Why is college tuition high, but academic salaries low?

Supply and demand. The value of something is what people are willing to pay for it.

  Why is college tuition so high?

Because students will pay it anyway. If you headed the committee to decide how much tuition to charge, what would you base your decision on? You would probably want to charge as high as possible, since you're trying to bring in money for your school. And you would find (as many current committees do) that you can go pretty high and still have millions of students crawl over each other for the privilege of giving you piles of money.

Why would universities lower tuition? Top schools already dismiss 20 applicants for every one they accept, despite the insane tuition cost. Clearly, either education is an inelastic service, or there is a ridiculous shortage - either way, HYP could probably charge 10 times what they do now and still have no trouble finding students. I would say that the main reason they don't is a combination of concern for their reputation and a fear of being sued.

You may ask why the students are willing to pay so much; but that's an involved matter which is outside of the scope of this question.

  Why are academic salaries so low?

Because professors will take the job anyway. If you headed the committee to decide how much salary to pay, what would you base your decision on? You would pay as little as possible.

In many areas, money is the prime motivator. So, at least the top companies will pay top dollar for the best employees, because the best employees have a string of job offers lined up and you have to give them something extra to take up your offer over all the other. Unfortunately, it so happens that in academia, money is not a good motivator:

Most eminent professors are old and content and they couldn't care less if their professorship made them $75k or $85k - they'll still want to work at that one school that they like for the reputation and the work environment (like colleagues and quality of graduate students). The ones that do care about money probably have a side business that brings in huge sums of money which makes their salary look like peanuts in any case.
Small time professors are either terrified of being fired (if not tenured) or can't get over the conflict between their ego and their lack of recognition, so they will readily take a pay hit to work at a more desirable institution if it means they can increase their own prestige.
Post-docs and other grunts will take pennies to work for a slightly more famous institution, because they think the association is vital to getting a faculty job after their post-doc. I'm sure many of them would pay (if they can afford it) to work like crazy for a guy who is famous enough.
Grad students are... Well... Grad students. The typical PhD candidate, when told that his job is essentially slavery, smiles and acts like it's a hilarious joke (even though he acknowledges that it's true). Many grad students already do pay to work like crazy, and not even for famous people.

How do you convince a thrice Nobel prize winner to be professor at your institution and not Next Door U? Pay him an extra grand every month? He's got three Nobel prizes, he doesn't care. And since he doesn't care, you might as well pay him a pittance - and as a nice bonus, you can tell all the other wannabes "Look, even he gets paid so little! Be content with your salary!".

If you ask why professors don't care, the answer is easy: Most people who care about money realize by the time they leave college that becoming a professor is not an optimal strategy for making money. To be a "greedy" professor, one must essentially wake up on their 30th birthday, and suddenly decide that even though all their life they haven't cared about money at all, from now on, money will be their chief concern. People who are old enough to have earned a PhD rarely have their worldviews change overnight so drastically.

  Where is the money going?

Short answer: Admin staff, marketing, sports. Things such as cleaning staff and building maintenance are also factors, but crucially they are less dependent on the school budget. Whereas those three mentioned areas will benefit the most from budget increases (but perversely, academic salaries will be harmed the most by budget decreases).

For details: Depends on the university, and may be determined by consulting the annual financial report of the university.


Heard of Chamber of Chartered Java Professionals International?

No.

  2. If they can [offer a degree], is it a reputable degree?

No.


The dominant cost of attending most conferences is not the conference fee but the travel costs (e.g., airfare + hotel). Moreover, most conferences (including most ACM and IEEE conferences) offer a reduced rate for student attendees, often half or less of the rate for professors. If you cannot afford that lesser rate for students, you probably cannot afford the travel costs either.

There are two good ways to try to get around these problems, however:

Some conferences offer the chance to apply for student travel scholarships. These typically both waive registration fees and help cover travel expenses.
Many conferences draw on student labor to help run logistics, e.g., manning the registration booth, acting as ushers. These students are typically compensated by free registration. They are usually drawn only from the hosting institution(s), however.

The best way, however, if you are a graduate student, is to see if your professor or your department can support you.


When is it appropriate to describe research as "recent"?

Good question. The semantics of the word "recent", in general, and in academic writing, in particular, is not clearly defined (that is, fuzzy), which makes its practical use quite tricky, as evidenced by your question.

While @vonbrand's answer offers some valuable insights, such as considering the fluidity of a particular scientific field or domain, I would suggest a more practical solution to this problem, as follows. Consider literature that you reference in a particular paper. What is the temporal range of the sources? I think that this aspect could guide you in to where the word "recent" is appropriate and where not so much.

For example, if you cite sources from the current century as well as 1930s, then a paper from 2010 should be considered recent, but not one from 1950. If, on the other hand, your temporal range of references is rather narrow, say, recent 20 years, then you should refer to as "recent" for sources that are from approximately last 4-5 years. You can come up with your own rule of thumb (10-20% of the total range sounds pretty reasonable). The most important aspect would be not the actual value (for the rule of thumb), but rather your consistency in applying it throughout the paper.


Is there a conflict of interest between me and the university if I get paid on teaching others how to apply for the PhD positions in my university?

Three thoughts:

(1) It's hard to see how this is a conflict of interest if you have no role (even informally) in the admissions process.

(2) Writing an applicant's personal statement for them is unethical. If you are advising students on the best strategies for dealing with particular individuals in your department, that also seems a bit like "insider information."

(3) You should consider the (not so remote) possibility that your department will become aware of your role on this platform. If you are okay with this, then it is likely ethical. You may even want to consider discussing it proactively with a trusted professor (e.g., the graduate program director).


What is the perception of foreign Universities (Non UK) in the US for prospective academic positions (Postdoc/Tenure)?

I don't think there's as much of a perception problem with foreign universities as you might think. I'd say the majority of postdoctoral associates are international, and most of them have not gone to universities as well known as Oxford and Cambridge. More likely than not, forging personal connections with the advisor you want to work for as a postdoc will matter much more than the university.

That said, individual professors may have a bias toward hiring people from "known" schools, because the risk factor associated with hiring them is presumably much lower than someone from a school they've never heard of. Such a bias is of course understandable, but it also means that they could lose out on some potentially promising candidates as a result.


When reviewing a resubmission, can I request a version with changes highlighted if the journal does not require it?

You can certainly ask for it but if the journal does not require authors to provide such files, you are not likely to get one. So why ask? Well, by asking you provide the editors with the wish from reviewers to see this as a permanent feature and in the end such changes may be made by the journal in their instructions for authors.

The reason why I think it is unlikely your request will be immediately heard is that editors usually handle many articles and may work under severe time constraints (often on their free time outside of work). Communicating back and forth with authors of varying background requesting new versions of manuscripts is usually a time consuming venture that could delay the process by weeks, depending on the responsiveness of the author.

So, there may be a good reason to make a request but I would not expect the wish to be heard in many cases.


Receiving a reviewer comments of the wrong paper from editor

Don't overthink this. Write a concise and polite reply. Here is an example that is not perfect but should do it.

  Dear Professor ...,

  we recently received the reviews for our paper ...., which we
  submitted to the journal ...., of which you are a/the editor of.

  While we found the comments by reviewer 1 very helpful, we noticed
  that review number 2 was written for a different paper. We'd like to
  hereby inform you of this likely administrative error. It is our
  understanding that there is a second review for our paper, and hope
  that its content will be equally helpful to improve our paper.

  Thanks,  Author name

If there is a submission number for your paper, include it as well (perhaps also submission date).


Countries where lecture duration does not exceed one hour

Well in the UK we usually have 50 minute lectures of which we might have 2-3 per week on each subject. The evidence from educational research that I have read is that you can't stay focused listening for more than 20 minutes in a lecture so even in a 50 minute lecture it is good practice to break it up with something a bit different in the middle.


What is the best PhD choice for gauge-gravity duality research?

At least in the US, your first question should be whether to do a mathematics or a physics PhD.  It's possible to work as a physicist with a mathematics PhD and vice versa (and I know people who do it), but it's hard enough to find an academic job (which is the only kind of job that will pay you for theoretical research of the kind you seem to be interested in) as it is, and having background and teaching experience in the "wrong" field makes it much harder.
It's important to understand that physics and mathematics are different fields with different ideas of what it means for a statement to be true.  In mathematics, a statement is true if and only if someone has given a valid mathematical proof for it.  In physics - well I'm a mathematician who is ignorant of physics, so I think it's best to let physicists speak for themselves - but it's not what I just wrote for mathematics.  Their definition (in the mathematical sense of definition) of truth is different.  Which definition of truth do you want to work with?
Also important - would you rather teach introductory physics or calculus?
In either case, you want to be at a university where the mathematics and physics departments have a good relationship with each other.  (For this purpose unlike many others, having no relationship does not count as having a good relationship.)


