how much input from someone else can a student have in an essay without it being collusion?

Interestingly our university undergraduate guidelines definition of collusion only specifies working with another student. So I guess this would count as plagerism rather than collusion.

I wonder however, if the rules for PhD students give a better definition of what is an isn't acceptable:

  It is acceptable for a student to receive the following support in
  writing the thesis from the supervisory team (that is additional to
  the advice and/or information outlined above, if the supervisory team
  has considered that this support is necessary:

  Where the meaning of text is not clear the student should be asked to
  re-write the text in question in order to clarify the meaning;
  English
  language: If the meaning of text is unclear, the supervisory team can
  provide support in correcting grammar and sentence construction in
  order to ensure that the meaning of text is clear (if a student
  requires significant support with written English above what is
  considered to be correcting grammar and sentence construction, the
  supervisory team will, at the earliest opportunity, require the
  student to obtain remedial tuition support from the University’s
  English Language Teaching Centre);
  The supervisory team cannot
  re-write text that changes the meaning of the text (ghost
  writing/ghost authorship in a thesis is unacceptable);
  The supervisory
  team can provide guidance on the structure, content and expression of
  writing;
  The supervisory team can proof-read the text.
  6 . Anyone else who
  may be employed or engaged to proof read the text is only permitted to
  change spelling and grammar and must not be able to change the content
  of the thesis.

In practice, the line between proofreading (which is generally considered allowable) and plagiarism (which is not), is  fuzzy and hard to define.

If you don't know how to prove this is happening, how do you know that it is? Someone's written work being better than their oral work would suggest is not proof, and having a father in the same field is not a crime.


How to engage in discussion after a presentation on an unfamiliar topic?

In general I agree to what @user46345 and the others said: If you do not have a good question (and no good reason to ask one anyway) it is better to be quiet.

However, sometimes it is important to ask a question. Two examples that come to my mind are:

You are the discussant of the talk (and you had no opportunity to read the paper before the talk or the speaker already answered all your questions in his talk).
You have a very shy audience that whats to ask questions but no one wants to be the first one to ask.

But there are probably others.

The best thing to do would be to read the paper first and think about a question related to it. If that is not possible there are still some other options to use:

If you haven't understood something during the talk: ask about that.
It is not your field of expertise, so no one expects you to know
everything about it.
In most fields a very common type of question is about applications. In economics this could be "What are the policy implications
of your results?". @JeffE has the following examples for (theoretical) computer science "Does your algorithm work well in practice?" and for non-theoretical computer scientists "Does your technique have any theoretical guarantees?".
"Sensitivity analysis type questions": Is the assumption A crucial?
How would your result change if you change assumption B? They still
require some knowledge of the subject but not as much.

These questions can be used as backup as long as you still have some knowledge about the topic of the talk and you have paid attention (asking something the speaker explained 10 minutes earlier makes you look really stupid). However, it is usually better to avoid asking questions than forcing you to ask one.


What to do with rejected papers in case of conflicting reviews everytime?

You seem confused by the fact that one of the reviewers only suggested minor edits whereas the other was quite against the whole thing. As an editor, I see this all the time -- and typically, it means that I chose the first reviewer poorly and that the second reviewer really knows the field, knows the other methods that are used today, and can compare what's proposed in the paper with what's being used today. The first one may have tangential knowledge of the field, but not enough overview to recognize that the method is not new.

In other words, to avoid a repeat, you do well to think about whether the second reviewer may be correct. If she is, you would do well to figure out what you think what is new about the paper, and whether that is sufficient to justify publication. An experienced co-author or colleague can certainly help you with this, and you should schedule some discussions about this topic before you think about where to re-submit the paper.


Almost all of the Postdoctoral positions requires to attach publications while contacting. Can a manuscript under review be sent to address this?

You can send it if you clearly label it as under review and not yet accepted. Name the journal reviewing it as well.

I don't see any problem with this as long as you are honest about its current status. Of course you should also include other publications if available. But in your labeling of this paper you can give your personal assessment of its importance in your work. People can do their own evaluation.


I guess you can contact the journal publication and ask them change your name in the online version. Printed book is probably already published. But the online is very easy to change. I never tried this, but I guess this would not be a problem. Just give it a try.

I see one problem here. In case you want to use that publication in future, lets say in your thesis, your misspelled name may induce some problems, because you present the verified list of articles you published.


Editor rejected paper because of insufficient reviews

It seems to me that the editor asked people to review your article, but not enough people were willing to do so. Apparently, the editor thought your article had enough of a chance not to give you a desk-reject, but your article (or your abstract) was not exciting enough to convince potential reviewers to review it.

Maybe it is not the article/abstract, but your article is dealing with a very narrow subject, thus limiting the potential reviewers. You had the bad luck that all of those few potential reviewers were all busy.

I don't think there is much you can do, other than have a good look at the abstract, and see if it is excessively boring. If that is not the case, then you probably just had bad luck.


I am in fourth year and didn't get to know any of my professors really well. Is it too late to ask for letters of recommendation for graduate school?

No it's not too late, but you're going to be disadvantaged - mainly because your letter writers probably cannot say much about you that your transcript doesn't already say. They might be able to comment on your coursework performance, but cannot say anything about your research ability, which is going to have a negative impact.
If you're interested in graduate school and can still do some research project, you should take the opportunity.


My research paper has been stolen on pretext of a book publication deal? What can I do?

This is an unfortunate situation. I would try to contact that person's current supervisor (if you can find out who) and explain all this, and maybe s/he can reprimand this person. Additionally, I would also contact the editor of the journal and explain the same to him/her. It might result in the paper retraction on grounds of plagiarism/academic dishonesty. However, I am not sure how would you be credited for the stolen work. Maybe an addendum saying it was your idea or maybe publishing it separately altogether.

Edit1: As @CaptainEmacs pointed out, "Add email date evidence. It is not perfect, but at least corroborates the dates."

Edit2: As @ASimpleAlgorithm pointed out, "Presumably there would be vastly more evidence possible in terms of prior revisions and incremental experimental or theoretical work. It only takes a very short conversation before it becomes obvious which person is the plagiarizer and which is the author."


Acknowledgment of funding and adding an affiliation in exchange of permission to use experimental data?

From what you describe here, the requests for the paper are fair: nothing is asked but a proper description of what you did where, and who funded you and who provided the data that is analyzed.
The crucial point is that you say paper 2 is an advanced version/extension of paper 1 you plan to do using data you got at affiliation 1, which I read as  both papers are part of wrapping up your scientific output at affiliation 1.

(To me this sounds as if paper 1 is describing the theory and paper 2 describes the application to experimental data - if that's the case, you have two papers closely related to project 1.
Also, how closely related is your project at affiliation 2? The more different that is, the more related to affiliation 1 will paper 2 be seen.)

  I am required to have affiliation of his research unit for paper 2. Second, in the acknowledgement section, I will have to strictly mention that the research of paper 2 was funded by a project grant from his research unit.

At least in my field (not geophysics) it is perfectly normal to list an author who changed affiliations with 2 affiliations. From what you say, you'll anyways need to refer to paper with something like "this is an extension of [paper1]" in the introduction. In addition, you can clarify your affiliations in the acknowledgements saying that you started working on the project while at affiliation 1, funded by project 1, and now are at affiliation 2, funded by project 2. If you like, you coul dbe even more specific in describing what was done where.
If your project at affiliation 2 is unrelated, you may give affiliations as "1, now working at 2".

  In reality, he had the data from the year 2008, from a private seismic survey company XYZ and such data is very regular thing to obtain in any seismic survey.
  I have such data as well from my previous job profile as a geophysicist. I can easily get more of such data and permission to use them from other companies without any hassle.

Whether you could have used other data as well does not matter at all. The point is that you give the proper origin of the data you actually use.
And, regardless whether you use data you got at affiliation 1 or at job 0, you need permission by the respective employer to use that data for new studies or papers. (I'm talking German legislation, things may vary somewhere else, but I guess this is something you can safely extrapolate to other parts of the world).

The only thing you describe that sounds somewhat unusual to me is that prof. 1 asked you to no not contact company XYZ on your own. But we'd require background information by prof. 1 to judge whether this is fine or not.

I do have the impression from your posts, though, that you are still thoroughly stressed about your situation and still too upset to think calmly. One point that triggers this impression in your post is that you write in length about prof. 1 being upset - and are - judging from what your write -  thoroughly upset yourself, but never mention taking into account even the possibility that you are also upset.
Seeing this, prof. 1 very clearly spelling out the IMHO usual points in wrapping up publication plans after a change of affiliation may even just be a reaction to you being as upset as you are. (Which does not mean that prof. 1 is not upset, but we academia.sx readers of your question do not have the neceassary background information to judge who else but you is upset.)


