Is it reasonable to request an exemption from certain degree requirements?

As a former Humanities Professor and Dean, my answer is "nope."  We heard so many times from the Engineering College that they wished their students would have more Humanities, that there's no way I can say okay, go ahead without it.  So many students would rather give it a pass, but I can say (besides my being on the Humanities bandwagon just in general), that my father worked for a professional organization of engineers, and the thing they wanted most at their professional conferences was work on writing and communications.  And that's what you learn in the Humanities.


When sending my final grades to one professional school, my transcript shows I am enrolled in another program

Does my unofficial transcript reflect how my official transcript will appear?

Only your university knows how they handle the two types of transcripts.  But it's possible.

If it does list Program A, will Program B regard this as an issue? Or can I just submit my transcript as-is with no explanation?

I think it would be reasonable to inform Program B that this is an error and that you have not enrolled in any program at A for the fall semester.
It's true that this might reveal that you have applied and been accepted to A, but I don't think that's a serious concern.  Every university knows that applicants apply to many different programs.
If anything, the fact that you've been accepted to another program would likely motivate B to try harder to recruit you, since it's confirmation that you are well qualified for professional study, and it shows B they can't expect you to accept a low financial offer out of desperation.

If this is an issue, is there a way I can circumvent it?

Sure; contact the office at A responsible for maintaining academic records (e.g. the registrar). Inform them that your transcript erroneously shows you as enrolled in the program, and ask for it to be corrected.


Is "lab" too informal a word for a formal cover letter?

I agree with you that both lab and laboratory don't sound good. Maybe you could use "group" instead?


What is more valuable: PhD degree or journal publication?

You will have to specify which country/system/subject you are talking about.
In the UK a PhD is pretty much a 100% requirement in most subjects. The only exceptions to this are subject where you would be doing vocational training, such as business studies, management, nursing, perhaps even law(?) where an exceptional standing and experience in the field might make up for a lack of PhD. The other big exception is medical school, where you could have an MD rather than a PhD.


What should I do if my parents are forcing me to study a career I don't want?

You are presumably an adult, you should not do something so important to your life as studying only for your parents wishes. Guilt-tripping children is very bad parenting, you should not feel ashamed to do your own thing.

However, before you start doing your own thing, think about what the consequences could be. Can you afford studying without your parents help?  Can you afford being at war with your family? Is there some sort of compromise you can find with your parents? Those questions only you can answer, and you (unfortunately) have to consider them. But never feel ashamed for studying what you want to.


academic dismissive undergraduate and research experience

The only proper answer will come from the admissions system of a university that you apply to. However, in any system that lets you make a personal statement or (better) includes an interview, you will have a chance to explain the issue. Most people, though not everyone, will understand that people change and grow. They also, normally, understand that the more recent work is a better indication of your future work.

I wouldn't worry too much about it, as long as you have a satisfactory explanation and have made up any learning deficit you may have from the year of poor work.


Should I withdraw my other PhD applications when I have a secured funding and a supervisor but I am waiting for the faculty decision?

No!

Until you receive an official offer of admission, you have not been accepted to the PhD program. Do not withdraw your other applications until you have actually been accepted somewhere.

(In fact, I would not recomend withdrawing your applications at all, but rather, if possible, waiting until you have all your official admissions offers and then deciding which one to accept.)


If you want to bring this up with them, you need to focus on concrete things you want done differently. "Try harder" is going to (a) antagonize them and (b) not change anything for you (except maybe for the worse). The professor, as you say, is aware that they are not putting in much effort, and it is very unlikely that they will change this habit unless forced to.

I suggest thinking about what, concretely, would help you most if done differently. If you need more in-class examples, raise the issue as "I feel the class would profit from working through more examples in class". If the inconsistent notation is a problem, ask him if it is possible to unify notation. These are not things that are an incredible effort for the teacher, so they have a realistic chance of getting addressed. Complaining and hoping that the teacher somehow sees the error of their ways isn't.

That said, there is a good chance that all complaints and requests coming from you directly to the teacher will be brushed aside. If the teacher is as badly prepared and unmotivated as you say, they are probably not the kind of person who would care deeply about student satisfaction. In that case, going one level higher (i.e., complaining to the programme manager or equivalent) is often more useful. While this will not typically improve things rapidly, it will likely improve the situation of this course over time, especially if complaints are raised from different classes (it's hard to continue to brush off student complaints if the same complaints come again and again for multiple years).


Master of Research (MRes) schools in the U.S.?

I've never seen the term "Master of Research" used in the US.  Many master's degree programs in the US do include a significant research component (either a thesis or project) while other master's degree programs consist entirely of coursework.  In either case, the degree can be called an MS (Master of Science) or MA (Master of Arts) degree.

In programs that do include a thesis, the thesis might be 6 out of 30 credit hours in the degree program.  This is nominally 20% of the program but in practice students often spend much more than 20% of their time on the thesis.  In my experience in mathematics, 3 semesters of course work plus two semesters of work on the thesis is more typical.


Contact reviewers/authors after the end of the review cycle for follow up

As has been stated in the comments to your question, contact between author and reviewer once the review process is complete is no issue. In a double-blind system this hinges on establishing the contact and in that case, as stated by Nate Eldridge, it will have to be a contact from the reviewer. In other cases where authors are known to the reviewers it depends on the willingness of reviewers to reveal their name.

The editors obviously sits on the information that could connect the two under any circumstance and you can of course always ask an editor to forward a request to an anonymous reviewer. As an editor myself, I am not sure I would be altogether happy with such a development since it would mean a lot of communication back and forth concerning matters with which I have nothing to do. I will add that many if not most editors do this on their spare time or time they take from their own research and are not salaried to do the work. This is why I would think twice about making the request and make sure the reason is very good and of such interest that an editor will see benefits to science to make the effort. As you probably realize, doing this once is no big deal but if it becomes routine it will occupy much time for an editor. I would then clearly opt for changing the review system to not be anonymous and try to convince the community that such changes has benefits worth considering. Another option is to keep the review process double blind but then provide all information to both parties once a decision (accept or reject) has been reached.


Is there a way to see which papers have used a particular R package?

Sometimes (not often) papers will formally cite the package.
This is more likely to work if the authors have published a peer-reviewed paper that describes the package; it makes it easier to cite/more likely to be cited. In the case of the tidytext package (which may or may not be the package you're referring to), you can find the citation info here. More generally, try citation("package_name") within R. On Google Scholar, this page lists the articles that cite Silge and Robinson 2016.
Or you can use Google Scholar, which does a full-text search and may pick up the name from papers that mention it even if they haven't formally cited it.

Silge, Julia, and David Robinson. “Tidytext: Text Mining and Analysis Using Tidy Data Principles in R.” Journal of Open Source Software 1, no. 3 (July 11, 2016): 37. https://doi.org/10.21105/joss.00037.


In what language do scientists communicate with each other in European research institutions?

From my perspective of working in multiple European universities in different countries:
In a "closed" conversation setting, it will exclusively depend on the people involved in the conversation. The prime requirement is to use a language that every participant understands and speaks. A secondary concern is to use a language that people are particularly comfortable in. As a result, a meeting of two German researchers and a German student in a Swedish university will usually be held in German.
In an "open" conversation setting, people usually prefer to use a language that will allow other people to understand and join the conversation (usually English). Exceptions happen and might be considered as rude by some.


A job application asks for a "sample of current scholarship," what is this?

"Scholarship" is effectively a synonym for "research".  Send something like:

a published paper
a preprint of an unpublished paper
your thesis, or one or more chapters from it

Your advisor may have advice as to what would be best.


What are the benefits of getting a PhD in statistics?

A doctoral degree is a credential signifying largely that you are capable of doing independent research at the highest possible level. It is not, in an of itself, a ticket to working in a particular industry or in a particular location any more than a bachelor's or a master's degree. In fact, PhD holders may have substantially more challenges in those aspects, because the additional qualifications make them unattractive for many positions in conventional businesses and industries. (You are unlikely to find a PhD working in a sales division of a multinational conglomerate, for instance.)

The reason to get a PhD is because you are interested in problem solving and doing original work. If this doesn't describe your motivation, I would recommend against pursuing a graduate degree, because it will be a very long few years of your life which are not guaranteed to achieve the objectives you've laid out.


Is it necessary to customize letters of recommendation with recipient names?

I can hardly see the need of addressing the reader in a letter of recommendation, but if your professor wants to do it, they can use a process called mail merge.

Common word processors have mail merge functionalities (e.g. MS Word).


You're going to find answers all over the map for this one (i.e., there probably aren't "standards").  I personally like having a private office so I can get the most work done, but I'm generally comfortable with a shared space if it doesn't get too loud.  I have found that it is rare for students to worry about how they perform if they are just trying to get help figuring out the material.  If there are conference rooms or open classrooms available, that's sometimes a good place to tutor students, too.