How much tweaking of figure design (not content) can I postpone until the final figures are requested?

As a referee, if figures are in a rough shape, I will absolutely call the paper out on that, and demand improvements. This will potentially set the acceptance back by weeks. Unless the figures will take weeks to get right—and in this day, that would usually imply  that more data needs to be collected—then it's better to just do it right the first time.


How much detail about mental health issues should one include in "Special Circumstances" section of graduate school applications?

You do not have to disclose your personal health history (including mental health) to graduate schools  when you are applying -- and even while you are enrolled.

There are occasions where you may want to. For example, if there is a semester in your undergraduate record where you did particularly poorly because of (mental) health issues, you may want to note this is in your diversity statement or special circumstances portion. However, you can be as vague as you want -- saying "In the fall of my junior year, my health declined which led to poor performance in a number of my classes. I recovered the next semester and you can see that my senior year grades were all of the highest rank."

If you have faculty writing letters of recommendation for you who know about this incident, you may want to tell them: 1) if you want them to mention it or not; 2) what language to use ("she became depressed following a family death" vs. "She struggled with the additional family issues following the death of her mother" vs. "There was a family crisis that took her away from school that semester", etc.etc.).

Otherwise, your (mental) health record  is your personal medical information. The professors in your department do not need to know it -- any more than they would need to know that you had HIV or were on dialysis. If you need accommodation (such as taking Wed and Fri off for dialysis, or for therapy) you may want to disclose that to some people but you should feel free to compartmentalize the information to certain people and to not disclose everything about your condition.

For example, it is entirely appropriate to tell just your advisor, department chair or director of graduate studies -- or external to the department: your university ombudsperson, disability services officers, or associate provost or dean -- some of the details of your condition and what accommodations you need to be a successful scholar, but ask that the information not be shared with faculty members in the department.  But again, this is your choice.


Advisor asks me to use plots that favor our approach, saying "the numbers in our paper don't matter; what matters is the message"

Standard definitions of scientific misconduct consider omission of conflicting data an instance of data falsification, see, for example, the guidelines as applied by the BMJ, or Gupta 2013 on fraud and misconduct:

  Falsifying data means altering the existing records. It is the deliberate distortion or omission of undesired data or results.

If your advisor asks you to deliberately produce a figure that downplays undesired results, he or she is asking you to falsify your data.

So, what should you do?

Speak again to your advisor. Tell him or her that you don't feel comfortable with the suggested plot, and explain that you feel obliged to report the data faithfully, including weaknesses of the analysis and conflicting observations.

If your advisor insists on using the falsifying plot, you should consider choosing a different advisor, because the present one may not teach you proper scientific conduct.


Publication dates: accepted date, version of record online, issue online – which one to use?

A journal citation looks like

  Last, F. M., & Last, F. M. (Year Published). Article title. Journal Name, Volume(Issue), pp. Pages.

Since it refers to a specific volume and issue, you should use the date that issue was published. (For your example, that is 25 January 2016.)


Why do companies fund academic research?

There is a variety of reasons, as someone who has worked on such projects, here are a few that come to mind:

Access to research facilities. It's often far more rational to fund a study in a university than to invest in building your own wet lab/cleanroom/animal testing lab, etc. In some fields and countries, there are also regulations that limits certain area of research to university institutions (example: research on human tissues).
Highly educated, relatively cheap human resources In the subsets of projects where academic researchers actually do the work from the project description, it is generally cheaper and bears fewer risks than hiring people directly.
Great way of recruiting scientists by establishing a close collaboration, the company has the opportunity to meet and see potential hires in action.
In some fields, it can be a form of advertisement. In particular for companies that have scientists or research labs as customers. Example: lab equipment manufacturer, metrology tools, lasers, etc.

  Do they get actual patents out of it?

Yes. It's frequent for industry-funded projects to result in patents. The patents are usually owned jointly by the company and the academic institution. Sometimes the technology is already patented and the study is only about testing an application. Publishing a technology in the scientific literature can also be a way to prevent other companies from claiming ownership, since you can't patent something that is already published.

Note that industry implication in academic research might diminish, as it becomes evident that they aren't always getting good research for their money. See: http://blogs.nature.com/news/2011/09/reliability_of_new_drug_target.html


Just to echo what's being said in the comments, in the United States, there are no distinctions with degrees... you simply have either earned it or you haven't.

Also, for what it's worth, "PhD ABD" is not a real degree, even if you list it on your resume. Just sayin'.


Will I get a negative LOR from my professor

I don't think that there should be any issue. Your professor is right - most LORs are submitted directly by the referee to the university (to avoid the risk of falsified references). I would thank the professor again, say something like "yes, I thought that it's kinda weird that the system asked me to submit the reference. It makes much more sense that you do it" (putting you and the professor on the same page, while placing the blame on the system rather than on yourself).

Generally speaking, it would be good to have a few referees to rely on, but I don't think that this incident "burned" one of your referees.

Good luck!


Writing letter of recommendation for someone I have never met

You shouldn't write a letter of recommendation for someone you have spoken to once, and you certainly shouldn't write a letter of recommendation for a friend of some you have spoken to once.
You should never lie in a letter of recommendation, but it is generally also bad form to write negative things in a letter of recommendation. If you can't in good faith write good things about a candidate, you should refuse to send the letter.
EDIT:
I'll add an answer to your first (not main) question from the comments:
It is very unusual for a first year grad student to be asked to write a letter of recommendation, particularly since he is asking you to say he is your best student, when presumably you have no students. If I were the admissions tutor here, I'd probably disregard such a letter. Unless it was obviously dodgy (claiming things which were clearly untrue), in which case, it would count (heavily) against the candidate.


Ordering Chemicals for a laboratory on a Student or J1 Visa

If you mean order as in "sorting the bottles", then you anyways shouldn't do that unless you have the proper training so you know what you are doing. If I should give a paranoid guess: getting the training would have been the point that got you listed as owner of a "hazardous chemicals certificate". That's much easier from a large scale administrative point of view than knowing who entered which lab to touch a bottle at a nation-wide scale.
If you mean order as in "administrative task to buy things": This type of ordering does not imply physical access to the substances. Lists of people who do that would be full of secretaries and administrative/procurement/bookkeeping staff.
If you're trying to be paranoid: the other thing that is much easier to know than who actually enterd a particular lab is who is working in that group/building. From that point of view, you may already be listed as "possibly had access to X" if anyone from your lab does the order.

(Disclaimer: I'm German and in Germany and not overly worried what types of US visa I can have. However, I'm chemist, so if they list people in relation to harzardous substances, I'd expect to be listed by profession [or by my publication list/affiliations] anyways - even though taking also into account the amounts the most important hazardous substances I usually handle are alcohol/bacillol for cleaning instruments and the lab table.)


Can I post on Arxiv a final paper published on PLOS ONE?

Yes, you can.

Read the CCBY license: you are allowed to share (copy and redistribute the material in any medium or format) and adapt (remix, transform, and build upon the material
for any purpose, even commercially) the material as long as you attribute (you must give appropriate credit, provide a link to the license, and indicate if changes were made). So you can put the paper on arXiv, as long as you attribute.


Contractions ("can't", "don't") in a mathematical paper

My experience has typically been that the more formal mode, with no contractions, is preferred for most scientific publications.  It is not a terribly strong or important custom, however, and in one of my more high-profile multi-disciplinary publications, I actually found the copyeditor introducing contractions into my writing!

In short: worth mentioning, but not a big deal.  As a reviewer, you might say something like: "I found the contractions distracting, and would advise removing them" but I wouldn't recommend being much stronger than that in your statements.


Impact on PhD application omitting a recommendation letter from research advisor in that field?

It would likely be cause for speculation if the applicant is promoting their research experience but does not include a letter from their advisor. There may be inert reasons and it does happen (an advisor that is too busy or too aloof; on a leave for medical or other reasons). There are also cases where the applicant and advisor do not get along well, or where their interests are not aligned. In these cases it may be worth a direct conversation to find out if they would offer strong support for the position and if not then ask why not. The applicant may be surprised to learn that the advisor with whom she/he argues holds them in high regard. At the same time, the advisor may have useful input to offer that the applicant may wish to weigh as they decide on an educational and career trajectory.

That said, if no advisor letter is provided then the applicant should succinctly provide an explanation for why the given recommenders were chosen, and leave it at that unless pressed. If the applicant has a good relationship with another recommender, she/he might ask that recommender to include a supportive explanatory note in their letter.


Someone referenced my work in a journal paper using my first name only, do I contact them or the journal it was published in?