PhD in pure mathematics for a student in computer science

Short answer: Yes.  Absolutely.  You are already doing mathematics.

A few bits of advice:

Ask your advisor and other references to specifically address your mathematical depth and maturity in their recommendation letters.
Include a technical summary of your past research, including pointers to ArXiv preprints if possible, in your statement of purpose.
Apply to math departments that employ computational algebraic geometers.  Three that come to mind immediately are Saugatu Basu at Purdue, Frank Sottile at Texas A&M, and Bernd Sturmfels at Berkeley.

(I know at least half a dozen former CS grad students who successfully switched into mathematics.)


Can I reuse parts of a chapter from a text book in my thesis?

I did this in my thesis - my introduction was going cover a lot of information overlapping 3 textbook chapters I'd written, and I really didn't want to write it all again!

I did check with the publisher first, however (just an email asking for their consent), and added an acknowledgement to them in my acknowledgements page. I'm sure this was probably over-zealous, but it felt better to err on that side of things.


How do researchers send unsolicited emails asking for feedback on their works?

The real answer is that they don't. I'm sorry, but I can't slice it any other way. You would need all the planets to align in order to receive an answer after such an email. You are asking someone who doesn't know you and who is probably very busy (like all academics) to provide you a big favor for nothing in return. Because let's be honest, giving feedback on someone else's work is taxing. The best case scenario is that you get very vague and superficial feedback about the first page of your paper.

Instead, ask your colleagues, or people you have already built a rapport with (an advisor or former advisor, a collaborator...). Or do it the hard way and submit it for publication. You will get (anonymous) feedback. But make sure first that your paper is close to being ready for publication, because you don't want a desk rejection, and you don't want to be known as that person who wastes referees' time by submitting drafts.


About completing Ph.D degree in the US Industry

I have known a number of people who have done a Ph.D. while in industry (in partnership with an advisor at an appropriate degree-granting university of course), often closely tied to the work that they are doing in industry.  This is relatively unusual, however, because it requires that one's industrial work be both at a high enough level for a Ph.D. and also able to be disclosed through scientific publication.

Thus, if you're in an industrial environment where people are publishing regularly (my company is an example of such), it's not too hard to make work, but in a "generic" industrial job it would be difficult.


Switch from pure mathematics to machine learning as postdocs?

1) How hard is this switch going to be? I guess I've all the required
  mathematics background, but will it be hard to pick up the necessary
  computer science skills, even if I work in more theory-oriented
  problems?

Not a problem: picking up the math associated with ML. You've got the right background and you'll find it easy to understand the papers after an initial learning phase.

Potentially a problem: understanding why certain questions get asked and what's considered interesting. This is where mathematicians and computer scientists tend to diverge, and translating your intuition for questions might take some time. But a more mathematical mindset can also lead you to ask interesting questions that CS folks are NOT asking !

  What exactly are the programming knowledge I need to master to work in
  ML?

Depending on how theoretical the postdoc is, anywhere from none to R, python and matlab, and maybe even some distributed large-scale learning framework like GraphLab. But you should definitely get some familarity with the first three - ML is a good example of "no problem formulation surviving first contact with the data".

  2) Is there a website/email-list where I can get notifications on jobs
  in machine learning? I'm looking for jobs in Europe mostly, but
  information on the US would also be welcome.

One good mailing list is ml-worldwide. Another is the Google group ml-news.


Are there any (online) communities for independent researchers?

IGDORE, a large organization for independent scientists, hosts an online forum titled On Science and Academia. This is by far the largest online meeting place for independent scientists to my knowledge. IGDORE membership is not required to participate. I am not a member of IGDORE, and I have seen others with traditional university affiliations participate as well.
I've found the website useful to meet like-minded people, and I believe they would be receptive to requests to collaborate on a particular idea.


Simultaneously submitting, one paper got rejected, other didn’t - what to do?

Team U can genuinely claim the following in a future version of their article:
"After making our result publicly available on arXiv, we became aware of a similar result obtained in \cite{teamTresultPublishedPaper}."
Team U can congratulate team T and ask the following:
"Dear Team T, congratulation on your result R in journal J. As you may be aware, we have been working independently on a similar result as your recently published paper; our article was available on arXiv on Sept 2019. We were planning on acknowledging your independently obtained result in the next revision on our article, and we were wondering if you would agree to do the same." As pointed out in the comment, this is potentially obnoxious, and might not have any benefits.
Team U can submit to paper to the same journal that accepted team T's paper. "Dear Editor, we have noticed a recently published article by team T in your journal on result R. The same result was obtained independently by our team and made public on Sept 2019, a few months before team T's result was publicly available. We are wondering about the journal policy regarding publication of two papers that prove the same result, when the public record shows that the results were obtained independently and contemporaneously."
Alternatively, instead of asking the Editor on the possibility of such submissions, Team U may directly submit the article to the same journal with a cover letter asking to be considered.
If members of team T were referees for the paper of Team U (the paper that was eventually rejected), this may constitute a conflict of interest. If a reviewer reviews a paper that proves the same result as an article written by the reviewer not yet public but currently under review, the reviewer should at least declare this as a conflict of interest during the review. Of course, reviewers are anonymous so there is no way for team U to know. Team U may contact the Editor that rejected the journal, saying     "Dear Editor, thanks for your consideration for our submission XXX that was rejected on $RejectDate. After the submission of our article to your journal, the same result was published and made public by Team U in OtherJournal. We are wondering if you could double check that no conflict of interest among the reviewers hindered the review process." this is potentially obnoxious, and might not have any benefits.

Beyond these, team U should try to have their result published. Team U can certainly claim the result in their CV, research statement etc.

There are numerous cases of independently obtained results in hot fields and many papers actually include a sentence as in 1. above. When that happens, curious readers and historians can lookup arXiv or other public repositories (e.g. PhD thesis, etc) to check the actual timeline.


How can I seek permanent Personalised Assessment Arrangements, rather than reapplying each year?

A quick review of the link you've shown suggests that the two classes you've listed, personalized assessment and alternative venue, are open to two completely different groups:

Personalized assessment is for students with recognized learning or physical disabilities;
Alternative venue is for international students.

You're effectively trying to conflate the two types of accommodations, by requesting an alternative venue as a means of handling your disability. Based on the response of the chair of the committee, they are proceeding according to this distinction. For this to be successful, you need to be able to explain medically why you need to be at home for the exam period. Raising financial costs as a reason will not be a sufficient reason—by that rationale, you're no different from any other applicant wanting an alternative venue.


Are magazines (journals) "Scientific American" and "Popular Science" peer reviewed?

From the Scientific American website:

Generally speaking, SCIENTIFIC AMERICAN presents ideas that have already been published in the peer-reviewed technical literature. We do not publish new theories or results of original research.
Please allow six to eight weeks for the review process.

From this and other submission instructions on that page I conclude that the manuscripts undergo a general review that is probably aimed at accuracy and style, which is different than typical scientific peer-review of original research.
No scientific peer-review is mentioned in the relevant page on the Popular Science website either.


How do I speak with my professor about my mental health?

A number of the things you mentioned you've been thinking about the situation, i.e. you're taking advantage of the teacher's kindness, how your reputation will be ruined etc possibly fall under the category of unhelpful thinking styles or cognitive distortions which are common misguided ways in which people think that often leads to an unhelpful outcome. People with depression and anxiety can be particularly bad at thinking in these misguided ways.

I would recommend seeing a professional mental health expert like a GP or Psychologist as soon as possible and not waiting one month for the councillor. There are lots of tools that professionals can teach to help manage stressful situations like these. Seeing a professional doesn't imply that there is anything wrong with you either. From your post, it seems like you're having a natural reaction to an incredibly high workload and that you haven't gone completely 'off the rails' so to speak. Seeing a professional can help prevent things from getting any worse.

In the meantime, I think the action you should take becomes clearer if you acknowledge that your previous thoughts might be the result of unhelpful thinking patterns. For example: You don't actually know that your reputation is going to be ruined. That impression is most likely the result of some assumptions about someone's reactions. In truth, there are a number of possible outcomes and it is futile to worry about the one possible negative outcome as if that outcome is certain.

I think that the best thing for you to do is to sit down and write out everything you need to do, how long roughly it will take to do and when you are going to do it. If you really need an extension, go and ask the teacher for one and explain the situation and the action you are taking to fix it.

You might find worksheets such as these useful to reduce anxiety levels about the perceived consequences of actions.


Forced out of an abusive advisor relationship, how to find an advisor in another university?

