Does any university require reporting of misconduct at other universities?

in case of publications and falsified data you are first and
foremost responsible to report it to the publication. They need to
first approve or review the technicality of the matter which can
become material for the ethics committee.
The Honor Committees of universities keep a record of students and
faculties, and when students or professors apply to other
universities they are generally being asked about the previously
notable issues with ethics in the previous institution. Lying in
those form can by itself be lying to the second institution even if
the matter can not be investigated with the first institute. That
being said Honor committees in university X might have a threshold
and limit before noting an offense or violation on the record
subject to citations and referral for future. In some cases in
universities, some mandatory 6 session therapy is being recommended
as a way to remove an item from someones active record.Those
therapies are subect to confidentiality and therfore can not be
cited by university Y.


How do you make corrections to a published paper?

It depends on what the error is.

If the error is the publisher's fault—for instance, if they failed to make a correction you specified in the proofs—then they have an obligation to correct the error. In that case, an email to the editors alerting them of the problem, along with some documentation of the original list of corrections, usually suffices to get the problem fixed. (This will usually be accompanied by a "publisher's note" alerting the reader to the correction, although the original article will usually be updated to provide the correct information.)
If the error is something discovered after publication, then the best way to fix this is to prepare a short comment detailing the error, the correction, and its implications on your work. The resulting item is then submitted to the journal as a "comment" (or, in some cases, an "erratum," if the journal offers that as a submission option). In this sense, it is like any other comment on a paper.


What is the correct APA citation style with two places and two publishers

From this APA library guide it says;

  If more than one publisher is given, use the first one or the one that
  represents the home office, if given.

This answer at writer stackexchange supports this as well

So for your example the following should be fine for APA

  Cazes, S., & Verick, S. (2013). The labour markets of emerging
  economies: Has growth translated into more and better jobs? Geneva:
  ILO.


How long it takes for a Mendeley Data repository review?

Mendeley Data moderated and accepted all 6 datasets, in between 2 and 3* days since submission.

I can't say when exactly it was as I received no email confirmation and I've checked last time the status of datasets 2 days after submission. Also, looking on the Mendeley Data UI, I can't find any clue about when it was approved.

However, 3 days is very good in my opinion :)

Hope this info will help someone else :).
Live long and prosper!


Balancing short-term academic position and pregnancy

If I understood right, she is not pregnant at this time.

If the post-doc is a one-year appointment, I don't see a problem.  Pregnancies generally last approximately 9 months.  It often takes more than one cycle to conceive.  If she wanted to be sure the birth wouldn't interrupt a 12-month appointment, she and her partner could always wait a couple of cycles before starting.

She may start to want to have an afternoon nap at some point; she'll probably want to bring some extra snacks to work; she would be smart to plan in such a way that she doesn't have to spend a lot of time on her feet in the lab in the last trimester.  Some women find their concentration isn't completely what it was pre-pregnancy.  She might want to build some flexibility into her project(s) in case she finds her productivity is a bit less than what she's used to.

Other than that, the only limitation I can think of would be if she works in a field involving radiation.

If the post-doc is a two-year appointment, then she may want to plan her work flow to allow her to ease back into work part-time after the baby comes, while still making progress with her research.

(How to combine work with care of a young baby is whole topic of its own which I won't get into here.)

Note, my answer would be different if she were about to jump into a tenure-track position, with a solid teaching load and having to build a lab program from scratch.  But this position sounds nothing like that.

Whether or when to start a baby is a very personal decision.  I see nothing objective here to stand in her way if she and her partner want to do this now.

(Note that in the U.S., employment discrimination against pregnant women is strictly prohibited.  I can't imagine things would be substantially different in the UK.  If in doubt, however, http://law.stackexchange.com can help.)


I am applying to a Philosophy Master degree which I have little experience on, what should I do with my CV and cover letter?

A taught master's degree are given in programs where the majority of the 'work' that you do is coursework rather than research.

In those cases, the assumption is that you are seeking more background in the field -- which implies that you don't have enough background in the field. I think that you'll find that if you get in, most of your cohort will have similar ... how shall we say it... diverse backgrounds.

I would write your statement just as you did, that you don't have much background but that you are seeking a PhD in the field and see the taught master's as a stepping stone towards that.


Graduate in three years and then apply for Ph.D. programs?

If it really is a risk that you might not graduate at all if you stay on another year, then maybe you could consider graduating early and hedging your bets. There are other ways to catch up and make yourself both more prepared and more desirable to PhD programs of your choice. For example, you could try and apply for a research position if you see any openings in labs, and either take courses simultaneously or or as someone else suggested, apply to a non PhD program first.

Either way, if there is an academic you know you would want to work with, it doesn't hurt to write them an email and ask them if they would be willing to take someone with only three years of college and if not, what would kind of skills and strengths they might be looking for. I did this when I switched fields right after college, and I was told that though I did not have quite enough qualifications, if I managed to do x, y, z I would be considered. That's what I ended up doing while working part time and two years later I got into the program (of course if you need a visa to work that's a different story).

However, if you can manage it financially, I would probably advise staying in college the extra year, and prepping for the GRE, taking courses relevant to your field, and getting those very important recommendation letters by making an impression on your professors. Also, most colleges have the option of doing a senior thesis, and if you want to go into a research career, while not a deal breaker, writing one can be very beneficial, no matter what area you write it in. Showing that you have the ability to do independent work is always a good thing when applying for doctoral programs. And it gives you a chance to work one-on-one with your advisors and can be as challenging and fulfilling as you make it!

Everyone is different, so you will have to decide on your own, but I'm always in favor of a little bit more rather than less time between college and grad school to be both psychologically and academically prepared. But that's just me. Good luck to you!


Which ranking is more meaningful for post-doc students?

None of them. At the postdoc level, you should already be familiar with the people and research groups in your field, at least at a basic level. Go where there is someone you want to work with, and maybe a good active research group, irrespective of the ranking of their university. That ranking could have been achieved because the university is great in a completely different research area, or because it has good conditions for students (as a postdoc, you don't care about this). And, as you state yourself, at high detail level many rankings are bullsinaccurate anyway.


What is the timeline for academic job postings in the humanities in Australia?

Universities in Australia take a slightly different approach from those in the US. Rather than recruiting serious academic positions almost exclusively at the assistant professor/level B level and recruiting in cohorts, they tend to advertise positions when they get new funding or when someone leaves, rather than on any particular timeline, and may hire (or cut positions) at any level of seniority.

If you look at the websites of universities, most of them currently have some academic positions open, with deadlines ranging from tomorrow to the end of July. You just need to be on the lookout for suitable positions in your field.

That said, the academic semesters in Australia run from about February to June and from about August to November, so it is likely that there are more positions being advertised in May-June and November-December, looking for people who will be ready to teach at the start of the coming semester.

ETA: Here's one for you to look at: http://www.jobs-monash.jxt.net.au/academic-jobs/lecturer-senior-lecturer-in-literary-studies/642748


Is it common for a publisher to offer monetary compensation for a book proposal review?

I was asked some time ago to review a book proposal by a leading academic publisher, and offered to choose between receiving some token monetary compensation or having them send me a few of their textbooks of my choice (I opted for the latter option and remember feeling quite happy when the "free" textbooks arrived :-) ). So yes, publishers offering payment seems not uncommon.

I do agree that the use of a personal email is suspicious and not consistent with professional email standards associated with large and respected organizations like Elsevier. It could be completely innocuous, maybe due to an employee with slightly rebellious tendencies who refuses to kowtow to his corporate culture and insists on using a gmail account, or it could be a scam, who knows. Caveat emptor - obviously do your due diligence before compromising any bank account information. (And let us know what you find!)


How can I re-use someone's mathematics thesis without plagiarizing?

I assume that someone's PhD thesis is a larger piece of work than a section of your report. Therefore, I don't see how you can avoid summarizing the thesis to fit your work. And while you are at it, you get the chance to deepen your understanding of the subject, because you will basically be writing a review of this someone's thesis in light of you report. That is a prospect you shouldn't miss, as in academia as well as in industry, you will be expected at some point of your career to "digest" some work and produce some implication of it.

Citing the thesis is a must, if it is used as a reference, there is no debating it. I would recommend writing your section "your way", but not just changing some details to mask your copy-paste trail. Put the material in the context of your report. You don't need a clear mind and conscience to use something you learned from a source. If it "looks like" the said thesis, that is not a problem, as long as it fits and you have gained significant understanding from it.

PS: If you did a simply copy-paste, you would likely find that the text still needs some polishing to fit your report. That can amount to a significant amount of work.


Submitting the same PhD proposal to multiple universities?

You should clearly tell this potential supervisor at your current university what you told us here: That your current university would be your first choice but, since funding is uncertain, you need to apply elsewhere also.  If this potential supervisor is a decent person (which most academics are), this should remove the difficulties that you are concerned about.  (If she's not a decent person, why do you want to work with her?)


The best way I've discovered to become a reviewer for a journal is to submit a paper there. In my experience this is almost always followed a few days later by a request to review a relevant article.