I would recommend approaching this problem through the following layers of triage:

First, is it a serious journal, or a predatory trash publication?  If it's not a serious journal, just ignore it and move on. It won't really count as a citation anyway, and there's basically nothing you can do to get a meaningful response from the people running it.
Second, if it's a real journal, is it in the final form or a "just accepted" pre-print?  Some journals give early access to "just accepted" manuscripts before any copyediting occurs, typically with a big warning label saying "Not yet final, things may change."  If this is the case, then you may be able to count on the production staff catching the problem and getting it fixed before the final form; if you don't want to count on the error being caught, it is reasonable to (politely) contact the authors.
If neither of these is true, and the paper is in its final form in a real journal you can write to the editorial staff to request a correction.


It is very unlikely that you can make such a radical change without having to take a number of additional make-up courses at the undergraduate level, and your current training does not appear to have much overlap with your future plans.


What is the process for PhD applications and contacting professors in France?

TL;DR: in France you have to find first the supervisor, then you apply for a funding. If you have a funding of your own, you have to find a supervisor to be admitted. In both cases : you need the supervisor first.

There is various things to know when you apply for a PhD in France :

It is forbidden to be a PhD without having funding. In France a PhD student is considered both as a student and an employee.
The funding can be a state funding, an industrial funding, a funding on a research contract (either from a national funding agency or a company), or you can also do your PhD while working elsewhere (some teachers in secondary schools are doing their PhD this way).

Industrial funding and research contract are basically given to the supervisor, who can choose alone amongst all candidates. So for PhD with those fundings you have to contact directly the targeted supervisors.

State funding is given by a committee to a bundle (candidate, subject), this means that a professor, with a subject, has to find a candidate and then propose to the committe this candidate on his subject. Then the candidate is on his own : (s)he will generally have to send an application letter, with a reference letter from the supervisor, and if (s)he is shortlisted, (s)he will have to make a short presentation (either on location or using skype or a similar service).

Last case: you are funded on your own (job, external funding for foreigners). Even in this case, the procedure is that you find the supervisor, then you apply.


How can I tactfully decline my supervisor's suggestion and set boundaries?

5h commute a day for 2 weeks is not acceptable, pandemic or not. To play it tactfully, I would ask the supervisor to pay for accommodation there for these 2 weeks. This will force your supervisor to:

pay for it, so reconsider whether it is worth it.
if she pays officially for it, she must check whether that trip is authorized by the university considering the pandemic, I know mine has forbidden all travel.
I think it is reasonable to ask for accommodation but would end up being a graceful way of dodging the bullet.


Royalties and advances from academic publishers: what should I look out for?

For academic books, there may often be no royalties.  And only a small number of copies sold.  Maybe if your first book has unexpectedly large sales, you could negotiate something more on future books.

Typically, though, academics publish books not to make money from the book, but to build their academic reputation.  And that may lead to promotions, tenure, hiring at more important universities, etc.


On one hand, you seem to have a research advisor who is quite supportive of you; he has already offered you a post-doctoral position when you finish.  On the other hand, you are concerned that he tends to attach himself to, and take credit for, work on which he is only peripherally involved.  This places you in something of a quandary, since your advisor has not made a meaningful contribution to your paper.

However, I would suggest that you show your advisor the paper to get his feedback.  Even if that feedback is not useful in terms of the content of the manuscript, your advisor probably has a good understanding of how papers should be written, and where they should be submitted.  Moreover, when other scholars are evaluating work done by graduate students, you are not going to be significantly penalized for having your advisor as a co-author.   Having a paper that is co-authored by your advisor, but with you as the first authors, is not going to be perceived as that different from  a single-author publication.

Perhaps your advisor will make some useful comments, but he will decline to be an author on the paper.  (This happened to me, in my interactions with my advisor, more than once.)  You seem to think that your author is not likely to be magnanimous in this way, which is, in the abstract, unfortunate.  However, as I stated above, having you advisor as a co-author is unlikely to be counted against you in a significant way, and maintaining a good relationship with your advisor (for whom you man continue working as a post-doc) can be extremely important for a future research career.  So I do not think that you have much to lose by showing your paper to your advisor and getting the advantage of your advisor's guidance.


How do you choose a textbook for a new class

These are some criteria I usually use:

Published within last 5-10 years, preferably in 2nd edition or beyond: This ensures the materials are reasonably up-to-date and major errors had been cleaned up.
Have physical and e-book versions: To tailor different types of readers.
The e-book version should be freely available through the institute's subscription: This is to lower the barrier for acquiring the book.
The titles have been commonly adopted by other syllabi: Perform a search using your course title or subject plus "syllabus" and "filetype:pdf" or "filetype:doc" will get some nice results. Sift through them and get some ideas.
For software book, I would also check if the publishers provide all codes and data sets online. In additions, I'd make sure the book's examples use the software with the same version that my institute has or the students have.

Some other thoughts:

From my experience in teaching statistical software, I found that books are really not that popular. Online workshops and support websites seem to be a lot more welcomed by the students. If you can identify any of online resources, I'd at least suggest that as a secondary option.

I elaborate to students in the first class on why I chose this particular title. When I teach a class with very diverse backgrounds I also suggest some secondary books that are more specific to their interests. For instance, if I have medical and veterinarian students in my class, I may pick one software book on medical data analysis and another one on analyzing zoological/ecological data, etc.

Another thing I do to show that I am serious about the text: I often put footnotes on my notes or slides pointing students to the relevant section if they'd like to learn more and try that particular analysis/function.

Once you have found a few candidates, read the forewords. All else equal, I often prefer books that were written with a syllabus in mind. The authors usually explain that in the forewords.

Isolate the "must learn" techniques in your syllabus and make sure they are all included in the chosen text. That would make sure the texts and your teaching are coherent, and lower the chance of getting evaluation comments like "the text has nothing related to what was covered in the class."

One format that always thrills me is inclusion of self-assessments and case studies. Even I don't end up using those titles, I often borrow the case studies to make all the codes that I teach relevant to the contents.


Is it acceptable for a student to ask a professor to be included as a co-author on the professor's paper?

It's fine to just ask.

But if you feel uncomfortable asking straight out "Can I be considered for authorship on this paper?" an alternative approach is to have a conversation about authorship that (1) makes it clear to the professor that you're interested in authoring a research paper, and (2) helps you understand the shades of "it depends" for your specific kind of research.

For example, you might bring up in conversation:

  In our field, what kind of contribution are students expected to make in order to merit authorship on the paper that comes out of their work?

Then you can ask,

  On this project, what additional work could I have done in order to have sufficient contribution to be considered an author?

and then, if you want very much to co-author a research paper and plan to continue working with this professor,

  I'm interesting in being a co-author on a research paper. On the next project we work on, can I have a role that (if I do it well) merits co-authorship?

Ideally, if you had just asked straight out "Can I be considered for authorship on this paper?", the ensuing discussion would also cover the points above.


applying to graduate school during the final year

Once you are accepted it is very unlikely that it would later be rescinded, except for serious breaches. But you won't do yourself any good if you give up your efforts. Your acceptance is probably contingent on successfully completing the bachelors, however. Don't jeopardize that.
On the other hand, don't start grad school in a state of burn out. You are only part way through the race.


homework testing method for schools - how to encourage good practices and design and reduce reliance on proofreading?

You are asking for a fully automated code review pipeline, also known as the Holy Grail.

By parts:

Faulty logic: this can theoretically be caught by testing. But if it were so easy, software will be bug free. If the assignment is simple enough so that there is one and only one way to do it, you can predict the algorithms, and design corner cases to test for. If there is more than one way (and people, specially beginners will find another way, however convoluted), you would have to review them, see which algorithms they are using, and get mean on them.
Code style: there are automated tools to check style and good practices, like cppcheck but they are quite stupid. Some settings are over zealous, and they are completely unable to see through the general structure, find too long functions, or enforce single responsibility. Plus, they are designed to give suggestions to the programmer, that he will evaluate if appropiate ("do I really need to document this 3 lines long auxiliar function with a perfectly clear name and signature?").

So, in general, no, that is not possible. The only way I can think is to make it easy to expand your testing and evaluation framework. When the TA finds a mistake in a program, a test shall be added, and all of them will go through the pipeline, and that becomes one less thing to check for.

To enforce good practices, the best I can think of is to make the application grow assignment after assignment. If it is poorly coded, expanding and maintaining it will be a major effort, and the benefit of good practices will become obvious. Building larger code bases is, in my opinion, the only way one can really understand and believe why patterns and conventions are useful and not just the product of some picky guys with OCD.

But you can cheat. For example, you can manually thoroughly check the submissions with lowest style scoring that pass all the tests (supposing they would be the ones more poorly coded), and find their corner cases where they would fail and add them to your battery of tests. This is unfair, though, as you are targeting your punishment to specific submissions.


How much does it cost the publisher to transform the draft of a textbook as given by the authors into a final publication (for web or print)?

The costs are going to depend on three factors: (1) how long the book is, (2) how well written the book is, and (3) how much layout work the publisher does.