For what it's worth, I never have closed door meetings with students because that has the potential to lead to allegations of improper relationships, etc.  If a student does have something private to discuss, I'll ask them to take a walk around campus where we are visible but can't be heard, or to go into a conference room that has windows into the hallway.


Is it unethical to add same environmental data such as temperature and salinity in two different papers?

Researchers frequently have to decide how to publish journal articles from a large data set. When it is not possible to write a single, integrative article from such a data set, the issue of publishing multiple journal articles arises. Here is good article about the issue


Should I be concerned about student access to a test bank?

As long as the test bank has enough questions to cover the material I'd not be concerned.  Those who work at it will learn.  I've given my own students "sample exams" for years, then put some of the sample questions on the real exam.  The students who were going to earn grades of A anyway got them right.  The students who were going to earn unsatisfactory grades anyway did not.

A colleague performed the experiment of handing out the course final exam a week before the exam date.  Students were encouraged to get help studying, but then had to take the exam again in class.  He says it did not change the grade distribution at all.


Is there a community driven unified article database?

Sadly, not yet...

Many publishers view their bibliographic metadata as commercial property and hold-on to it fairly tightly.

Mendeley will release little bits of the article data they have accumulated from all their users, but they will not let anyone download all of it - it's valuable property that they want to keep 'in-house'.

There are a few truly community-driven projects trying to change this e.g. Open Citations & Open Citagora.

These projects aim to build truly public & open databases for anyone to build upon & annotate. The other tools mentioned in the question aren't really public or fully open.


Why do researchers in areas requiring minimal resources apply for grants?

I am a theoretical computer scientists in a top-10 US computer science department.  To first order approximation, the only reason I apply for grants is to fund PhD students.

My research does not require PhD students, but it's part of my job as a university professor to advise them, I enjoy working with them, and I am considerably more productive when I work with them.
Students in my department that are not funded by research grants or fellowships are funded instead by teaching assistantships.  Being a TA requires a significant time investment, decreasing the time that these students can devote to research.  Being a TA can be incredibly valuable experience, especially for prospective academics, but the first-order criterion for judging the success of PhDs in computer science is the quality of their research output.
My department competes with peer departments — and I compete with researchers in those departments — to attract strong PhD students.  If we/I want to attract strong students, we have to make credible promises of future funding to do research, because that's what our peer departments do.  Prospective PhD students understand the previous point.
I work in a public university in a state with rather significant budget problems.  TAs are paid from state money, which is limited.  Thus, my department can only support a limited number of TAs.  So if I want the department to admit more than a small number of students into my research area, I have to demonstrate that we can fund a majority of those students through grants.
Students need funding to travel to conferences to present their research results, because they need to build a reputation in the research community.  I could pay for my own travel out of pocket if I really had to, but most PhD students don't have that luxury.

There are a few second-order concerns as well.

The day-to-day functioning of my department requires a steady stream of incoming research grants.  Grant overhead pays for a lot of basic infrastructure in my department, including the salaries of all the staff our business office, half of the salaries of most other administrative staff, support for non-instructional non-research computing resources like our graduate admissions database.  Grant overhead is also the source of startup packages for new faculty (for which we are again competing with our peers).
The only equipment I need is "pencil and paper"—or more accurately, a laptop with a stable LaTeX distribution and a drawing program, and basic internet access.  NSF no longer allows research funds to be used for general-purpose computing equipment, so I can't include that in my grant budgets anyway.  But my university returns a small fraction of overhead directly to PIs, and I can use that to buy new laptops, to pay for additional travel (by me, my students, or visitors), or even to help fund RAships.
Tenure and promotion decisions, and to a smaller extent raises, do depend in part on professors' proven ability to attract funding, especially in a department (and college) like mine where most faculty are extremely successful.
Oh right, I almost forgot.  I can pay myself an extra month or two of salary over the summer from my grants.  The university pays me for only 9 months of each year (although that pay is spread over 12 months), so each month of summer salary is actually more than 10% of my annual pay.


How narrow or broad should I look for undergraduate research?

I suggest you greatly broaden your search.  There are common features to all research.  Perhaps even look at research projects and programs in adjacent areas, like combinatorial research in computer science.
Since you could easily wait until the following summer to get involved in a research project, you can write programs and professors (in the area, or where you might want to visit) and ask about what you might do to prepare for the projects that exists.  If you do not know computer programming, perhaps that is a gap needing a fill.
It would be good to be exposed to many areas of mathematics before you decide on what you focus upon in graduate school.  I was convinced I wanted to to algebra when I was an undergraduate, but then topology started to be appealing.  In graduate school I switched to analysis.  Now I mostly do applied math research related to physics.


Is it ethical to present the same paper in two different conferences?

The issue is highly field-dependent. In computer science, it's probably still considered highly unethical, but in my field—chemical engineering, where papers are not normally "published"—presenting the same talk in multiple venues is not normally considered a problem. Other fields lie somewhere in between.

I think that, regardless of the ethical dilemma, the issue is that the more likely you are to have overlap between the two audiences who will hear your talk, the less you want to give the same talk—even if it's ethical to do so. At the very least, you should have enough new material in the later talk that it's worth the audience's time to hear the second version if they've already heard it at the first conference.


What does this mean, "We recommend that you consider submission to an alternative venue"?

From what you've said by itself, it's ambiguous. That is, if your paper really is on a topic not usually covered by that journal, then their remark is completely bland, just meaning what it says. If, at the other extreme, you are pretty sure that your paper's topic is exactly what is covered in the journal, then, yes, their "recommendation" is just a polite form of rejection.

If you are a beginner at this, it is possible that your understanding of what your own paper is about may have some quirks or limitations, or you've presented it in a way that dis-served you, or you've presented it in a way that confused or mis-directed the editors/referee, etc.

For example, giving inappropriate/inaccurate keywords can get a paper sent to an inappropriate referee, who may think the paper is misguided, while if you'd given different keywords, a different referee might think it was mainstream and wonderful.

Similarly, unfortunate choices in title, abstract, and introduction can set things off down the wrong path. Getting an opinion from an experienced person about the actual appropriateness of your paper for that venue is necessary before it's possible to understand the situation.


How to cut ties with abusive supervisor?

I was going to just leave this as a comment, but I feel like it's worth an answer (even if it's effectively only one half of the answer), given the other current one:

Your current therapist (psychiatrist) has tried to guide you through this in a way that has caused you to mistrust them, by calling your account into doubt in a way that questions your grounding in reality and as a sole means of directing that line of inquiry, rather than something such as a strategy leading you to find (should they even exist) other symptoms that can serve as evidence of differences between what you recall and what may have actually occurred, should there even be any such discrepancies. All they have done is put you purely on the defensive and add an element of antagonism to a situation where you are already highly pressured from external sources, and where your issues stem from a situation where your trust was horribly abused. From how you are discussing the experience, it sounds like you are unlikely to receive meaningful therapy with them at this point, if trust with your therapist can't be re-established.

Find a good Clinical Psychologist. (PsyD or PhD)

If you do not have other, local avenues of seeking a referral you trust (and assuming that this is in the US), the APA maintains a Psychologist Locator service. You should probably first check if there aren't any state based referral networks available to you, if you can't get a personal referral from someone you trust. One avenue can be through your University's psychology department, not necessarily in terms of seeking care but at least a trusted referral.

A good psychologist will also be positioned to help you move on socially and professionally/academically from this as specific to your situation, with setting up both coping strategies and boundaries, and helping reflect on your own behavior, thoughts, and feelings in relation to both what happened and in moving forward from it. Not every psychologist is a perfect fit for everyone, and not every form of therapy as administered is a perfect fit personally or situationally: it's ok to tell a psychologist who you're trying to work with that things aren't working out with them and you feel you need to see someone else. Every clinical psychologist I personally know would be more than happy to refer you to a colleague who might be a better fit, in that situation.

If you feel you need medical (psychopharmaceutical) support to help manage things like immediately severe (acute) emotional issues while working on recovering, then seek a referral to a psychiatrist for that. There's nothing wrong with needing more or more immediate help than what therapy alone can offer, but I would suggest being upfront with your psychologist about that too (and usually they can be a good source of a referral to someone who can handle the medical side of things in a balanced manner) as it will affect how therapy proceeds in relation to corresponding changes.

A Psychologist will also be able to administer any well validated instruments that are appropriate, or refer you to someone who specializes in related testing, if there is a need for any.

  I cannot relay what has happened since I am afraid it would be
  dismissed the same way as with my psychiatrist?

This is, ultimately, part of why this answer focuses on seeking out a psychologist to help you through this, because while your focus is on what happened (which is completely understandable), you may need to work on processing it as something unfair and unjust that happened to you and work on moving past it without relying on the particulars of the event as justification for how you choose to do so.

Sometimes when we are in the middle of a situation, all of our attention remains riveted on what happened, and we lose sight of simple answers to moving forward where what happened isn't a relevant matter to doing so. Some of @aparente001's answer focuses on suggestions that would fall under this.