Edited to add: I did my first reviews while a graduate student because my PhD supervisor was the editor of a journal. He would send me things occasionally because he considered it part of my training. So, another way to become a reviewer is to know an editor.


Should I apply again to the same research group where I used to work and haven't got any PhD offer from the professor?

You got scooped. That sucks, but it happens a lot; and it is definitely not the end of the world.

If you think your work was good in the group, I would say go ahead and apply. You could explain to him why the project was delayed; a polite discussion cannot possibly hurt you, and you can figure out in which terms they are with you. Remember that even if you were in your best conditions, some other group may have just more people working on the same problem, or they started one year before you, or any other reason.

By the way, you have now a working implementation of the analysis, and perhaps you can improve it to do something the other group didn't; implement other algorithms, etc.


Is it OK to inquire about paper status after 7 months (2nd round) review?

I inquired the status about 4 months ago and only got a reply from the journal staff, basically saying that my message has been forwarded to the handling editor ...

is telling me that the journal has not forgotten about your manuscript. They are still processing it.

As you are well aware of, reputable math/applied math journals turn around time are very long in general. I have read on this site that two years is not unheard of. Please see this answer for example.

If you are anxious to know the status of your manuscript, I think sending another inquiry is okay since last time you inquired about its status is four months ago. I don't think the inquiry is too pesty. They'll understand.


Dear XYZ,
thank you for considering me for this position. Unfortunately, for personal reasons I am no longer considering this option. Hence, I have to decline this invitation.
With best regards, clearseplex

In other words, like you would politely say no to any other opportunity - polite, short, and without going into details why exactly you changed your mind.


Difference between internal and external doctoral studies in Germany

Keep in mind that most German PhD positions are not funded through "scholarships" but instead through standard labor contracts. Consequently, any listing of "scholarships" will likely include all forms of funding for graduate students. Filtering by internal or external positions will allow the database to select if you are being "employed" by either a university (internal) or a company (external).

There may be some nuances and particular issues depending on the school and faculty with respect to residence time, composition of your thesis committee, and format of the defense (among other issues) according to whether you're doing an interne Promotion or an externe Promotion. However, it's hard to say in advance if you'll run into this or not.


Should I be concerned that my (successful) application to grad school only barely survived the first cut?

we were in the bottom of the pile.

Not really! You were in the very top of the pile. Many departments get more PhD applications than they can accept. Typical acceptance rates are about 10%, although I don't know about statistics specifically.
So if they offered eight spots, you were applicants #9 and #10. That's good. Unfortunately, when it comes down to choosing eight people out of the top 20 or so, it comes down basically chance. There is no objective way of measuring how good a candidate might be. So there is likely no real difference between #9 and #10, or more critically, between #8 -- the cutoff -- and #9. That a professor was asking for you specifically means a lot more than the overall ranking come up with by a committee.
Because "ranking" in the top 10% or so is meaningless, it doesn't really correlate with performance. Likely, you and you cohort study different enough things that it's hard to compare anyway.
It is quite inappropriate for a professor to reveal students' "rankings," especially to other people, though.


Pursuing the field of computational physics professionally with a physics PhD

So for starters, I want to comment on your interest in writing everything from scratch. I feel for you with that, I felt similarly when I was starting out. While writing codes for some things that exist in great software packages already can definitely make sense, I will specifically say that writing code to do numerical linear algebra work is a terrible use of time. These numerical linear algebra packages are optimized to the extreme both with respect to algorithm approaches and with their software implementations.

Now implementing some of these things yourself is a great learning experience but don’t expect your code will perform nearly as well as the popular and proven packages. Also note that when it comes to being a productive researcher, you will have to be smart about optimizing your use of time. Building up your own numerical linear algebra package is likely not going to be a very productive use of your time. Feel free to comment.

As for how to learn, you should see if you can find more specific courses in other departments in things like computational mechanics so you can develop some general computational science skills, if you cannot find computational courses with your desired niche. From there, you’ll want to find some good textbooks to supplement your learning, depending on what things you need to learn more deeply or that fit your domain of interest better. You’ll obviously want to also develop some of your own solvers after you’ve covered the theoretical side of things to validate your understanding.

Outside of the straight up computational physics learning, you should try learning about some topics that could be useful, such as High Performance Computing, numerical optimization, and perhaps some minimal computational geometry.


Is a 2.5 year shorter tenure clock a benefit?

Getting tenure is (technically and in actuality) a promotion and comes with at least one benefit (not easily getting fired) and usually there is a (modest) pay jump. Whether you consider these benefits against the additional responsibilities that tenured faculty have (especially in terms of administrative/service work) is up to you.

A shortened tenure clock could be a good thing as it gets you that promotion sooner. It could also be stressful if you're at a place where the tenure hurdle is clear and you don't think you'll make it (e.g. 7 peer reviewed articles when you have only 2 in the bag and will only get 3 more done by tenure-time)

The best would be to have the option of coming up early -- but also the ability to delay your tenure bid and return to normative time -- but also retaining the ability to count all of your materials from your postdoc period in your tenure bid.  There may be resistance to this, though, as it might be seen as having your cake and eating it too.


JCR publication required to enrol in PhD program - is it common?

Admissions requirements and research expectations for graduate students vary wildly across different disciplines, subfields, countries, individual departments, and even individual advisors.  I would be surprised to discover a PhD program that actually required prior publication before admission, but at least in computer science, it is a fact that strong PhD programs regularly attract applicants who have already published.

In particular, students are much more likely to produce publishable research in a Master's program than they are as undergraduates.  Again, I'm unaware of any Master's program that requires publication as a condition of receiving the degree, but a good Master's thesis is publishable, and Master's students do regularly publish.

Strong PhD programs are looking for students with potential to become good researchers.  Nothing provides evidence of potential for becoming X better than demonstrating that you already are X.  So PhD applicants whose have published good research (in a reputable and visible venue) have a significant advantage over applicants who have not.

The absolute best PhD programs in a particular subsubfield, especially if those departments are small, attract enough published applicants that a significant fraction of their PhD students had publications when they applied.  (For example, theoretical computer science at Princeton.)  But even in those departments, I'd be surprised if "a significant fraction" was a majority.


My affiliation after I moved to another institution for Ph.D

Most of the work was done at affiliation A and your adviser for that project was at affiliation A, and now you are at affiliation B. I disagree with Buffy's answer, which is to list your affiliation as B rather than A.
The most common approach is to put affiliation A with a footnote that says: "Present address: affiliation B", or to put both affiliation A and B.
You might also like to ask your advisers at affiliation A and B whether or not to include those affiliations on your paper, so that neither adviser can get angry at you for doing what they don't want you to do or not doing what they do want you to do.


The straight forward answer is that you can publish the work as you see fit. A well-written sound manuscript submitted to an appropriate journal is always welcome.

That said, however, your actions is not likely to smooth out any existing "conflict", for lack of a better word, between you and your advisor. And, just because one can does not mean it is the best solution. I am not about to judge who is is right or wrong in your situation, only someone close to you plural) would know. But, one question that immediately pops if you really have tried to discuss the matter in detail or if you have the position that your adviser should solve the problem. Lacking your advisor's side, only you can make such an assessment.

If you are in the position that your adviser is one-sidedly not communicating with you, the situation  is difficult. I understand your eagerness to publish but will also mention a few things that can cause the actions to back-fire. First, you will most likely want letters of recommendation from your advisor so publishing work done in the advisor's lab without sanctioning from the adviser can become a negative aspect. You really need to objectively assess this proposed action. Second, if you are close to finishing, the timing is perhaps not optimal to ignite a conflict with your adviser. Again, you need to really assess your situation to know what ramafications can come from your actions. One partial solution, is of course to try to talk to other faculty for whom you have more confidence.

In the end, I can only see one solution: communicaton; and I can only advise to tread carefully over possibly mined territory so make sure you prepare your map carefully before running into solutions out of frustration or even anger.


No vote from department, up vote from university level committee. What does this mean?

The tenure process usually has many steps, with decisions by the department's tenured faculty, the department head, the college's tenure advisory council, the college's dean, the provost, and the board of regents (or board of governors, or whatever other name they have at your school). At some schools, some of these steps may be omitted, at others there may be more steps.

A friend of mine, who happened to be a dean at the time, told me once that he's pretty sure that every combination of positive and negative votes has happened before. I know of at least one case where the department's faculty voted no and the department head recommended yes anyway.

In the end, you are right that the ultimate decision lies with either the provost or the board or regents. (Though I would suggest not taking this as legal advice -- the situation at your school may be legally different.) So you can take solace in the fact that the department's vote does not determine the outcome. Of course, the negative vote will likely be considered when the provost or the board make their decisions, and so it is still possible that you will not get tenure.