For example, in Math, the publisher might provide a LaTeX template and expect you to hand tweak underfull and overfull lines, float placement, and hypenation. In other fields it is more typical to give the publisher plain text with minimal markup.

The Editorial Freelancers Association publishes recommended editing fees. A typical book might have a round of "line editing" at 4 cents per word, a round of layout at 4 cents per word, and a round of basic copy editing at 2 cents per word.

If the book is poorly written, two rounds of line editing might be needed. If there is automated layout, the layout costs could be saved. There is also the cost of creating an index at 2 cents a word, which depends on who makes the index.


How to describe a program written by the author?

"in-house" program is the term I always use myself and see in other people's papers.

In the corporate context, Wikipedia defines it as

  In-house software is a software that is produced by a corporate entity for purpose of using it within the organization.

Here's an example in an academic context

  Energy minimization is done with yammp, an in-house molecular mechanics package.

Here's another example from academia

  All analyses were done with a battery of in-house codes and external analytical tools.

I wouldn't say "in-house" strictly means "the source code is private". I have sometimes seen people use "in-house" to mean "code our own research group wrote and uses, but which we also make available as open-source code". But if I see a sentence in an article like "All analysis was performed using in-house code", and no reference, then I read it as "We used some code we wrote ourselves which we haven't published anywhere", which sounds like what you want.


Policy regarding grouping of papers in Google Scholar

One rule of thumb would be that any set of related papers that would be considered separate for a paper CV should be considered separate in what amounts to an electronic CV. Especially if one version clearly contains more material/data/argument than another one.


Do language skills impair students' ability to assess their skill in other subjects?

I've taught esl  for international students trying to get into graduate school. One thing that I noticed is that the students did not know there is a difference between conversational English and academic English. They were totally convinced that since they could tell me their name and where the bathroom is that they were ready to begin graduate school. Literal ideas are easy to share in a second language but abstract ideas require real mastery.

Perhaps in your situation the students have the same misunderstanding in regards to conversational and academic German. When you lack expertise in any subject everything tends to look the same.

Another potential concern could be language ego which essentially means that nobody wants to look dumb using another language. This may also cause students to inflate their language ability in order to fake competence they lack. Toning down the complex German and explaining everything in the simplest way possible with the simplest words will encourage them to indicate when they don't get it.


"Do you need travel support?" Questions on Conference Applications

What you should answer will depend on the conference you're attending and the country it is hosted in. Different conferences will have different amounts of money available for travel support and there is no single set of criteria that is used to determine who is eligible. Often travel support is aimed at students and researchers with a very low budget, for example those from poor countries. It is typically not intended for people who have the budget to attend several conferences, but want to attend more.

So figure out what the eligibility criteria are. If they're not listed on the conference website you can either just fill in "yes" and hope that you are provided with documents that provide further information.

But as is often the case, the simplest way might be to just ask. Send an email to the conference organizers asking what their criteria and intended target audience are for travel support.


Reference on abuse of stimulant medications among professors to enhance academic performance?

There were several prominent publications in Nature, spurred by a survey that they conducted of their readers who were able to broadly identify their area of work.  See this link here for information about the survey, which also cites the papers that were published in Nature.  http://network.nature.com/groups/naturenewsandopinion/forum/topics/1309

In researching this topic, I used google scholar and the search terms "stress stimulants faculty -students" and published 2008 or later to arrive at meaningful search results.

The most likely reason there is more work published on student use is that students as a demographic group are both easier to study and are a more similar group of cohorts than faculty as a demographic group, which are more diverse in age, race, ethnicity, etc.


How to find out whether potential advisor will retire soon?

By asking, "are you accepting PhD students in the coming academic year?" you will find out not only whether they are openly planning on retiring soon, but also critically whether their docket of students is full.  You can do this via email without risking offending them.  In your email, also justify why you are interested in working with them.

I personally have experience with this, and unfortunately the person I contacted was retiring in the next year, and they told me so when I emailed them.


Is there a self-consistent citation system?

Work out which journals you are most likely to be publishing in. Read their authors' guides. Pick the citation style that occurs most frequently.

Start using that now.

That way, you'll have all the tools you need in place for when you start submitting to those journals.

I think reference management software these days typically includes the ability to incorporate new citation styles, often encoded in CSL (Ctitation Style Language), as well as having the most commonly-used ones built in.

Any decent reputable citation style will be internally consistent enough, and will have rules for papers, books and various species of grey literature.


What are the primary causes of conflict between PhD advisors and their students?

The biggest causes of conflict, beyond personality-related issues, I believe stems from a point made in the linked article—lack of communication.

When advisors and advisees are not on the same wavelength, either because goals have not been clearly communicated, or because the frequency or quality of contact and correspondence between the two has broken down, conflicts can result. This is especially true when it comes time to graduate: the advisor may have specific expectations on what the student is required to provide; however, unless this is directly communicated to the student, there will potentially be a lot of conflict in getting to a point where both are satisfied with the final results.

Often, this can be solved by having a direct discussion about the unresolved issues. However, if there is a pathological problem—in other words, one that can't be resolved through communication between the student and advisor—it may become necessary to invoke the thesis committee, graduate officer, department chair, or other authority who can help to resolve the problem.


Update #0: Case Study: Logistic Regression
As an example, consider the origins of the logistic equation as a model for population growth. I came across "The origins of logistic regression" , Cramer 2002 on wikipedia in the context of machine learning. Cramer traces history back to the independent rediscovery of the equation by Pearl (Bio statistician at Johns Hopkins) and Reed in the 1920s which appeared in the "Proceedings of the
National Academy of Sciences", in "The Quarterly Review of Biology" and others. Cramer notes that the name Velhurst is first mentioned in a footnote in one of their papers which he cites by year but does not appear in the bibiliography (Pearl and Reed 1923), and on page 560 of pearl's 1924 book  Studies In Human Biology we get the following:

(This criticism distorts the facts, according to Cramer).
Pearl and reed cite Verhulst which published, in french, in the 1844 proceedings of the Bruxelles Royal Academy, but actually earlier in 183/8
in a journal published by his teacher Quetelet (Who Developed the Body Mass Index], in the Netherlands.
Du Pasquier cited this work in a paper published in 1918, 74 years later after Verhulst, in The " Vierteljahrschr der Naturforsch" ("Nature Studies Quarterly"?) which was apperently a german general published in Zurich, though Du Pasquier's paper on population models, "Esquisse d’une nouvelle theorie de la population" was in French. How did Du Pasquier learn of this 75 year old paper? According to WP he studies in both France and Switzerland, and was not only a mathematician but also "a historian of mathematics and mathematical sciences" (!). It seems plausible that Reed and Pearl could have been aware of a paper published 2 years prior,even in foreign language and journal. And if not directly, their wider circle could have turned their attention to it. Though, reading the quote, they seem to  possibly be saying that they reached the Verhulst paper by a different and unspecified route.
So, in this case, a polyglot European mathematician with a passion for math history, discovered (again, in 1918, from a foreign journal) an obscure 80-year old work, cited it in his own paper, which was enough to get it over the ocean to america two years later, where the same ideas had been redisovered, but much more effectively publicized. With that, the citation link was forged, and now we have the Pearl-Verhulst logistic process.
One conclusion is that you don't necessarily need someone who knows the obscure paper, you just need to transitively traverse the citation graph and hope that someone cited it at some point, and that you hit the natural limits of exponential growth before you stop looking.
Update #1: Before Information Overload
a suggestion received from an unexpected source. In reading the 1988 article "What's Wrong With This Lagrangean?" by David Mermin, he suggests a fact which explains how knowledge of sources used to be work:

We've known for some time that, roughly speaking, nobody any longer
reads anything but preprints, the archival journal of choice, which
for many years now has been Physical Review Letters, and secondary
references cited in these two primary sources. But the preprints have
been coming thicker and faster. And Physical Review Letters now
publishes almost as many pages each month as all of Physical Review
did back in 1956, when I was starting graduate school.

[...]

the disaster looming over science libraries, and therefore over
science itself, as a result of the irresponsible way we have allowed
scientific journals to proliferate; and, not unrelatedly, the
lamentable decline in the quality of scientific writing.

In other words, a hundred years ago, before volume became unmanageable, people actually used to read what was published.
Update #2: Memory In Judaism
Regrading the role of persons possessing exceptional memory abilities, specifically in the scholarly context of judaism, here is an extract from "The Esential Talmud", Ch.6, by Adin Steinsaltz:

The work of preserving and codifying the vast body of oral law went on
for several generations, but its importance waned as the main focus of
Torah scholarship shifted elsewhere. Those scholars who engaged in
memorization of the vast number of baraitot were still known as
tannaim, but the term took on new significance. Tannaim were no
longer creators of the oral law but individuals gifted with
phenomenal memories who did not always comprehend the full
significance of what they were memorizing. They were to be found for
many generations in the larger academies, serving as living archives
utilized by the sages in order to clarify and elucidate various
problems that cropped up in the course of the study of the Mishnah.