I can think of at least a couple of Psychology Professors who also do clinical work, who I'm personally well acquainted with who have "seen it all" in academia and would give whatever story you have complete face value credence: if you can't find someone willing to give what happened to you a fair listening without immediately jumping to questioning your grounding in reality simply on a basis of what happened, then keep looking, because they are out there. At the same time, it's important to understand that questions of whether your perception of what happened might differ from the actual events is also not necessarily an attack on your state of mind. We are all prone to remembering things in ways that are not perfectly genuine to actual events.

Someone who approaches that line of questioning should manage to do so in a way that doesn't leave you completely distrusting them, however.

  Things escalated to a point where I was on the receiving end of a racist declaration from him

It's unfortunate that you apparently have no documentation of your supervisor's behavior (although there may be more evidence of that behavior than you believe exists), because I realize the reality is that it can make filing a grievance difficult. I do think it's likely that you probably should file one either way (not about the letter, but about the behavior you experienced) from even the little you've relayed here, depending on the political situation within the department, but given how that may impact you professionally it's probably best to explore a discussion of that with someone you trust and with whom you can discuss it confidentially (which again, leads to the recommendation of seeking out a clinical psychologist you can form a strong working relationship with). I think if I had friends/allies in the department who were familiar with the Dean in particular and the political situation with your adviser in relation to the rest of the department, I would sound things out with them after receiving some counseling, and then make a decision of how to proceed with anything more formal based on their feedback.


It is ethical and common that a professor ask the student to write their own recommendation letter?

It's not common (in my experience).  I have requested letters of recommendation from professors in a couple of different fields, and was never asked to write my own.  Nor have I heard of anyone who was asked to.  That said, it might be something that varies by field, institution, culture, etc.  I wouldn't rule out it being common in some contexts--I just don't know of any.

It's not unethical. There is not an ethical requirement that a letter from a person was actually written by that person.  Even though I've never heard of a student being asked to write their own letter, it is well known that, often, professors don't actually write the letters themselves.  Secretarial staff often do much of the actual writing (hopefully with the professor giving input about the student's strong points, things to emphasize, etc).  In a broader professional context, it's quite common for people to sign the name at the bottom of letters that were not written by them, for a variety of purposes.

Who wrote the letter, ultimately, doesn't matter.  What does matter is that the person signing their name at the bottom agrees with all the content and is willing to stand behind it.  As long as your adviser is happy to agree with what you said, there is no ethical problem here.

That said, it's not ideal, either.  I would argue that a professor who asks you to write your own letter is not doing a great job discharging their academic responsibilities.  Really the content of the letter ought to come from them, even if someone else is writing it up.  This is an opportunity for them to assist you in your career, and they aren't really taking that opportunity seriously.  In addition, it puts you in a rather awkward situation--many people would not be comfortable putting complimentary words about themselves in someone else's mouth.

So, I sympathize with your situation, it's not great.  But you probably don't have a good alternative other than writing the letter as requested, at least from your supervisor.  You want a recommendation from your supervisor, and substituting someone else wouldn't be equivalent.  At least you get to make sure it says what you want!  Just make sure you get someone (who is actually interested in helping you) to review it, both for content and to catch any errors.


Does your institution have a policy regarding policing online student feedback?

No policy that I am aware of at any of the four universities and two high schools I've been associated with.  When the sites first appeared in the U.S. about ten years ago, questions came up about whether anything could be done about it, and the institution I was associated with then decided that there wasn't anything legal that could be done.  I believe that libelous material can be appealed directly through some of the websites, but I've never heard of anyone having success with that.

Personally, I love anonymous feedback, and I've had my share of good and bad reviews.  I've tried to use the bad reviews as a means for informing where I can improve, and I've tried to limit my head from getting too big at the good reviews.  Teaching takes a certain amount of thick skin, and sites like these can be a good way to test if you've grown enough of that calloused layer to ward off any long-term effects.


Can I ask a professor (via e-mail) for a citation for a result presented in lecture notes?

Sure, it can't hurt to send a brief, polite email. Just make sure that the reference isn't already given somewhere in the notes, or the professor's course website, or his/her list of suggested reading.

Of course, you should prepare for the possibility that your email will go unanswered. Professors tend to be busy. There is little-to-no benefit to them (other than the pleasure of helping out another human being, that is) in tracking down a reference for someone who isn't a colleague, student, or potential collaborator. There's also the possibility that this professor didn't prepare his/her own lecture notes, and the grad student who did is long gone, etc.


Are these responses from top journals just boiler plate? or anything atleast miniscule to salvage from them?

I think you should treat them as honest statements. They may be boilerplate, of course, since journals often get more submissions than are possible to publish on any reasonable time scale. They therefor have such "boilerplate" ready to ease the editor's work.
The first implies something lacking in the paper itself wrt the standards of that journal, though the paper may have merit otherwise. The second doesn't necessarily imply the same.
But, an exceptional paper, by their standards, would probably be put into the process.
As they suggest, move on with the paper and try for a different venue. Alternatively, improve it dramatically and try again.


Is it accepted/common to answer factually inaccurate reviewer comments in case of rejection?

I have not read your paper and it's likely that you don't work or publish in my field, so you will need to take this advice as it is given: without conditions or obligations.

I have decades of experience helping edit some of the top journals in my field. If I've learned anything, it's this: as much as academics like to think otherwise, peer-reviewed publications operate in much the same way as [insert trashy supermarket checkout rag here]. Journals are human institutions operated by humans with the same human concerns as everyone else. Things would go a lot smoother if they stopped being placed on pedestals.

Despite everyone's best efforts, mistakes happen all the time. From an editorial point of view, it is important to us to receive reports of factual errors so that we can consider the best information to reach the most appropriate decisions.

If you were to write to us about this issue, I promise you that we would consider this seriously. While we value the work our reviewers do, we also need to know when our reviewers are making factual errors such as this. This is actually a red flag for us.

Why did the reviewer fail to pick up that these statements were referenced in the text?
What else did the reviewer misinterpret?
Is this behaviour consistent with other rejoinders or complaints we've received?
Is it still worth our while keeping this person on our list of reviewers?

It is for this reason that I recommend that you compose and send a letter to the Journal making these corrections. It is unlikely that the issues you outline will overturn the decision and, by your own admission, you're not seeking an appeal. Nevertheless, I believe that this is an important step. There's no need to be uppity about this. Just lay out the issue and sign off.

In addition, you might want to reconsider the manuscript to see whether it could be improved to prevent this issue from being raised when you submit your work elsewhere. For example, you might have wrote

  We collected and analysed blood using standard techniques. Levels of serum bicarbonate...

when something like this might be more specific

  Analysis of serum bicarbonate was conducted using the process outlined by Nikishima et al. [5].

I'm making this up, but you get the idea. Could your statement be modified slightly so that there is absolutely no way for a reviewer to raise the original concern?

Anyway, good luck to you.


Sara, I would wait another working day (Friday), and on upcoming Monday morning, I would send the following email, so the he/she could respond the beginning of the next week:

Dear Prof.X

I would appreciate if you could let me know about the outcome of the interview?

Kind Regards,
Sara


I was a rapporteur of the main session of an intergovernmental forum, should I add the final report as a publication in my CV?

You should ask the organization specifically what is appropriate. It might be fine, but I know of other such international collaborations in which it is specifically forbidden to claim authorship. The work is attributed to the committee as a whole, by name.

An additional reason for not doing this is the question as to whether it is a creative work on your part. I can't judge, of course, but it seems unlikely.

You can, of course, include your participation elsewhere in the CV.


What do I put on my publication list if I have no publications?

If you do not have publications (including papers "in press") then the publications list can be left empty. If you have papers. You can, however add headings for publications "under review", if you have any or "manuscripts in preparation", again, if you have any. You may also have unpublished reports of different types. Such contributions can also be listed under a separate heading. What can be included is difficult to say but in my case, I used to include annual reports I had to write to a super-computer center and a research station, both which were collated with others and printed by the organising body. So any report sitting in a drawer is not valid.

Obviously the a "manuscript in preparation" will not be very strong but it will at least indicate that something is ongoing. But, note that a manuscript in preparation should be something worth reading to make it to such a list. In a situation like yours any written material prepared for some official body and with some distribution, can  be used to indicate your activities. There is a grey zone which is undefinable (which is why one generally avoids such listings later in the career), so do not put in anything. In short, you need to be able to show these "claims".


Asking for a change in rules to get a MS rather than end the program with no degree

In addition to the suggestion given in Nicole Hamilton's answer, and provided that you are making good progress in your degree, you still have several options:

You could see if someone else in the department has funding to support another student.
You could see if colleagues in other departments at your institution doing work related to your thesis area.
You could ask if the department will help you in transferring to another program.

The big question here is why you're being let go. If it's really that funds are low, and it's through no fault of your own, then the department owes you the right to continue in the program, or help you to continue your studies. On the other hand, if they're saying "we don't want to spend more money on you," then it'll be a lot harder to get help.

As far as awarding a duplicate degree, that's probably not decided at the department level, but instead probably requires a higher-level signoff.