(Written as if directly to your friend.) Depending on where you are, "starting over" may not mean starting at the beginning. In a new program you would likely be already more advanced than you once were. In particular, you may be much closer to passing any necessary comprehensive exams. And you have a more sophisticated view of research in the subject.
But, to remain where you are, with your current co-advisor, I'd suggest that you first try to work through that person rather than cold-emailing people and having to explain a difficult situation. While the blame for the current situation might lie completely with the former advisor, it won't necessarily be interpreted that way by people you contact yourself. "Why would I want to work with someone who ...?"
But your co-advisor has contacts, I hope, and they can contact others. The explanation of what is going on and your potential for success will be better believed coming from a third party.
Of course, there may be other faculty level advocates you can also use.
But at least you should explore this possibility with the co-advisor. Likewise, the possibility of moving can be discussed and the co-advisor can also help with that if necessary.


How do journals and conferences verify if the results in paper are genuine

Since you're referring to computer science, I'll talk about conferences. Peer review, as Dave Clarke mentions, is primarily how papers are scrutinized. But conference reviews are often on a severe time constraint. So for an experimental paper, the reviewer looks at the main ideas, sees if the experiments are convincing and handle the cases that the reviewer thinks are important, and evaluates the overall work for "general excitement". But the reviewer has no ability to check if the work is correct.

In a theoretical paper, a reviewer might skim proofs, and see if the main claims pass a "smell test". If the result is important, or surprising, the reviewer might try to verify key claims in detail, and expect the authors to argue why their techniques should work. But even there, no formal proof checking happens (that happens in the journal review).

Ultimately, there are two (imperfect) safeguards against incorrect claims:

author reputation - you don't want to get a rap for writing faulty papers
reproducibility - I might reproduce your work, or ask for your code, when writing my papers.


E-Mailing a Professor about interest in his research group during application for a master and before admission(in Germany)

It is usually the case that the information you intend to include in your email about your studies would be asked for in the application, so preemptively providing that would be unnecessary.

It may be useful to email mentioning your interest in the research group, and ask any questions about the research you may have.


What if the author I am seeking his permission to use part of his work has passed away?

Find out who inherited his copyright, and ask them for permission.

If he's long dead, his copyright may have expired and the work entered the public domain, but this period depends on governing law, jurisdiction, and numerous other variables. A century since the death of the author is probably a safe buffer but not infallible (and gets riskier the more well-known the author or work is).

Better to find the copyright notice for the work and follow the thread from there to the current holder.


Can departmental funding combine with fellowships/grants?

In general, the rule of funding in graduate programs is that external money is used to replace internal money. That is, if your department gives a stipend of, say, $20,000 per year, and you win a fellowship that pays $15,000 per year, the $15,000 will be used to offset part of the $20,000.

However, most departments that I'm aware of will also guarantee that fellowship and grant holders don't suffer relative to their peers by bringing in outside money. That is, they guarantee to make up any shortfall between the value of an external award and the department's standard. (In the sciences and engineering, I would steer clear of any department that doesn't have such a policy!) Many departments will even incentivize bringing in outside award fellowships by giving a premium or bonus that supplements the outside award. This might be done either by multiplying the standard award by a percentage (so, for instance your total would be 125% of the department's standard), or by giving a lump sum on top of an outside award (if it exceeds the standard, for instance).

One thing to watch out for, however, are restrictions placed on the outside fellowship: your department may have to certify, for instance, that you will not be assigned teaching duties or other non-research duties during the fellowship period. If you are unable to attain such a certification, the award may not be given out.

For the PhD phase of a program, the tuition should be covered by the department and the outside fellowship; however, in general the student does not receive part of the tuition payment back. In general, the tuition charge is a negotiation between the university and the fellowship program, as this is at the graduate level usually a financial transaction. Also, if the student were to receive the tuition payment which was then forwarded to the school, this could be called taxable income, which would make things very messy for everyone.


How important is it for your website to have a unique domain when applying for academic jobs?

I don't think there is any real downside to the weebly.com domain name.

There isn't really an expectation that you have a personal website in the first place in academia.  It is "something extra", and the fact that you have it hosted on a free service doesn't seem like a downside to me.

Note, however, that if you do want to register a personal domain, you can do it for about $10 or so a year, much less than Weebly charges.  You can't map a Weebly site to a domain without a paid plan, but you could still have the domain redirect there.  Also, there are other free hosting services (e.g. Google Sites) that allow mapping the domain without extra charges beyond the domain registration.

Also note the suggestion of Nate Eldredge and others that you could use your university web page as an alternative that is free and looks more "professional".  Also, it may help your work be more discoverable.  It does have the downside of not coming with you when you change institutions, though.


Is it legal and is it appropriate to display religious items in faculty offices in the United States?

There's a big difference between inconspicuously displaying religiously-themed materials in one's office and effectively proselytizing, as the retired faculty in your example apparently did. The former is I think entirely reasonable, as it's a personal display that does not put any burden on a visitor or guest to the office. Putting religious materials in their inboxes is unwanted, and is inappropriate for a faculty member to do (particularly given the power imbalance involved).

I don't think I've ever received (or heard of) a legal notice that one is not allowed to display religious imagery in a personal office. Is it a good idea? Again, I think it's a question of degree. There's nothing wrong with displaying a small cross or Star of David or moon and crescent in one's office. Having a large and ostentatious display, though, would probably put students ill at ease. Similarly, having those materials where you actually meet with students (say, at a conference table in the office) is more "aggressive" than just having it on a bookshelf.


Should I include code in my research paper?

Depends on the field and journal - check other papers in the same journal on how they do it. In my field (Bioinformatics) we usually do not put code into the paper but provide the full source code via the department web-page and/or git.


Which journals make peer review history documents publicly available?

The publisher Cooernicus has an open peer-review process, i.e. all peer-reviewer reports as well as the answers of the author(s) are published open access.


How to react to an angry email / argument as a third party

I would suggest that the proper etiquette here is similar as to how you should behave if you were to witness two people arguing in public. You may listen—the argument is, after all, public—but you probably shouldn't interject unless you are directly addressed. As stated in the comments, this is a very common tactic for raising the stakes in any discussion. This currently isn't your fight... don't get involved unless you want it to become your fight (pro tip: you don't).


My university does not do anything to prevent cheating in online exams, and grading is relative. What should I do?

Given the comments, you have eliminated the two most obvious responses: Exit (leave for somewhere better) and Voice (complain to the administration for improvements). There may still be more available to you than you think. A good resource is Exit, Voice and Loyalty by Albert O. Hirschman.
Because marking is relative, you are dealing with a tragedy of the commons problem. The total available high marks are made scarce because your professor has a particular mean and distribution in mind. There are more people who want high marks than are marks available. If everyone cheats, all the allotted marks are worthless as a measure of coding or other talent. Everyone has an incentive to cheat because not cheating does not prevent the cheaters from being rewarded.
In a commons problem, you will not be able to resolve the ethics on your own. The problem is social-structural, therefore the solution also needs to be social-structural. Your options are as follows:

Brainstorm ways to associate a cost with cheating. For example, you could launch a honeypot for an assignment with an answer that is wrong in a specified way. Then you can take the students to task for stealing your intellectual property.

Work with administrators via the institutions available to you (Student unions, associations, political movements etc.) to punish cheaters more harshly.

Establish a network of students who recognize the same problem and seek to establish norms across your colleagues against cheating. For example, raise some money to establish an award for merit for students who succeed while following the rules. Elinor Ostrom, the nobel economist, is the expert on this kind of solution. I would read her work, but summaries of her ideas do exist.

The ethics of cheating, even where you are disadvantaged are pretty straight-forward. Contributing to the cheating makes for a worse society from utilitarian (everyone loses from coders who do not know how to solve problems), deontological (a world where everyone cheats on everything is not a world I would want to live in) and a virtue (people will not improve if they always cheat) ethics perspective.
Assuming that your institution is indeed not interested in fixing this problem, it is corrupt. The World Bank has a list of actions to deal with corrupt institutions. There may be something there to help you.
Beyond that, you should know that blowing the whistle on an issue almost never benefits the whistleblower. Take a look at where your favorite whistleblower is now, and you will see I am correct. You will need to evaluate for yourself the degree to which you can fight this problem. I do recommend fighting from the inside first, assuming that everyone is interested in resolving this problem. You should go all the way to the top, explaining your understanding of the problem as succinctly as possible. You should also offer to be part of the solution as much as possible.


What do postdoc advisors/hiring committee typically look for in a potential theoretical high energy physics postdoc candidate?

Typically how many recommendations, does "the more the better" hold true here?

The job advert will usually tell you how many references to provide. I'd be wary of exceeding the number they ask for -- you want to demonstrate basic competency by following the instructions about the application. The same goes for any formatting of CV, cover letter or research statement that they require.