See also the related, tragic, short story "Mendel the Bibliophile" (1929) by Stephen Zweig. These persons are rare, but have played an important role in preserving knowledge throughout history. I've ran into more than one, behind the counter at this or that second-hand bookshop.


When is a proper time to consider quitting a phd?

There are a few subproblems I want to respond to, then an overall answer.

If an advisor is not invested enough in a project to spend time on it, the student is going to have to struggle with avoidable problems, i.e. issues which the adviser could have quickly addressed. It's still not impossible, and some students might even flourish without micromanagement, but it's not ideal. So then, is it that this advisor doesn't care to spend time on the project, or that they have many other commitments and are just doing a poor job allocating their time? If they earnestly want to meet but are being pulled away by teaching and committee work, then the student might be able to help out by tracking down the advisor when they are available.

Pressure to publish is almost universal in academia and if we want to be successful we have to embrace this as a delicious carrot rather than a heavy stick. However, for many PhD students there is a gap between what the program tells the students to do and what the median student who receives a PhD actually does. If you want to pursue a faculty position, you need to aim substantially higher than the median--in terms of publication counts, everyone should aim higher than the median in terms of personal achievement--but if that's not your path then it's less critical.

Now, those issues aside, I generally feel that if a student is bothered enough by a working environment to make a list of the reasons they think the environment is awful, then regardless of how common any individual factor might be, it isn't working out. Don't torture yourself. If you love the work you do, then look for transfer opportunities. You should quit a PhD as soon as you know it's not working, regardless of how much time has actually passed.


German doctorate (Phd) in industry; Working in a company or University?

I'm from Austria but the system is the same.

Only universities can award PhDs, so no matter where or how you do your PhD you need a supervisor at a university and you need to hand the thesis in at your university, get reviews like every other student has to and defend your thesis at that university. This is always the same.

In principle you can do your thesis wherever you want or got a position, as long as it's research based and your supervisor (and the dean of studies) approves the topic. The actual details on how everything works depend on the industry partner and the university, but there are two main cases.

1) You are doing your research directly at the company, in that case you don't need to be at the university except maybe for some courses you have to take and of course meetings with your supervisor. Usually you enter some kind of "PhD contract" that says you should meet your supervisor every X months or something like that. In this case you are usually paid by the company to do research and the university might not be involved.

2) The university is working together with a company on a research project, in that case you will work wherever you are needed. This is often the case if (smaller) companies need help in projects they cannot or don't want to do in house. In that case you might be paid by either the university or the company.

Be aware that in both cases you have to write a thesis which will be publicly available, which can be a problem when working with companies. There's usually the possibility to "lock" the thesis for a certain amount of time (some years) to get patents for example, but all of this is something you need to clarify beforehand! This is extremly important!


How to interpret the phrase "experimental approach"?

I use the term "discovery" when I am using approaches where I don't really have a "control," but am trying to investigate phenomena to determine the underlying causes. (I use a simulation technique which is essentially "deterministic" in its results, so it's a matter of trying to find a model which explains the phenomenon in question, or determining results for a new system).

So this would perhaps be an example of "experimental discovery."


What are the general rules for faculty attendance?

It varies very widely depending on individual faculty, departmental, and institutional culture, norms, and rules.

For example, many faculty at my institution live in a city two hours away and only come to campus twice a week for classes and meetings. Faculty performance at my school is measured by lines on the CV, so one can argue that not going to school is a more productive use of time if you have a home office.

Meanwhile, while in Japan, I noted that some faculty had to punch timecards that showed their daily attendance. There, faculty performance seemed to be measured by the appearance if diligence rather than actual productivity.

On the extreme other end, adjunct faculty in the USA may not even have an office (or library privileges) to even have office hours.


Is it reasonable to ask update on recommendations letter twice?

You can stop worrying.

It is not unusual for professors to wait until the last minute to write letters.  Although busy, they are experienced at meeting deadlines and will get it done.  It only really takes an hour or two to write a recommendation letter, and submitting it to 7-8 places is no big deal at all.  What you've asked of them is completely reasonable.

It is certainly fine to contact them, though I don't think I would phrase it as "asking for an update".  I would write an email like:

  Dear Professor X,

  Thanks again for agreeing to write me a recommendation letter.  I just wanted to send a friendly reminder that the first deadline is April 1 (for University Y).  The remaining schools and dates are in the list I sent you previously.

  Please let me know if you find that there is anything else you need.

  Sincerely,

  truvaking

Also, if you have recently made any significant accomplishments that you think they might want to mention in the letter, you can communicate this in your email as well.

I really don't think you will upset anyone by doing this.  It would be incredibly petty and unprofessional for a professor to go back on a promise to write a recommendation letter, solely because the student sent some reminder emails.  Likewise, I think it is still fine to re-contact the fourth professor if you think their letter would be helpful.  They may have simply overlooked your original request (professors get a lot of email).


What is the proper way to ask a professor to be your PhD supervisor?

I don't think that your approach is not good.
It is always preferred to be straight to the point with direct focus on your aims and how would they fit into your potential hosting lab vision and goals.

Always, Keep It Short and Simple (this is called KISS principle).

However,
Some suggestions to enhance your odds:

0- Set your objectives and your target areas.

1- Get prepared by identifying your potential advisor' research interests by visiting his web site and his lab activities to see if it's fit to your needs.

2- Make a balance sheet between your strengths and weaknesses.
Don't be shy to identify your weaknesses, because you shall be providing an improvement plan on how to address them.

3- Try to come up and suggest some research topic that sticks with your potential advisors research interests.

Like this, your advisor will be more than glad to offer his/her expertise and embrace your proposal.

I believe by doing the aforementioned steps, you show that you are already on your way to a PhD. Such thing would be visible to your potential advisor and would be certainly appreciated.

Good luck.


What are the key components of being an effective supervisor of undergraduate researchers?

I have had some pretty good success advising undergrads by:

Making sure that the problem is extremely well-defined. That is, don't throw them into the water and see if they swim. Think a lot about what the expected outcome will be, and what the foreseeable steps, challenges and problems will be. Yes, this is a lot of work and means that you could (almost) "do the work yourself" in the same time, but for undergrads you can typically not yet expect that you can just drop them a research question and see them run with it.
Have regular meetings. Make sure that there is progress, and if there isn't, make sure that you know what the blocking issues are. Don't expect them to necessarily come to you first with any issues. In my experience, undergrads often are a bit shy about asking for help, and sometimes get stuck on (for you) relatively easy problems unnecessarily.
Make sure that you would be able to do the project yourself given enough time. I know that this is somewhat controversial, but for grad students, I am perfectly happy to accept projects where I myself wouldn't know how to do every part myself. That is, I expect a grad student to be able to solve her/his own problems. For undergrads, I do not do this. I want to be able to help undergrads in a meaningful way if they get stuck, technically.
Conversely, make sure that the work is not just random grunt work. In my experience, the best way to make sure that the undergrad research project is not interesting for the student is by letting them do something that everybody else either considers unimportant or terribly tedious to do. Undergrads are not yet experienced, but they are still colleagues and not some sort of scientific minions.
Somewhat related: make sure that you are excited about the project, or at the very least be able to convincingly pretend that you are. Again, having the feeling that nobody cares about their project is a surefire way to make for a terrible research experience.
Integrate the undergrads into the lab. When there are talks, the undergrads are invited (i.e., expected to come). When the grad students are expected to regularly speak in the internal seminar, the undergrads need to do this as well. If there is a regular lab beer night, the undergrads are invited as well. If the lab usually goes to lunch together, the undergrads are asked to come along. You get the idea.
If at all possible, give them a fixed work place in the lab, and require them to be there at least some percent of the time.

To summarize, the best undergrad projects in my lab always worked on a well-defined project, which was still an integral part of the research agenda for the lab that others were enthusiastic about. On concrete example from my research: some members of my lab are currently working on benchmarking compute cloud providers. That typically means hacking up some automation scripts, deploying benchmarks, gathering some data, and analysing the results. This is rather tedious and error-prone work. Hence, I got a computer science bachelor student to build a web-based platform, which students could use to define, schedule and execute benchmarks using a relatively simple DSL (domain-specific language). The platform the student built technically wasn't terribly complex, but the solution worked well, tackled a common community problem, and most importantly saved multiple grad students a ton of time. We also published the tool as open source software and wrote a small paper about it, allowing to student to go to a conference to another continent. During the conference, a number of professors asked the student for details on his tool, and expressed interest to also use it for their research.


Is it legal to have a collection of interesting articles printed for personal use, in the form of a book?

I don't see how printing a paper for one's personal use could be legal, but printing 2 or 10 and binding them together would be illegal. As long as it is actually strictly for your personal use, if printing a paper for your personal use is legal where you live, then certainly binding them together is.