How does the testing method and possibility of cheating in an entirely online degree affect the value of the degree?

Being online and thus open to cheating on tests certainly reduces the value of the degree, as you suggest in your question.


PhD: Online philosophy courses and their worth when transitioning from an unrelated field to philosophy

My guess is this depends on what sort of on-line course it is ...

(1) In the course, you write one or more papers, which are critiqued by them, and at the end they issue some sort of credential to you

(2) You listen to lectures on-line, do assigned reading, and nothing else

Perhaps (1) would be of value in applying.  But not (2).  Of course (2) could still be of value to you, personally.


Is copying numbers from published scientific articles considered plagiarism/copyright infringement?

No, it's neither:

It's not plagiarism because you cite the original source and you don't try to put others' results as your own.
It's not a copyright infringement because there's no copyright on data.


Student missing exam for “medical reasons”

In my experience dealing with these types of things correctly takes more time and effort then letting them slide. Continue scheduling exam times for her until she takes the exam or the incomplete automatically converts to a fail. I would even reuse the last remediation exam instead of making a new exam. I would only schedule the exam at times that are convenient for me.


These kinds of issues are normally fixed later in the publishing process.  If your paper is accepted you'll be asked to submit a final version of your paper in LaTeX.  A professional type setter will process the paper through LaTeX and should fix it up minor issues like these.  You should then be given a chance to review page proofs before final publication.  If the problem is still present in the page proof then you should mark up the page proof to request that this be fixed.


Position in mathematics after Ph.D. with publications but without recommendation letters and teaching experience

I can't imagine taking on someone who wasn't able to provide any recommendation letters, even if the candidate had several Science and Nature papers. However, I would be happy to consider strong recommendation letters from an employer in another field in combination with a very strong publication record.


Including "Thanks Card" in my graduate application

Honestly - unless this card is speaking to something very particular and relevant to your statement of purpose I would not include it. Think about this from the perspective of someone reviewing your application. In most US grad school applications, you need to have people provide letters of reference. What would this thank you note contribute in addition to those letters?
You don't say whether you have a letter of reference from this internship, but it would be odd either way.
If you don't have a reference letter from the internship, someone looking at your application might be confused by it, and not know how to judge it. It might raise questions such as "why is this person including this letter from their co-workers when they don't have a letter of reference from it?"
I will also say - generally the more specific a recommendation letter can be, the better it is. Maybe it depends on thank you letter, but in my experience, those tend to be "thanks for a great summer, great to get to know you" which is probably of less interest to an application reader than "During the 3 months Danny worked here, he worked on projects X, Y, and Z, and made contributions U, V, and W"
Anonymous Physicist is right. Show the letter to the person writing your recommendation letter, don't include it in your application.


How to persuade my advisor to keep working with me even if my grades are poor?

scaaahu has given the most pragmatic answer in a comment:

  Study harder or leave.

If it is very important to your advisor that your grades are better, those seem to me pretty much the options.

That being said, I think most people don't really care so much about grades that they would kick out a perfectly fine grad student for grade's sake alone, even if he is well above the formal requirements. Honestly, I would assume that this is not, or at least not only, about grades.

How is your research going along? Are you progressing at least as well as the majority of the other students in the lab? Is your advisor still enthusiastic about your topic? It is not entirely unlikely that your supervisor is not super-happy with some other part of your work, and just using your suboptimal grades as a simpler, more objectively validatable reason to put pressure on you.


Just graduated with a master’s degree, but I internalised nothing

You asked,

  How am I supposed to find work if I barely know how to program?

It sounds like you're looking for a job in industry, versus academia, so I will answer from that perspective.

Employers are generally looking for people who can get things done and will consider the ability to program as a means to an end. While technical skills (i.e. mastery of a specific programming language) will be important, it's never the only factor evaluated, and it's sometimes not even the most important factor. Combine that with the pace at which technology develops, and having a specific technical skill ends up becoming even less important, as that skill may be obsolete rather quickly. Go find a dozen software engineers who have been working in industry for a decade or more since getting a degree, and ask if they're still using the actual content from any of their classes. You may be surprised at the answers. What they will probably talk about is how valuable it was to become a "learning machine" rather than a knowledge repository.

You've described the process you used to get good marks on tests. That's a valuable skill. Employers don't inherently care about test scores, but they will care about someone who can pick something up, and learn it well enough to complete a task. In many programming environments, the ability to learn something, apply it, and then move on to the next thing is incredibly valuable - even if you "forget" that thing as you're picking up future things.

Further, Resumes and interviews are sales tools - you're selling yourself to an employer. Focus on the value you can add and match that value to their needs. There's a job out there for everyone - don't just spam every software job you see and hope one sticks despite your shortcomings - instead, focus on understanding your own strengths and then look for jobs where your strengths are a good fit. Write your resume to emphasize the skills you do have and be ready to talk about them in interviews.

Taking a bit of a tangent, there's a concept in motorcycling called "target fixation." Riding instructors working with new riders will emphasize the skill of looking where you want to go when in a difficult situation. This is because new riders who are surprised by a piece of road debris, or a vehicle out of place, tend to focus on that thing to the extent that the ride right into it instead of avoiding it. Apply that to yourself since you're undertaking the new pursuit of searching for a job: Don't become fixated on what you perceive as weaknesses or you may end up in a mindset where all you have to offer in an interview is nervousness about what you see as your own shortcomings.

As a final point, to address your comment of,

  I also haven't worked professionally a single day in my life

I have a feeling that the quicker you can change that, the less significant your problem will seem. Once you have a few years of work experience, you will see life through a different lens - on the one hand, you probably don't want a menial job for the rest of your life, but on the other hand, your first job doesn't have to be the job - it's OK to just take a job and get some experience to give you some confidence and expose yourself to a professional workplace.


it only takes time and effort

I think the answer to the question is already there. It takes time and effort. So it means it takes at least the money to pay the people for a long time. And effort means you need a lot of people.

More precisely, for medical research, reagents, animal model, clinical test are really expensive. Many different drugs need to be developed to have only one working in the end. Finally when a drug seems promising, you have to do year-long clinical tests, just to ensure patients safety.

So time and effort == lot of money


How should project based assessments be implemented in order to prevent cheating?

I can, perhaps, give you a few ideas, but note that I've never had to deal with this scale. Many of my courses (CS) were project based.
First, make it very explicit what you expect of them. Have some sort of honor code that they agree to by taking your course. Don't assume that the already know what is right and what is wrong. University wide honor codes are effective in some places. And also make it clear that the purpose of the exercises is less to "get answers" (which you already have) than to "get learning". Shortcuts are a form of self-defeating behavior.
Next, is that if you want to prevent cheating you won't be able to do it. You can, at best, reduce it, unless you are willing to run the course in a way in which cheating can't happen because it is irrelevant. I don't think that a first course in math analysis is especially amenable to this, but the idea is that students are allowed to use any source that they cite, just as if they were actual researchers. But to make learning, not just copying, happen, the questions you ask of them need to be a bit deeper and require some reflection beyond what they are likely to find in print or online. It is difficult, of course, to create such exercises.
The next idea has two parts. The first is to make all of the projects team (or at least pair) based so that the scope is reduced a bit. For 500 students you have 250 pairs or 100 teams. My preference with pairing would be to have a lot of small exercises where the pairs switch for each exercise. This may be easier now, in the zoom era, that it was when people mostly got together physically.
The second part of that is to use some form of peer assessment with the pairs/teams. Search this site for that or for peer evaluation to get a better idea of how to do that. Note that it isn't peer grading, but each member of a team can give you some idea of who the best players are and what those people contributed as well as listing their own primary contribution. Over many projects you will get an idea of who is doing a good job and you will sometimes be surprised.
One alternative you might be able to do is to partially "flip the classroom" so that the "tutorials" become work sessions and the projects are then done under the eye of someone with some skills. If the instructor can also do this twice a week then you have seven smaller groups, to which the "graders" might also contribute. Having students work in pairs in such a situation reduces the number of questions that must be answered by faculty and TAs, since partners will have the answers to some questions. If they work alone, then there will probably be too many questions and people will get stalled waiting for help. It might, however, be necessary to make the "tutorial sessions" longer and to move some of the content to videos and other online resources. And having students to their graded work under the eye of staff reduces the opportunity for cheating (but doesn't eliminate it in large groups).
One of the big problems with huge classes is that you have such a variety of ability, but also a huge variety of student goals and expectations. One way to make it possible for students to define and meet their own goals is to use cumulative grading rather than percentage grading. See this answer to a different question for a description. Not every student needs to reach for top marks. And this grading scheme lets every student know exactly where they stand in the course and what needs to be done to meet their goals. With a lot of smaller projects, every team member gets the same grade for a given project. In bigger projects you may need to make occasional exceptions.

Notes: I will probably add to this over the next day or so.