I do wish you luck in the process. Going through this is stressful, and will likely occupy a substantial fraction of your mental energies until it is resolved. After that, however, you ought to also consider what happens if you do get tenure but you have to face the colleagues in your department every day. Half of them did not think that you should get tenure. This is something that will follow you for many years to come. It will affect your standing in the department, and you will feel insecure opening your mouth every time you speak up at a committee meeting. Assuming you do get tenure, it would probably be useful to think in detail how you want to deal with this: Are there things that you think you might have done wrong in the past and for which you could atone in personal conversations with colleagues who may not have been in favor of your tenure? You might eventually find that you don't feel sufficiently welcome in the department to spend the remainder of your professional life there, even though you ended up getting tenure, and might want to look around for jobs elsewhere.


How to revise a paper when the reviewer has not understood my work?

Make sure that the reviewer was wrong not you. S/he is definitely an
expert in the field and might see your work from a different
perspective. In this case, it is not a matter of being right or
wrong.
Assuming that s/he have not really understood your manuscript. This
suggests that there is something confusing about your manuscript. If
s/he, as an expert, has misunderstood it, this means many other
readers will not understand it too. Things might be crystal clear to us, but our expression can be confusing but we do not see the confusion from our perspective.

As a general advice, see peer-review as a gift instead of a fight.


Do STEM professors retire from research at age 65, while continuing to teach classes?

This is very much a function of the regulations of the institution in question, and the health and desires of the faculty members in question.

I have known a number of faculty members who start to wind down their research groups at age 65 or even a little earlier, while others wait until about age 70. I also know of schools that don't allow faculty members over 65 or 70 to bring on new students, thereby effectively "shutting down" the groups. But I do know a handful of faculty members who were active as researchers into their 70's and even into their 80's.

In countries other than the US, policies are much stricter. In Germany, for instance, professors must retire at 65 unless their successor allows them to continue to supervise students and conduct research.


Where can I find research papers to read? (not currently in academia)

This is going to depend a lot on your discipline. Some disciplines are very good at keeping papers and preprints publically available. For example, most math and physics papers get papers put up on the arXiv but this is rarer in other fields. Some other fields put papers up on SSRN, but some fields don't up up almost any preprints.

It isn't clear from your question if you've completed just your undergraduate or did some graduate work. Given your statement about not having looked at papers before, I'm guessing this mean that you have either finished just an undergrad or finished a master's but nothing beyond that. If that's the case, I'm also not sure that finding papers will in general be useful for you. It might help to clarify why you want to find papers and what your goals are.


Benefits to supervisor presence at viva in the UK?

I would suggest that you should only bring your supervisor if you have a specific, positive reason to do so. If you are in two minds about it, it sounds like the answer is "no". But as your supervisor says, it is entirely your decision.

Although it is permitted to bring your supervisor into the viva as an observer, most PhD candidates do not do this. The main exception is if it would be reassuring for you to have them there. There might also be an argument for having them as a kind of "quality control", but really this is the job of the internal examiner, so unless for some reason you don't trust your internal (perhaps if they were very inexperienced), that's not necessary.

For most people, having your supervisor there would be fairly harmless, but provide no real benefit. It could be a little distracting having them in the room (given they are not allowed to say anything!) and might just mean that you start second-guessing yourself, looking to your supervisor for reassurance instead of being self-reliant. Given that it's uncommon, it's possible that it could make you look less confident in the eyes of your examiners.


Does writing code for an assignment after seeing similar code online count as plagiarism?

I think this is very subjective question and will depend on who the judge is. I would suggest you communicate exactly what you wrote in the question to your professor and let him be the judge. If he thinks yes, he might assign you some other relevant exercise to evaluate your learning.

By actually being honest about your situation, you will likely be treated in a positive light.


Do evaluation / recruiting committees respect "co first authors"?

In theoretical computer science and mathematics, authors are (almost) always listed alphabetically. There is simply no such thing as a "first author", except lexicographically.  Equivalently, all authors are co-first authors.

In my experience, recruiting committees generally understand and respect this practice, but (at least in computer science, where order by contribution is more common) they do occasionally have to be reminded, especially for candidates whose last names start late in the alphabet.  One sentence in the CV and/or in a recommendation letter usually suffices.

For non-theoretical CS, I have seen CVs that indicated equal contribution of co-authors. Again, one sentence in the CV ("Stars indicate co-authors who contributed equally") made the notation clear, and the recruiting committee understood and respected it.

As Ari and gefei say, having a local advocate is much more important that having another (co-)first-author paper.  If nobody on the faculty is willing to pound on the table and demand that you get an interview, you won't.


How to get confidence in myself after making several errors?

I see three different issues in what you have described:

You make some mistakes in computations.  That happens to all of us, but whether you should be concerned about it depends on what type of mistakes you are making.  You need to look at what mistakes you are making and how, and see whether they are "sloppy" mistakes (in which case you can develop a checklist for yourself to avoid making them) or whether they are just coming form the fact that research is hard.
You submitted to a paper without consulting with your advisor (and maybe dual-submitted as well).  This is a serious problem, especially if you did a simultaneous submission to two journals, which is almost always forbidden and unethical.  If your advisor is a co-author, then you are definitely in the wrong to submit without approval: you are not taking responsibility for yourself, you are denying responsibility to your co-author.  Even if you did not commit either ethical sin, most advisors want to help advise their students, and submitting without consulting is a good way to make mistakes that will reflect badly on both yourself and your advisor.
Your advisor has been angry at you, and you are losing self-confidence.  Maybe you need to lose some of the undergraduate-style self-confidence, and to develop a more mature self-confidence.  What you describe as "being responsible" and "working your hardest" does not actually sound like responsibility to me: it sounds like you are not yet reflecting on how to manage your own behavior and its impact on others.

For all of this, I think self-reflection and learning from your mistakes is the solution.  If you can understand how you have been making mistakes, then you can act to make them less likely in the future, and all three of these issues are likely to improve.


I think everything you're asking about is within the scope of the reviewer's role. Generally speaking, I divide my review up into three sections:

Summary: A summary and free-form critique. Here I communicate what I think the "gist" of the paper is about, its strengths, and offer some weaknesses that might exist in the paper as a whole. For example, if I think the authors were slightly too timid in not offering a interpretation of the data, or if they've missed or glossed over some major point.

Major criticisms: These are things that must be fixed in order for me to consider it a publishable paper, and if I have the chance to review the revisions (some journals do this), things I expect to either see changed, or have very good arguments for why they're not. Stuff in this category includes:

Flawed or inappropriate methods
Major intuitive leaps that aren't supported by the data or analysis
Study design problems that need attention
Major failings of interpretation
Journal specific problems, like failing to properly report your protocol to established standards for a clinical trial, or the inappropriate use of p-values in some journals.

Minor criticisms: These are all things that are essentially "The advice of someone reading your draft with a critical eye". Importantly, these are things where, if they all made it in, while I would possibly be annoyed, I wouldn't be upset that the paper hit the press. This does include things like advice on graphics (my pet peeve is graphics that are unintelligible when printed), missing citations, etc. Things that are above the level of a copy editor, but aren't going to move my decision on the paper one way or another, unless there are a lot of them.

Occasionally I'll put in one or two small copy editing notes if something jumps out at me (insure vs. assure vs. ensure, etc.)

The cut-off I use is "Will this irk me when I see it in print, and will I think less of the authors that produced it?" To use your example of bad graphs, yes, this would annoy me, and it results in a less usable finding than one with the appropriate graphs - just like garbled language in the Results section might. If its minor stuff, like a turn of phrase I wouldn't have used, or a slight fondness for run-on sentences? That falls below the radar.

As for friends vs. anonymous reviews, I think the scope does change slightly. For a friend, you're helping them polish a paper - I think a great many more things fall under that umbrella, including things like "That's really not what a semi-colon is for" or fiddling with the graphics parameters on a plot. For a reviewer, you're one of the last gatekeepers before this goes out into the world - but you aren't an editor. Your focus should be on the research, and the appropriate presentation of it, unless the errors are so bad as to impede one of those.

In either case, you should be polite.


What to do if your research idea has already been published?

It is hard to give advice specific to your case without knowing more, so I'll mostly restrict to general comments here. What you do depends on the field, to some extent, and to the individual paper and kind of research.
But, if you use a known technique to reach a known result, your results are probably not going to be published. It is, at best, a learning experience.
Independent researchers have a number of problems, but they often come down to lack of professional advice in getting started in research. Working with a guide can help you avoid dead ends. The big problem is that there is a lot to know about any given narrow subject and it can take a long time to absorb it. A guide can help you find an appropriate path to learning what is already known and what is still valuable to pursue. Ideally, you'd like to know about the earlier work before you spend time that might not be productive.
You don't suggest that your research is in mathematics, but there, it is possible to publish new proofs of known theorems under certain circumstances. A proof give insight into why something is true as well as the fact that it is. Sometimes those insights can be transferred to other problems yet unsolved. So, a new proof, using a novel technique, can be valuable in itself and might get published.
Another kind of research depends on statistical methods. Social science and some of the "hard" sciences can use such methods. Some of the published results here are worth replicating, since statistics alone only give evidence, not proof, that something might be true. But, again, you need some variation for the new study to be valuable. Sometimes a paper will contain assumptions that may be unwarranted (normal distribution of a variable in a population, say) and a new study making fewer assumptions might be worth doing. Likewise, some medical studies are extremely important and may affect people's health. So, a lot of evidence for what is really going on is needed and replicated studies can be essential. And some studies actually refute the results of others, thus requiring more study. Statistical studies, if done well, have a measurable probability of producing misleading results. Replication reduces the probability of error, provided that things are done properly, and probably with some variation on the original.


