As a TA, what should I do about an error in the professor's lecture that I repeated in the lecture notes?

Just tell the professor: "The transcription of the lecture included an error, and many students made the same error on the midterm." (It really doesn't matter whether the mistake was made first in the lecture or the notes.)

He will decide what to do about the midterm.

He will almost certainly be very happy to hear about his error from you, rather than from a large number of irate students (which is likely to happen if you don't tell him).

Nobody is infallible - not professors, not teaching assistants, not students. If he gets mad at you for preparing "bad lecture notes" for proliferating one mistake that he made, he is completely unreasonable.

As an aside: this evening, I gave my students a quiz, and during the quiz my TA - who was helping me proctor - pointed out an error. I thanked him and told the students to disregard that question.  Then, after the quiz, I had the students get together in groups and work on "fixing" the question (the nature of the error made the fix non-trivial). It was an interesting and helpful educational exercise, for my students and for me. Errors can sometimes be an opportunity for good things.

Of course, I told my students that this is an important lesson on the dangers of taking code snippets off the Internet or from a book without carefully checking them :)


Referencing the papers at the end is not sufficient.

Generally, the litmus test whether or not something is plagariasm is whether the reader is given an adequate impression of how much of the text is other peoples work. Readers don't always read entire papers, and in particular may not make it to the end.

In your case, I would suggest to state at the beginning what your two main sources are, and give some indication of how heavily you are drawing from them. Then, throughout the paper reference each bit you've taken from elsewhere by where it is coming from.


The advantage of EPS over PDF? And why so many journals ask for EPS alone?

The eps format used to be the only possibility for including graphics in (La)TeX. Now the more modern alternative is using pdflatex, which also supports other more common graphic formats natively (such as pdf).

Most journals have outdated LaTeX processing pipelines, so they are still using eps. (And, frankly, they have little incentive to get more modern, since they are in a strong oligopoly position.)


Why do universities require international students to show language proficiency?

The short answer is that when people want something, they often experience cognitive distortions that prevents entirely accurate assessments. Dunning-Kruger is a good example of one of these effects, where a student thinks, "Oh, I'd love to study in Paris - and lots of people speak French, so I'm sure I could pick it up!" Learning a new language to a college-level of proficiency in reading, writing, and speaking is incredibly challenging, yet some people inevitably misjudge this.

Sure, the student would eventually figure this out and face the consequences, but in the mean time there are lots of reasons the institution wants no part in such a situation. For one, it's sad - a student will struggle, feel isolated, and most people end up blaming others for their situation and don't take complete responsibility ("why did they let me in if they knew it wouldn't work?!"), so it can be really unpleasant. I saw a student from China try to make it in English-only classes, and I couldn't make out if he even understood more than a few words in English - he only ever nodded, looked confused, and looked back down at his paper. It was just sad to see, and I can't imagine how this was helpful to him - the only way he could succeed was to have an interpreter (he didn't have one), or cheat, and that's just a terrible situation to be in.

Most institutions also have various statistics like drop-out and graduation rates, as compiled by an office like Institutional Research, often reported to the government (for "public" institutions, and others who take government money). Institutions have a lot to lose for regularly taking on students they have a very good reason to think will fail in their program, or will require disproportionately high resources to support. So they want to try to avoid such situations, when possible. Finally, positions in a class/program/institution are often limited, and accepting one student can mean necessarily rejecting some other student, which makes administrators even more keen to be careful of offering a spot to a student unlikely to succeed.


What are the common criteria of evaluation for a Post-Doctoral or Tenure-Track faculty position?

You seem to be most interested in a primarily research position so I'll say a few things about that and then give a broader answer.

Every candidate is different, with a different mix of positive and maybe negative factors. Every hiring committee is different with its own concerns. Every university is different, and usually they have a well-defined "mission."

But it is up to the candidate to make the case to the specific committee. Nothing positive that you do professionally is likely to hurt you unless your interests are wildly different from the "mission." So, for a research focused position at a university with a research focused mission all of the things you mention are good and any of them can be stressed in your application.

All universities love that sweet sweet grant money and some fundamentally depend on it, so be aware of that in seeking employment. It is hard to get tenure in some places without quite a lot of grant support. Other places it means little, but is still valued. Especially if the grant can support students.

However, you should try to match your own interests with the mission of the place. If you are very hot to do research you will be very frustrated at a place with little research synergy. Likewise there might be little future for a person interested primarily in teaching and advising at an R1 university.

Note that some small Liberal Arts colleges have a strong research reputation, others do not. In the US, some state universities stress a teaching mission over research. Others are just the opposite.

At one Ivy League college/university that I know of, faculty in Computer Science were (and maybe still are) given a choice of focus - teaching or research. They valued both and didn't require that every faculty be equally invested in both. But you had to excel in the one you focused on and be "acceptable" in the other. You couldn't ignore one aspect entirely. So, just as you need to make your own case for getting hired, you need to make your own case for tenure and the value of the various things isn't fixed in stone.

Note also that some R1 level universities in the US have a special category for teaching faculty. The criteria for hiring and retention are quite different from that of the research faculty. There can be a place for both.

If you want to do research today, but are at a small place that doesn't support it well, you will need to establish and maintain a wider group of contacts, possibly world-wide. This was impossible before the internet and relatively cheap travel, but is now a possibility. In my later years I collaborated with an international group, a few of whom I only met face to face a few times. But it takes extra effort if the coffee-room crowd can't help you explore your current interests.

Technical note. In some fields, such as CS, conference papers are extremely valuable. In other fields, not so much. Much of the intellectual life of the field can be carried on in good conferences.


How to find an editor for a statistics book?

Students can make good people to give you advice. If you pick someone who already has the knowledge they can probably give you good feedback on how what you say will work, assuming this is a text and not a professional work.

Graduate students in the field are often needing a bit of extra money and can often be recruited to help, especially if you also give them an acknowledgement. They are also good for providing solutions for exercises that you might include.

However, even advanced undergraduates can verify a book, both for readability at the level you are aiming for and for pointing out where they don't understand the formulas and technical terms you use. That can be especially valuable.

You are wise not to depend solely on your own reading. It is too easy to "see" what you think you wrote, rather than what you actually wrote. And for a textbook, someone who has taken the course in the not too distant past can have a valuable viewpoint.

I assume, of course, that you don't need someone to actually make corrections, as that may be beyond some students. You can do that yourself, certainly, as long as you learn where there are issues that should be addressed.


How hard is it to change universities after one year in a graduate program (USA, PhD in Chemistry)?

In chemistry (or physics) it would not necessarily be hard if your 1st year grades were great and you made progress in other activities during that year that showed you would be successful in US PhD system. The application timing is the difficult issue, as you apply in the fall to new school and you would have had no convincing track record by fall the first year.

People are accepting of helping (recommendations, etc) a good student switch if it is clear that no group within the department is suitable for that student due to funding, or subfield interest.

However, your email appears as if you are asking how to work the system to apply to one school  to get into the US, but then go somewhere else? Faculty are not clueless and some will be pick up on what feels like a lack of good faith or transparency during your year or two at the first institution. It will not lead to faculty being helpful. (And some resentment if it felt that scarce resources as TA or RA slots were 'wasted').


How to deal with unnecessary stress introduced by the supervisor?

It is not unreasonable for a supervisor to write emails in the middle of the night. I do it myself, and frequently at that (sometimes because I am honestly just working late, sometimes because I am in a different time zone). However, it is unreasonable to expect immediate response when you do so (more accurately, it is unreasonable to expect immediate response for basically any email, as the medium is fundamentally asynchronous and nobody should expect you to have your email open all the time).

That said, a significant part of the problem also appears to be your own mindset. You can't realistically change when your supervisor sends you work, but you can definitely change when you read it, and when and how you react to it. Just not reading emails in the night is a big start. Many people do it, and you do not need to have a bad conscience when you do it as well. A second part of this is also to not interpret every email as implicitly highest-priority. Try to assess what a realistic timeline for any given work task is - if your supervisor does not specify you don't need to assume it needs to be done next thing in the morning.

One problem that you may face is that you have by now trained your supervisor that you read and react to every email at any point in time. Even if it's unreasonable, it is somewhat understandable that this is by now how your supervisor thinks you work. The most pragmatic way is to change things gradually over time, combined with a non-accusory one-on-one talk with your supervisor that you are unable to deal with your current work mode. Don't use the words "you are stressing me out" or anything else that puts the token and blame on him. Say that you are stressed out and need to change how you work. The goal is not to elicit a different behavior from him (although this may also come out of the meeting as a sideeffect), but to communicate to him how you plan to address your stress-related issues going forward.


Is it possible to guess the purpose of my potential PhD supervisor inviting me to lunch?

No one can really know what the exact motive is of the professor. However, if he or she is willing to take time to meet with you (especially for lunch, which means the person is also investing money into your meeting), I imagine that the program is able and willing to provide you with support and he or she is assessing your fit to work together.