  Also does it matter if referees give okayish recommendations but are well recognised versus strong recommendations but not-so-well recognised?

An okayish letter from a well-known researcher is a waste of a letter. You want (at least) three strong letters, ideally from people who have worked closely with you, and on different topics if possible.

  Is there a threshold to the number of papers published, and typically how many?

Individual people doing the hiring may have their own prejudices, but there is no community-agreed upon minimum number. One high quality first author paper trumps five weak papers where you're in the middle of the author list.

  Also are preprints on ArXiv taken into consideration, if not published in a journal?

If you've submitted the paper to a journal you're probably fine. I can't answer your question about single-authored papers as they are extremely rare in my field (cosmology).

  How important is demonstrating here that the candidate has a well defined career plan ahead?

Writing about your long-term career plans is less important than writing about the research you plan to do in the job you're applying for, and how working at that particular institute, with the particular person who's hiring will enable you to do that research better than if you went anywhere else. (This obviously depends a bit on the job being advertised; some postdoc positions already have a well-defined research plan laid out in the advert, in which case you need to emphasise how your skills and previous experience make you the ideal person to work on that project.)

You may be asked about your longer-term (2-5 year) career plans at interview. This is another opportunity to emphasise how doing this particular job will get you to where you want to be in that time frame.

  Any other relevant factors?

Above all, people want to hire strong researchers, who they know will get the job done. Your strengths are best demonstrated by your published research, but there are other skills which are important for academic success. These are things like verbal presentation skills, the quality of your written English, networking ability (particularly if you can build a network distinct from your PhD supervisor's), organisation and committee experience, teaching and supervision experience (this becomes far more important as you progress in your career)... the list goes on. You need to consider if you have evidence for each one of these points that you can highlight in the appropriate place (CV, research statement, cover letter or interview).

However, I reiterate my comment: talk to your supervisor. They are the person best placed to evaluate your application before you send it off and help you to improve it.


When is it expected to write someone's name correctly?

I think "correctly" is the wrong word to use here, and it will cloud the issue. What's "correct" for a name is somewhat ill-defined (I've known a Risa and a Lisa who both had the same Japanese name. Which of them was incorrect?). The real standard is to spell in accordance with the person's wishes.

As a German person, the blanket assertion "the German name "Müller" is expected to be spelled correctly" is not in my experience true. Rather I would say, as the ease of writing the umlaut electronically increases, the likelihood that someone will be unhappy that you didn't bother to make the minimal effort increases too. There are still plenty of systems that only take ascii characters and people will make do with Mueller or even (sigh) Muller. Japanese people know quite well that you probably couldn't read "田中" nor "タナカ", and they will themselves sign their correspondence to you "Tanaka". They won't expect you to make the effort to learn how to read and type kanji, because they know it's exceptionally more difficult than finding a diacritic. (They will however be quite happy if you do manage.)

For citations, the issue is a little different: it is expected that you cite the authors as written on the paper. If you are citing an English-language paper, it is very likely that you will be citing "Ryouichi Tanaka and Robert Müller", because that's what they called themselves. If you are citing a Japanese manuscript, you are expected to cite "田中良一　ロバート・ミュラー". Maybe as "田中良一　ロバート・ミュラー (Ryouichi Tanaka and Robert Müller)" if you are yourself writing in English.

To sum up:

When is it expected to spell someone's name correctly? Always, but correctly ≠ in the original alphabet, or following some specific romanization rules.
When is it expected to spell someone's name in the original alphabet? When you can reasonably do so without major effort, and it does not hinder communication.


How to follow up the result of postdoc committee?

Just ask them if a decision is imminent as you are keen and motivated.

Trying to write some form of « I have an offer from X, should I take it? » may not help...


How to deal with the frustration of doing PhD at a low-ranked university

Stop whining and start kicking ass.

Work hard with faculty (and undergrads!) that you respect, do some awesome research, and then (if you are very lucky) move to a better department, either as a PhD student, a postdoc, or even a faculty member.

Meanwhile, own your past mistakes, but forgive yourself for them.  You put yourself in this situation, but holding onto your frustration and loneliness, instead of doing the best with what you have now, is only going to keep you frustrated and lonely.

(My undergrad GPA was 2.4/4.0.)


What happens if letter of recommendation to a university contains a wrong fact?

These kinds of mistakes happen all the time. Don't worry about it, just move on -- the people who will read the letters understand that these things happen.


Can I quote from my interviewees before the methodology section in my dissertation?

I have been working with qualitative (semi-structured) interviews for years and I read a lot of literature that uses such data. I am neither aware of any rule that prohibits or any convention that discourages quoting interview statements before the methodology section/chapter; nor could I see any reason for such a rule to exist. It makes sense to describe the methodology before the analysis and results sections, in which you will draw on your interviews most extensively, but individual interview quotes are not equal to "analysis" or "results". They are just that: Quotes. I would also add that a catchy interview quote can be a good way to introduce a paper/book or to illustrate an empirical result or theoretical conjecture.


Since you are using 'will use' in your question I assume there is still time to make asjustments and will just quickly mention some things that you might still want to change in order your get it 'passed' as your thesis.

You say you do not use a Likert-scale. Why not still change it to a Likert scale? (I will also suggest you use a neutral (midpoint) option for all bipolar scale questions you use)
Another important change to make in your questions is that you are now (judging from the few example questions you posted) biasing your questions by how you formulate the stem. You are doing this atm in two manners (you should change this):

"..on Internet is more reliable than advertising?" should be
something like "..on Internet is more or less reliable than
advertising?"
"Would you agree that.." is likely to lead to acquiescence bias, you can change this to something like "do you think that..".

Getting back to your actual question.

The analysis is dependent on what you wish to 'test' and the 'sort' of data you have.
Most commonly you would have a research hypothesis that is 'tested' by seeing if scores (e.g. averages) on question/construct A are associated with (/'can predict' but not te be confused with causality) differences on question/construct B.
(e.g. you ask people how tall the they are in questions A and what size of pants they wear in question B, to test the hypothesis 'taller people tend to have pants in larger sizes. This would be tested by taking both averages and going for a simple t-test (if the variable would have been categorical for example we would have needed to choose a chi-square test instead)

So the actual test you would choose (e.g. SPSS) depends on this design/hypothesis (or you using 1 variable to predict 1 other variable?) and the datatypes of both the predictor and the dependent variable (nominal, ordinal, ratio etc).

This makes it difficult to answer this question without having a lot more information.
Here is a link to a simple in-browser tool that asks all those question about your research design and variables and rolls out the acceptable significance test (tool).

Hope this helps!


What would it mean if a professor of interest (POI) emails me after April 15th asking if I decided where to go for my PhD yet?

Seems to me like you did the right thing. They may really have been impressed by your qualification; or they just wanted to gauge your interest in remaining on the waitlist, to which you replied "yes".
There's little else we can guess the person might have wanted to ask. You didn't burn any bridges and expressed interest. There's little else anyone could have done in your place.


Thematic synthesis in a systematic review paper

Please excuse me for recommending my own work, but I've done quite a bit of work to address the problem: "I need to do a literature review. How do I organize it in a way that is useful to myself and to my readers?"

Actually, I answered a somewhat similar question before; I'm adapting my answer from there for you here. In brief, I recommend adopting a theory-extracting approach. That means to explicitly look for theory in the source articles and then to synthesize the theory as the contribution of the review. What I mean by "theory" is very simply "A is related to B". This is distinct from literature reviews that simply summarize what people have said about A; that is not theory. Theory is about explaining how and why phenomenon A is related to phenomenon B. In my academic field (information systems), I have found that this focus on theory is the most useful thing that can be done with literature reviews (in terms of citations by other researchers). Although my literature review approach focuses on social sciences, I believe it would be relevant in a case like yours.

I have two main relevant articles to recommend:

The View from Giants’ Shoulders: Developing Theory with Theory-Mining Systematic Literature Reviews: this describes the idea of theory-extracting reviews and focuses mainly on theory (I used to call them "theory-mining reviews")
A Guide to Conducting a Standalone Systematic Literature Review: this provides more practical details on how to actually conduct a general literature review


Try exercises or look at the solutions for self-study

Some of the exercises are very hard. That is expected. But it depends on how deep you want your learning to be. If you are happy enough with a superficial understanding, then just read the solutions.
But if you want "operational" knowledge. The knowledge of how to put all of that to use and to extend it in your work, then you need to do a lot of the exercises. Mark them off when you succeed and come back to the ones you can't do later on. Or, find someone more knowledgeable than yourself, who also understands learning, who can give you minimal hints when you get stuck.
The issue is in the way the brain works. Long term memory works not by seeing something once and having it immediately imprinted somehow, but through rewiring of the neurons through repetition, reinforcement, and feedback. If you don't do that, you won't develop a deep understanding - or even memory of what you've seen.
But, since many of them are hard, and there may still be a few research problems hidden in there, don't work until you get frustrated. But instead of giving up and reading the solution, put it aside and go on to another. Come back to the hard ones occasionally and see if you can do better.
The more you do, the more it will enable you to do others, even if it doesn't make them easy.
In some books the exercises are what give it value. If you can do them, you have some deep knowledge TAOCP is like that.
But the same is true of the books you have for your coursework in CS and in Math.