What should I start doing to improve my prospects since deciding on an academic career?

Try to find active researchers who are willing to let you do a research project with them (easier said than done, but if you're offering to work for free in your spare time without huge amounts of hand-holding then people will sometimes give you a chance), and then collaborate with them to write a paper. Papers, particularly high-quality papers in good venues, are the primary currency in academia. Writing a technical blog might be fun, but realistically won't affect your academic reputation one way or the other (it's unlikely that many academics will see or read it). Similarly, joining organisations isn't on its own going to have much impact on your academic reputation - people generally don't care if you're a member of e.g. IEEE, they just care if you've done any useful work lately. Helping organise seminars that are popular in the field (if you can find a way to get involved in that) might get you noticed to some extent, but only counts a bit (people hiring researchers don't want to know whether you can organise talks, they want to know if you can produce interesting research).

Basically, the main thing that matters is (good) papers - try to find ways to write them, preferably with other people, but on your own if necessary (the latter is hard and less effective, so try to avoid it if you can). Try not to waste too much time on things that consume your energy but for which you don't get any reward. Enjoying them can count as a reward, incidentally - by all means do fun things just because you like them, just don't expect them to have a huge impact on your reputation.

Source: It's Sunday, and I'm writing a paper, so at the very least I believe the advice I'm giving :)


What are the benefits of PhD students working on projects where they won't be first-author?

In disciplines* where the PhD thesis consists of a set of published articles, the PhD usually - but not always - must be composed of first-author papers. Yet there are many reasons why it might be beneficial to be involved in other projects as well, so long as one is also making reasonable progress toward the dissertation.

Perhaps the two most important reasons are:

Training. Early on in graduate school, it may be valuable to simply have the experience of going through every stage of a research project from conception to publication, without having to be in charge every step of the way. Often a first of second year student will be involved in a research project on which a more senior student or postdoc is first author.
Portfolio-building. For most students the goal is not merely to finish the dissertation, but to do so in a way that positions the student for future success. It may be preferable to graduate with 3 first-author and 4 mid-author papers instead of 4 first-author papers, for example.

Additional reasons include

Research assistantship duties. If one is being paid on an RAship, this often contributes substantially to published research that may not be directly relevant to the dissertation.
Reciprocity. Sometimes students collaborate on a series of papers and alternate first authorships as they go.
Too good a thing to pass up. Sometimes the lab hits on something so cool that one would be a fool not to be part of it, whatever the authorship position.
Networking. By establishing collaborations with researchers beyond one's home lab and institution, one builds up one's professional network.

This is only a partial list, of course, but it should provide a sense of some of the reasons that graduate students should not shy away from projects that will lead to mid-author publications.

Authorship order does not matter in all disciplines. In economics and some subfields of computer science, for example, authorship is alphabetical by convention. Clearly this distinction does not matter in those fields.

[ Edited to include suggestions from the comments and other answers. ]


Should I address my professors by first name in emails if my peers are doing so already?

In the US-influenced culture of international Academica, closing an email with the first name can most of the time be interpreted as implicit invitation to interact, at least in further email communication, on a first-name basis.
So yes, most likely you can address your professors by first name in emails. Not because your peers are doing so, but because your professors are inviting you to. For other communication, I would just ask: "Is it OK if I call you Jane, or do you prefer Dr. Doe"?


How high should I rate a good student for PhD admission?

The question of gauging inflation in these situations is both serious and important. It affects peoples' lives!

The difficult task of the letter writer is to visualize what other letter-writers will say, their degree of effusiveness. "Being brutally honest" is obviously stupid and naive to the point of destructiveness.

The operational issue is about achieving the desired effect. And, in particular, if your recommendee is fairly exceptional, it would be a grievous error to praise them "modestly". Yes, the problem is to discriminate between "fairly exceptional" and "exceptional" and "truly exceptional". And these are not things that can be rationally discussed about young people by committees...

Thus, consider the noise in the system into which you put your information...


Publishing figures: Serif or Sans-serif fonts?

When it comes to typographic design, it can be dangerous to adhere to rules of thumb. Sometimes (actually most of the time) sans-serif fonts work, sometimes they don't. It would depend on tradition, trend, and overall feeling that the fonts project.

If the journal does not specify. I would usually favor sans-serif. The reason is that unlike my texts, I am not always sure how much the editorial team may size down my illustration. Sans-serif has a pretty good property that they are quite resistant to shrinking, and can still be legible at relatively small size.

In the mean time, if the publisher uses any software to smooth out the edge of the fonts after resizing (e.g. through aliasing,) serif fonts can sometimes appear broken at their thinner strokes.

There are, however, some illustrations that just don't look right with sans-serif. For instance, line labels and angle labels of trigonometry problem sets and formula like this one are much nicer with bold and/or italicized serif fonts, monotone ink-drawn anatomical charts (like this one) will just look very odd if we put on sans-serif labels. This timeline describing Shakespeare's Life may look ridiculous if sans-serif fonts are used.

In those difficult situations, look for serif fonts that are beefier or with more uniform stroke width. As they can likely withstand shrinking and aliasing. In addition, look for fonts that are slightly wider, and have a good "x-height" (literally height of the font "x"). Some possible candidates are Caslon, Baskerville, Garamond, and Palatino. Avoid cursive fonts, or fonts with some very thin lines like Times New Roman. A more in-depth discussion on squint-free fonts can be found in this blog page and this thread on SE UX.


Is it acceptable to post a brief and speculative paper on ArXiv?

In general when is "I have a general interesting idea for solving problem X but don't have tools Y to determine if it really works" worth publishing? It depends on how important the advance would be, how big a step your paper takes relative to the part remaining, and how easy it would be for the remaining work to be done. I agree with Captain Emacs that you should not be using readers as your beta testers. Let me propose three categories:

A) Not worth publishing: Is (a+b)^2 = a^2+b^2? Simple question, which could be resolved by actually doing the algebra.

B) Probably not worth publishing without extra work/collaboration: Our mathematical model predicts cancer correlates with gene X. Potentially important result, but this is something a bioinformatics person would know or be able to find out easily - so why are you spending so much time writing this up without asking someone to check first?

C) Worth publishing: "The Taniyama-Shimura conjecture, if true, implies Fermat's Last Theorem" (https://en.wikipedia.org/wiki/Ribet%27s_theorem). Linking two unsolved problems, or providing a potentially new attack on an old problem, can be a useful contribution even if it doesn't solve everything.

I think you are probably in case B, because if the issue is just that you don't have many programming skills, you can either learn enough to implement your ideas or find someone to collaborate with. If you can't, this means your question is probably not well-posed enough to interest the broader audience of arXiv. I suspect this is the case, because your question is not too detailed "Data analysis" is a huge field -- you could be trying to speed up an algorithm for a known process (something where you could have a theoretical result -- but it shouldn't be too hard to implement to show you are right), or find a better way of extracting some detail from data (need to test on real-world data to make sure you are not fooling yourself), etc. Your question doesn't sound like you need super-specialized skills, or a giant investment of time to fill in the later details -- so you should try to do this before publishing. Otherwise, you run the risk of spending weeks writing up a draft to wait a month for someone to test your idea to find out that, if you asked the right person, they could have found out in ten minutes that it didn't work.


Is it a bad idea to ask my erstwhile PI to say in a recommendation letter he "forgot" to acknowledge me in a prior work?

You should ask the professor to describe your contribution to the database and the relationship between the database and the publication.
No matter what the reason is that you are not an author on the publication, there is no benefit to including the reason in your letter of recommendation.  A correction to the author list could benefit you, but only someone familiar with the details of your work could determine if that is appropriate.


How to cite three things in the same sentence

The original "I use A, B, and C [1] in my paper." is not quite clear for the reasons you've mentioned.

Better:

  I use A, B, and C in my paper [1].


Difference in length of study between Europe and the states?

Your understanding of the duration of PhD programs in the US is a bit off- the average "registered time to degree" beyond the bachelors degree for PhD recipients in the US is more like 7 years.  See

[http://www.nsf.gov/statistics/infbrief/nsf06312/][1]

In recent years there have been some attempts to reduce time to degree, and the data reported in this link are more than 10 years old, but the situation hasn't changed very much in the last 10 years.


A scam publisher offers me to publish, but it seems that I lose nothing if agree

(These comments are not intended to be specific to the named company, but to any that are generally considered to be suspect.)