Be aware that this could be something of an interview where he or she is assessing a few applicants to see which one is best suited for working on their project. Therefore, I urge that you to prepare for the lunch as you would any other type of academic interview (e.g. review some recent work of this faculty member, prepare questions ahead of time for him or her). When I applied to my PhD program years ago, one faculty member invited me to meet with her, but ultimately chose another applicant to work on her project. I received support from another faculty member to work on a different project, but the invitation to meet by the initial faculty member did not indicate a guarantee. Best of luck!


Should I submit a major revision if it seems that AE has the intent to reject?

Your call, of course. Either would be a step forward. But consider how much the revision will actually improve the paper. If a lot, then it is to your advantage to just do it, no matter where you submit. All suggestions should be, at least, considered for revision, as usual.

And a new submission will take its own time, of course. And a "top journal in the field" is probably worth some effort and even time.

As for the last question, each paper is different and each editor is different. A general answer does you little good. It is your paper that you care about.


Paper for software tool - Medical Domain

If you want to publish software in a quality scientific journal it is usually required that it represents a significant advance over previously published software, which is usually demonstrated by direct comparison with available related software. There will be no way to get around this.

I would also recommend to put the code on github (http://github.com). Github is more and more recognized as THE resource for code hosting. It is a free service for public repositories, and it is widely accepted in the community, e.g. you can register your Github repos with Impactstory (http://impactstory.org).

"Source Code for Biology and Medicine" (http://www.scfbm.org) might be an appropriate journal for you.


How should a job market candidate leverage his or her network?

I should not contact my network about potential jobs at any particular university because I would sound too “desperate”.

Oh, please. Your chair probably remembers the Good Old Days when you could submit three applications with your one publication "in progress" and get two interviews and four offers.

Yes, of course you should contact people in your professional network.  The academic job search is no time for shyness or modesty. You need to sell yourself. You need other people to sell you.

Ask them if their departments are planning to hire, and if so, what their hiring priorities are. (And no, you cannot get this information from the text of their ad.)
Ask some of them to write recommendation letters on your behalf.  At least in computer science, you must have at least one reference letter, preferrably more, from someone who is not from your home institution and not a coauthor, but who can still write in detail about the quality, depth, originality, and impact of your work. Congratulations, you've cultivated the perfect environment to find such people.
Write them to let them know you've applied, and ask them (directly, shamelessly) to put in a good word with their hiring committee.  You will not get an offer from any department, and you may not even get an interview, without a local champion inside that department; the champion doesn't have to know you personally, but it certainly helps.  (Of course, a better way to cultivate a champion is to knock your interview out of the park.)
Always thank people for any information or help, even if they just say "Sorry, we're not hiring in your field this year." or "Good luck!"


I can't speak for everyone, but 6 weeks would be fine for me personally.  Less than 2 weeks I'd be grumpy about, if there weren't a good reason.


Encouraging team-work while discouraging free-riding

I assume that your goal is not just to catch and fail the free riders but to see to it that they actually do the work that will result in learning.

However, I'll note that having a goal of "sharing the work equally" is unattainable except over time and/or averaged over many different interactions.

The most radical suggestion here is to flip the classroom so that people do the active work of learning under your observation. Rather then passively "consuming" information in a group and then working to solidify it outside your view, the opposite occurs. Now, you can watch how people are contributing and you can encourage a true exchange of ideas and sharing of skills.

Note that for large groups flipping is much harder, requiring space and possibly help. But working in groups is easier to monitor than individual work in a flipped classroom, no matter the scale. People help one another and so there is less burden on the instructor and any TAs

But another idea that is less radical is to have students simply do peer evaluations of all group experiences. Students are reluctant to bad-mouth their friends, of course, so you need to use a scheme that they will consider "safe" in their social interactions. In pairs, you can ask two questions. First, what was your partner's chief contribution. Second, what was your own chief contribution. These are done separately. Note that both questions are positive and are less subject to simple opinion.

In larger groups, say five, I would ask to name the three most important members of the group and to also say why for each of them. The question about your own contribution is also needed. Note that a student who is never given praise is probably contributing less. But I didn't try to reduce these comments to numeric scores.

Knowing that others will have something to say about your contributions encourages them, I think.

To make this work you need to have a hand in forming groups so that the same people don't always work together. Different tasks can use different ways of forming groups, but some of them need to be under your control, even if it is just random assignment.

I would have students answer these questions on index cards so they can be sorted. Now you can look at a set of comments about each student and make judgements as needed, but you also get an idea about who needs coaching.

My own experience with this is positive. In one case, as student who was not standing out in the classroom was said by his peers to be an outstanding contributor to their project. I wouldn't have noticed it but for these comments and thought he was a bit of a slacker. In this case the work was done outside my view and so would have missed the interactions.

Note that both of these suggestions are for group work. One of my chief goals for groups was that team members could help each other learn. Not everything a student learned needed to come from me.


Need help and advice concerning how to apply and look for grad schools

The first advice I have to give you is perhaps the most important: in the immortal words of The Hitchhiker's Guide to the Galaxy, DON'T PANIC.

First, identify the schools to which you'd be interested in applying. You should find a reasonable number (6 plus or minus 2 is typical), and plan on some "long shots," some "typical" schools for you, and one or two schools which you would have as a "fall back" option—in case none of the "long shots" and "typicals" work out for you.

You should also find people who can write letters of support for you. This is perhaps the hardest part for you. Luckily, you've finished relatively recently, so you should be able to find people in academia who can write some letters of support for you. If you have a few people such as employers who can vouch for your work ethic, that could also work.

Doing well on the GRE will also help, but it isn't likely to make a huge difference except in "borderline" cases.

One thing that might help your case is to get directly into contact with people at the various schools you'd be interested in attending. If you can organize a meeting with some of the faculty there and present your case in person, that can leave a more positive impression than just submitting an application "cold."

The other thing you can do to help your case is to have a clear and compelling explanation for what you want to do, and why you feel a master's or a PhD is the right way to accomplish those goals. I see far too many applications from candidates who otherwise might be viable who can't elucidate a single reason to go to graduate school beyond. Having a compelling plan can go some ways toward convincing skeptical faculty members that you are serious about graduate studies.

In addition, you can consider all of the advice about getting a bad transcript past admissions as additional suggestions for how to proceed.


Is there a "Facebook" for researchers? (to collaborate on projects)

Facebook is not a collaboration tool. It is a tool for advertising companies and the government to gather information about people; that is the business model and the primary intent. Interaction and collaboration are at best secondary effects.

Now, other social networks controlled by commercial entities and many have business models which involve advertising, but Facebook is among the worst.

At any rate, have a look at:

https://researchgate.net
https://academia.edu
https://linkedin.com

The first two are sites intended for researchers to showcase their work using a generic UI/UX. Users of both complain about their spamminess; and Academia.edu apparently has most functionality limited by a paywall. I personally have found ResearchGate less spammy than Academia.edu, but some comments below suggest otherwise.

The third one, owned by Microsoft, is more geared towards recruitment/head-hunting, and is about presenting one's professional profile rather than research. But I've found both ResearchGate and LinkedIn to be places where I've discovered people who are potential collaborators or sources of useful material for my research. I have not, however, used these networks to actually engage on collaboration.

But of course, that is also true for scientific conferences and journals, or rather their on-line form of websites and downloadable proceedings.


Is it okay that I don't meet my project supervisor until I can reach a certain subgoal of a long project?

It is useful to meet with your advisor on a regular basis, even if (especially if!) you haven't achieved everything you had hoped to since the last meeting.

Otherwise, you risk getting stuck in this "Avoidance Cycle":

(Source: PhD Comics)

Also, meeting with your advisor may be helpful because:

If you haven't achieved your goal because you are stuck on something, your advisor may have a suggestion to help you get un-stuck.
If the project is delayed because some part of it took longer than expected, your advisor may want to re-arrange or re-prioritize parts of it to adjust for the new time frame.
Having to report back on a regular basis motivates you to keep making regular, if incremental, progress.

But these are only possible if you keep your advisor informed of what's going on - whether the news is good or bad.


Biological data being used by an unpublished research paper is considered proprietary

The copyright is probably on the full database release flatfile and the formatted entries ... you will find similar conditions for UniProt/SwissProt so it is not so unusual.

The restrictions on scripts are common to prevent server performance hits from a large number of requests.

You can simply invite reviewers to download the data from some other server, for example from the EBI SRS server. The URL for entry A00673 would be

"http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?[IMGTLIGM-ID:a00673]+-view+FastaSeqs+-ascii"

You can also use a list of accessions, for example A00673 or A01650

"http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?[IMGTLIGM-ID:a00673|a01650]+-view+FastaSeqs+-ascii"

If downloading many entries you should pause between requests, but putting lists into the URLs may reduce it to few enough not to cause a problem. I doubts EBI would be upset by 200 requests - they would be concerned about thousands.

There are various fasta formats available for IMGT data, you need to find a server that produces fasta files compatible with your input requirements.

Alternatively of course your reviewers could download the whole database from IMGT or any of the other servers (including ftp://ftp.ebi.ac.uk/pub/databases/imgt/) and generate their own fasta subset from the list of accessions/ids

Hope that helps!


What are the responsibilities of the Publication Chair of a conference?