How to stay motivated and optimistic about an academic or industrial career with an extended PhD?

I'll say something only about your first concern.

You can't change the past. You are where you are. However, I wouldn't be overly concerned with anecdotal remarks about what is expected or not. You have a history and if asked about it, just recount it honestly. Don't apologize for taking a few extra months or even years.

The funny thing about (real) research is that you can't do it on a schedule. The insights and the background work take time to mature. It isn't like manufacturing a complex artifact like an automobile that can be optimized to the second. Research problems worth the effort are hard and the solutions come when they come. Sometimes spending more hours on them helps. Sometimes taking a break, especially a mental break, helps.

But anyone who says "I will do this significant piece of work and be done in three years" is deluding themselves. I expect other people with research experience to recognize and respect that. If they don't, I expect that they haven't really worked on anything difficult lately and carried it to completion.

You do what you can do with the constraints that you have. Hopefully you learn something valuable and are able to write it up and get your degree. But the path is both winding and difficult.

When I went to grad school it was still possible to get a math PhD in four years out of undergraduate. I took seven. My career wasn't what I expected, due to economic factors beyond my control, but I had a rewarding career in academia. Nowadays seven is closer to the norm, unfortunately.


Alice and Bob should not worry about it.  Collaboration with Alice and Bob does not prevent Carlos from working on closely related research independently.  Maybe Carlos will even succeed in bringing additional attention to the collaboration with Alice and Bob.

There are two ways this could become a problem:

Alice and Bob insist on coauthorship of Carlos's paper, even though their only contribution was a brief discussion.  They very probably have not earned it.
Carlos does not attribute results from the coauthored papers correctly in his sole-authored work.  Since Alice and Bob apparently have not seen Carlos's paper, it's not time to think about this yet.


Distributing your own papers in your thesis

I don't understand why you are repeating the same material twice in your thesis. Each of your three papers is re-cast in a separate chapter in your thesis, and then verbatim in an appendix.

You most likely have assigned your original copyright in your papers to the journal that published them.

I think adding the papers as an appendix is unnecessary, and may fall foul of the journal's copyright. The interested reader should be pointed to the journal article relating to each of the three chapters.

If you reproduce substantially the same figures as that which appears in the journal -- to whom you've presumably assigned the copyright in the figures -- then you will need to ask for a license to reproduce those figures.


Is it fine to ask my advisor if I can appear as first author in our paper?

Yes, of course you can ask, and give the reason. But it may be moot depending on your field. In some fields, alphabetical listing is the norm. In others it is vitally important and fought over.
If you are in a field in which it is important, then I hope your advisor is a bit generous in this since you are starting out. But if you aren't the main driver of the ideas in the paper then you should be prepared to yield graciously. Other papers will come. Your first paper isn't, hopefully, the best work you ever do. There will be future opportunities but they depend, somewhat, on cooperation with others. You can also be generous. Especially if you are willing to take a long view.


TV-L 13 contract before the official masters degree

I know some people who signed their contract with "4,0 Bescheinigung" and got the final mark afterwards. As far as I know submitting your thesis is not enough, you have to prove that you passed your masters.

But it would be better if you ask your supervisor or the people in the HR.


How do I add an article that is already in Google Scholar to my profile?

Sign In to Google Scholar.
Click on My Profile.
Click on the + button above the article list
Click on Add articles in the context menu


Minor revision changed to major revision

In my field, biomedical science, it is highly unusual to hear back from a peer-reviewed journal within 2 days of resubmission. I would recommend double-checking whether the journal is a peer-reviewed journal and whether the papers published in this journal provide a significant contribution to your field. It is important to always check that as there are multiple predatory journals out there. As Roland said, you have two options. Certainly, you should always consult with your supervisor prior to any action.
Another point I would like to add is that usually when the reviewer finds issues regarding the quality of the manuscript, the reviewer will point out the specific issues in order to clarify where the authors have to work on before resubmission. It is very strange that you did not receive a detailed review.
As for the change from minor to major revision, that can happen. Particularly because not always the same reviewer will be available to review all versions of a manuscript, so in some cases, your manuscript may be sent out to a different reviewer after resubmission.


The American Bar Association has a nice explanatory essay that answers exactly this question.

In essence, in the United States, the J.D. degree is quite new, with lawyers having previously received a professional degree that was not called a doctorate.  As such, it has generally been considered problematically confusing to call a lawyer "doctor" and also possibly unethical as undue self-promotion (lawyers used to be prohibited even from advertising in many areas).


In Indonesia, are research grants extra income that go directly into academics' pockets?

I did my advanced studies in southeast Asia. One of my professors was from Indonesia. When I was talking to him one time he shared that when applying for a grant the researcher should put in a "consulting fee". This fee covered the researchers time.
I can't say if this is standard practice but it is first person testimony from the country.


How do I get published in Nature or Science?

First, don't obsess about it. In chemical engineering, Science and Nature papers are rather rare, and probably even more so if you're doing theory. So, while a paper in those very high profile journals can give your career a great boost, not having one is not a career-breaker.

Now, if you want to know how to orient your research to things that get you a greater chance of being published in such venues, my first advice would be: do something you're excited about, something you think challenging and you want to address. If you enjoy solving the problems you work on, you'll do much better work and get a better chance of getting that shiny paper. Also, you might just be happier doing stuff you like, obviously, even if you don't publish it in Science.

However, it is true that some fields and subfields are over-represented in journals. This depends on journals, but very high profile journals tend to prefer:

Hot topics. In your field, it used to be carbon nanotubes. Nowadays, I'd say “nano” is a good keyword, metal-organic frameworks are a widely published system. But… that's not entirely foolproof, because this will change and it's not certain that the choice you make right now will still be a hot topic in 4/5 years.
Theoretical work that addresses very basic questions that are not yet fully answered: dynamics of water, the nature of the hydrophobic interaction, the Hofmeister series, that sort of stuff.
Controversies, work that challenges common assumptions.

Oh, and if you make it, I claim co-authorship based on the above contribution!


Do I have any chance to apply to a graduate school after a bad junior year?

I think you should not worry about the 'junior' days. You are now equipped to apply anywhere.  If you are concerned about not making at the top schools, also apply at say five second choices.  If you get accepted at one or more top schools, you can pass the others. Get best testimonials in your hand so you are ready for the next move up.  Best of luck.


What can a biostatistician do to earn money on the side?

This is more of a brainstorming session/life hack than an answer specific for academic, hopefully this can spark some more inputs. As a disclaimer, I identify with you as I am also working in the field of biostatistics and epidemiology, though I have not actively sought after extra income. However, I have always been a financial life junkie and I used to love to daydream how to be rich or at least to enjoy retirement with dignity. Here are some of my thoughts and, well, refined thoughts.

Saving = Income - Expenses

We should first recognize that you can save money by either getting more or spending less. Before going to get more, I'd recommend sitting down with your spouse and go over the financial situation. Here are a few exercises that I found easy to pick up, and once you have started, you may see if this route is good:

Create a happy matrix for your spending: Print out your credit card statement(s), item by item, grade how each of them makes you happy (Likert's scale, etc. you know the drill.) Identify things that are not contributing any satisfaction and avoid making the same purchase again. For those that truly make you happy, evaluate if you can cut back (usually, from all my reading, the culprit is often the $7.90 something Starbucks grande latte and a scone for the breakfast), or substitute with cheaper options such as shifting to other vendors or make them at home. I especially recommend everyone to check their credit card bill, bank bill, and cell phone bill: When I first started this routine, I found out that I have $280 sitting in my credit card as cash back! I just never claimed it.
Have an energy audit of your house: Most local government should be able to point you to some free energy audit service. They will evaluate your house's insulation, electricity usage, conditions of the heating system etc. and provide you a list of improvements and expected return on investment. For example, you can spend about $1,200 to inject foam in between inner and outer wall, and drop your heating bill by more than $200 per year. Other gadgets like motion sensing switch, smart thermostat, and CFL light bulbs may also help.
Take public transport or bike: I actually use this method. I don't drive and I live about 9 miles away from work. I commute on bike in spring, summer, and fall; and use subway in winter.
Commit to be green: This sounds like quite off. But I have come to realize that once you want to cut down on trash, you can't help but cut down on consumption. For example, I bring my travel mug and a collapsible box everywhere in case if I need to buy a drink or food. Since packaged food is automatically out of the equation (which are usually more expensive per weight), I save some money there. I also go to wet market or farmer's market for food, and I don't consume processed food. If I need an item I check out local flea market and freecycle websites (I give away stuff through freecycle as well.) For level 2 difficulty: Commit to be a vegetarian or vegan. Meatless lifestyle simplifies life tremendously.
Use your educator's identity: Many vendors provide discount to educators. Since you work in a university, you can flash your staff card and get some good saving here and there. I'd also encourage you to check with your university's benefit page. I got a 24% discount on my phone bill just because I filled in an extra form.