But I would advise against actually binding them. Let's say you do, then the next day you find a new paper on the same topic. You will want to kick yourself, because you will not be able to add it to the collection. I think that most people have bunches of physical folders, with papers consisting of stapled (or otherwise kept together) stacks of papers, but separate papers not being bound to one another.


Is it worth going to an academic conference if I'm just attending?

Academic conferences are pretty good to make networking between the participants. If you are looking for some collaboration into your project, maybe it could be a great idea to attend.


Are editorial management systems helpful to journal editors?

I served as editor-in-chief of an IEEE magazine for 4 years and have been an associate editor on various editorial boards for the past couple of decades.  For as long as I've been on edboards, I'd say they have used some flavor of online management system.  Pretty much everything I'm on now, not to mention everything I submit to, has coalesced on "manuscript central" from Scholar One.

I fully agree with @Nate Eldridge's comment about the "paper" trail.  That is definitely a plus, because I can look and see past correspondence -- was someone reminded at the right time, etc.  And to be honest I couldn't imagine managing this offline.

That being said, I find the system (and the others I've used) frequently painful.  Aside from the bug about being negative days late, my biggest problem is that the system tends not to remind anyone that a task is outstanding.  In particular, as an associate editor my job is to line up the actual reviewers.  In two cases recently, I discovered that I'd invited 3 people, and usually more (as people might decline), but in the end 2 from each of 2 papers had agreed to review and 1 in each case had never responded.  The system sent them a reminder or two, then from what I can tell, it neither reminded them nor told me it was time to find someone else!

There are other minor difficulties, such as finding reviewers within the system rather than creating duplicate accounts for them as new reviewers, that sort of thing.

Bottom line: they serve a purpose, but they can be improved.

Are they helpful to journal editors?

Absolutely.

Can they be improved, especially from the standpoint of reviewers?

Absolutely.

But don't throw the baby out with the bathwater.


Relating job hunting and PhD preparedness

(tailoring applications, organizing application materials, networking, interviewing etc.)

During your PhD and in your future academic career you will spend a significant amount of your time:

Tailoring applications to grants
Organising materials for those grant applications
Networking at conferences, workshops, online, etc across your discipline and in to other disciplines
Presenting your research and selling yourself as a researcher as you present papers at conferences etc (not entirely unlike a very harsh interview)

It seems to me that you've answered your own question. Your experience has prepared you for many of the academic extras that happen beyond simply being able to do good research. I think that's probably your hook there.


Is my adviser supposed to be assigning me my research?

This depends very much on:

How much interests and your advisor's interests align
Where your funding comes from

First, interest alignment: Starting a grad program, you find an advisor with interests that overlap with your own, do the foundational things that need to get done, then expand on it with your own ideas.  Later, when you are pitching grants, very much the same thing but with program officers: you have a great idea, and you find a way to dovetail it with their calls for proposals.  Finding the common ground between your research and others' research is a fundamental academic skill.

Second, money: if you are funded through a grant that needs image processing research done, do you think that your advisor or the funding sponsor will give you a big thumbs up when you say, "Actually, I have some great ideas for embedded security devices I would rather work on."  Nope.  If you were in their shoes, shelling out $30-60k on a student for a year, wouldn't you expect them to help get the grant completed successfully?  If you want full control over your research, become independently wealthy first.

Successfully doing your own research in academia, in grad school and beyond, involves a lot of meeting in the middle.  Given the huge disparity of research topics you mentioned (image processing versus security), I genuinely wonder about the overlap of interests.  If there really isn't much overlap, it might be worth looking for a different advisor.  You won't become an expert in one field by being mentored by a guy in another field, even if your advisor lets you run wild with any idea that comes into your head.

Update

Since more info was added about the funding and interest overlap, I can note a bit more here.  It sounds like your funding is relatively portable and not tied to a project.  In that case, you should have pretty strong control over what you want to do.  You should not be using this control to just pitch ideas and run with them.  The benefit of a PhD program (as opposed to learning how to research while living in a shack) is to apprentice with people who are experts in what you want to do.

However, having your own "batteries included" funding means you should be able to match with the best advisor for your interests. It sounds like you need to discuss the issue of overlapping interests with your current advisor.  If you don't want to go in the same direction as the lab, maybe they can suggest another group who does something that is a better fit.  Alternatively, maybe they will hit topics that you find more interesting during other phases of projects. It's not uncommon to switch advisors in the first year: I knew a professor in undergrad who actually recommended avoiding even starting in a given lab, so you could just meet with professors to find the best match.


In general, for any scientific paper, the key question for being able to publish in a reputable venue is: "Do we learn something new and interesting?"

In this case, I think the key questions to ask in this regard are:

Is there a set of real-world (or otherwise interesting) problems that fit the more general case of algorithm D, and for which A/B/C are not applicable (or perform badly)?
Does algorithm D also out-perform even-more-general algorithms (e.g., some of the foundational algorithms), or do they not apply for some reason?

If the answer to both question is yes, then you've probably got a nicely publishable result.  If the answer to either one is no, then you've probably got something new but not particularly interesting: that may still be publishable in some venue, but probably not well and probably won't have an impact.


Are professors allowed to participate in political activities?

Since you are concerned, it must be a good idea to look into the rules, as @Penguin_Knight suggests.  But it would be absolutely shocking if you were not allowed to volunteer for a particular candidate or party: by restricting you from doing that, the university would be infringing upon your own political freedom.

  I am concerned that I am in a position of power, and thus if I were to be out campaigning for a particular candidate, this could affect my students' freedom to vote, should I run into them while I am volunteering.

I'm honestly not sure what problematic activities you're envisioning here.  A university professor is allowed to be a real boy or girl.  Students may run into you while you're outside doing real person stuff, and they have no right to being "protected from you" any more than anyone else they might encounter.  How does running into a student affect that student's "freedom to vote"?

  Are there any rules in the university that forbids professors from participating in political activities? How much is acceptable? Can I help out with phoning people to get them to register to vote? Can I knock on doors in person? Could I run for office eventually?

Again, the answer to the first question is that if you want to know the rules of your university, you should not ask us, because you know which university is yours and we do not.  (Added: As Tom Church points out, there is a small but positive number of US universities for which the answer will be very different from the general case!)  The answer to the last three questions is that I would certainly expect you to be able to do all three of those things (again, you're a real person; you have the same right to knock on people's doors as anyone else!). If you successfully attain office, then this might interfere with your academic schedule and commitments, but it would be up to you to resolve that: e.g. if you live in a small town and get elected to a town council that only meets on Thursday mornings...probably okay.

If you feel strongly that (i) you want to be openly political and (ii) that you do not want your job to be even slightly at risk, here is some advice for that: I suggest you keep a clear separation of your political and educational activities.  When you bring up politics in the context of a course or student supervisory relationship, it should be in the service of an intellectual/academic point you are trying to make, not your own political activity.  When political ideas come up naturally in coursework, you should make an effort not to signal or imply that your own political beliefs are "the right answer".  You should certainly not try to politically proselytize with your own students or suggest that their grades will suffer if their political views do not align with yours.


What does it mean when a paper is rejected but encourages resubmission without a suggestion of new experiments?

Many journals are now encouraged to publish the data on the "efficiency" of the review process, e.g. the average time before initial submission and publication. Expected time to publication may be an important consideration for authors, along with the journals impact factor.

So, imagine that you run a journal, where a paper on average goes through 2.5 rounds of review and each round takes 3-6 months. If you sum it together, 12+ months from submission to publication would not look too attractive. But you only need to sum up if you invite revisions. If you "reject and resubmit", then technically you look at a completely new submission, and it counts as a new paper in your statistics. So, your processing rate gets shorter (which authors like), and your acceptance rate gets lower (which makes your journal sort of a prestigious one, tough to get into).

This is the main reason (in my personal opinion), why so many journals now rebrand "major revision" decision (and often "minor revision" as well) as "reject and resubmit".


How would I go about doing a PhD after an M.Eng in Biomedical Engineering?

Generally speaking, the main difference between an M.Eng and an M.S. is in research. An M.Eng is usually a course-based degree and usually does not involve any research. There is often some sort of "project" course which students will be required to take for credit, but that is still far from research.
An M.S would usually involve a research project and thesis, and it would give you exposure to the type of work a PhD student would be doing. That being said, many schools also offer course-based M.S. programs, so the name of the degree does not really mean much.

I would not recommend enrolling in an M.Eng program if you wish to study for PhD. In the U.S. in many schools having a master's degree is not a requirement for getting into a PhD program. I would advise you to inquire whether it's possible to be admitted to the PhD program at Cornell instead of the M.Eng.