I've been publication chair of an IEEE conference before, and it's pretty straight-forward.  IEEE has a well-arranged process for managing conference publications, and you basically just need to hold up your side of the deal and make sure that nothing falls through the cracks.

In particular: you should have an IEEE CPS publications contact.  You can get this from the current general chairs, since they're dealing with IEEE, or (since its usually the same from year to year) you can ask the previous publications chair.
Set up a meeting with that person ASAP and they can walk you through the process and make plans with you; I've had very good experiences working with their publications personnel.

The key responsibilities that you should expect to fulfill are:

Set a schedule acceptable to IEEE and the conference chairs
Work with the general chairs to fill out the required forms and get them to the IEEE on time, so that you can get the publications IEEE CPS contract signed.  This will include setting the various different types of publications (e.g., main track, short papers, workshop papers, tutorial abstracts, etc), as well as pages sizes, expected number, delivery method (I recommend USB sticks) and budget.
Send information about camera ready from IEEE to the various conference chairs that need it (general, program, workshops, tutorial, etc.).
Work with chairs to get all of the front matter prepared in a timely fashion and within the schedule negotiated with IEEE (cover, index information, introductions, sponsored material, etc.).
Immediately after the conference, report to IEEE whether there were any no-shows (who should have their papers removed).
One month after reporting whether there were and no-shows, everything should appear online in IEEE Xplore. If it doesn't, then you need to keep pinging IEEE's representative to make sure things get into IEEE Xplore as promptly as possible.


Is it possible for an international masters student to get into teaching role in US Universities on completion

I understand that teaching positions are mostly reserved for Full time Phd Holders and is getting increasingly tough. So how difficult it will be, post MS, for an international applicant to secure a full time instructor job.

In the US, community colleges (i.e., two-year colleges) sometimes hire faculty with master's degrees.  At four-year colleges and universities, it's basically impossible to get a regular faculty position without a Ph.D.  (It might theoretically be possible, but only under extraordinary circumstances, for example a pioneering industrial researcher who never completed a Ph.D.)

So that means you would have to target community colleges.  How difficult that would be depends on the circumstances, and it's important not to assume it's easy to get such a job just because the institution is less prestigious.  I don't think you'll be able to get a full-time instructor position without some prior teaching experience, since you'll need to demonstrate your teaching abilities.

Being an international applicant shouldn't be a big deal overall (assuming you have authorization to work in the U.S.; see Paul Garrett's comment below), but it may come up in several ways, such as English proficiency.  The most annoying may be that teaching experience is other countries is sometimes not taken as seriously.  It can be difficult for evaluate for people unfamiliar with the system it took place in, and it may involve students who are very different from typical U.S. college students.

  I have seen certain Master students get a faculty position in the uni itself where they completed the course.

I've never seen that happen for a regular faculty position in the U.S.  Occasionally, a master's student may be kept around for a while as an adjunct to teach low-level courses nobody else wants to teach, but this is generally not a well-paid or respected position.  Someone with truly exceptional teaching skills might be retained long-term in a position with a title like "senior lecturer with security of employment" (not a regular faculty member but reasonably paid and without fear of abruptly being fired), but there are not many such positions and they are not easy to get.

  What other degrees/certificates can help tip the scales in my favour?

I don't think any other degree or certificate will play an important role.  If you find an opening for which the hiring committee genuinely doesn't care about having a Ph.D., then teaching effectiveness will be the primary criterion.  Any evidence of excellent teaching will be helpful, but other degrees or certificates are not generally a compelling form of evidence.


Why are journals used in modern scientific academic research?

Why are so many people publishing [on ArXiv]?

You have to be careful with terminology when making statements like that. ArXiv is certainly "publishing" in the literal sense of "making public" but would you say that you'd "published a book" if you'd just put it on your website? Probably not.

  My question is, why were journals used to begin with?

Because they predate ArXiv and the web by hundreds of years, though the format has changed over time.

  Why are they used now?

Partly through inertia, partly through a lack of alternatives. On a purely scientific level, ArXiv itself is not peer-reviewed. On a non-scientific level, ... People have an intuition about the quality they expect from a paper that appears in a particular journal and we don't have alternatives that allow us to make this kind of judgement. Correspondingly, certain journals have quite a lot of prestige, which is important for students early-career researchers who are looking for promotion; a large fraction of papers have at least one such author. It's easier for people like Tim Gowers to work outside that system.


Can anyone provide insight on a Master's student struggling with research?

I would say this is your opportunity to explore and find a (hopefully small) gap in the literature that you can fill. Reading literature reviews is the best way to start. I had a similar experience a little earlier in my degree (masters), and I was able to pick a topic that I loved, and it kept me going; I am almost finished, and it has been, IMO, a successful endeavor.

If you are applying to a PhD program after, you will have experience exploring a little on your own. Your advisor will be able to say in their recommendation letter that you took initiative in your research.

The difficult part will be carving out something meaningful that you can do in 7-9 months (1 month to research and decide & 2-4 months for thesis writing and defense at the end). Your advisor should be able to help you to narrow the scope to something manageable.


Is it looked down upon to do a second PhD (vs a postdoc)?

I guess I would approach this from the opposite end. You want a faculty position, what is the best path to that goal? And would your feelings change if you had to fit your future research plans into a more acceptable box?

You say "no one" is working in the field you want to work in, and it's not a sufficiently interesting topic to catch your current advisor's interest in letting you play around in that space. Have you reached out to anyone in X field at your university? Do they seem interested or supportive? Are they willing to commit cold hard cash to your training or research?

To me, the idea that you're interested in a 100% new out-of-the-box field suggests that actually finding a faculty position in that field would be close to impossible, because from a hiring committee's point of view, your chance of landing big papers, big grants, finding students who share your interests, etc., would be next to zero. You'd be fighting uphill the whole way.

The reality is that academia is hyper-specialized at the moment, and academic careers have probably always been very prestige-/stature-driven. Someone doing computational medievalism (or whatever) risks seeming like a dilettante by the medievalists, and imho most science-minded folks sadly don't hold their humanities colleagues' research in very high regard. [aside: i very clearly remember attending a career panel back in grad school where a physicist casually suggested that humanities papers don't undergo peer review. The indignant English prof in attendance lost no time setting the record straight!]

Therefore, you might consider whether your research direction, however novel/interesting it is to you, has a place in your academic ambitions? Or maybe once you land your CS professor job, you could always try and learn something during a sabbatical? In any case, before you put years of your life, not to mention your own money (my understanding is that most humanities PhDs are self-funded or require substantial time spent doing teaching work for a small stipend), you should get more perspective from others whose opinions you truest in the two fields you want to bridge.


Is using an old book's solution considered cheating?

One more thought in addition to Buffy's answer:

Transparency is maybe the solution here: tell your prof "I remember this problem, I met it studying book last summer. How shall I proceed with the assignment?"

This will ensure that there won't be any ground for accusing you of cheating
Prof may give you another assignment, from which you can learn more.


Succes in research, awful in solving in basic things

I have seen my fair share of mathematicians failing basic tasks. Probably more iconic ones are related to arithmetics but that is more understandable.

For example I have seen a +40 years old working mathematician volunteering to teach differential equations because s/he didn't feel confident in his/her ability do solve them and wanted to force him/her-self to improve.

I don't think it is detrimental to fail basic tasks as long as you behave accordingly. As long as you discuss with others while doing your research and prepare before you teach, you can avoid most of the potential issues and fix them along the way.


What your looking for looks a lot like the wikimedia project wikibooks.org.
Here a quote from the main page :

Welcome to Wikibooks,
the open-content textbooks collection that anyone can edit.
3,072 books with 83,999 pages

Also there are a lot of old textbooks in the public domain published in different languages. One repository of such books is project Gutenberg, where I find the category page helpful to get books in the right context/science.
Also some books, event recent ones are published with a open licence and as such you are allowed to read, copy and translate them at will, such books are for example published by framabooks (mostly in french).
These are must have books and there are some others to be found.
Also some book are freely readable online, copyright holder being aware, eg see VMLS if interested in maths or Motion Mountain for physics, but a big mouthful, not just 100 pages.  (not sure for the licence, couldn't check it).
These are more often than not typeset in latex... So you might also ask on the author for the sources.
(I hope this answer isn't too much out of the context of the question)


Why don't many textbooks have electronic versions?

tl;dr-  Many books aren't available in ebook form for money and pretentiousness.

Money can be impacted because it's really easy to pirate ebooks.

Pretentiousness is relevant because there seems to be a stereotype about printed books being more prestigious.