Then up a notch

If you have mortgages and complicated insurances, etc. Consider talking to a financial planner. Most of them can point you to some restructuring to make the system more streamlined. Simple things like grouping the insurance to one company can save monthly payment. I have even read about an extreme case that a couple actually ends up saving more by having one of them stopped working because the commute, childcare, and other expenses were eating into the take-home income so much.

Now, zoom out

I do understand that you value your biostatistics skills. But when it comes to making money, you don't have to only work on biostatistics. For me, after 9 hours of coding and reading outputs, I'd rather see something else. Once you have broken out from the box, you'll feel more liberated. Reassess your passions and hobbies, and see if you can pursue an instructor position somewhere. For example, personal trainer, yoga teacher, musical instrument teacher, handcraft, carpentry, gardening, etc.

On my own spare time, I write video game walkthroughs, and post them on various websites and my own wiki sites. In the walkthrough I put affiliated links to vendors and in the wiki I earn Google Ads money. Given I am not very prolific, I don't earn a lot, but I can usually pocket about $300-400 a year if I happen to have written a walkthrough for a popular game.

Finally, zoom back in

Now, back to your question. There are many ways a biostatistcian can expand their job repertoire. Here are some examples:

Consult your local classified websites such as Craigslist: Check for consultant type of jobs. You may even post an ad if you are so enticed. I used to do some consultation on and off as a student and got to charge $50 to $100 an hour.
Propose a course to local adult learning center: Most cities should have some adult learning centers the provide classes on hobbies or professional skills. Meet with the director and propose a course (on R, for example). You can build clientele and enlarge your social network as well.
Statistical editor and reader: You can also contact local editors and discuss on possibility to be an ad hoc statistical editor. I am actually working towards this direction. In my institution there are a lot of orphan data: grants ended, staff left, no body works on it and publishes the work. I found my niche of being a data undertaker, and I grew to be very interested in writing as well. Other than editors, you can also sell your skills to students who are writing their thesis. Most of their works can benefit by having a round of quantitative examination.
Look for an adjunct position: I know you don't want to, but I'd urge you to be a bit more adventurous on this option. Since online education is actually picking up traction, your skill in biostatistics and website building may actually be a good combination for some institutions looking for a way to move their program online. For remote course you usually just need to meet the student in the first 1-2 weeks or every other week, which can still preserve your flexible time table. Use online chat or billboard for office hour, give students feedback using track-changes, etc. You can do most of these at home.

Closing remarks

I hope I didn't sound patronizing. But I wholeheartedly hope you may find some of these useful. I used to have mindset like you do, thinking of how to expand my income sources (I have my own expense and family in my home country to support), but after a few rounds of thinking, and sorting out what are the most important, I didn't feel like that any more. Now I make sure I have good pre-tax saving taken out first, save at least 10%, allocate money for family, allocate minimal expenses, keep about 5% or so for entertainment, buy used, give away or sell my own used goods, bike to work, stop all cable TV, lend to people on Kiva.org, simplify my closet, practice the motto of "buy the experience, don't buy the stuff"... etc. I realize that I still have enough, and I am not really sure what I was fussing about in the past. I'm happier, calmer, and definitely feeling clearer about what I want. And I certainly hope you'll be able to find your solution as well!


Correct answers were visible in a test; should I notify my instructor?

My guess is that it would be appropriate and pretty safe to note to your instructor that "some students" noticed that the correct answers were printed in bold. Sort of a "heard it on the grapevine" comment during an office visit. You could add "didn't notice it myself, hence the lower grade."

The instructor will take some action or not, but you will have done your duty.

You might, of course, know more about personalities that would make this unsafe for yourself, in which case, possibly let it go.

But if the instructor doesn't know about it then it will probably happen again.

I think this is a more serious issue in a medical related field, where people need to know things, not just get good grades.

It might also be a judgement call as to whether this is "cheating". The others just noticed an anomaly.


Does this statement seem arrogant? How do I put this humbly?

The only time I would ever make this statement is if I actually won the Most Diligent, Intelligent and Focused Undergraduate Student Award.

You didn't include the rest of your statement, but it's hard for me to believe that an undergraduate outcome has the capacity to demonstrate these three qualities. Course marks or a cGPA are hardly an indicator of diligence or focus, and certainly not a marker of intelligence the way I would define it.

I find that the best statements don't so much state the personal characteristics of the applicant in so direct a way (a la the conclusions of a lab experiment) but relate how these personal characteristics are demonstrated in real life. The reader is not so much TOLD that you are diligent, intelligent and focused as much as he or she UNDERSTANDS that you are these things.

If you really, truly wanted to include this statement, I wouldn't position it in the end. I would start somewhere at the beginning:

  My peers have remarked that my most endearing qualities are my diligence, focus and intelligence. During field experiments in my final year, we spent 17 weeks in Borneo tracking a potential new species of shrew. Our equipment broke down by the second week and we were suffering from malarial fever by the third week. I jury-rigged a camera trap made from vines and the bottom of a coke bottle and stayed in a single position for 14 weeks. My perseverance paid off when I captured short (2-second), grainy footage of the animal. By then, my entire team had long since abandoned me. I thought they were weak.


Is there a reliable indicator for which which NIH RFAs are open to post-docs?

Ask your institution's Sponsored Research Office (SRO). These organizations are often called by other names like Office of Sponsored Projects (or Programs), the Sponsored Programs Office, or something similar. It's their job to understand the rules and regulations associated with external grant funding for research institutions.

In my experience with NSF (not NIH), the eligibility requirements for institutions and PIs are spelled out in each RFA/RFP. I have frequently seen limits on the number of proposals that a PI or institution can submit, and there are frequent limits on the types of institutions that may submit (e.g. 4-year, degree granting colleges and universities only, etc.), but I have never seen a limit in the RFA/RFP for the qualifications of the PI or co-PI.

My institution, however, does put limits on who may submit. Post docs, as far as I can remember, are not given blanket authorization to submit. They, and even more junior staff, are allowed to submit grant proposals only with an exception as approved by their unit head (dept. chair, center director, etc.) and, I think, the VP for Research's office. These are, in my experience, always granted for post docs.

That being said, the proposal preparation guide requires you to describe your qualifications for submitting the research, including prior work, prior grant support, and other relevant material. If you haven't been a co-PI before, a proposal with you as PI probably won't look as strong to the review panel. It's probably best to start as a co-PI with a more senior, experienced researcher as PI. This is true even if you will primarily lead the day to day work of the project.

This is all based on my experience with NSF, but I don't think NIH is much different.


In mathematics, it is possible to have a successful career while publishing rather few papers, but they need to be very good and important papers. In my own field, set theory, an example is Jack Silver. MathSciNet lists only 11 publications by him, starting in 1970, but these include five extremely important advances, which have become fundamental for much of contemporary set theory.  Although 11 looks like a small number in this context, 5 is very impressive.


No specific license & no copyright transfer agreement: do I retain rights without restrictions?

What we "think" about it is of little consequence. The laws around copyright vary over the world. I think you are being a bit blasé about it. You need some explicit statement of any license you grant. If the publisher makes assumptions and does things you don't approve of with your work you may have little recourse other than a lawsuit that will probably cost you money. As Anonymous Physicist suggests, you shouldn't deal with such people as they are probably not reputable.
If they aren't willing to be explicit prior to publication and ask you to actually sign a clear agreement, then it is a giant red flag.
The risk is yours and yours alone. You may be fine, but no one here can provide any assurance of that. Talk to an IP lawyer to get knowledge of the local laws that will apply.
My worry is, if you give them an implied but not stated license, whether they can pass that license on to others. And, again, if they assume that, then it is a lawsuit that would be necessary to stop it. What "I think" is that you are stepping into a minefield. Don't do so blindfolded.
If you are associated with a university, they may have IP lawyers with whom you can consult.


Is there a standard approach for grading sequence-based questions?