By publishing with a company, you are partnering with them. Associating yourself with something you know to be dodgy is not a helpful contribution to your 'personal brand', in any respectable career.
It's unlikely they are being honest with you about the associated costs. They may not actually mean it when they say it's free for you, despite their advertising. Or, as suggested in comments, they may intend to use your work as bait to convince someone else to give them money.
Depending on the exact terms of the free licence you used, not giving them some copyright permission might mean they don't actually have the permission they need. If they don't need any permission from you, why did they bother to ask you rather than just going ahead? Alternatively, if you haven't used copyleft, perhaps they think they can try and limit what others can do with your work.


It depends a lot on the field you are in. In some fields, almost everyone who ends up being a professor has had a previous career outside academia. An example is education where your previous background will be considered a plus and there is no stigma attached to being older.

But there are also fields where yours would be a very uncommon career trajectory and where people have the perception that researchers' best contributions come when they are still young. Mathematics would be an example. In these fields, you will probably have a harder time finding a career as a researcher in academia, though I suspect that it makes little difference if you are going for an industrial research position.


What are the economic incentives for professors to hire and train graduate students?

Since you mention economic incentives, one obvious answer might be for teaching, at least this was the way it was in Germany. Even the most theoretical professor is supposed to teach a certain number of classes each semester. Generally the work involved in this is too much for one person alone, that is why the professor is supposed to do the lectures and the PhD students handle exercise classes and organisation. So its either supervise a bit on a research level or spend twice the time dealing with undergrad students having missed the deadline for their homework again because their grandfather died for the fifth time in this semester. Personally I'd know what I'd choose...
To this end each professor has a number of positions available, which can only be used to hire PhD students or postdocs. In particular it is not possible to hire someone to just help with the teaching without supervising them scientifically (Not that many qualified people would be willing anyway), or use the money for something else. Also like with any budget item, not using positions for too long is a great way to have them reallocated to someone else.
Regarding incentives to have them graduate on time, that one is also simple, if a bit unrefined: There is a maximum amount of years one can be employed in such positions. So in order to supervise the next student, the old one should be finished.
But I have to say that homo economicus is a spectacularly bad model for professors in theoretical subjects. Most of the ones I know are primarily motivated by science and would gladly work with a gifted student even without receiving any compensation.


PhD Bioinformatics academic career outlook

Like many other answers I am sure you will hear, it really depends what you want to do. Either path will be fine, what it will matter more in terms of job searching (academia or industry) would be:

You research project
Your PI
The reputation of the program you enrolled in (unfortunately)

In general, doing a PhD requires patience, dedication, and hard work. Focus more on what types of projects you want to spend 4-5 years on rather than worrying about what field degree you will walk out with in the end.


How could I become a mathematician with only a bachelor's degree in computer science?

Undergraduate math has a wide variety of free or cheap resources online.  Youtube, udemy, and khan academy are your best friend. You will quickly learn how to spot a good teacher / course.  Some books are public and many are available at libraries or online. And of course stackexchange is an option when you feel stuck. As you said, you have a number of years before you would try to make this transition.

This is coming from someone who went from being a teacher to learning python and getting a job at more than double the pay with just 3 months of online learning (mostly udemy and youtube) and a 3 month internship after that

As you learn more and gain a stronger grasp on undergraduate mathematics, you will begin to answer your own question about what topic you really want to pursue.

Although, even now, it does not hurt to send out a few emails and ask professors about topics.  The worst that can happen is them ignoring you.  You might "waste" 3 minutes of 100 professors time but a single answer could inspire you or help you make a more informed choice about your future careers.  I think it is worth is.

If you are unsure the topics you should study on and the recommended order, find transcripts or graduation requirements for a mathematics degree in a school you respect. It might take a little digging, but finding exactly what you would need to take at x school for y degree is not impossible (heck, send emails to counselors there and just ask if you cant find it easily online)

for an undergraduate reference

https://webapp4.asu.edu/programs/t5/roadmaps/ASU00/LAMATBS/null/ALL/2018?init=false&nopassive=true

Even vague terms like "upper division depth course" can be clicked on there and it leads to a list with descriptions of what they are and what is taught.

I found this by just googling

course requirements for math degree ASU

similar searches should yield fairly similar hopefully helpful results


Does every professor need to do research?

In the Netherlands you can have a "buitengewoon hoogleraar", who has a professor position of typically one day a week and another position somewhere else. Often this is an external entity like a company, but this has also been used to give a professor title (but not the pay) to someone who does the managent of some institute.


"Required review completed" means that the reviewers who were assigned to review your paper have all submitted their reviews. The next step is that the editor who is handling your paper should take a decision based on these reviews such as "accept", "reject", "minor/major revision", or invite more reviewers.
It is a bit unusual that it takes 1 month after the reviews are completed. From my experience (as author of more than 200 papers and as editor-in-chief of some journal) it is usually more like a few days or a week but it can vary depending on the journal. There can be various reasons why there is a long delay such as the handling editor being very busy.
What you should do is to send an e-mail to the editor to let him/her know that your paper is waiting with that status for over a month. Write a polite e-mail and ask gently to check what is going on with your paper. I did that recently for a paper that was in that situation for 3 months... The editor told me that he was busy and since he was only a guest-editor he did not handle the job quickly, but after my e-mail, he processed it quickly. Don't send more than 1 e-mail because editors are usually very busy.


personal motivations in job applications

Should I mention my personal willingness to move to Norway?

You can, but I don't expect it to have too much influence on the decision.

Strictly speaking, a committee loves to see that a candidate really wants to come to a specific country or university, and a "personal motivation" is as good (or better) than any other reason.  The big problem with "personal motivations" such as this is that basically anybody can write the same thing - there is no way for a committee to decide whether you truly want to come to Norway, or if this is just a thing you write into every application (cp. the treaded "It was my lifelong dream to pursue a PhD in XYZ" that seems to pop up in every other PhD student application I receive). As such, it is hard to take such a statement all too seriously.

In my opinion, where you can make this argument rather effectively is during a campus visit, when you can actually talk to people and explain that, and why, you would truly wish to come to Norway, in a way that allows people to judge whether you are actually sincere. I have seen such "smalltalk" to become a surprisingly positive factor in committee discussions.


Questions about research assistant posts

Q1: Is it weird or stupid to apply for a research assistant post at some university or research institute, and not a company in industry, with the purpose to gain research experience to boost profile for graduate studies, and why/why not?

Not at all. In my field (biology), this is quite common, the only reason not to do it is that you think you can get admitted without it and are trying to save time. However usually the experience is also very valuable in learning what research is like and whether you even want to do it, or whether you like the field. In other STEM disciplines it also seems to be very common. I've heard of it happening in social sciences (psychology, sociology, history) as well, but I'm not sure how things are exactly there. Usually it's up to the PI if they want an assistant or not. There is a lot of variation there. Some PIs love it, some have zero interest. But there's no easy way to tell, and asking rarely hurts.

You should absolutely mention future grad school plans, firstly because many PIs strongly prefer people who are planning to go to grad school (they're seen as more motivated, there is less commitment as opposed to an indefinite employment contract, and hiring assistants in this way is seen as part of a professor's responsibility to future generations). I am not sure if the same can be said for people who seek similar posts in industry - most of my personal acquaintances have worked in university or national institute labs, not in companies. However, honestly it would be naive in this day and age for a company to expect 22 year old BS grads taking a lab tech position and be fully committed "lifers" - and if they really want you to not run off to grad school after a year, they should put it in the contract.

I'd say it's very different from a baby version of a postdoc. Postdocs are often expected to independently come up with hypotheses, design experiments, locate and order equipment/materials as needed, write grants and submit manuscripts to peer-reviewed journals. Rarely they may also teach and mentor others. As an assistant you will most likely be part of a postdoc's project - duties may range from mechanically doing some simple technique over and over (like running gels or feeding mice) to semi-independently doing a small part of the postdoc's project under constant supervision (but ideally you would always be expected to demonstrate good understanding of the science in discussions, even if you are doing pretty monotonous experiments). You may be expected to help write small parts of the paper, such as methods sections for experiments you did. Should you end up with a PI who encourages independence, you might design experiments or even provide feedback on equipment purchases, and if you are really lucky and hardworking you may even have the opportunity to submit a first author paper. But that would be exceeding everyone's expectations; needless to say, it will look very good on your application.

  Q2: Who are the usual applicants of research assistant posts?

I can't say for sure since I've never been in a position to hire such people. But based on experience and what I heard, the vast majority are either undergraduate students or recent grads planning to apply to a PhD program. Sometimes there are premeds but academics look down on them. There are occasionally people who don't necessarily have future plans, and are just curious about science, or maybe they want to do something related like patent law and decided to get a taste of what it's like in the trenches. I've never heard of anyone doing it just to pay bills, those people will usually have very long term positions (which may sometimes be called "technician", "scientist" or "assistant" etc).

  Q3: What's the difference between a research assistant post and an internship in industry?