Worth noting that I'm obviously against this practice, as I see it to be contrary to the mission of spreading knowledge and making academia more broadly accessible.  I would encourage instructors to select texts with electronic formats available whenever possible.
1.  Ebook availability makes pirating easier
It's pretty easy to pirate an ebook.  A quick automated script can take screenshots that're easily enough pasted into a word processor and saved as a PDF.  Common ebook apps attempt to have defenses against this practice, though they tend to be fairly easily defeated (which I won't elaborate on for obvious reasons).
The same can be done with hardcopy books, e.g. as demonstrated by Google Books, though it's a lot harder and typically produces lower-quality results.
2.  Many feel that hardcopy books are more prestegious
I have to stress that I truly despise this point.  However, the one book that I've written isn't available in ebook form as I wrote it as the request of a PhD advisor who insisted that it not be available in electronic format.  I protested this on multiple occasions, so while I strongly disagree with their logic, here I'll explain it.
First, we wrote the book primarily due to the publish-or-perish regime that rules much of academia.  My advisor felt that, by writing the authoritative book on a topic, it would establish recognizable authority across the field.  Students would know our names because they had to buy the book, and academics in the field would need a hardcopy of it on their book shelves.  And, of course, publishing books looked good on their faculty activity report, an annual report to their supervisor (typically a department head, or the school's president for senior professors).
My advisor had also expressed the opinion that readers respect a book more if they can feel it in their hands, especially as a hard-cover book.  The formality and expense impressed upon the reader the stature of the topic and the writers.  We've recently seen an example of how some students can feel that electronic materials are less respectable in this post.
And while my advisor didn't say this, I think that it's important to note that, until recently, ebooks and the internet weren't a thing.  Many older folks completed their education using only hardcopies, and due to that background, they have a strong emotional association between hardcopies and legitimacy, while electronic copies can feel cheap by contrast.


One option would be to create a tags P1, P2, P3, P4 ... and assign "rating" to articles how much priority they have. Tags could be updated as priority changes.

(similar system could be used with Delicious.com tags to websites)

Tags are more flexible then folders. Mainly - Multiple membership in more than one tags


strategy of looking for external reviewers in grant applications

For external grants that ask you to suggest reviewers (common in UKRI grants for example), you are expected to suggest someone who has the technical, theoretical, or methodological expertise to evaluate the proposal and who would have no conflicts of interest in doing so. In other words, no one that you have an active research project with, no one who you have had significant past research collaboration with, no one that you go down to the pub with as friends, and likely no one in your institution. You can and should suggest people that you know to be collegiate and who are generally friendly to your work, that's expected. The granting body will then consider your suggestions and will likely select one or two of those you suggest mixed in with someone you don't suggest just to balance things out. It is unwise to try to game this any further than suggesting someone who you know generally likes what you do as reviewers are asked to disclose any conflict of interest. For them to reveal there is a conflict that you did not reveal does not sit well.

For an internal grant, that will likely be a bit different and it is best if you get clarity from your institution as to what they expect. They may expect reviewers to be internal.


How to take notes while reading textbook?

I tend to have problems documenting-while-reading as well. What tends to work for me is either:

Read all of the resources on your topic that you find, and then write a summary of what you've learned immediately afterward. Try to have enough detail that someone following behind you can make sense of what you write. (In a few days, you will be that someone!)
If I have a specific need (say, to defend a point I'm trying to make), then I'll quickly jot down bullet points while I research, but no more than that. Then when I'm finished with my research, write the summary described above.


Supervisor asking me to fabricate papers (and other problems)

Never ever fabricate. I repeat: never ever fabricate.

If you do not manage to get a suitable reference from your superviser, your career may or may not take a nosedive, depending how lucky you are to find someone else to write you  recommendations.

But if you fabricate, you will be found out if your research is of any relevance whatsoever (and if it is not, why do this research in the first place?) and then your career, sooner or later, will be destroyed with no hope of recovery.

Addendum: in my personal opinion, the two capital crimes in science are plagiarism and fabrication. But, in my very personal opinion, fabrication is the worse of the two, because it wastes many people's time and effort in trying to reproduce the results.


Clearinghouse for Physics Postdoc positions?

There is no clearinghouse or standard way of advertising postdoc jobs in Physics. Opportunities may be advertised on the Physics Today Jobs or Nature Jobs websites.  But more often they are listed on an institution's job website or a research group website.  Positions may be advertised on mailing lists.  Some just are not advertised at all.  You have to ask.


Supervisor takes my results to type a manuscript. Is this normal?

I don’t know about normal, but certainly not helpful in making you an independent researcher. Perhaps they want to make sure you see how it’s done right, perhaps they really need a paper fast, but I can see why you’re frustrated. I suggest you politely suggest that you help write things that you contributed with: like the data analysis, or the experimental setup. Ask her if she’d like a draft by a certain time.

  She listed herself as the first author and me as co-first

This is tentatively good though author order importance greatly varies by field. Contribution is a tricky thing to establish. You say you generated 95% of the data; even if this is true, maybe your PI and the rest of the lab managed most of the grunt work allowing you to generate so much. What do other lab members think of you getting first co-authorship?

  Does the number of papers/ or amount of contribution listed in the papers matter to PIs who are employing potential post docs?

Very much! When I hire postdocs I want to be sure that they’re “fully baked” and able to conduct research independently, so they can help drive the lab forward, and perhaps advise students (as you were advised).


Does careful selection of graph colors in a manuscript have any positive impact on reviewers?

Some people will tell you that colors shouldn't matter because only data should matter.  Those people are wrong.

All human readers (including reviewers) find some graphical presentations easier to digest and comprehend than others, and the choices that matter include color.  Of particular note, it is often important to consider color-blind readers, who are up to 10% of males, depending on population, (though many fewer females).

Color sets that work well for color-blind readers often work well for non-color-blind readers as well.  You can find a number of good resources online to help you decide what colors to use, such as this "Color Universal Design" site, among many others.


Do supervisors take a person as PhD students who abandoned his graduate program?

I would consider it, but only after having a talk with the student. In addition to the usual about background and research interests, I'd want to know about why it was abandoned and how we can have some assurance it won't occur again.

But for many this might also depend on how much support the advisor was expected to give. In a situation in which a lot is required (such as a lab), the situation gets more difficult. In other situations, where the professor provides mostly feedback and a few ideas, it is less critical. In CS, it could go either way, depending on the topic of the dissertation research.

But your activity in the interim indicates some seriousness (assuming "a person" means yourself).


How to best leverage resources offered at small undergraduate school to be a competitive applicant to top law or architecture + planning schools

As you mentioned, your career interests may change, and at the moment seem to be rather varied. However, there are a few things you can do to prepare for a graduate career.

1) Research the programs you are interested in (Harvard, Stanford, MIT) as well as similar programs that you would be willing to apply to. You will likely need to split this into two groups: architecture and law. Once you've identified approximately a 6-12 of each type of program, look at their admissions criteria, recommended coursework, and suggested extracurricular or work experience. Most graduate programs will indicate the grade point averages, standardized test scores, and subject matter experience they desire in applicants. Generate lists of the most frequently mentioned criteria.

2) Examine the offerings at Hamilton College in relation to those lists. If the law schools all request you take Intro to PolySci, be sure to work that, or an equivalent course, into your schedule. If the architecture schools all require you to submit a drawing sample, plan on taking at least one art class so that you can develop a portfolio (and possibly a letter from the professor). If certain specialty courses are unavailable at Hamilton, see if you are able to take the class at a nearby university, or complete it as an independent study.

3) As you narrow your career interests, use the summers (or possibly the school year) to engage in internships or jobs in those fields. Entry level work in a specific field and internships are often seen as markers that students are driven, organized, and mature. You may also consider joining undergraduate student organizations in these areas, such as the American Institute of Architecture Students (https://www.aias.org/website/article.asp?id=8), which can engage you in the field at a national level.

4) Regardless of where you apply, you will eventually need letters of recommendation. Be conscious of this while in school and develop strong relationships with your professors. Speak up in class, volunteer for projects, and seek their advice on your career.

I attended a small, private liberal arts college and used similar steps to prepare myself for possible graduate careers in biology and psychology, and found them to be effective. Although the school may not have been a tier 1 research institution or offer classes in every subject, the flexibility to complete independent projects and faculty support were invaluable.


Reality check on advice for statement of purpose

All good advice.  In addition, may I suggest that a statement of purpose should answer the question, what will you do if they admit you?  It should be
future-oriented.  What are your goals and what are your plans for getting there?


I have noticed GPA calculation "bug" in our University, what should I do?

What is the clever thing to do when one finds such regulations in own University which can be used on one's own good?!?

I'm so glad you asked.  The clever thing would be to realize that the best way to raise your GPA is to do excellent work in all your courses.  Aside from being the optimal strategy GPA-wise, this has the fringe benefit that it is the only strategy with inherent rewards beyond the GPA game.

Look, I don't know where you're enrolled, but your university has taken a step down a dark road by playing with weighting GPA's differently than the number of credits or course hours (which is the weighting which corresponds to the actual instructional time and, ideally, to the workload of the course).  You're contemplating a further step down this dark road by trying to play games with their game.  It is up to them how they compute the GPA.  I disapprove of their strange weighting system, but do you know what's even worse than a globally enforced strange weighting system?  A student who asks for "a specific GPA calculation for myself".

Just rise above.  See if you can recapture the quaint idea that your goal is to learn the course material rather than attain a certain number at the end.  Or, if you feel that the world has moved on and that number that you get at the end is too important to your future to so naively dismiss, then respond by GETTING BETTER GRADES.  Merciful Minerva, we live in strange days.


Why are all these papers exactly 10 pages long?