You could give points for the longest subsequence in the correct order.
Alternatively, you could make it an open question: "Describe the process step by step, make sure to include in your answer 1, 2, 3, 4 and 5." Then grade by a few essential insights that need to be in the answer. This eliminates any easy guessing and shows you why the student misorders the process.
Also a possibility is to only let the students place 1 element of the process in the correct spot. For example:

Where in the process does 1 happen?
A. before 2
B. after 2, but before 3
C. after 3, but before 4
D. after 4, but before 5
E. after 5

Another possibility is to focus on the parts of the process that directly follow each other. Suppose the student answered "1,2,3,4,5", you could look at the pairs (1,2), (2,3), (3,4) and (4,5). Then give a point for (1,2) if 1 directly precedes 2 in the correct sequence, give a point for (2,3) if 2 directly precedes 3 in the correct sequence etc.


When is it appropriate to consult with the publisher/editor prior to manuscript submission?

This really depends on factors such as the field, the reason for contact etc. In my experience it is usually appropriate to consult with the publisher/editor in two cases, when:

(1) you have a short question about something that is not answered in their submission guidelines, or;

(2) you would like to send them an abstract to determine whether they think the potential submission fits with their journal.


How to decide whether the amount of study material provided to students is enough?

Use backward design, start with what you'd like the students to become or to achieve at the end of the course. Then, according to each of these "wishes," determine the best way to collect evidence on learning, and according to each of these evidence, design the teaching/learning experience. Formats should not drive the contents; it's the experience you wish to achieve that drives the formats. If lecture with slides is the best way, then lecture with slides; do not add lecture with slides because it's your institute's status quo.

Here are some of my anecdotes addressing your points:

  First of all, every presentation should have slides. Who takes a
  lecturer without slides seriously? (with the only exception of,
  perhaps, really senior professors).

Teaching in a US university, I have started to see students showing excitement because a certain lecturer does not use slides in the class as early as 2010. That got me start thinking if slides are still a viable teaching tool. After some thought, I made the decision to go slide-free and have complete done away with slides two years ago.

I like the format so far because slides had been acting as an invisible wall between me and the students. Just because I have clicked through them does not mean I have taught them. However, I felt safe behind the screen, and perhaps had grown to relish that false security too much.

I replaced the slides with what I call a "learner's package" (more details below) and I immediately felt a lot better. There are more discussions, questions, and interaction. The questions became a lot more spontaneous. In the beginning it can be daunting, but once I got into the rhythm I can never go back to the slides. As of now, four cycles into this new scheme, 80 students taught, and none of them complained the lack of slides in the evaluation.

  If one dares to use a black- or whiteboard, students will take
  pictures on their iPhones instead of following the lecture, pretending
  they will follow it at home, which they never do.

It's not if they will or will not follow up; it's if you have structured the activities or evaluation exercises to make them follow up or not. If there is no reason, why would they be motivated to look at something they have already archived?

  And students who miss the lecture will complain, since the slides are
  not available.

Many technological solutions here: e.g. First, make it clear in the syllabus that it's their responsibility to solicit notes from their peer if they miss a class. Second, consider video-taping your lecture. Third, consider using screen capture with audio recording if you will be using slides. Talk to your IT folks for possible supports.

  Secondly, some question / exercise sheets are important to keep
  students entertained and busy in class / tutorial.

While I love the idea of enriching the types of formats and interactions, it should be based on the desirable outcomes of the course, and not based on entertainment (though I sense that your questions are portrayed with a bit of sarcasm). Different types of format have their pedagogical pros and cons and they should be used to best fit what you want to achieve.

  Question sheets imply answer sheets, with (some) of solutions worked
  out, to help students prepare to the assessments.

I'd disagree with making it a routine to provide answers; this can cause them to rely on the eventually available right answers. Instead, I'd suggest base the questions on a defined set of skills (that you can point to at a section of the text, or on a certain page of the notes) with mild to moderate modification. That way, you can point them to the section to see how similar questions are solved, and encourage them to revise their answer.

If possible, base your answer scheme on instant feedback of the class's performance. E.g. if last week's quiz shows that only 35% of the class got question 6 correct, then consider making a detailed answer scheme for that.

Use your teaching assistants. Make them try your questions. They can i) find typos or errors, ii) give you a sense of how much time was needed to complete each question (multiply it with a factor of 1.5 to 3.0 to factor in the fact that the TAs probably can complete the exercise in a shorter time,) iii) draft the model answers.

  Lecture notes, to collect all relevant information in one place, and
  save students some trouble looking for it in various textbooks. Helps
  with those students who are hip enough to never use a library.

I agree a one-stop reference point would be helpful. It can be a set of notes or a list of materials hosted on the online learning website (like Blackboard.)

In my "learner's package," I included the followings:

List of learning objectives
Learning resources, which include corresponding sections in the textbook, readings, videos, etc.
Self-assessments. This section contains a list of activities and exercise with answers for students to test their own understanding. It's not graded.
Lesson evaluation. This section details how the students will be evaluated formally. I often put the link to the weekly quiz here. And if appropriate I also suggest some mile stone that they should achieve in this week with their personal final project. (I provide rubrics and so, but this answer is long enough so I'll save it for another day.)
All the notes, with citations.
In-class exercise and activities.
I use the Tufte LaTeX codes to compose the notes. I picked it because of its pleasant layout and ample amount of space for students to write.

Lastly, here are some titles that have inspired me with trying different instructional designs (I'm not affiliated with these authors nor Amazon.com):

Wiggins and McTighe. Understanding by Design.
Smith. Conquering the Content. It's for online course design by the contents helped me greatly in designing the online teaching platform.
Dirksen. Design for How People Learn
Ambrose et. al. How Learning Works
Davis. Tools for Teaching


How to approach a professor for an independent study course?

Yes, at least in mathematics, beginning grad students often cannot make informed choices about worthwhile directions of study, and there can be advantages to getting more-expert opinion. This is not at all to say that you should not follow your own curiosity and intellectual impulses! But only that you should also be open to expert advice. So you might best view arranging your independent/directed study as an enterprise whose goals can be negotiated, hopefully with all parties thinking of your best (long-term?) interests.


Asking a faculty member at my university that I have not met(!) about his research, and about courses that deal with his specialty/my career goal?

It is completely fine to send an email. Your request is totally reasonable. You are a student, at university to learn. The professor is at university to teach. If they get offended by a simple enquiry that shows interest in learning more about their favourite subject then you have a bigger problem on your hands.
It will not be the first or even the hundredth time this professor has received an email from a student they don't know and writing such an email is not going to cause offence in any way, shape or form. The worst that can happen is you get a polite "Sorry, I am too busy" or perhaps no reply. The professor will not be offended by you asking -- in fact, it's more likely they will be annoyed or frustrated that they don't have the time to help you, not at you for asking.
Finally, I would not start off with such a grovelling/self-deprecating tone. There's no need to apologise for sending a perfectly innocuous email. However, please bear in mind that academic cultures do differ, and I'm writing from a UK/Western European perspective, where the culture can be a little more blunt and far less deferential towards authority (i.e. professors) than in the USA (where I assume you are from). To me it would come across as more professional if you write to them as though you are a peer wanting to initiate a scientific discussion, rather than as a lowly student who isn't worthy to interact with an esteemed professor.
In summary, the best thing to do is make sure your email is short, polite and to the point. Briefly introduce yourself, ask your question and thank them in advance for their time.


Is it appropriate to ask for recommendations, which I'm not sure if I'd use eventually?

You can ask several people whether they'd be willing to write recommendations for you.  Do not ask them to do any actual work until you need it and intend to use it.  Recommendations will generally go directly to the institution to which you are applying, so "keeping them updated" doesn't really apply.  You'll never see the letters that get written.

When you are ready to ask for the actual recommendation, be sure you provide all the information the referee needs. Substitute "research" or "lab work" for "classes" below as appropriate.Here is what I tell students:

Tell me what the deadline is!
Include your student number.
Remind me which of my classes you have taken, and when.
How did you distinguish yourself in those classes?
How would you describe yourself? What are your strengths? What are your weaknesses? I am going to have to answer those questions when I write your reference, so the more details the better, but these have to be things I've observed myself.
What are some of your academic and nonacademic accomplishments that I may not remember?
What makes me particularly qualified to write a letter for you? That is, why should the recipient of the letter value it over a letter from someone else?

Be sure to tell how and where to submit the recommendation: online link, address for paper letter, etc.


May I cite an unpublished exercise from a lecture?

You always cite your source as best as you can. If your best citation is “unpublished solution to a lecture exercise”, then that is what you should cite. If you can find a better citation, fine. If not, cite it this way.