Spreading the grading out over many projects also means that no single project is "high stakes". This means that there is less incentive to cheat on a given project and to "cheat your way to success" means you need to do it repeatedly, increasing the chance of being caught.

Requiring writing projects rather than computational ones makes some kinds of auto checking for cheating a bit more reliable, reducing false positives (at least). For a mathematician, learning how to write is a valuable skill of its own. But this is admittedly difficult for an analysis course.

Permitting students to resubmit work is very useful for learning, though the scale is probably out of whack here. In fact, I think the scale and the ratio of students to staff in this scenario makes any sort of learning difficult. It is very difficult to give feedback to individuals to permit re-work to have a valid effect.


What are books and websites I should look at before trying to write a grant?

The form of a successful proposal varies wildly from organization to organization and often also within different programs in an organization. Many grant organizations thus provide "model grants" or "writing guides" somewhere on their website that you can look at to see what they are looking for (they aren't interested in wasting their time either).  See, for example the NSF's grant-writing guide.

Government organizations also generally allow you to search a database of previous grant recipients: you can look for some who are close to your area (thematically and/or geographically) and ask them for advice or to share their examples of winning proposals.  People are often willing to help out like-minded colleagues in this way.


Paper in revision stage but a similar paper was just published

Sad for you, but things like that happen.
Something that might help: Usually, there is a note in a paper making transparent when it was initially submitted, when a revised version was submitted and when it was accepted for publication. If the other paper was accepted after your initial submission it is obvious that you could not have known the contents of that paper. In that case, as a neutral observer it is nice that two independent papers describe similar findings, i.e. reproduce the results. In that sense, your paper is worth publishing in any case.
You might be able to use this as an argument in a possibile discussion with the editor. However, there is a realistic chance that neither the reviewers nor the editor have heard of the other paper, so will not ask for any information in this direction.
Of course it would be best practice to make your current knowledge transparent to the editor anyway and maybe include some discussion about the other paper in your own paper. If I was the editor, and if the other paper was discussed properly, I would probably accept the paper for publication, given there are no other reasons not to do so (but this is my opinion).


Can a scientific article (of an non-tested idea) in computer science be accepted in a high-ranked journal?

Ideas are cheap. Most researchers have more ideas than they have time to develop them. It's the development which has value. Or to put it another way, in order to advance the field you need to convince other people that your idea is interesting, and the fact that you believe it will not be sufficient. Depending on your subfield the way to convince people may be a mathematical analysis, empirical measurement of an implementation, or a combination of the two, but you need something.


To stay or leave PhD after having completed 4 years

Firstly, no apology needed, your question is thorough and easy to read and understand.  It sounds like you are in quite an unpleasant situation.

Don't take any advice I may give as gospel, but in answer to your questions:

You are most certainly not foolish to wait until now to stand up to your advisor, you have had several leads and have given many chances for the project to kick into gear. You have every right and reason to feel skeptical about the current promises and project direction.

Ultimately, how you proceed is up to you (you're probably understandably sick of hearing that), but look at the following considerations (no doubt many other members will add to this):

The new direction could well be a winner, leading to papers, conferences and most of all, fulfillment.  It could also be a good one as now, you have made your feelings clear to your supervisor.
Could this be just another academic 'false positive'?

Perhaps outline a couple of potential papers and present them to your advisor (this is something I do).  This could be an ongoing thing, alongside your research - outline potential papers.

As for the timeframe, 17 months - I would not be too worried about that - I have been able to get three papers published in less than ten months, with a 4th on the way and the 5th planned (I finish my Ph.D. at the end of the year).

I hope this helps, and I hope it all gets sorted out for you.


My suggestion is that you continue your job as Master's programs in engineering departments in the US (at least for many schools) value the experience in the industry before taking on a Master's degree. As for personal projects, it is always useful to be able to present a few in your application materials; however, don't feel like you have to learn everything about computer vision, machine learning etc. before you apply for the schools. It is what the degree is for.

Having done some amount of work is surely useful, as it shows your genuine interest in the field and being able to effectively articulate why you want to study a certain field in your application statement also carries some considerable weight when it comes to admissions. You can try to focus on a single, but a considerably impressive project on a related topic and present it in your application, rather than trying to take all the MOOCs out there (although Andrew Ng's courses are quite useful).


How can I put myself in the best position to get a postdoc in a different field?

I'm in the same boat as you, but then for my thesis I added a few elements of the thing that I want to do later in my career, so I can use it as background. If you can incorporate something related to experimental physics in your plasma physics research, that'd help. Otherwise, you may join some research lab that works in the field of exp. physics, that'd look good on your resume.


How does applying to work with multiple potential advisors at a university work?

The picking/assignment of adviser varies dramatically by institution and department. In some institutions - for instance, in some of Carnegie Mellon's departments - the student chooses their adviser (and optional co-adviser) during the first month of their first semester after admittance, and the adviser needs only to agree. Advisers usually can say yes to any request they want because the department funds all new PhD students for the first year - and thus only becomes responsible for funding the student after that year. But some departments don't have the same policy!

A friend at Berkeley told me that their adviser actually saw their admissions packet and reached out to them to say, "I know you said you wanted to study X, but I think you'd enjoy topic Y that I'm working on" - and the student accepted and thus gained their adviser (in an entirely different field than they applied).

As yet another variety, I'm told that at some institutions the student is admitted with no adviser and the expectation is they will work with various potential advisers in different semesters for the first 1-2 years before being expected to formally have a permanent adviser.

The variety of systems is heavily influenced by the nature of how funding is handled at the school, as well as how admission is handled. In many institutions only the admissions committee decides on who is admitted and then advising comes later, while at others at least initial advising is part of the admission process (students are paired with potential/initial advisers before admission, and if you don't fit a professor with an open student slot then you don't get admitted).

Luckily this process is usually not a big secret, so you can talk with graduate admissions coordinators at departments you are interested in to find out just how things work there. Current PhD students are also often helpful in willing to share how they got their adviser, but be aware that their experience may or may not be typical (and sometimes they don't actually know).

Finally, there is great variance between institutions, and between departments within the same institution - and even greater variance between countries - and yet more variance across time as departments change their policies and strategies to recruit and retain students. So in the end - you'll really have to ask that specific department near the time of application to find out how thigns work


Should I be credited for my programming contribution to a dissertation?

You did work for hire for a research group. Since you say you were strictly involved in developing the tool and not in the research, authorship of subsequent publications is not to be expected. An acknowledgment in the thesis would be appropriate but it would have very little weight in a CV, inside or outside academia.

At any rate, you can definitely list your contribution to this project in your CV regardless of which kind of acknowledgment you might get. In fact having delivered a working software and gotten paid for it will be much more helpful than any kind of authorship/acknowledgments when applying for jobs outside academia.


Academics with ADHD or autism: What workplace accommodations have helped you?

This is a very difficult question to answer because people with ADHD/LD aren't treated very well in higher education in general, so (anecdotally) they seem to be extremely underrepresented among both academics and grad students. Even though ADHD/LD people make up at least 10% of the population, there doesn't seem to be much interest in diversifying faculty to include them, or in consulting with them about how to help better serve the needs of ADHD/LD students.

Plus, there's a worse problem of fundamentally misunderstanding ADHD/LD and thinking that a few minor changes is the same thing as "accommodation." You often hear ADHD/LD described as having "attention problems" or "learning problems" (as someone on ASE did here). But in the case of ADHD, the underlying issue is actually difficulty regulating attention, which results in differences in how attention gets used. And in the case of LD, the underlying issue is difficulty processing certain information formats. In both cases, there is a significant mismatch between natural strengths/preferences and the way neurotypicals are expected to do things. (I am not autistic, but I have heard that ASD people are in a similar situation.)

The standard accommodations you mention are the product of what I call the "test in the envelope" mentality, which is as far as 99% of academics get in their understanding of ADHD/LD. It's a horrible accommodation because it sends the message that having ADHD/LD basically means that you're just like everyone else but slower. Needless to say, that creates a lot of false negative assumptions and stereotypes, especially in a career where being smart is prized above everything else.

In other words, in the current academic environment of widespread ignorance and unwillingness to really deal with people with learning/attention differences, ADHD/LD accommodations are nearly always reactive rather than inclusive: the person with ADHD/LD has something "wrong" with them, so they posture as "needing help," for example by asking someone else check their Excel tables. This raises the question of whether it's necessary to work with Excel tables at all if it's a task that you know is going to be problematic. Is there some completely different approach that is better suited to your learning differences? What should universities be doing to provide an inclusive environment for that, rather than going small potatoes with Excel proofreading?

So at this rather benighted point in time, it might be more on-point to reframe your question as: What are examples of nonessential expectations that are typical in academia, but which put ADHD/LD people at an unfair disadvantage?


Advisor getting married, should grad students chip in for gift?

I laughed here; can't imagine my supervisor getting married.  It is just nice to see the supervisor involving in life..