Most American computer science conference papers are precisely 10 pages long, because most ACM conferences have a strict 10-page limit on proceedings papers.

(ACM is the Association for Computing Machinery, the primary professional society for computer science.)


Is it bad if my mom comes to a conference with me?

You ask about "stick together". This is probably not an ideal idea.

Generally, in a conference, you want freedom of action. Going with your mother may induce you to "talk to the known" person whenever you are unsure; i.e. you talk to her whenever you are not sure how to approach people - the notorious "escape route" - but this is exactly what conferences are not for.

When I went to my first conference, I made a point to talk to as many people as I could. At the beginning, it is quite a leap of faith. But later you find, it is fun, you get to know people, and you get to know new research directions and ideas. Sometimes it feels difficult, but remember: all you people have one thing in common - the topic of the conference. You are very unlikely to go wrong starting a conversation about that.

If you are unsure how to start, start with people which look like they are alone at the conference, and probably a bit lost. They will be grateful to get somebody to talk to; you may meet interesting colleagues (don't think that, because they are alone, they are not good scientists - good scientists may not be good at socialising), and notch up a good deed, to boot.

It is fine to take your mother to social events and the like, but I recommend that, if she joins the conference, say, because she is interested, that she stays mostly in the background and does not send signals of "supervision" to others or - even more importantly - to you. If you can keep that balance, then, by all means, bring her with you.


What happens when a PhD student finishes the thesis but is forced to defend way after the contract ends?

It is fairly common (at least in Germany) that the date of final defense is after the contract/funding ends. What should happen in this case is that this is discussed between the PhD student and the advisor as soon as possible. And with "that" I mean the funding/employment situation. Actually, there should be a discussion about the future plans of the PhD student somewhere around the last half year of write-up and if the advisor does not initiate this, the student should do it. Indeed, PhD students can have different plans, e.g. "having a job outside academia secured an wanting to start as soon as possible", "wanting to apply for postdoc positions", "continuing at the current place in some way", "applying for a fellowship somewhere"… In each of these cases advisor and student should proceed differently and without knowing the situation, things may go the wrong way.

  Is this treatment considered fair for A (given that other PhD students in the same office stay 5 or 6 years without anyone being bothered)?

I can't judge "fairness" but for sure it is unfortunate. But if nothing regarding the defense date and the further plans of the student has been discussed, delays in the defense date are common (and in some cases no problem for anybody).

  Is there anything A could do to avoid being in this situation? Or A should just accept that "that's how things are" and move forward?

See above: Discuss exactly this matter as early as possible.

  How can A then ask for a recommendation letter with such treatment?

I do not see how recommendations letters are influenced.

  And finally: What does this say to the external committee? Is it possible that this would create a very bad image for A to the reviewers?

Since procedures for the review of PhD theses are quite different at different places, I don't think that the process has any influence of the external reviewers.


How to get an advisor for my amateur research?

You've mentioned that you intend to apply to grad school.  It would be helpful to know where you are in the academic process: high school, started university, finished university?
Regarding asking for help, I see two distinct phases:

If you have not yet started the project (and you are not currently a student somewhere), then I think most professors and professional researchers would be very wary to spend any time helping you.  Complex systems, is, in particular, a field that attracts a lot of crackpots, and even the most well-intentioned projects of interested amateurs usually fizzle.  I think the best bet would be to find someone you already know to provide early consultation, rather than cold-calling a professional at this stage.
If you are enrolled in a university of some kind, then the story is different: the faculty has something of an obligation to talk to eager students. (-:

If you have already made significant progress and have specific technical questions, I think almost anyone would be wiling to help.

One other piece of advice: don't worry too much about talking about your idea.  Many 'amateurs' get obsessed with the secrecy of their amazing idea -- this is the road to crackpotdom.  I think it would be quite reasonable to state your idea on a site such as mathoverflow and ask whether it is a credible research proposal.
If you can cite recent publications in refereed journals that indicate active interest in the area of your proposed work, then this is a good sign that you have both done your homework and identified an interesting subject of investigation.
That said, even if the thing you are investigating turns out to be interesting only to you, it could still be worth continuing.  It might lead somewhere more interesting later, and you would certainly develop useful skills in the process.

If I don't get anyone on board, what are my chances of publishing, or at least getting a pat on the back from admissions committees when I apply for graduate school? Do they appreciate this kind of thing?

A successful independent project, especially one resulting in a publication, would be great material for your grad school app.   If your project does have interesting results, it should not be too hard to publish, regardless of your credentials.
Even if it turns out that your work is not publishable in a refereed journal, it might find a home in your school's "journal of undergraduate research" (or something similar), which would also be a nice resume bullet during the grad school application procedure.
Finally, it's probably best to simply avoid the word "amateur".


Is a software-simulated experiment enough?

This is impossible to answer without reading the actual paper, but I will do my best to give you an indication.

If the hypothesis is exciting and the simulation is well-executed and also gives the expected results: probably publishable. Otherwise, probably not.

Given that you need to ask this question here, it looks more like a "no", but don't let me (or any other random person on the internet) stop you: if you think it is publishable you should definitely try it. In the worst case it does not get published and you have learned something.

Also, you should ask this question to your supervisor (if you have one), or try to find someone to work with who has experience publishing papers: support from someone with experience publishing will probably be very helpful (read: necessary) to get your paper into a journal or conference.


Is there any information about the trend of journals preferences regarding Word over LaTeX?

Both ACM and IEEE accept LaTeX publication format, which represents computer engineering to a large extent.1

Based on this list which categorizes publications in various fields by their 'friendliness' to LaTeX (primarily linguistics-related), many linguistics publications accept LaTeX (especially those related to computational linguistics / natural language processing).2

1 Cf. http://acm.org/publications/latex_style/ and http://ieee.org/conferences_events/conferences/publishing/templates.html.

2 The list was last updated in January 2010.


Accepted article still not assigned a Volume or Issue number in a journal

Do write, very politely, to the Editor in Chief. In most cases he just wants to pursue other topics or maybe wants to bundle your work with a similar one which is not yet 100% ready.

Rarely, though, even editors might make mistakes, and it is not impossible that your work had been involuntarily shelved.


What is the average salary of a life sciences post doc in Singapore and what is the average living cost there?

I have found that a good general source for salary information in Glassdoor.com: everything on it should be taken with a grain of salt, but it's a good starting point for getting a general sense.  Searching there at the moment, postdocs in Singapore seem to be reporting around $5K/month.

Combining that with the cost of living estimator recommended by Fabio Dias, it seems to be survivable, though you'll likely not be saving much.


I believe this is an institution-dependent issue. Different departments and schools may have very different approaches as to what is formally allowed. In this day and age, however, collaborations, particularly between different departments or institutions, is generally looked on favorably. Whether it rises to an "official" arrangement or not, however, is clearly a different matter.

I don't believe that this is normally done via an employment contract; I think this is handled according to the regulations of the department—so the chair or graduate officer (or whoever normally approves student-advisor matches) would have to sign off on the arrangement. The responsibility for making sure all appropriate procedures are followed, however, lies with the advising team. (In general, this only matters with respect to the thesis committee and matters related to the thesis defense itself.)

The only other situation which might complicate matters is if both advisors are jointly funding the student; then the situation is certainly thornier. However, for such purposes, usually one advisor is the "hosting" advisor who has the primary responsibility for the student, which normally obviates the need for a complicated contract.


None of this would be illegal, at all likelyhood (but I am not a laywer).
The more important question is whether it is ethical or not.
With regard to theses (i.e., bachelor, master thesis, also PhD thesis), I don't see any issue in posting the thesis somewhere public. (Indeed, PhD thesis usually must be published.) After all, your thesis is your work (certainly this is the formal point of view), and it is up to you what you do with your work.
On the other hand, if you have a supervisor who wants to publish results from the thesis as part of a journal article, it might be better not not publish the thesis before that, such as to protect your ideas until the paper is out. However, this is more about being smart than about being ethical. Also, as far as I see there is no such issue involved here.
Note that the situation is different for results which are not part of the thesis, and which is not solely your work: In that case, you cannot publish them without consent of your coauthors. (Again, this is not about being illegal, but about research and publication ethics.)
Finally, even if it is fine to post your thesis, a bachelor thesis in practice often does involve contributions from the supervisor, so it is probably smart to ask them for permission. As has been pointed out, they might well be happy to showcase good students.  And last, since your supervisor does not seem to care much about publishing, they should not mind those ideas being publicly available (unlike when they would like to use towards for a publication).


How to make good use of compulsory study plans in connection with PhD studies?

I can sympathise with your sentiment about the study plan. The idea is generally good but it will only be as good as one makes it. In my department we started with study plans long before it became a mandatory requirement. The reason was mainly to establish a contract (although strictly speaking it has no legal meaning) where student and advisor agree to the terms of the work. We had instances where both students and advisers were not doing their part and lacking a paper trail made discussions difficult, usually both parties blaming each others for the catastrophe that emerged when it was too late.