For schools, the advantage of admitting students without master's degrees to PhD programs is that they will be around longer and probably have more time to do good work. In the case that the student doesn't quite meet up to their expectations, the can arrange for the student to leave with a M.S. halfway through the program. This to some extent compensates for the risk involved in admitting an undergrad (since they will likely not have much research experience).

M.S. students on the other hand have research experience. They have also written a thesis and possibly some papers. This gives the admission committee better insight into the applicants capabilities. Furthermore, a student with an M.S. degree will likely need less time to get started on their research and will not need to take as many courses, so they will probably hit the ground running once they enter the graduate program.

A student with an M.Eng degree will have a shorter PhD than the students coming in with B.S. degrees but will not have the experience the students with M.S. degrees have. So they will be at a disadvantage compared to both groups. Because of this admission to a "top 10" school would be a bit more difficult with an M.Eng degree.

Another thing to consider is that if your goal is a top 10 school, many of them give priority for PhD admission to students already pursuing M.S. degrees at their school. These are typically the schools which require master's degrees for PhD admission (such as Stanford and MIT).


How to correctly mention people in a PhD thesis?

Generally you should ask your advisor on that. It strongly depends on the discipline and probably the requirements of your parent institution. For example in my case the correct method was Method X was invented by Doe, but I have written a few works where the citation style was customarily Method X was invented by J. Doe as well as Method X was invented by John Doe.

On the other hand I can't remember any paper where an author would introduce biographical data of the people whose names are referred. You are generally not writing about those people but their ideas. Moreover, sometimes you may be unable to find the birth and death dates - what would you do in that case? Omit the data in case of few people where you were unable to find it?


Is it “legal” for a Senior Vice President and Provost of a College to be Intimate with a PHD Candidate in their editing?

The law varies widely, but I doubt that there are many places that would have laws against this. But university regulations are a different matter. More, but not all, would have rules, usually to forbid it. It would be, in most of those cases, a violation of the VP, not the student, I think.

But the situation can be fine, provided that the VP has no influence whatever over he grading/ranking/prospects of the student. This might be the case or not. It would probably be unethical if the student's future depends in any way on actions of the VP, rules or not.

Whether it is wise is another matter. Reputation is important.


Should I make my research students' pay contingent on completion of tasks (such as reading/summarizing papers)?

Do not do this. At best, you will appear merely stingy; at worst, perhaps financially abusive. (I also suspect your university would not even allow it, but I think that's not as important because it should not be done anyways)
I strongly, strongly advise you to reconsider how you think about students. It seems you are thinking about them like employees you want to squeeze some work out of, with some sort of benefit that you deserve for providing funds. This thinking is wrong, and leads to many of the student horror stories here about abusive advisors.
A student should never be under threat that their financial security is subject to the whims of their supervisor on a regular basis. Any process that leads to a student getting paid less than their full salary* should be a structured process with warning and opportunity for improvement. You write that "students need a reliable source of income" - exactly, so don't make it unreliable.
Students in research are not mere employees, they are future researchers for whom you are taking on a responsibility as an advisor. You pay students so that they can focus on their research and education. You pay students who you think have good potential as researchers that are worthy of your time investment. You are not paying them to do a job, you are paying them to learn.
If you think you need to add incentive for students to focus on things like reading, do that incentivizing outside of the regular compensation structure. One option is to have regular meetings where students present papers or literature reviews of a subset of papers. Students are typically quite motivated in that setting to look good in front of their superiors and peers and they will put in the effort. You could also use a bit of peer pressure to offer some sort of group reward, like buying lunch for the whole group when a student wants to schedule a presentation over lunch to summarize what they have read (harder to do now during pandemic times, but hopefully that won't be permanent).
I'm glad you've asked about this here before implementing it, because I cannot stress enough how bad this would be.
*Exceptions: for someone who is a part-time employee, like an undergraduate student, there is nothing wrong with hourly compensation, but it should not be based on production but rather on time worked. You can decide at the end of a semester if it's worth taking that student for another semester. There could be graduate students in special circumstances that work and study part-time; they should be paid a salary relative to their part-time level of commitment.


How to stay in touch with professor after graduating?

As far as my experience goes, this 'we should stay in touch' with no concrete suggestion as to how you should stay in touch, means he does not expect you to actually stay in touch on an ongoing fashion.

The way I interpret the meaning of this phrase as it appears in the email you quoted, it means roughly the following: "I am a busy man, and I have no particular thing in mind that we should cooperate about at the moment. But I like you, I am thankful for your comments, and I am impressed with what you achieved so far and by your potential. So if at any point in the future you see a concrete way in which our relationship can be put to use please contact me, and I will do the same on my side."

So I would just answer back saying something like "I'm glad were helpful. I'd be happy to chat more if you ever want [more comments about the current paper or anything related to the it or the job that you are doing now]."


How do you judge the quality of a journal?

The way I usually choose journals is by looking at where people I trust/follow publish, and where previous work was published. It is usually not too hard to compare the quality your work to the quality of the work you are citing, and chose a target based on that. Unless your field is highly mutli-disciplinary, you will see the same journals/conferences popping up again and again in your references; submit to one of those.

Before submitting, however, it is always important to look at a few articles from previous issues. This will give you a second gauge of quality for the journal and also let you pick up on any formatting and presentations quirks that might be present in the publication.


Taking a course on Pass / No Pass Basis for Grad School

I have been to Ph.D. admissions committees both as a grad student and as a faculty member. Generally speaking, if those courses are not very relevant to your major and your intended area of research, I wouldn't pay much attention to "Pass" grades (whereas low letter grades would probably stand out) We get plenty of domestic and foreign applicants with very diverse backgrounds and there are much more important things to look at in their application package.

I assume that the genesis of your position is that you want to be challenged in class, but not at the expense of risking a bad grade staining your otherwise impressive transcript in a subject that probably won't define your career. While this is certainly not the only approach, it seems sound thinking to me.

If they do affect your GPA in a negative way, however, I would consider a bit more carefully--perhaps not in a binary way, but in regards to how many courses to do this with.

By the way, remember that as a Ph.D. student you can also take courses outside your major you feel curious about. I certainly did that.


Factors contributing to Research apart from publishing Technical Papers

A senior thesis (or, if you're engineering, your senior project, if you did one) would probably be a good thing to showcase, as it demonstrates both your ability to perform work in a group as well as your ability to write.
Internships are great. They show that you can work and it also can serve as a reference.

If you've done anything else particularly notable (e.g., won a nationally recognized science fair), you can mention it, but the number of people who've done stuff like this is pretty miniscule.


Should I include written evaluations (from courses I took) in my transcript as part of the job application materials?

If your course evaluations range from good to excellent and there is nothing harmful in them, including them can only be helpful.

In the worst (and probably more likely case) people will simply not read the additional 10 pages of transcript. This is, of course, exactly where you would be if you didn't send them in the first place.

A thick application file is not a problem. Just remember that it falls on you to help narrate and explain what you include. For example, if there are a few choice quotes from the evaluations, you might want to call those out in your application front-matter.


Is there something between auditing and taking for credit?

This depends on your institution, so you will have to ask someone there, a general answer is not possible.

My undergrad institution allowed for taking some courses (specifically, those not part of the specific requirements towards your degree) as pass/fail rather than graded, which meant if you scored at least a C you got credit and if you scored worse than a C you didn't, and the course wasn't included in your GPA.

However, auditing a course typically gives you the same access to course materials as taking it for credit; the opportunity to learn should be the same however course credit is assigned. Auditing is not typically a way to prepare for a course, but rather for self-enrichment and perhaps to learn material outside your area of expertise without being evaluated to test your interests.

edit: The OP has since indicated that their reason for auditing these classes was that they hoped to prepare ahead of taking the course for a grade, due to disability they experience. I would recommend consulting with the institution's disability office to get proper accommodations rather than using the audit or pass/fail system directly.


How to resolve disagreement with project teammates over which professor to work with?

To expand the comments above into an answer: ask the professors what they think is a good idea, ideally both at the same time (e.g., at the end of a class where they are both there).  You have less chance of coming off as disrespectful, since you approach from the perspective of a student desiring guidance.  If they say you should work with both, then that's probably a fine plan to follow as well.


I am only familiar with the humanities through my wife. When she reads writing samples for admissions she seems to talk about the quality of the research, organisation, and clarity. She doesn't seem to care about topic so much. It seems many Art Historians change their topic area early on during the PhD process in the US.


Search for certain keywords in all articles which cite a given article

Yes, Google Scholar has the functionality that you are looking for.

First, find the article that you want other papers to cite on Google Scholar, then click on the Cited by link.

Now, click on the Search within citing articles box, and either type your keywords into the search field (you may need to enclose your keywords in "quotes") or do an Advanced Scholar search and type your keywords in the appropriate field(s) there.


Second Masters in maths after master's in physics: how does it help getting into PhD in Europe?