For the question, Why not? It is a big day for your supervisor. Just make sure the gift come from group of students not only one student. If you missed the first day after his return (assuming he's going on vacation for marriage), then no need for a gift. Either ways, a verbal congratulations is a must here :)


How to respond to an editor's post-review comments suggesting major changes I'm not willing to make?

I would suggest the following thought experiment. Take a day (or at least a couple of hours), and fully embrace the editor's suggestions. Think about why h/she made them, and think about how you would revise your paper to fully incorporate his/her suggestions, and in what aspects it would make the paper better.
Sleep on it a couple of days. Then, if you decide you prefer not to take the editor's suggestions, you will be in an excellent state of mind to write a reply.

I carefully considered suggestion X. As pointed out by the editor, this would have advantages Y and Z, and W. [It is especially helpful to not just say the same thing word-for-word, to show that you thought about the editor's suggestions carefully.]
Nevertheless, I feel that for the most part the paper is better as is, for the following reasons: ...


Supervisor choosing PhD topic for student

In short, if the advisor chooses the topic for his student in any field without taking student's opinion into consideration or a proper discussion with him about his interests – that is a very unhealthy dynamics in student-advisor relationships.

The good supervisor definitely should:

determine the student's interests
take into account the student's strongest/weakest skills and his goals of getting the PhD in the first place
offer him several directions that are interesting to the advisor and might be interesting/are promising for the student
be prepared for a reasonable flexibility within the general direction

However, it is unreasonable to expect an advisor who specializes, say, in PDE to be open for research in mathematical logic. Particularly in pure math, the initial choice of the advisor might already dictate very strongly what general direction of research you are going to work on. However, even within the general direction, there are many possible topics and approaches; thus, the list above applies anyway, in my opinion.


My R01 application was re-assigned to a study section that doesn't seem like a good fit (NIH)

I think the problem is that you "misunderstand" the sections, and whether that is right or wrong, you have to change that perception.  I have a PI with a similar problem, and she decided to resubmit and "play along".  R01s are hard to get funded when you're new.  Plan on that  -- average age of new PIs in the 40s -- not 30s.  That said, I would say if you can ask for clarification (playing coy), that might be your best option.  The PI I support said, "we had X-topic expert on our proposal and they still said we didn't have enough expertise on x-topic!"  Sure, she could misunderstand what expertise in that topic looks like, but I think in general, if she wants the funding, it behooves her to ask the relevant NIH person more specifically what expertise one needs to be convinced that this PI knows what she is doing and how to get the proposal funded. Sometimes you have to bend (who you include, how you write them in); other times, we have to convince the agency.  Do your docs help convince the agency of your POV?

In general, I don't advise faculty to antagonize the PO, but they are supposed to be the public face of a program, and they should be able to answer some of these questions.  Asking questions about submitting is not too much.  That is the job of the agency, to answer your questions on the application process.  Forge ahead there!


License issue: publishing an image of famous person in the scientific paper

Assuming the photograph is still under copyright, yes.

The copyright owner of the photograph. This will usually be the photographer.

You are probably liable, but they would probably complain directly to the journal who would then shout at you. Under a Creative Commons license, you are still the author and "owner", even if you have given permission to people to use it under the license.
(I say "probably" - it does occasionally happen that you transfer rights to the publisher, who then release it under a CC license with themselves as the owner, but this is pretty rare.)

Short answer: yes, you do need to get permission, and you can't just say "I found it on the internet and it's the journal's problem for not checking".


Is it considered normal to publish job offers inviting candidates to apply based on their gender and/or race in academia?

These statements, in many variations are quite common. But they are not discriminatory, as you suggest (universities do not "discriminate against white males"). All the statement is saying -- and that is true in actual practice in the discussions of hiring committees -- is that women and other minorities are specifically encouraged to apply. This does not imply that they get special treatment or preference. It is simply a reaction to the fact (statistically proven by research) that women rarely apply for jobs that they do not perceive as a "perfect fit" whereas men do. So if a committee has a bunch of applicants where none is a perfect fit, more often than not a man is hired because there simply are not enough women in the pool.

See: Why Women Don’t Apply for Jobs Unless They’re 100% Qualified.

I do want to also comment on one of your comments while we're here. You state

  I think job offers should only focus on the candidate's skills regardless of his background and gender.

That is true, but how do you define "skills"? Let's use "qualification" instead. If you're, say, a typical math department where 50% of undergraduates are women, 35% of graduate students are women, but only 20% of tenure-track faculty are women, wouldn't part of the qualifications you are looking for in an applicant be that that person is a good mentor to many of the students in your department? Does it not diminish the quality of the department in its ability to teach and mentor if every single faculty was a white male? It is important to recognize that the role of the faculty extends beyond just writing papers in obscure journals; "qualification" is a term that ought to be understood much more broadly than you may think.

(I think it's important to say that the role of women in math departments is not to be there as mentors. All I want to say is that I want diversity to be part of the many considerations when deciding who is "best qualified" for a job.)


How to cite Arabic translation of a German book in an English paper?

Unless your specific field indicates otherwise, I would consider German and French to be more widespread as scientific languages than Arabic. Thus, the primary version to cite should be the original. To safeguard against potential mistakes through translation, you can add a note that you accessed the Arabic translation.

As there is no English translation of these books, translating the titles into English would be massively misleading. Don't do that.

[I am not familiar with APA or ASA citation styles, so this is just a "common sense" answer.]


Are faculty positions more competitive than government research lab positions?

Of course the answer depends on the university and the lab.  There are plenty of university departments with low standards, and some labs are truly excellent.  However, I think your comparison is right on average for top universities vs. national labs in the U.S.  There are several reasons for this:

Many researchers at universities aren't professors, and in some universities the non-faculty research staff outnumber the faculty by a substantial factor.  To make a fair comparison, you should not restrict your attention to professors, but rather compare all research staff in both institutions (or look at especially noteworthy or high-level employees at labs).
Some research labs are huge.  For example, Los Alamos and Sandia are each the size of a whole university, but they cover a much narrower range of fields.  The top researchers at these labs are exceptional, but the sheer number of positions makes it difficult to maintain the highest standards for everyone.  (And you can't just keep positions open for years while you look for the perfect candidate, since that would compromise the lab's mission.)
Researchers at national labs in the U.S. do not have tenure, and their jobs are subject to availability of funding and political interference.  In some cases they face as much or more pressure to get grants as faculty do.


I don't think a research question is every “closed”, as you say, though it's of course a matter of vocabulary. In the example you mention, it seems clearly that there is no current incentive to design better solutions, but unless it is actually proven that there can be none, it's not a solved-and-closed question, it's a “we don't actually need to do better” question. This makes all the difference in the world.


How to balance learning and solving assignments during coursework

You may be interested to know that this problem doesn't go away when you finish classes.  It's easy to struggle with the same question when you're doing research.  Simply put, you don't have time to learn everything.  You need to estimate how important a topic will be to your future studies (and future research).

Similar to what you're describing, I feel a sense of security when I can reproduce the details of all the relevant proofs.  However, taking this approach to everything I learn is simply infeasible.  Perhaps you can take comfort in telling yourself that for the stuff that is most important, you'll reread it later and learn it in more detail.  The difficulty is that right now you most likely can't really tell which material will be most important (to you).

As I continue to listen to talks and read more papers (or take more classes, at an earlier stage of my career), I watch for which ideas keep coming up.  When I hear about a topic repeatedly, I often become convinced that it's really worth learning in depth.  In the time between first seeing a topic and finally sitting down to really understand it, I'm also likely to learn about many connections to other areas, which give me more motivation.  In addition, I often grow in intellectual maturity, which makes it much easier to grasp ideas that were quite challenging the first time around.


Changing level of difficulty of assignments for a course based on average class performance

I would suggest that you step back and ask yourself why you are giving these assignments. Some people give out assignments purely so that they can grade students and then they think about fairness of grading, etc.

But, if you consider that it is through reinforcement and feedback that students actually learn then the solution becomes clearer. If you consider that the human brain works by actual physical rewiring - connecting synapses - then you see that students need these exercises to make the material clearer in their minds and so that they can move the ideas from short to long term memory. This is discussed in the book The Art of Changing the Brain by James E Zull. It is pretty fundamental to learning theory in general.

Thus, the exercises should be there to enhance learning, primarily.

So ask yourself whether the exercises you use are enhancing learning or not. Or are they just a stumbling block that some students can't get over? If it is the latter, then you should use different exercises that better enable learning.

My goal was always to teach every student. If I had a reasonable number in a class and if they were willing to do what it takes to learn, then I could be successful. But for many students it takes a lot of practice to come up to speed, as well as a lot of feedback.

But my goal was never to just deliver information and use what you want of it. Wikipedia does that job pretty well.

However, for your weaker students - those who are willing to do the work, anyway, there are other options. If your current exercises are good in some ways and you don't want to drop them, you can provide additional exercises for those who want to try them. These might be chosen to better enable good performance on the current set. But you should also provide some mechanism for the students to get some feedback on these new exercises. From you is probably best, but sometimes peer-review might be sufficient. Or even set up study groups among the strugglers.