So, I still look at the study plan as a tool when things go wrong, actually to identify when things start to diverge and nip it in the bud. There are students who do no appreciate the plan but as subject responsible (and in our case the discussion involves also me) I try to make it a good and reflective discussion. I do believe it is good to take the opportunity to reflect upon what has been done so far and try to lay out the plans for the next year because in a PhD project the nose is often close to the work and perspective may be difficult to get. Providing an opportunity to express the plans can therefore be enlightening for all parties.

I must, however, add that the bad cases which the study plan is supposed to reduce, still are very difficult and the study plan is not enough to resolve such cases. So my recommendation is to try to find a format for the discussions so that they become useful and positive for you. I would not expect everyone to experience these discussions the same way so in the worst case, try to make it as pleasant as possible.

EDIT in response to comment.
As with most things that are forced into action from "above", the way to handle study plans and how to relate to them has become unclear. I can personally see that different departments view the document differently and although the Science faculty of my University has issued guidelines, my suspicion is that they have no clue what they are trying to say. So it is all confusing.

Now, recently I heard a lecture by Bob Harris at the Karolinska Institute, Stockholm which concerned the so-called Intended Learning Outcomes (ILOs; another fancy term). You can listen to a talk similar to the one I attended on BrainShark, however, a warning is issued for the poor sound quality. The talk was for director's of graduate studies and the Faculty. The point made here is that we need to decide what it is that we do during a PhD and it is only then [my interpretation] that we can make use of the study plan to see if we meet the expectation from the side of the Higher Education Act as well as from our personal viewpoints. All of this becomes very involved and I am myself in the process of changing the way we look at the study plan to also include the goals of the research education as formulated in the Swedish Higher Education Act.

A problem with study plans as they stand now is that everyone must be involved in the process and as with everything else, they are not necessarily so and opinions will vary. Some will find it very useful and some will not. If a study plan is merely a meeting where one says 'done that; will do this' then its use is very limited. At best it is a time to actually reflect upon the progress or lack thereof. In the end, I think we have all lost track of the purpose of a PhD, we do not see the forest for all the trees. Publish has become the (only?) goal but all the other skills are not highlighted well or even considered. Integrating the wider goals with the study plan to record and view progress, could in my opinion be a useful tool but it requires more or less reorganisation and additional adaptation by many.


How much cost a graduate student to a supervisor?

As stated in the comments, this is impossible to give a general answer to; you would need to choose a field and a country.

That said, I think the factors you list are generally pretty negligible. The major expenses are usually the stipend, tuition, and overhead on the stipend+tuition. That can easily be $60K USD per student per year, often more. Also, students require considerable training (i.e., faculty time) before they start becoming useful. Those are the main drawbacks of hiring a student; no one is too concerned about the extra pens or an occasional conference fee.


Emphasizing previous sales skill in finance PhD application?

TL;DR: Don't over emphasize work experience, It doesn't "speak for itself" in academia like it does in business. Think instead of using it as examples of how you will make a good PhD student

This is a very interesting question because the answer depends pretty heavily on the field you area looking at, the university you are applying to, and the program that is looking at your application. I and a current Computer Science PhD student, and my path here involved a Masters Degree, then working in my field for 3 years, and applying to PhD programs twice, the first time after 2 years of work ( failing to get accepted anywhere) and the second time after 3 years of work. After I didn't get in, I reached out to one of the professors (at MIT) that I had shown interest in working under in my application. He read my resume and said, "Well theres the problem right there: you haven't done research in 3 years!" I worked at an R&D company all those years, and was surprised that what I thought would be an advantage was actually a disadvantage. The next year, the only time I mentioned my work (which was still pretty often, after all it was most of what I had done since I finished my Masters) was to exemplify how it made me a good researcher...and the rest, as they say, is history.

Really what it comes down to is, just like in business, how are you going to present yourself? You can highlight your business or not, but from my experience detailed above, it seemed to matter much more how you use your work history as an example, and less how much. The people reading our application are likely contextualizing it with their own experience as a person who once-upon-a-time was trying to get into a PhD program and is now a researcher, and the successful cases from their past students. They are going to look at your application and think, "Does this seem like a person who could really contribute to this field?" For me, when I focused on work experience as a part of what made me an applicant, set apart from other applicants coming straight out of school, it actually hurt me in the top schools. This is because all of the people reading my application were researchers and they wanted to cultivate more researcher from their students. As such, my emphasis on work experience hurt me. The following year, when I emphasized what research I had done at my job, as opposed to the general experience I gained at it, I got in to a bunch of top schools.

From what I understand, PhDs in Econ and Finance have very different goals internally (e.g. People who do a PhD in Econ want to do research on markets, trends, and math, and influencing policy vs. People who do a PhD in Finance want to work in finance, maybe do research in Finance, and get job in Finance). Knowing this, what the goals of your PhD are, and the goals of the application readers will help a lot in deciding what is the best way to use your work experience in your application.

Last piece of advice: don't be afraid to reach out. The worst you'll get is a silence or a "I don't talk to prospective students;" no one will hold it against you. You think that some school or someone's research is interesting? If you can get them on the phone or email they will tell you exactly what they expect of their incoming applicants. Was the best decision I made in this long journey of mine...

Good Luck!


Dropping a Course in my Field Before Applying to Graduate School

I wouldn't worry about it. You have a perfectly valid reason for dropping. Your advisor can give the best advice, of course, knowing you better than we do, and also knowing other options you might have.

But a poorly taught course won't give you much of a push toward your goal in any case.

But if your advisor is "on board" with you dropping and supports you generally, then you should be fine for the more important task of getting good letters of recommendation, which will count much more heavily than a W on the transcript.


What to do when one my co-authors is openly insulting me but the others remain silent?

Things have gotten personal, it is best if you remove yourself from the fight. Anything you say, no matter how sensible or innocent, is likely to be poorly received.

Instead, talk with your most trusted collaborator and ask them to defuse the situation (and follow up, to make sure they do!), preferably someone who has received the insulting emails first hand. Once your difficult collaborator has calmed down, you can all meet and discuss the paper. (NB: it is possible that some have already started to talk to him about this in private, or they are just waiting to see what on Earth is happening with you two, so silence doesn't necessarily mean inaction).

I'd say it is rather unusual for someone to snap at you, so there may be something else going on here, and perhaps you should look into it. On the other hand, some people are plain rude. In any case, personal insults are not acceptable, and this behaviour should not be tolerated.


Do high-ranking US grad schools typically interview PhD applicants?

I have not seen anything to indicate that PhD programs no longer interview candidates. I was interviewed in person by many (~75%) of the schools I got into for my PhD program in 2015. I doubt this has changed in 4 years. In fact, I helped interview several candidates in 2017 and 2018 at my school. I was invited to tour and interview at several well regarded schools in my field.

Note that some schools do not interview candidates. This is especially true of lower -tier schools in my anecdotal experience. But I had colleagues who interviewed at some rather prestigious schools in Massachusetts.


Is autism more prevalent amongst students in well-ranked universities?

There is research to suggest that the general belief (or stereotype) is accurate relative to subject area - specifically, some (but not all) areas of STEM (science, technology, engineering, mathematics) have a greater amount of autism prevalence than would be expected by pure chance. There is no research I can find that considers rank of University comparatively, but there is research that compares the prevalence of autism spectrum signs/symptoms/behaviors/classifications between various fields.

Science, Technology, Engineering, and Mathematics (STEM) Participation Among College Students with an Autism Spectrum Disorder

  Findings suggest that students with an ASD had the highest STEM
  participation rates although their college enrollment rate was the
  third lowest among 11 disability categories and students in the
  general population. Disproportionate postsecondary enrollment and STEM
  participation by gender, family income, and mental functioning skills
  were found for young adults with an ASD.

Selected quotes:

  Young adults with an ASD had a higher proportion of majoring in STEM
  related fields (34.31 %) than any other disability groups. The
  difference was significant for seven out of the 10 pair-wise
  comparisons. When we broke down the STEM related fields into computer
  science, engineering, math, and science, we found that the high STEM
  participation rates among young adults with an ASD was mainly driven
  by a high concentration in science or computer science majors. Young
  adults with an ASD were significantly more likely to major in science
  (12.12 %) than their peers with LD (4.72 %), SLI (4.71 %), ID (5.40
  %), HI (4.80 %), OI (1.45 %), OHI (4.55 %), TBI, or MD.1 These young
  adults with an ASD were also significantly more likely to major in
  computer science (16.22 %) than those with LD (4.06 %), SLI (5.90 %),
  or OHI (5.19 %). However, the high prevalence in STEM majors for young
  adults with an ASD was not found in non-STEM majors, such as health
  science (7.64 %) or social sciences (9.52 %)...

  When focusing on STEM majors, the odds of STEM majoring were 13 times
  higher among males with an ASD than females...

  These results provide the first national picture of postsecondary
  enrollment and STEM participation for young adults with an ASD as well
  as their peers in 10 other disability categories. Our analyses suggest
  that young adults with an ASD who attend college are most likely to
  pursue STEM majors. However, they also have one of the lowest overall
  college enrollment rates...