Interns are usually expected to be short-term (3-6 mo) and part-time (<20 h/wk). The internship will often be coordinated with the university, and may be required to complete the degree, and result in a grade or certificate. These days governments try to crack down on unpaid work, but in practice there may be an (arguably unethical) expectation that interns work for free. Assistants should be longer term (>1 yr) and paid (and thus officially employed and eligible for benefits - interns sometimes "just come"). But the terms aren't too reliable - the goal of the posting is usually marketing first, accuracy second.

The linked post is for an MS student, those can often become involved in their PI's side-ventures depending on how things go. Usually it wouldn't apply to assistants both because their contribution is smaller, they are less independent, and they will soon begin a PhD program where they will be too busy to follow up. It can happen, though, if the professor really likes the assistant and the assistant isn't totally committed to going to grad school right away.

  Q4: To confirm, if research assistant posts are indeed on temporary contract or short-term, is there indeed a risk for someone to quit their regular full time industry job hoping that a research assistant post will boost their grad school application profile?

Anyone can quit a job any time. Nobody can make you show up. That's one of the few aces employees have in their deck against employers. However, grad applications give a lot of weight to recommendations. The experience you have won't be as well regarded if there isn't an accompanying letter from your boss praising you to the high heavens and saying in detail what a great job you did and what a golden grad student you would make. Obviously if the boss is pissed off at you for quitting out of nowhere, obtaining the letter might be an issue. However, if you worked with your boss on this, discussed your plans ahead of time, did whatever you could and the boss was still unreasonable the admission committee might take that into consideration. Sometimes there are people who did a stint in a lab and did good work but for some reason their supervisor really didn't like them so when they submit the letters and none of them are from this place they worked at. Then you have to sweat a little explaining all of this in a positive way while writing your SoP and other materials, bragging about how great your experience was but at the same time stepping around the fact that clearly you got your boss so mad you couldn't even get a letter from them.


How much time are UK PhD admittees typically given to accept/decline an offer?

Its completely context specific. It might even depend on the quality of the applicants - if I have two good candidates, I might want an answer from the first choice quickly so as not to risk the second choice taking up another offer if the first choice says no.

Conversely if the first choice is really good and I really want them, then I am more likely to be willing to agree to wait for an answer, so as not to risk them being rushed into saying no.


Which would be more beneficial when applying to theoretical physics PhD programs, Math M.S or experimental physics M.S.?

If your MS in physics will be experimental and you want to do theoretical physics, the math route could work. But we are basically guessing at how an admissions committee will see your application;  so I encourage you to keep asking. Hopefully other answers here will help.


Is there something like withdrawal charges?

Don't pay them a penny/euro

This is a scam.  Cut all ties with this journal/company.  I've never heard of any reputable journal charging thousands (or even hundreds) to publish an article.

In the future google the journal name first.  There is also

https://beallslist.weebly.com/

to help filter out scam publishers.

Rules of thumb for vetting publishers

1) Don't pay to get published.  Journals generally work on a subscription method where subscribers pay administration overhead.

2) If you do have to pay, it should be a conference paper with a date, and location.  Some conferences require that at least one of the paper's authors attend.  Be sure there are a date and city attached.

3) Paper retractions/withdrawals are generally big deals triggered by incompetent or unethical research practices.  Fees associated with this would obviously be a hindrance to accurate reporting by authors.

Edit:
You're not the only person this has happened to.  See https://web.archive.org/web/20130903150917/http://www.jfdp.org/forum/forum_docs/1013jfdp1040_1_032912094346.pdf


Why would a grad school reduce fees to a trivial amount rather than reduce stipend?

Actually, it’s almost certainly easier bureaucratically to simply charge the fee and increase the amount of money they pay you. You have to think of this from the point of view of budgeting. Each of the different fees you pay gets deposited in a different department or organization’s budget. Let’s say it’s a fee to the gym. The gym has a responsibility to manage its own budget in the university, and it pays for its services out of those fees.

Your stipend is being paid by the graduate school, and yes technically the grad school could just pay the gym automatically and give you less money. But what would happens if something goes wrong and the grad school doesn’t pay the gym for your membership?  The director of the gym now has to go figure out why the grad school didn’t pay. But how is the director of the gym supposed to know how many grad students were supposed to have been paid for? How is the dean of the grad school supposed to be able to verify that the gym didn’t receive payment for the full complement of students?

It’s way easier, from the point of view of both the gym and the grad school, to just make you responsible for the fee, and to give you the money to pay it with.


Ethics: Is it ethical for a professor to conduct research using a student's ideas without giving them credit?

On more than one occasion, a student has pointed out a resource to me that I am already familiar with. In those situations, I always thank the student but don't always mention that I was familiar with it. I don't lie and say that I hadn't seen it before, but see no reason to bring it up (since doing so might make them feel slightly disappointed). If it is open data which has relevance for their field of study it is quite possible that they were already familiar with it. Perhaps in their e-mail they meant that they were unfamiliar with a certain source that contained the data, even though they were familiar with the data itself from another source (such as, from research colleagues who presumably were aware of the source).

The fact that he published a paper several months later is strong evidence that this is indeed the case. The time frame seems too small for him to have begun the research after your email exchange, found something which was publishable, written the paper, and gotten it through peer review. Obviously I don't know the specifics of the case, but I find it implausible that he was unethical in the way that you claim.

I don't see any reason for you to switch advisors. If you unjustly accused him of dishonesty, the real question is if this advisor would still want to work with you as a student. Unless you have evidence which goes beyond what you have communicated here, an apology might be in order.


Career advice - Getting a Math PhD admit in a good program with computer engineering background

A concern (raised by your background) that occurs to me is that do you really have a clear idea what graduate programs in math are all about? I don't think that any reputable grad school would allow you to study numerical analysis alone ... [Edit taking note of Willie's remark] within a graduate program in pure math - the scene is markedly different if you are applying into a program in applied and/or computational math. I apologize for not knowing that such possibilities exist. My smalltown background left me with the false impression that math and applied math always come together. Such programs may be better suited for you![/Edit] (continued rant) ... For the simple reason that doing research in math requires familiarity with a variety of tools and theories from adjacent, nearby and occasionally relatively remote areas of mathematics.

Is entering a computer science/computer engineering graduate program not an option? Probably you can specialize in scientific computing/numerical analysis in such a program. It may actually be easier to find an advisor in such a topic at a CS department? I don't know for sure, but it sounds like such a plan would entail less risk.

Our resident experts on numerical analysis/scientific computing can give you more useful advice. Below I will say my bit.

Before you burn your boats I would recommend, as an extra-curricular activity, that you take a look at what the obligatory 1st year courses of math programs have in store for you.
The core math at a typical US grad school (for 1st year grad students) contains at lest topology, abstract algebra, real analysis (sorry the link is only to measure theory, couldn't find a more fitting Wikipedia article at this time) and complex analysis. Some places would offer/recommend/require also mathematical logic. After the first year, you are expected to display a working understanding of the theories and results that those articles link to, and be able to reproduce their proofs on demand (ok, the committees will likely give you some slack on the more esoteric proofs, but don't count on it). The depth of those course probably depends on how much ivy the school has. I cannot give details on that for the simple reason that my experience is from a reputable but not top notch grad school, and I have only heard rumors about the others :-).

Only after having covered those basics can you start specializing on a topic that interests you the most.

I don't want to dampen your enthusiasm. I just had a few fellow grad students who were surprised by the graduate curriculum, and either dropped out or had a hard time making through the 1st year. My concern is that you may not fully appreciate how limited your exposure to math actually is (given your background). GRE is a joke, but it does test that you can speedily pick the correct calculus concept/theorem off the shelf in your brains and apply it.

So if going through those links just makes you hungry to learn more, then 'full steam ahead!', but otherwise you may want to reconsider.


Is it possible to work full time and do a part time PhD in software engineering in England?

Answering the question as asked, the answer would be yes. There are part-time PhD positions available at many UK university Computer Science departments. There are currently part-time PhD students currently attached to many UK Computer Science programmes and the regulations and fees are arranged for both full-time and part-time students. However, that being said, the situation is far from being that simple, as indicated in the many comments.

The majority of part-time doctoral students are likely to be experienced industrial practitioners who are enhancing their qualification portfolio with a PhD or are working for a commercial research based organisation and have linkage between their work and a potential PhD. It is less likely, and indeed less acceptable that the student is working purely to fund the PhD. This will be considered by the university to be an unacceptable situation which does not give the student sufficient hours to perform the necessary work.

There are also further hurdles to this route. One is employment. Would an employer take on someone who is planning on a part-time PhD? Perhaps; but if you are not from the UK or the EU, then there is the issue of study visas and work-permits  to contend with.

If it is finance, then as also mentioned in comments many departments have fully funded PhD research positions available and often advertise these in the academic press and online. The main database of these funded positions is hosted on behalf of UK universities at jobs.ac.uk and in that database there are 94 advertised PhD positions in Software Engineering as of today's date and four of those are advertised as being for part-time students.


Why do a second PhD in a "neighboring" discipline?