Regarding the Ph.D. part of the question, only a school can grant a Ph.D., and no school will grant you a degree if you are not enrolled as a Ph.D. student.  Your best bet is probably to contact the mathematics department at a nearby research university and ask if a faculty member would be willing to look at your work.  If you have really been doing original research on your own, then you can probably be admitted as a student and begin working toward a degree.

Regarding the journal part of the question, most journals do not charge fees to authors (they make their money from subscription fees).  Most journals have web sites that explain the format and process for submitting a paper.  See http://en.wikipedia.org/wiki/Academic_publishing#Publishing_process for a description of how this works.


Being "good enough" to do research with a professor? ( cse, undergrad )

Research means diving into the unknown.

Committing to work on a research project with a mentor is also diving into the unknown.

What I can reassure you about is that

Professors are used to undergraduates signing up for research projects with less preparation than would be seen in grad students
The stakes will not be as high for this as they would be as a grad student.  If you don't have any original findings to show for yourself at the end of the project, that won't be a disaster.

This is a chance for you to get your feet wet, to ask, I wonder... and then figure out how you might start working on an answer.

Give it a try!


Can a rejection be appealed after reviewer says comments were addressed, but paper is not original enough for the journal?

Is it still possible to write an appeal to the Editor-in-chief against the decision?

Sure, it's always possible to do that.  Whether the appeal will get you anywhere is a different question.  In this case, I feel like you think what you told us is grounds for an appeal which has a reasonable chance of being successful....but I didn't see anything in your post that would make me, if I were an editor of your journal [disclosure: I am not a journal editor; but I have dealt with journal editors regularly for some years now], reconsider the decision.

Basically they are saying that after addressing the comments they agree that your paper is solid and publishable, but is not worthy of publication in their journal.  More specific words like "originality", "difficulty", "novelty", "value", "depth" all amount to this same judgment.  Does a journal have the right to reject papers that they think are perfectly sound and publishable but not good enough for them?  Of course they do!!  The journal's right (and even obligation) to do just that is what allows the entire system -- in which some journals are more prestigious than others, and for which publication in the most prestigious journals (e.g. Nature and Annals of Mathematics) is a career-making accomplishment -- to function.

Unfortunately it is quite hard to successfully appeal this kind of verdict.  In the rare case that you happen to know that the editors lacked some specific, objective, important piece of information that would have impacted their decision -- the referee's report dramatically mischaracterizes your work, say by neglecting to mention that you solved an important and well-known problem -- you can bring that to their attention.  More often you suspect that they didn't properly appreciate your work, but your recourse is to resubmit to a journal of equal or greater prestige, and look forward to the (usually implicit!) "I-told-you-so" when your paper gets published there.

Maybe you thought that being asked to make revisions meant that the paper would be accepted conditionally on making those revisions in a way that satisfied the referees?  Well, if you were specifically told that, then: Yes, appeal.  You have a strong case. Otherwise: unfortunately, no, that need not be the case.  If a referee feels that even if you made the revisions she would still not recommend the paper for acceptance, then the ethical thing to do is to reject the paper and make clear that the suggested revisions are for a version of the paper to be submitted elsewhere.  However, even if the referees recommend the paper, then the decision to accept rests with the editors.  As a general rule, the better the journal the more likely it is that a paper which was satisfactory to all the referees will still not be published.  Some of these journals presumably don't even have the space to publish all the papers that their referees recommend them to publish, so they have to make hard choices.

There is one small word in your post which shouts to me: still.  This suggests that one of the referees mentioned in her original report that your paper did not have enough originality to be published in the journal you sent it to.  Is that right?  If so: well, then is it really true that you addressed all the comments of the referees?  In my experience, lines like this are often  hints that the referee is not going to want to publish your paper even if you make some revisions which in your mind measurably improve the paper.  Since "originality" is quite subjective, it is very hard to be confident that you are adding originality, and when you get a report like that it is often a good idea to check in with the editor to see whether s/he views that comment as a deal-breaker.  (I can think of one instance where I got a comment like that, was asked to revise, and wrote back to ask the editor whether he really wanted me to revise the paper under the circumstances.  He said yes and the paper was published.  However the journal, while solid, was very far from the top one in my field.)


Discussing sole author vs first authorship in ML/CV with supervisor

Just go with co-authorship
You're an undergraduate researcher.  This is a case where having co-authorship is actually better than sole authorship.  You said yourself it isn't groundbreaking.  By doing co-authorship you've created a google trail back to this professor.
When people are googling the professor's name, your paper will come up.  When people google your name, they will see your research network back to the professor.
Ph.D. students in the group likely talk about first/sole authorship more.
That's because Ph.D. students are expected to do high-level research and come up with novel ideas.  The next step in their career is (maybe) being a professor.
The next step in your career is getting into grad-school
The prestige of the professor your working with is a factor in admissions.  He'll probably write a recommendation anyway, but drive it home to admissions committees with a co-authorship.
From your post it sounds like he's pretty hands-off.  Write up the paper and put your name first and the profs second.  Let him tell you to swap them.


Suggestions needed in my tricky PhD situation

I'm addressing your particular goal of "I wish to change the direction slightly and explore more relevant techniques to solve the same problem I am dealing with".

One particular suggestion is to use a kind of "red herring" strategy: Work on two directions in parallel. The one direction is the boring/phony stuff that your supervisors want you to do, and that you will mainly discuss in meetings, thus giving them the impression that you buy into their game. The other direction is the direction you actually want to follow. The time to first mention this direction is when you have made some substantial results - you may then calmly announce that you plan to submit them to a specific conference.


Learning new topic: read literature from oldest to newest or the other way around?

Neither.

First, identify the "important" subset of your 400+ papers and read those. Second, try to identify the "good" subset of the papers and read those. Then, (if at all) read the other papers; perhaps you are doing all this with the intention of writing a review, in which case it makes sense to read oldest-to-newest to get a sense of the history.

The most obvious metrics which you can subsitute for "importance" are number of citations (these will likely include review articles) and the ranking (pick one) of the journal of publication. Note that "important" does not mean "good", "honest", "well-written", "reproducible", etc.

For a second sweep, focus more on what you actually do consider to be "good", based on authors and journals that you have found to be of consistent quality.


I am missing deadlines for coping with anxiety. What should I do?

The first, and most important, step should be to find a good therapist to work with you on your anxiety if you don't already have one. If you already have one, talk with them about how you are feeling about this rejection. They will be in a much better position to talk you through your options than we random people on the Internet.

Keep in mind that this isn't an academic question per se (even though it often comes up in academic contexts), and professors and fellow students are not necessarily the best people to help you. Speaking from a little personal experience and seeing the same process in others, getting help with anxiety, burnout, and stress-related symptoms is not about finding a magic bean strategy that will allow you to put in the same hours as before, but somehow don't mind it anymore - it's about guiding you towards acceptance that you cannot and should not work quite as hard as you used to, along with the consequence that you may produce less output than before (but in exchange get a much better life, as you yourself said).


Is it possible to improve(fix) a paper after its acceptance by the conference

Generally, papers presented at conferences include the preliminary results, and the purpose is to receive feedback on your preliminary results and improve them for the final study. If this is the case with your paper, I think you could consider making the improvement after the conference, since you are going to improve the study anyways later on based on the inputs you receive at the conference. However, if you strongly feel that making the change would improve the paper significantly, you can write to the Chairman and explain your concern. If he agrees, you can make the change.


(Soft question?) Sharing knowledge to students, what are the limits?

For actual legal advice, you should consult with your institution's legal department.

Having said that, in most countries, the legal concept of Fair Use protects you from getting in any copyright trouble for normal educational activities. There are limits to fair use (you're not allowed to photocopy a textbook and pass out copies to all your students), but making lecture notes that are based on a copyrighted textbook should be fine, as long as they are tailored to the lectures you are actually giving, and not presented as "here's my summary of the textbook so you don't have to buy it." The exact line where fair use ends is hard to define, and would be up to a judge's discretion if it got that far, but in practice, as long as you don't do anything blatant, you should be fine.


How to find size of academic literature in a given discipline?

It is not that easy to determine the current trend. Many search engines for publications give the number of the search query.

It is important to continuously dealing with your area of expertise. The best way to identify the current trend is to go to conferences and read professional journals. In addition, one also needs a lot of expertise to be able to assess as something.


Working with the 'my way or the highway' attitude from advisor

Given that your advisor sounds stubborn and does not respond well to the students disagreeing, I don't think responses along the lines of 'No, I don't think so' will be productive. In your given example, it seems like the advisor is giving a specific order, and not interested in hearing your opinion on what's right or wrong.

Your second hypothetical response sounds confrontational and involves using the authority of 'ZZ' against your advisor. Playing off one co-advisor against the other is rarely a productive long-term solution; nor am I sure your co-advisor necessarily is willing to go into direct conflict with your main advisor to help you.