Nothing compensates your low GPA in Physics. I think you have to learn to live with that. But there are several ways to improve your competency for the PhD application in theoretical physics. First let me share my experience with the application procedure in Europe.

In France, from my experience, there is a well structured process for PhD intake. Your application will undergo an initial screening using various criteria, one among them is the GPA, other is the masters thesis. Next step is the interview(expect several rounds). I had a completely different experience in Germany. I was offered a project associate position for 6 months as an entrance to the PhD, predominantly on the basis of my current work(master thesis) and the recommendation from my adviser. I know several others who had similar experience. I recommend you the following.

Find a shot term internship in the field of your liking. If you do really well such that you may get a publication or at least if the supervisor could give a good recommendation for your application, then you have good chances of getting admitted.
Have you considered the US? A great deal of research is going on there. Appear for GRE if your GPA meets the minimum requirements. I cannot say for sure a good GRE score alone can get you a position, guess someone from US could say more about that.
If the above options seem impractical, try applying for a MS in theoretical physics. There are some specialized MS offerings like astrophysics, photonics etc.
Do an independent research in the field of your taste. There is always a possibility for collaboration with others in the field if you could convince them you have the potential to be a researcher.

Bottom line

IMO, doing a masters in mathematics for the sole purpose to be a potential candidate for PhD in theoretical physics because you think you can't be one due to your low GPA is not a good idea. There are other options to consider. If you are really motivated to do math, nothing stops you.


Why do open access consortia affiliate themselves with questionable publishers

Why do these consortia affiliate themselves with questionable
  publishers?

Hindawi is a founding member of the OASPA and MDPI, whichever opinion we might have about the quality of its journals, is a major player in the OA business. The OASPA apparently conducted an internal investigation about MDPI and seem to be happy about the results. The question might be more: is the OASPA questionable?

  how can the academic community pressure open access consortia to
  consider their members carefully?

I would recommend not to consider open access consortia as relevant. Then, not submitting papers, not serving on the editorial board, and refusing reviewing tasks for sketchy journals.

On a more general level, one thing we could do is reduce the demand for low-quality, pay-for-publish 'OA' journals by challenging the hiring policies based on publication volume in our local institutions.


Can a thesis not answer the research question and still be good?

The short answer to your question is yes, you can have a good result even if you don't (completely) answer the original question. However, the advice you really need is from your professor. Don't express negative feelings about how he "forced" you or anything like that. Ask him for his analysis of your work and how to best position it.

Many research questions take a long time to resolve. Don't be discouraged by that.

But the work isn't a failure, and you, especially, shouldn't think of it that way. You want to ask yourself, however, "What, exactly, did I demonstrate in this work". Your wording of the rest should revolve around answering that question and showing how you did a good job of it.

You can have a final section that discusses how this work is part of a larger work and briefly describe the problem you started out to solve.

However, some of your statements confuse me. You seem to be saying that at some earlier point you gave a title to the university that makes a claim of success to the earlier question, and that that can't be revised. Such a policy would surprise me and I would make doubly certain that you are correct. But advice from your professor would also be valuable here.

When it comes time to publish your work, there is no rule anywhere that I know of that restricts you in the title of the paper(s) that get produced. So even if you are sort of "stuck" with an inappropriate title, you can just treat it long term as an anomaly. You then have a little joke you can share with future students if you stay in academia.


What is the fair way to grade in this pandemic?

It depends, of course, on what you mean by "fair". If you mean correctly distinguishing top performers (high marks) from average or low performers, I don't think it is really possible without assessment. Certainly depending on a mid term exam is not fair.
But if, by "fair", you mean "not disadvantaging any student" then something like a universal "pass" for everyone is fair. This would come with a note on any transcript that grading was cancelled for this term.
One university in the US has decided that there will be three possible grades for the term just ended: Pass, Fail, and Incomplete. But even there, it depends on some sort of assessment to make the distinctions.
Even cancelling the term and returning everyone's money isn't fair.
The bigger problem, of course, is that we (myself, at least) no longer trust that this situation is temporary and we may need a fundamental re-thinking of both course delivery and student assessment. But, in the short term, some sort of bridge to whatever will follow is necessary.
Chaos requires extraordinary action.
One thing that can be done, I think, is an informal, personal, assessment to each student making suggestions about what they have missed and where they need improvement to continue. This doesn't scale well, of course. But even an ungraded "exam" will give the student some feedback that they can use, if they choose, to advance their education. But making "grading" decisions on such things is difficult to do as, then, cheating is difficult to control.


Is this statistic about how many Latinos/Hispanics have a PhD in the USA correct?

This information came from a tweet I shared to express my excitement for finishing my PhD and, in the process, increase by 1 the number of underrepresented minorities in the US with a doctoral degree. I did not expect for this tweet to get the attention it has, but I'm glad it's opened the doors for more in-depth discussions about diversity and representation in academia.

To clarify, I got my information from the following sources:

  < 2% of people in the US have a #phd

–United Stated Census Bureau, Educational Attainment of the Population 18 Years and Over, by Age, Sex, Race, and Hispanic Origin: 2014

  Of those, 6.5% are Hispanic

–National Science Foundation, Survey of Earned Doctorates 2016 (this number only includes Hispanic/Latinos that are also US citizens)

These were back-of-the-envelope calculations based on limited information I had at the time. I appreciate that others in this thread have provided further sources of information regarding this statistic. It seems like my back-of-the-envelope calculations were not far from the most recent figures of Hispanic/Latino representation in doctoral degrees.

My goal was not political or inflammatory in nature, I merely wanted to bring attention to the low numbers of Hispanic/Latinos with doctoral degrees, share my excitement for finishing my degree, and connect with others in a similar position. I hope this response can bring some clarity.


Doing a PhD in physics after doing bachelors and masters in mathematics

First of all, please remember that PhD is not about learning; learning about many different areas/fields/subjects. More specifically, it is not about increasing you knowledge in breadth, i.e., you know Mathematics, you can now learn about physics, then you can learn about computer science and so on.

PhD is about training in research.

Ask your self this question:

How can I contribute to this area (may be theoretical physics or any) in this particular topic by utilizing the knowledge I already have (say, acquired during bachelors and masters) in this specific field (say, in pure mathematics)?

Once you get the answer to this question (it should be in the form of a nice research proposal) you will definitely be able to do your PhD in that area, which you would select and do homework for.

2nd part:

It really depends upon the institute and the department you are targeting to: what actually is the requirement there? And remember, some might not need GRE subject at all.

So, please make a list of the institutes/departments based upon your interests/priorities and mention their requirements. Then you would be in a better position to decide which one should you go for. Maybe, only because it is unavoidable or simply you can perform better in that.

I would suggest you to have a profound focus upon the first part. Chances are that you might end up targeting a Mathematics department only, still being able to contribute in physics. Even, otherwise would give you a clear vision of what should you do and what you don't.


What does a textbook look like while you are writing it?

Before you spend a lot of time on formatting, contact a publisher or two and see if they want to work with you and publish your book. If they are excited enough then they will sign you up. You normally talk to an acquisitions editor at this stage.

But each  publisher may have different preferred ways of working with your manuscript and it can affect how you work and the tools you use.

For the content of the book, work with whatever tools you prefer, but as you get closer to publication, the publisher will want its own formats.

Normally, for a textbook, you will be assigned an editor (in the sense of one who edits - a content editor). They will make suggestions about your wording and such. You will need to work with this person, using some mutually acceptable set of tools. It might be Word or something else. If LaTex is required, they might do that formatting themselves, and if not, will probably provide a required template for you to use. Even if they prefer Word, they will most likely have a template for you. Perhaps a required template.

You will have only limited control over placement of figures and other such things, and only limited control over layout. But the publisher will somehow prepare the manuscript for printing using its own preferred layouts: margins and such. They may even want you to use, or avoid, certain fonts.

I think that very few publishers will just print a photocopy of your manuscript. There is some processing done before production. So, don't obsess over formatting until you are working with a publisher.

Some publishers will want separate files for any figures (or even for chapters). High resolution images. Others will prefer to create the image files themselves. You may need permissions for any figures (or photos) that you don't create yourself. If the permissions need to be paid for then that may be your responsibility, or you may be given a budget by the publisher for that.

Once the manuscript is reasonably complete the acquisitions editor (or a representative) will probably send your manuscript out for review to a few people they trust. You will get suggestions for improvement of the text, possibly a lot. Especially for a first time author. Your book could get rejected at this point, but I think that is very unlikely. But you will be expected to respond appropriately to all suggestions, usually by modifying the text. This stage can be maddening for a first time author and there may be several rounds of review.

Once they have a printable version, they will send you galley proofs for your approval. These might just be pdf files and you can usually make minor edits, but a lot of money has been spent at this point, so too many changes will be problematic. But your prior work with the content editor should make this moot.

They will try to accommodate you, but you need to work with them as well.