I've seen two reasons for this.  The more worrisome reason is the one mentioned by EnergyNumbers in the comments, namely that some people just collect degrees.  In particular, they may feel having two Ph.D.s would look exceptionally impressive, or they may be unable to settle on a specialization, or they may feel that getting another degree is somehow preferable to getting a job.  These could be legitimate as personal desires, but they are counterproductive for a research career.

The other reason is to recover from a bad career start.  Sometimes someone's grades keep them from getting into a good graduate program, or they face other constraints (geographical or financial) in their choice of programs, or they fail to connect well with their advisor.  They may eventually get a Ph.D., but not under good circumstances, and a second Ph.D. might lead to a much better career.  The difference between this case and the first case is that these students don't actually want a second Ph.D. as such.  They regretfully feel they need one to achieve their career goals, but they wish it had been their first and only Ph.D.

Recovering from a bad start is a less worrisome reason to seek a second Ph.D., but of course the challenge is figuring out which students have moved beyond their past difficulties and which have not.


How important is the Ph.D. Thesis?

It depends on what you have in mind for "importance".  The intellectual content of the thesis is vitally important, since it stands for what you have accomplished in graduate school.  You should make sure it contains your best work, since early in your career you'll be judged partly on this basis.

In the long run, there is little direct value to the dissertation as a document.  (Aside from any sentimental value, laying out the historical record, and satisfying bureaucratic requirements.)  Any valuable content should be published, and the resulting publications will be the definitive source that the community will rely on in the future.  If people are still reading your thesis five years after your graduate, then that's a sign that you have not done an adequate job of publishing your work.

Opinions differ on how seriously to take the dissertation as a specialized form of academic writing.  For example, how much additional background, commentary, or literature review should it contain?  Should it be written in a different style from published papers?  This can vary between countries, fields, universities, departments, and even individual advisors.  There's no universal answer, and you'll have to investigate what fits your particular circumstances.

In particular, one fundamental question is whether your dissertation is nothing more than an account of research that has been or will be published, or whether it's an important academic exercise in which you demonstrate your perspective and thoroughness in a way that would not fit in a conventional paper.

I see the former as the default answer for mathematics in the U.S., but the latter is not completely unknown.  (There are advisors who insist that their students write far more detailed proofs in the dissertation than one would ever actually publish, to demonstrate that the student can in fact do this.)


I believe you are asking the wrong question.

You are asking: Can one demand to see code used to generate an article?

To which I would answer: Assuming you're in a country with free speech, you can "demand" the code. Just make sure you do not threaten the author or otherwise break the law with your "demand". However, you are unlikely to be successful in forcing the author to share the code with you. A "demand" for code to me would come off as arrogant and I would ignore or decline a "demand".

I think a better question is:  How can I get the code from an article I am interested in looking at or using?

To which I would answer: It depends upon your subfield and why the author will not share her or his code. Some subfields now require/expect authors to share code and data. For example, the American Statistical Association recommends sharing code to create reproducible results. Here are the steps I would follow to get the code from an article I wanted:

I would first try reaching out to the author and asking nicely if she or he would be willing to share their code with you.
If the author declined, I would ask the journal editor if they could get the code to support the conclusions article because you wish to reproduce the article's results. Also, some journals now have open code/open data requirements. Check the policy of the journals the author published in.
If you end up in hostile situation with the author, and you think they are being misleading based upon their findings, I would contact the research integrity and ethics office at the author's university (e.g., Illinois or Rochester).
If you truly suspect scientific misconduct as the reason behind not sharing code, you could take this farther by writing a response article questioning their findings and state that they refused to share code with you. For example, watch how this author investigated a cancer scandal. The end result was prison time for the fraudulent scientist.
If the author's funding agency requires open access to code, you could contact them and request they force the author to share their code. For example, all data and code development funded by the US Government is required to be open.

I would suggest working with the intellectual property office or similar office at your institute if step 1 fails. They can guide you on what options, if any, you have.

Last, you might need to accept that you cannot force someone to share his or her code with you.


How can my colleague use our joint results in his PhD thesis?

Don't worry, be happy (and be truthful). There's nothing wrong in including in one's thesis stuff that you didn't do yourself, as long as the delimitation between what the candidate did and what others did is clearly marked. And by that, I mean no lies, but also no half-truths either.

Basically, the presentation will thus depend on the interaction between you two and his part in the analysis (which ranges from “nothing” to “he suggested ideas that I tried” to “he ran my code himself”). In the first case, he could say:

  As part of project X, I sent these results to Dr. John Doe at Big U. for him to perform his widely acclaimed topological Bayesian half-filter analysis. This analysis revealed that …

There's nothing wrong with presenting results obtained by others from your work, as long as they shed light into the phenomenon you're studying. I once had a student who published a work, which was built upon by another group during his PhD, and he presented this at some length (and critiqued their extension) in his thesis. That's part of the whole story.

If the collaboration was closer, just make sure the thesis clearly indicates its nature and the contribution of everyone. Then, no fuss!


How to propose collaboration, when I have an idea for analyzing another group's data?

I would contact the postdoc you previously talked with. He could be senior enough to run the whole collaboration without keeping his supervisor in the loop all the time. At the very least he has close access to the supervisor, and would prevent you from "cold-calling" the PI with your idea. Why try that again when you already have a contact? This is of course assuming the talk went well and you think he would be welcoming the collaboration.

About how to suggest it: Don't tell them that your method is better than theirs. You could tell them you have an alternative idea that might give better results. As far as you could test it, this seems to be the case and you'd like to try it out with more data, preferentially in the form of a collaboration. This avoids telling them you're better than them / they're wrong. Nobody wants to hear that, and in this case they also don't need to hear it.


Getting the best out of a book-reading exercise

First, I would like to comment on some of your sentences. Then I will answer to your 2 questions.

Often the PhD may run into huge tomes of material which he has been introduced to by Wikipedia: I am not sure that I understand this sentence well. Are you using Wikipedia for bootstrapping and then proceed from page to page in wikipedia, hoping to find something useful, or do you use another source of idea, but jump to wikipedia to understand in a faster way the entities/concepts you find in the first place ? BTW, in most cases I am not sure Wikipedia is something we should use at the research level. The quality is clearly increasing, but this is far from perfect, and some essential intuitions are missing sometimes (almost always ?).
Intuitively he/she may feel that somewhere in those volumes lies a theorem or an idea which can provide vital keys to solving his own problem. This sentence makes me think that you maybe focus too much on a specific problem.

Now, my answers :

When I read a paper or a book, I proceed the same way: First I quickly go through the whole thing (for a book, the whole thing is generally a chapter). Then I try to understand the key intuitions and results. At that point I don't try to understand how they are proven. Then I switch to other things. When I am thinking of a problem, or when I am on other concepts, sometimes a flash occurs and I have the intuition that something I have read can be useful, then I go back to the paper/book and try to totally understand the result. Here, this means more or less homework like in the old days ;)
Reading tangential materials is a necessity. I proceed as stated above, and to make sure that I will not spend all my time on this, I decided to always spend the same amount of time reading on other fields. For me this is roughly 1 day a week, which is 1/3 to 1/2 of the time I can use for research.


Usage of Videos or Images from Youtube/ Google-images as data source

I think this depends on more than what you state here. In particular, it depends on what you intend to do with the data you analyze and how you intend to present it. If you copy/replicate/publish the material, then you need to deal with copyright as anyone would. But if you are only extracting naturally anonymous information from it you should have no problem. Your suggestion that you "reference" your dataset not by providing a copy of it, but by giving (with the date of access) the search terms that generate it, you should be fine.

As an example, if you are researching how many people pass by a certain street corner on a given Tuesday, you can gather the counts without getting "informed consent" from everyone that passes. No issues there. But if you intend to publish, somehow, the names (or images, or other information) of those people then it is a completely different story. You will need to judge where on that spectrum your study lies. I think you can even categorize things in the aggregate as long as you don't label individual items with your categories. To say that "60% of the videos we examine have blue backgrounds" is benign. Even saying "40% of the videos in our sample present conservative positions" is fine, as long as you don't "name names" and point fingers. (I am not a lawyer, of course.)

If you were in the US, then your IRB would give you guidance on this. In your country there may be institutional rules to guide you. You should seek those out. But generally, the "academic use" exceptions to copyright that were in place in the past have been fading out as copyright holders try, usually successfully, to extend their control over the culture. Not a good thing, but the law can be used against you.


There is no fine line that separates the subfields of software engineering and there is a lot of overlap. However, below is a list based on my experience in the software engineering research community (and you can find one or more credible conferences that focuses on each of these):

Formal methods
Program analysis
Software engineering process
Requirements engineering
Models
Automated software engineering
Software maintenance
Testing
Empirical software engineering
Human factors
Program comprehension
End-user software engineering

I'm sure there are more, but this should get you started.


Does the GDPR cover reviewer blacklists, and if so, how?

The GDPR of course doesn't cover all possible scenarios. However, it's fairly logical. You're not allowed to have and use personal information, unless you meet at least 1 of 6 specific reasons. "Consent" is the best-known, because we've all been asked hundreds of times in the last year. But obviously that's not going to fly for a blacklist.