Instead of responding in the negative, a more diplomatic solution would be to go along with the decision for now and convince them to change it afterwards - nicely and reasonably (perhaps when it is clear the situation has gone for the worse). By being too confrontational, it is unlikely your advisor will be inclined to listen to you in the future. Remember, you are stuck with this person for several years (unless you decide to switch).


Potential rotation advisor reaches out -- with her entire academic record!

I think you may be overthinking this
slightly. It’s neither a red flag nor necessarily a practical way to demonstrate anything (although it might actually demonstrate something useful, I have no idea).

People are quirky and sometimes do things that don’t make complete sense to other people, or even to themselves the next day. This is true of everyone - including, I’d bet, you. I’m sure you wouldn’t want other people characterizing every slightly unusual or eccentric thing you do as a red flag.

Since “ordinarily this would be awesome”, I suggest that you be happy a faculty member (who has won many grants and awards since 2009!) is taking an interest in you, and talk to her to evaluate the rotation option as you would talk to anyone else in a similar situation.


Endnote: citing highlighted text from a PDF as direct quote

You asked a follow-up question later (here) but this contains a specific aspect - pulling a highlighted citation directly from the PDF for an in-text quote. There is not a way to automatically pull highlighted text from a PDF so I would recommend the following:

Open the PDF and find the quote and page number. Type the quote carefully so that it is accurately represented.
Insert the citation as normal following the quote.

For an APA example you might have:

  "This is an important quote which justifies my research" (Jackson, 2017, p. 1)

or with the field codes visible the citation would be {jackson, 2017@1}.


Academic journals aimed at publishing work by high school students

Publishing in early career

If the research is good enough, it will get published.  The challenge is to do good-enough research as a sixth-form student. Actually, that's a challenge for any of us, at whatever stage we're at. The best example I know of, of young researchers getting published, is a paper in Biology Letters from a class of 8-10 year olds. The paper, Blackawton Bees, is a good bit of research and an entertaining read.

  Principal finding ‘We discovered that bumble-bees can use a combination of colour and spatial relationships in deciding which colour of flower to forage from. We also discovered that science is cool and fun because you get to do stuff that no one has ever done before.

Actually, never mind the rest of this answer for now. If you're reading this, whoever you are, and you haven't read the paper before, just go read it now - it's free to view for all. You'll thank me (so remember to come back here afterwards ;-).

Journals for students

As far as journals specifically for students: well, they all are, really. Pretty much all of us who are reading them, are reading them for study. God knows, they're almost always so dryly written that no one would read them for pleasure.

There are exceptions.  For easier reading, there's New Scientist and Scientific American; though the science sometimes suffers in the cause of circulation-friendly journalism, particularly for New Scientist.

More digestible science

And there are quite a lot of science blogs on the web, which make for more digestible reading of recent research. Unfortunately, there's also a much higher number of pseudo-science blogs on the web, that, unless you know a lot about the subject, are hard to distinguish from real science, but contain pure unadulterated nonsense.  For example, Real Climate is respectable science by respected scientists; Watts Up With That is unadulterated pseudo-science nonsense; but to the unwary, they are both climate science blogs. So, for finding new science blogs, reader beware. Even well-established science blogs sometimes go off the rails, when they stray outside their area of immediate expertise.


Did I make a mistake in being too honest in the PhD interview?

I want to make two points here, both are indirect answers to your question, but still open to interpretation with regard to your specific interview.

Interviews are less like taking an exam, and more like going on a date. It is possible to do everything right, and still not click. Equally, it is possible that you do many things wrong, but the other person is willing to take a chance on you, because they see something they like and willing to invest on. It is therefore not really worth it mulling over the details of the date in any meaningful sense, since you'll never really know what it was that did or didn't click. Having said that, just like a date, you would want to sound honest, but not arrogant, and generally not put the other person in an uncomfortable position for the sake of 'honesty' if you expect to establish some sort of relationship with them going forward.

There is always a way to rephrase a negative into a positive, and it typically pays off to do so. You come across as a more approachable, less negative person, who sees the good and the opportunity in things, as opposed to the negatives. It's generally a good way to go through life, too. So, in your case, you could have rephrased

"it was boring and it was the prof's fault but I'll look at it if I really have to"

into

"I am reasonably comfortable with the topic; however, I felt it was not given the time it deserved in uni, and my exposure to it so far has been more theoretical. Therefore I look forward to seeing an interesting application of this field in a real-life setting, and to improving my skills in this area: I'm very thankful for the training opportunities on offer in this job -- this is in fact one of the reasons that led me to apply here (blah blah, continue on positive spin)".

Regarding the second point, as a personal anecdote, I was taught this by my own PhD supervisor during my PhD. A large part of my PhD involved improving a field in which one of the most influential papers had many (in my opinion) naïve assumptions which weakened its conclusions. I approached this in my work from the point of view of "we build Y which doesn't suffer from the errors in X, who did bad things x,y,z". My supervisor thought this was unnecessarily harsh and had me rephrase it as "X pushed the field forward by proposing X. We improved on this idea by addressing improvements in areas x,y,z, which we believe make the general direction proposed by X even stronger".
Now, "technically", both versions say exactly the same thing, and both are 'honest'. However, imagine I wanted to invite Prof X to be my external examiner in my PhD viva at the end of my PhD. Which of the two formulations do you think would predispose them more positively towards my thesis?


Is it normal for a journal submission to show "awaiting assignment" for more than a month?

It really depends on the journal. Have you been contacted by the editor upon receipt of your paper? If not, I would contact them immediately just to check up. A month is a long time to go with no word. My paper submissions (all to the Astrophysical Journal) have all been followed up by the editor within a week of initial submission.


How to make the most out of a one-on-one reading course with a faculty member?

Ask the professor about his/her expectations on meeting. A short meeting once a week is probably the norm (comment of Nate Eldridge). But ask. And try to schedule a regular time for it. I think that what is expected is that you would give a short report on what you learned and that you would ask questions. If the prof is being vigilant, you might need to field a few questions also, some that might be hard/impossible to answer. The intent will be more to get you to think in a certain way than to test you.

But don't treat it as just "reading". Find a way to do some practice around the readings. If it is a well studied subject there will be exercises available and you can report on what you have done with those. In a more "state of the art" situation you will want to think about "what if..." to get a sense about where this subject might be extended. That would be for a quite advanced set of readings, of course.


As a PhD-Advisor: How do I discourage a student from continuing?

Do you want to dissuade the student from continuing because

You think the student is not capable because of a lack of ability,
You think the student might be capable, but just isn't engaging in the work,
You don't see the student is worth investing your time in,
You think the student is wasting his/her money?

If (1), then a frank discussion might be the best way. I have seen other PhD supervisors directly let their PhD students know that they think a research career is not for them.

If (2), you ought to move from dissuasion to a frank discussion in which you try and figure out the reason for the downturn in engagement. Is all well at home? Is it just the usual mid (?) thesis malaise? Has the student lost the big picture and therefore the drive to do the research? Why did the student start the research in the first place? Has the situation changed - e.g. has the life goals been redefined/changed?

If (3) and/or (4), if the student is  paying for themselves, then it's their money they are potentially wasting so I wouldn't concern yourself on how other people spend their money. However, the money is presumably paying your salary in part so your obligations to the student remain in that regard. In return however, you can set reasonable expectations on your student. If you make it clear that you expect your student to achieve reasonable goal A by reasonable deadline Z, and the student doesn't, then that opens up another opportunity for a frank discussion along the lines of the need for effective prioritisation of research work and for-money work.

EDIT: To bring this answer into line with the edited question, I would set out an agreed plan of work - and behaviour (esp. showing up to meetings) -  with deadlines for the next 2/6/12 months. You might want to work with your Head of Department/School on this to ensure that your requirements are reasonable. It appears that you have already said to the student that in your opinion the student isn't PhD material. In setting out your agreed workplan, you are giving - formally - the opportunity for the student to show that he or she is capable of working to an agreed standard. If, as you say, the student isn't capable, then the student will fail and you can reasonably excuse yourself as his PhD supervisor.

I am suggesting this cautious approach, as I am sure your Faculty will want to know why things went this way, and that you offered the best opportunity for your student (or fee-paying client) to succeed, before you ceased to be his supervisor.


While teaching how should I give justice equally to both female and male students?

If you really can't change your actions, find a different profession.

You're aware of the issue - you admit you spend more time helping the females than the males.  Find a way to equalize that problem.  Be sure that you make your time available to all genders - use office hours, or clarify to all students how to get help from you.  Look for the patterns where you realize that you cut off help from the men and continued to help the women - there's like an unconscious bias that you may be able to over come with a pattern.

Changing a pattern like this may not be easy - but it's what's rightfully expected.

Also ponder - why - why do you give women more time?  Are you hoping for something more than a teacher/student relationship?  Is something more pleasing about them? What's causing the problem, and can you reduce the factors that lead up to it?

I suppose the other alternative is to find a place where you teach only one gender.  Then you don't treat your students unequally.  Personally, that seems like taking a short cut.