  Despite a previous lack of national evidence, the idea that people
  with autism might be predisposed to choosing and succeeding in
  STEM-related majors and jobs has gained a footing in popular press
  stories and among advocacy groups (Moore 2006; Morton 2001; Ross 2006;
  Safer 2012). Our findings confirm that individuals with an ASD are
  more likely than the general population and other disabilities groups
  to gravitate toward STEM. The STEM major rate (34.31 %) for young
  adults with an ASD was not only higher than their peers in all 10
  other disability categories, but also higher than the 22.80 % of
  students in the general population that declared a major in
  STEM-related fields in postsecondary education (Chen and Weko 2009).
  In addition, this study found that young adults with an ASD in STEM
  fields were more likely than the general population to concentrate in
  science [12.12 vs. 8.3 % (Chen and Weko 2009)] and computer science
  [16.22 vs. 6.6 % (Chen and Weko 2009)].

Note that this indicates that people on the autism spectrum are more likely to choose certain fields, such as computer science and engineering, than is the general population - but people on the autism spectrum are also less likely to enter college at all compared to the general population.

This study links to many related studies, but only notes one other similar study in a single United Kingdom university that showed a correlation between autism and mathematical skill. All studies in total still make it impossible to compare higher and lower ranked institutions.

Finally, note that the mention of MIT is notable not simply because it's high ranked and famous - but because it is famous for a specific set of technological developments, related to AI (the topic of much of the interview in the OP), as well as engineering and computer science generally.

You can go about this in a rather sideways manner, however, from this one note from the above study:

  Young adults with an ASD were less likely to enroll in a 2-year
  community college (27.66 %) or a 4-year college (14.95 %) than all
  other disability groups except intellectual disabilities (ID) or
  multiple disabilities (MD) (Table 3).

This shows that autism is less prevalent at unranked/low-ranked institutions period, so you could roughly infer that those with ASD who choose to go to college at all do so primarily at institutions which are more likely to be ranked (or ranked relatively highly). This is a rather weak argument, but it's about all we seem to have to go on.


How to proceed if email asking for a recommendation letter hasn't gotten a response after 3 weeks (during COVID-19 pandemic)?

Send a follow up email reiterating your request and the deadline. It's likely the professor has just lost your email in their inbox. It happens, pandemic or not.


Is it a good idea to include "research interests" section in CV for PhD admissions? If so, what to include in it?

The section on research interests should help to identify these quickly. In principle one could deduce your interests from your publications, talks, thesis and so on, but an exposed lists makes life easier.

However, you can not just tailor your list of research interests arbitrarily to the position as they should be in line with the rest of the CV. If you state that something is one of your top interests but this topic does not appear anywhere else in your CV this looks suspicious. My advice is, to be totally honest here. Do not include anything which is not truly your research interest, and if you include something that does not show up in your CV, have some explanation for this somewhere else (e.g. in a research statement or cover letter). Don't write one of these applications where everything looks like a perfect fit for the position, but nothing is backed up with evidence.


I found published results of my mentor to be wrong. How to tell her?

As a matter of fact, I believe there is no such thing as guilt or ruin
for other people's work when it comes to the academic aspect of the knowledge.
Actually, if you do not share this with your mentor in order to be fixed, you
may ruin many other further research...

I suggest you do this respectfully and carefully. You can go to your mentor and talk about this problem. You can show her your code and your understanding from the paper, then confirm whether or not you are right. Let her decide what she can do about this. There is also a slight chance you have made a technical mistake while investigating their work, so keep this in mind when you discuss the issue.


Is asking your PhD supervisor a basic question considered inappropriate?

If your colleagues in the department—presumably also PhD students—don't understand the concept, either, it doesn't strike me that the question is truly "basic." That said, if your advisor is aware of your background, then he should know that there will be some things that might not be "obvious" to you.

Now, in this case, you have already "done your homework": you've searched for an answer on your own but couldn't find one. Mention this to your advisor when you ask the question. A good advisor will recognize that you have done what you're supposed to and provide some guidance to help you. He may not provide you all the answers but should at least be able to point you in the right direction.


Sounds like you'll be doing interviews. If this is the case I would call them respondents


How can I tell whether a mathematics journal seems reputable?

For academic mathematicians, it's not so hard to avoid predatory journals. We have a sense of the journals that we "typically" publish in, and the journals we "aspire" to publish in, and we stick mostly to these journals. For journals we don't know yet, we can ask colleagues to get their opinion. One (possibly unfortunate) goal of publishing in academia is to build a vita and maintain/advance your career, and it doesn't help as much to publish in a journal that none of your colleagues or supervisors has heard about.

For people who don't have that kind of professional experience, there are several easier questions you can ask. The better answer to each of these is "Yes".  On their own, none of these questions indicates that a journal is necessarily reputable or nonreputable. But, if the journal gets a "No" answer to many of them, then I would be very hesitant to submit a paper.

Does the journal publish with no cost to the author? Reputable mathematics journals almost never charge fees for publication. Some very good journals offer an open-access model as an option, but it is almost never the default at the moment.
Is the journal indexed by MathSciNet and/or Zentralblatt MATH? These sites aim to be very comprehensive for mathematics journals. Being indexed is not really a sign of quality, but not being indexed is a red flag.
Is the journal ranked on the Australian Mathematical Society Ranking? Even C-rated journals can be OK, but if a journal is completely omitted I would take that as a reason to be cautious.
Is the journal either published by a well-known publisher, or affiliated with a university or mathematical society?  Most reputable math journals fall into these categories, but not all. Some journals run by professional publishers are still not very reputable, of course.
Does the journal have a professional looking website?  Grammatical errors or parts of the website that seem to be entirely missing are a cause for concern.
Does the journal have a long history of publication (say, at least 20 years)?  Most predatory journals are very young; most math journals are relatively old.

The "American Journal of Pure and Applied Mathematics" has a "No" answer to all of these questions. If they really did have a 10-day turn around between receiving a paper and accepting it, as described in comments, I am even more skeptical of the quality of the journal - that is an almost absurdly fast turn around time for a mathematics journal.  I would not pay them anything to publish a paper of mine, nor would I recommend it to anyone else.

Of course, you can publish in a predatory journal, just as you can publish in a for-hire press. But if you are an amateur or "outsider" looking to publish in a math journal, you are likely doing it to get a sort of "seal of approval" on your paper. Journals that mathematicians view as unreputable will not give your paper that kind of recognition among mathematicians, just as degrees from unreputable colleges are unlikely to impress others.

If your goal is just to disseminate your mathematical work, and you don't require peer review, you can often use arXiv.org instead. Depending on the area, you may need to have a professional "sponsor", but the arXiv will keep your paper available for free for the indefinite future in a way that is widely accessible to the public.


Should unsavory but otherwise scientifically correct experiments lead to retractions?

In human and animal work, the Declaration of Helsinki was written in 1964 and was designed to provide ethical oversight of medical research. Work that was done without proper ethical oversight cannot be published in most reputable journals. If it was somehow published, it would be retracted. Most journals require a statement in the paper that good research practice was followed. Other fields presumably do not require such statements since the frequency of such unethical and dangerous behavior is rare. That said, research that wad conducted in a manner that was more dangerous than necessary should not be published, and if published should be retracted.


Is getting back to normal life difficult after PhD?

To answer your question, we have to clarify some misconceptions it seems to carry. First, a fixed routine is a staple in most jobs you'll come across. You're going to have to accept this. Even at Google, employees are given the freedom to take time off anytime they want -- but this time has limits, and it's on the promise that they'll return to work for a chunk of hours. The vast majority of jobs, no matter how flexible, will not be lax enough to let you work at a coffee shop in the long run.

The same goes for academia. As a professor or academic, you'll be required to teach, do some forms of public service, and, of course, do research. A lot of things from the first two will be fixed beyond your control in terms of task variation and scheduling. As for the rest, there's some freedom to allot time to tasks as you see fit, but given the amount of work you'll have to do, it will come to be structured in some way or another.

Second, it's more accurate to say that a lot of people aren't staying in academia after their PhD. The market today is vastly different than it was twenty years ago. Academic jobs are harder to come by, and tenured positions are an endangered species. Most people will find themselves working as adjuncts or lecturers for a large chunk of their careers. And so PhD grads are now more commonly seeking employment outside academia -- industry, governments, NGOs, etc.

Third, most importantly, no one chooses or should choose a job because of a free schedule. That's far too limiting. Choose a job whose tasks click with your interests, something that motivates you to work. Consider the reverse for your own background: if you hated research, I'm sure that no matter how many hours you were allowed to spend in a coffee shop, you wouldn't have enjoyed yourself or done well.


Asking a professor to supervise research done with a different professor

It is a bad idea for a professor in your department to enroll you for research credit under his supervision without actually supervising. This is taking all the responsibility without any control, contribution to educating the student, or simply a pleasure doing the research.

However, you probably should connect those professors from different departments, so that they determine their shared interest and responsibilities in this project. Between them (and probably the undergraduate advisor) they might determine the formalities to follow department's & programs's regulations; but if somebody's name appears as an advisor of a work, he must actually do some part of advising.