No, the reason which can justify a blacklist is (6e) processing is necessary for the performance of a task carried out in the public interest or in the exercise of official authority vested in the controller. Academic publishing is probably not done "in the exercise of official authority", but it definitely is "a task carried out in the public interest".

Having established that there's a reason, most of the other GDPR requirements become technical. There's a right to ask for factual corrections, but if the facts are in dispute you only need to record the objection. You are not forced to decide.

Now the biggy is of course the "right to be forgotten"/right to erasure. This is not an unconditional right. The person invoking this right must state a reason, and this must hold. "Withdrawing consent" is a reason, but it only applies when consent was originally necessary, which is not the case for the blacklist. "No longer necessary" might make sense if someone retires entirely, but we know that in academia retirement is often not a black&white matter.

The good thing here is that you can reason about actual removal requests if and when they arrive. There is not much preparation required other than the general GDPR rules for good recordkeeping.


Do conferences accept entry of those who didn't register before the deadline?

Most large scientific conferences will allow you to register at any time, even while the conference is running.  In this case the "deadline" is instead one or more deadlines for getting reduced rate registrations: they charge you more, the later that you register in order to get most to register early and have a good estimate of attendee numbers.

Some conferences, however, have size limits or require advance planning of other sorts, and so actually do have a strict deadline.  This is more often the case with small meetings than large ones, but the only way to know for certain for a particular conference is to check their website and, if it doesn't have information, contact the organizers.


Why are dissertation-based books looked down upon?

Simply compare the number of dissertations and books published in a field. A dissertation can be strong enough to provide enough material for a technical book, but it is rarely the case. A dissertation is normally focused on a specific research work, but a book is expected to be comprehensive. In rare cases, a PhD student has a comprehensive perspective of the field to write a flawless book.

It is legitimate and understandable that a publisher (university-based or independent) pays a particular attention to the marketing factors. The readers normally expect a book written by an experienced academic rather than a PhD student.

The publisher simply avoids highlighting any point, which might have a negative impact on the potential buyers, and leave them to judge the book based on its contents. They simply want to avoid prejudice about the book.

So, don't worry, they do not undermine the quality of PhD dissertations.

And believe me, marketing is as technical as your field of study, and has its own rules.


Citing newspaper articles (primary vs secondary? no references)

Whether a newspaper article is good to cite or not depends on the purpose for which you are citing it.

If you are writing about a factual topic, then newspaper articles are highly unreliable secondary sources, with a well-known tendency to be blatantly incorrect.
If you are writing about newspaper articles, however, then the newspaper is a primary source and can be cited directly.

So what should you do if you find a really juicy fact in a newspaper article with no reference?  The same thing that you do if you hear something with no reference anywhere else: spend some quality time searching the literature and other sources to see if you can track down an actually reliable reference.  And if you can't find one?  Then you should reluctantly conclude that this "fact" is probably made up, whether intenationally or by accident.


Should I do anything if I am cited for something that wasn't in my paper?

Since you never mention their technique, it is quite likely it's a "typo" (they accidentally cited a different paper than they meant, which, at least, in my field happens more than 0% of the time), or they just misunderstood your paper (or you misunderstood your paper).  I agree with @aeismail that there's nothing you need to do, but if you want to get to the bottom of this, you could contact the authors, saying something like:

I noticed you cited my paper in ... about X.  However, that paper didn't consider X.  Did you mean to refer to another paper?  If so, I'd be interested in knowing which paper.


You can, without doubt, but it might not be a good idea.

The first question is, of course, if the content of the paper is good.

The second question is, if you can find a more reliable source. Given the reputation of Vixra, almost any other source is more reliable, generally speaking.

I would suspect that, most of the time, when something is posted on viXra, either the content is not of high quality or you can find comparable material elsewhere.

But if you do happen to find a gem on viXra, certainly cite it. Just be very, very certain of the quality.


What is the etiquette for making an appointment to request a letter of recommendation?

The reason to want to talk in person is to be able to have the space for discussion and nuance that may be impossible over email.  But you can certainly start the discussion over email.  Why not send an email saying your plans and that you are interested in getting a letter of recommendation, but then close by saying that if the professor is willing, you think it might be a good idea to meet to discuss?


How do I politely and tactfully tell my advisor that I would like more consistency in meetings?

Tell him you would like to have more guidance, and ask to have regular meetings with a fixed schedule, same time every week. This way he will have a permanent entry on his calendar, and be more likely to reschedule tasks around it.

Some weeks you'll have more results, some others you'll have less, but it will be good if you can keep having at least a short chat every week.


Will a top journal at least read my introduction?

No, there's no such guarantee.  A top journal gets an awful lot of submissions, and you can expect them to be aggressive in rejecting papers which do not make a strong case for their importance, in the way that involves the least work for the editors.

If the editor, after reading the abstract, does not understand why the results would be highly interesting and significant, I would fully expect them to reject the paper without reading the introduction or any other part of the paper. (I can even imagine cases where they could make such a judgment by only reading the title.) As such, your abstract definitely should provide motivation for your results, such that a reader who is generally familiar with the area can see why they are of interest.

If your abstract just states the result ("we show that every snark is a boojum"), then it had better be such a well-known topic that every reader in the field would immediately know why it is of interest to know that every snark is a boojum.  If that is not the case, then your abstract should briefly explain why people should care, perhaps relating it to previous work.  ("Previous work of Smith showed that every reticulated snark is a boojum.  In this paper, we show that the assumption of reticulation is unnecessary, thus resolving a conjecture of Jones.")


What should I do when teaching maths for unmotivated undergraduate students?

Start each session with a quiz.  Have students exchange papers to grade.  Have full hour tests every 1-2 weeks.  Do lots of in class exercises that students work on.  (Put the animals to work.)

Emphasize calculations and problem solving.  Not theorems.

Emphasize efficiency in terms of grading exams.

Follow the text closely and spend minimal time on your lecture prep.


What is expected in a 5 minute postdoc interview presentation?

With only 5 min maximum, keep it to the point and interesting to them. They made clear what matters to them in their question

  How does your previous experience in vascular biology equip you to fulfil this post?

Find out about the post as much as you can and also the department (what do they specialize in). Find out what and who they want. Understand what your role will be, what their goals for this position are, in what direction to head. For example, research topics, but maybe also teaching duties etc.

Then use the presentation to show them why you are the perfect candidate for the post. Tailor it to their needs, no unnecessary information (you only have 5 min). This really depends on the requirements, but could be experience with relevant methods, openness to learn and use new methods / technologies (examples?), tutoring students etc. All the relevant experience for this post.


Do I need in text citations for an article on a historical event if I have links?

This is a pretty clear-cut case where you need in-text citations, especially given the multiplicity of possible translations and editions available. Not doing so could definitely get you into trouble with plagiarism accusations if discovered after submission.


Writing style when discussing other people's research in discussion/introduction

Neither alternative is good or bad.
I would put the citation first if the author or the history is important:

Darwin [On the Origin of Species, 1859] argued that natural selection ...

but the citation last if you just want to tell your reader where they can look to check your facts:

Darwin's finches continue to evolve [J. Wiener, The Beak of the Finch,
1995 (reprint)].

So it's a case by case choice. In this case I think your advisor is right.


Unless you're presenting joint work and had worked out your attendance with your coauthors in advance, not attending a conference is always your choice.

Not attending a conference for religious reasons is also completely standard and understandable. (Though your claim that Yom Kippur is just like Christmas is a bit unconvincing.  83% of Americans identify as Christian, whereas 1.4% identify as Jewish.  Moreover, a lot of Americans who identify as Jewish do not fast/atone on Yom Kippur and would be happy to attend a conference on that day: I do and I would.  Though not with as much glee as I would attend a conference on Easter, I admit.) I think it's an A-class excuse: i.e., if you tell this to your faculty advisor he will accept it without any comment.  I would keep to yourself however the fact that your amount of Jewishness is enough to get you out of a conference that you view as inferior but not a really important one.  That's not the most mature perspective, and if in your later life people observe that you seem to be using religion as an excuse to improve your schedule, they will not be so thrilled with you.

By the way, I would think that there would be a lot of other reasons that a high school student could not fly to attend a conference.  Saying "Sorry, I've just learned that my schedule doesn't allow me to attend" ought to already be more than sufficient (B+? A-?).

I think you may be off in your appraisal of the situation and the opportunity that going to any part of an academic conference is for any high school student.  My advice would be to, when you say that you can't go to this conference, tell your advisor that you really appreciate the mentorship and would be eager to go to a different conference, possibly a bit later on and/or during the summer.

Finally, your faculty advisor does indeed sound extremely nice.  Academics are extremely busy, and quality mentorship takes time and energy.  Your estimate that he spent half an hour looking at two drafts of your paper sounds rather naive to me unless he explicitly told you that.  I would spend more than 15 minutes looking at a student's cover letter, let alone their paper.  By the way, the fact that he is willing to spend the time probably means that he thinks you are extremely talented, so I hope you do not give up too easily.