Comparison of student involvement in research in different countries

Poland

Below I describe the default setting as general as possible. Things of course differ across fields, universities and even faculties. I base my generalizations on friends' experience on other fields/universities/faculties. Of course, there will be individuals who could have had a different (exceptional) path.

This can be of course expanded into hundreds of pages, but being to detailed is not the point here.

People finish high school at the age of 19.
Regarding academic education - studies - nowadays the Bologna Process is applied in most European countries. This means that studies are divided into three levels:

Licentiate (not to be mistaken with bachelor's) - lasting 3 years (mostly attainable at universities), or engineer's - usually lasting 3.5 years (attainable mostly at technical universities). One studies a particular field from the very beginning - e.g., when studying physics, one does not have courses in biology (well, in general, as there is also biophysics, which obviously joins both) and vice versa, etc. It's common that this level ends with a preparation of a small thesis (under an advisor's supervision) - usually something between 10-20 pages - some might call it simply a student project. In most cases a few weeks of research is enough for completion.
Magister - in many aspects equivalent to master's - lasting two years, being a bit more specialized - for example having a licentiate in physics, one can pursue a magister degree in astrophysics, or condensed matter, atomic physics, particle physics etc. Theoretically, one should spend most of the two years doing research for their master's thesis, but usually people choose a particular topic halfway through, and start research during their second year. Especially that there are still several courses to complete; usually more during the first rather than the second year.
Doctor or PhD - lasting four years. During the first one or two years there are some courses, sometimes taught by visiting professors, or senior faculty members. These are usually about the field of expertise of the lecturer - and these can change from year to year if the lecturer changes, e.g. once it can be about accretion disks on black holes, but the next year will have a course on relativistic magnetohydrodynamics. Usually, but not always, there's a seminar that has to be attended throughout the whole studies, or some other minor courses that need to be completed. However, usually there's only one course per semester, and rest of the time is spent on research.

To sum up:

One mostly learns;
one learns a lot and starts to do research based on that knowledge;
one learns a bit, and does a lot of research.


What are the pedagogical and institutional implications of implementing a Lecture Capture system?

I was involved in the installation of lecture capture systems in many of the classrooms on our campus with funding from a grant from the US Department of Education.  Overall, this has been a very positive addition, and both students and faculty seem to be happy that we've introduced the technology.  However, there were and are some concerns.

Student concerns.  The lecture capture system records in-class discussion.  Some students have been concerned about their privacy, but a policy that the lecture capture recordings will only be used for the current system and be made available only to students in the class takes care of most of this concern.  A related privacy issue is that instructors should be careful not to have sensitive discussions with students (e.g. about grades, absences from class, etc.) while the system is turned on- this could easily lead to FERPA violations.

Faculty concerns.  Some faculty were concerned that students would stop attending class if recordings were available.  Our experience has been that having lecture capture recordings available to students has little or no effect on attendance.  Faculty have also been concerned that the recordings would be used in ways that they didn't approve of (e.g. for administrative evaluation of teaching or to offer the course to other students without paying the faculty member to teach the course.)  You should have clear policies in place to address these concerns.

A major faculty concern had to do with how they present written content in the lecture.  For practical reasons, video recordings of material written on a blackboard (with chalk) or a whiteboard (with dry erase markers) simply don't work well with lecture capture systems.  Some faculty simply use prepared slides for their lectures.  An alternative (the one that I use) is to write the lecture material on a tablet or digitizing display.  Some folks use a document camera and write notes on pieces of paper that are displayed by the document camera.

Distance ed concerns.  Instructors and students can use lecture capture recordings as an informal way to have distance education courses without official permission.  This might not be acceptable to your administration or your accrediting body (or the US DoED- such a course would count as a "correspondence course" because of the lack of two regularly scheduled two way interaction with the student) but there's no good technical way to prevent it from happening.


How to obtain citation metrics for a low-profile journal that is not indexed in major journal databases?

Not a full answer, but I just want to point out that you can to some extent retrieve citations from, for instance, Web of Science (WoS) to journals that are not covered by the citation index per se. For instance, by doing a "Cited reference search". There you will find citations to documents, based on the citation information given in reference list of WoS publications, irrespective of whether the "target" publications (the ones receiving the citations) are covered by WoS.

For instance, when searching for "BRIT ASS STUDY RELIG" (a generalization of "The journal of the British Association for the Study of Religions", which seems to be found in WoS) as "Cited work" I find a ten citations in total to the journal.

This is probably not completely what you are after, but might be useful to know.


Is it a good practice to end a mathematical equation with a comma or a period in a scientific article?

In-line formulas are punctuated as required by the grammar.  For displayed formulas there are two conventions: punctuate as required by the grammar; or no punctuation.  See if the journal specifies this in their style (most don't).  Example

[Jahnke & Emde, Dover Publications]


Inquiring about PhD status and mentioning standing offers

Is it OK to send an email asking about application status and explaining that I have other standing offers which I have to make decisions about quickly?

Yes, it is more than okay.  If you think you might prefer school X over your current list of accepted schools, definitely let them know.  At worst they will be indifferent to this information.  At best, they will be very grateful to know this and be given the opportunity to enroll you.  They may for instance fly you in on short notice to interview / recruit you.  In no case (well, no reasonable case...) will they respond negatively.

  Would this have any negative impact on my application?

As mentioned above: absolutely not.  Rather it could have a positive impact, including in some cases resulting in better funding for you.

Added: The above is general advice without factoring in the thought that school X may be better than the schools to which you've already been accepted.  The advice is still valid, but the response from a top school may be less dramatic: top programs tend to make their admissions decisions more independently and tend to have good funding anyway.  (Nevertheless they would be happy to know that you are still interested in them before you make your decision.) A (fairly long) while back an old friendly acquaintance of mine was visiting the Harvard math department as a prospective student after already having been admitted to MIT (which is not a measurably worse department, I should mention).  He expressed to me the hope that MIT's interest would engender a "bidding war" between the two schools.  This did not happen and in fact the student did not stay in any graduate program for very long.


Commercial publication of your PhD thesis

The answer to this question is very field- and country-dependent.  In the sciences, a thesis is very rarely transformed into a book (except in certain locations, such as Germany), while in the humanities it is a relatively common end for high-quality theses.  To a first approximation, this is because science theses are often best "republished" or "prepublished" as a set of several peer-reviewed journal papers, whereas it is more common for a humanities work to be a single large monograph not suitable for such sub-publication.

There are a large number of pseudo-scam organizations which will contact you and offer to turn your thesis into a book.  Don't bother with them: they will merely waste your time and taint your reputation.

Instead, I would recommend beginning with a discussion with your advisor, who will know the common practices in your field, and may be able to help assess whether it is a good idea to publish your thesis as a book at all.  You may also contact a reputable university press, who can help assess your work and guide you through the process of transforming it.

No matter what, however, don't expect to make any significant amount of money from such a venture.


How to contact the Department Chair or Graduate Program Director?

First of all, the graduate program director is definitely the person to talk to.  There isn't much point in talking to the department chair; they don't necessarily have any direct involvement with the graduate program or admissions, beyond some nominal level of oversight.  (Note that in some departments, the MS and PhD programs may have different directors, so make sure you get the right person.)

I think it's fine to ask to talk to the graduate program director.  Graduate recruitment is typically part of their duties.

I would not necessarily expect that this conversation will directly improve your chances of admission.  Graduate admission decisions are usually made by a committee of the department's professors, and at best the graduate director is only one of the votes on that committee.  So no matter how good an impression you make on the director, the effect is limited.
Furthermore, the director will want to keep their decision based primarily on the objective information in your application file; it would be unfair if applicants who were able to visit the campus to meet them in person got a significant advantage over those who were unable to do so.

But it could be a subtle benefit.  They might also have suggestions about things to emphasize in your application.  And at a minimum, you can get more information about whether the program is likely to be right for you.

Email is usually the best way to get in touch.

  Dear Professor Wu,

  My name is Toby Ps.  I am a student at the University of Wossamotta, and I am interested in applying to enter your department's MS program.  I will be in your town between Octember 8-11, and I was wondering if I could meet with you or one of your colleagues to learn more about the program.

  One question I have is about admission requirements.  My overall GPA is X.XX, but I think this understates my preparation for graduate work because [reasons].  Can you tell me anything about how this affects my eligibility for admission to your program?

The second paragraph gives the director the opportunity to say "Sorry, we have a minimum GPA requirement of Y.YY, and we don't make any exceptions."  If that's the case, it will save either of you wasting any more time.

Assuming that you are at least eligible to apply to the program, you can proceed to arrange the visit.  If the graduate director is not available during those times, he/she may try to set up a meeting with another professor in the department who is knowledgeable about the program.  You may also be offered the opportunity to tour the campus, sit in on classes, meet with current graduate students, etc; do as much of this as you can.

During your meeting, you can discuss the likely strength of your application.  The program director (or other professor) won't be able to make any commitment about whether or not you would be accepted (admission decisions are usually made by a committee), but they may be able to tell you something about the qualifications that their successful applicants usually have, and that may give you a sense of your chances.  They may also be able to give you their personal assessment of how strong your application would be; you can ask for this, but if they don't feel comfortable giving it, don't press them.