Since you don’t want to rely on something unproven, you should include the proof. One reason to have a citation is to allow others to verify the result, so the proof should be somewhere where I can read it. If there’s no other place than your paper, that’s where it should be.

And to avoid accusations of self-plagiarism you should probably mention how the proof was created.


Grade conversion for PhD application: Masters in France -> Phd in the US (Math)

I do not tick any of the boxes in your requirements, but as no one seems to, I will try and help. I am a graduate student in the US in a different field than yours, but have had a similar question regarding conversion.

Admission committees acknowledge that different countries have different grading schemes, some schools are stringent and some have grade inflation. First of all, do not try to 'game' your GPA to reflect what you think would be the comparison. That would come back and bite you in the... back. Often the schools will ask for the original grades in your native scheme, and sometimes to translate it to a GPA using their own calculator - which you should use. I wouldn't write an explanation about it for two main reasons - (a) it doesn't look good, and mainly (b) you are not a source of authority and they have no reason to trust you on this. Even if they did it does not mean that you can give a proper conversion.

OK. What should you do? The best possible thing will be to get your class rank from your department and mention that in your CV/Resume. Unless your grades are abnormally low, it is my understanding that the CV will be looked at - especially if you have a decent GRE, recommenders that are semi-known, or decent experience. Rank beats GPA.
If that is not available, just assume that foreign students are given somewhat more leeway in the GPA department and your profile will gain a fleeting look if it is not all borderline.

Good luck!


Progression through Computer Science Path

This is a bit of a snarky answer to your question but... did you try Googling "PhD in Computer Science Security"? Perhaps even more useful have you looked at the offerings of your own university to see what a Masters or PhD entails?

To be a bit less snarky in PhD programs, at least, it's less about what the degree is called and more about the research and lab you become involved with. If you are interested in focusing on security, which is a broad field, in Computer Science you will often get a degree in 'Computer Science' but you will work in a lab focused on security.

With that in mind my first recommendation to you is to do some research. Find out what folks are researching at your current institution, see if you find it interesting. If you can, get involved! This is probably the best way to find out what programs exist out there for your interests.

Even beyond your local school - do some digging. I was about to do a quick Google search and find that there are a couple of schools that are considered to have the 'best'(subjectively of course) Security Information programs. You should be able to find this out as well! Start looking into other schools, see what they offer and also what their researchers are researching. See if anything seems interesting. Start reading papers. Do some research into what you want to do.

So, in short, do:

Figure out what research is happening at your school. Try to get involved.
Figure out what are the 'best' programs for the topics you are interested in. Who is the 'big name' in the field? Read those papers!
Find 1 person who you want to be when you 'grow up'. In other words find one person whose job you want to have one day. Research how they got there! See if you can build a road map to your own success based on how they got to where they are.


Effectiveness of grouping students to balance skills

I have a practical suggestion based on a course I used to attend.
It was a natural continuation of another course (which was a requirement), and the majority of the student body from the first course was proceeding to take the second course.
The only team leaders were picked by the professor, in a sense that the best students from the previous class were team leaders, and were free to form their group as they wanted.
This ensured several things:

no "elite" team with only the top students

the groups were formed mostly to students liking

some degree of balance was naturally present
(e.g. we grouped on purpose with 6:4 in favor of "stronger" students, because we were allowed to distribute the assignment grade on our own, and that way non-perfect score still meant everybody got approximately the grade they wanted which coincided mostly with their effort: non-perfect project was not a tragedy)

on the previous class, a small number of students were actually "pushed" to go the extra mile, do exceptionally, and provide a team leader for their social group

From the student perspective, at least, it worked pretty well. If you say the student body is not changing that much from class to class, maybe something similar could work.
The downside might be that an "elite" group is clearly identified, but if it is based on objective criteria, and not seemingly the random whiff of a professor, it does not seem so bad.


Accepting a graduate offer of admission and then turning it down

Traditionally, the recommendation is that as soon as you are accepted you withdraw your applications to schools that are out of the running. Then as soon as you accept an offer you withdraw your remaining applications. If a school make a decision early and requires a decision before you hear from schools you may find more desirable, it is best to ask for an extension.

I go against the norm a little and believe that if a school/employer will not give you and extension and wishes to put you at a disadvantage that it is not unreasonable to reneg on your acceptance. As this is not the norm, it will burn bridges.


How do I find similar research problems in other fields?

Here are some pointers that one can start with; on the multidisciplinary aspects of Combinatorics.

See Annals of Combinatorics

  Annals of Combinatorics will publish outstanding contributions to
  combinatorial mathematics in all its aspects. Special regard will be
  given to new developments which have yet to be given proper
  recognition, but which in the opinion of the editors show promise of
  eventual mathematical breakthroughs.

  Papers published in Annals of Combinatorics will not be limited to the
  field of combinatorics in the strict sense. They will range over
  problems and theories that have arisen, or will arise, in applications
  to computer science, biology, statistics, probability, physics and
  chemistry, as well as over work of a combinatorial nature in
  representation theory, number theory, topology, algebraic geometry and
  the theory of special functions.

See also Journals in Combinatorics and Related Fields and Preprint Links in Combinatorics. The site also has a list of  Open Problems in Combinatorics.

From the list of journals, find those are closely related to your requirements and subscribe to their email alerts or RSS feeds using Google Reader or the likes; for latest articles.

Hope these wiki articles (and the external links there) are already looked into; Combinatorics, Combinatorial chemistry, Outline of combinatorics, Combinatorics and physics


Unless you are 100% that you will run this lab until you retire (and even then, plans can change), I do think it makes sense to keep both websites and decouple them a bit. You and the lab are two different entities, possibly with different relevant recent achievements to publicize, and in any case, presumably you’ll want to grant employees/students of your lab access to modify the lab website, but probably not to modify your personal website!

For your personal website, I’d include:

material for courses taught
personal research interests
your CV
link to your lab page
etc.

For the lab website, I’d include:

lab publications
lab projects
recruiting info
list of personnel and links to their personal pages (including yours, of course)
news/media coverage/events
etc.

As for pros & cons, I’d say the pros of distinguishing you vs the lab are:

enables personnel to feel more “ownership” in the lab, thinking of themselves as part of an organization rather than just as your employee
I actually think a lab named for what it does (e.g. “Climate Dynamics Lab”) is not “generic” but actually more transparent and meaningful for communicating what your lab group studies (at least until you become so famous that your last name becomes synonymous with your subfield)

Cons:

you’ll have to maintain two slightly different websites, so synchronization becomes a pain


This questions will vary greatly depending on your research area. Many people in applied fields will have no more issue than any other scientist, while those working in, say, algebraic geometry tend to have a tougher road. That said, here are a few principles I have found helpful:

1) Find the smallest question that captures the key idea. You don't have to explain your particular problem, so much as give a flavor of the sort of question you work on. For example, in Schubert calculus, everyone always leads with the question "Here are four lines in space. How many lines intersect all four of them?", even for other mathematicians! You can then allude to higher dimensions, broadly say how your work ties in (or just assert that it does!), and so on.

2) Return to the specific. Use vivid metaphors as a way to overcome abstraction. For example, I often describe a permutation as a row of line dances, and a simple transposition as two people dosey-do-ing to swap places. Now I can talk about the dancer's motivation as motivating my questions, and it somehow seems less arbitrary. Providing something tangible to visualize helps a great deal. This is completely at odds with the usual mode of mathematical communication, where we wish to abstract away every specificity.

3) Inject narrative. Talk about the history. Mention peoples names, and say what they did. Give a scope of the human endeavor that is (a) mathematics, (b) your field and (c) your specific problem. "Littlewood and Richardson came up with a rule for multiplying these polynomials (Schur functions) in the 1930's, and said the proof follows from 'simple combinatorics', which they thought beneath them to do. Forty years later, Schutzenberger finally figured out how to do the simple stuff, after many failed attempts by famous mathematicians, some of which were published!" It would here be appropriate to mention some details about Schutzenberger's fascinating life.

Edit: Explain why you care! Talk about how you came to the problem, your motivations (beyond glory) for solving it, why you think it's worthwhile.

4) Create opportunities for dialogue. Obviously this only applies to someone who is genuinely curious, as opposed to being polite. If you provide the over-arching perspective (1) and provide a specific and familiar framework (2), your listener will have a framework they can use to start asking questions. Metaphors will be abused, and their limits exposed, but that's okay. At the end of it all, someone might call you a "math detective".

5) Be willing to sacrifice a little (or a lot) of accuracy. It's okay to describe the overall thrust of your area, rather than the particular question that you work on. It's okay to give a wishy-washy description of something that glosses over many complications. Despite working in the field that most prizes accuracy, mathematicians regularly gloss over subtle issues with each other. The standard should be much lower when dealing with non-mathematicians. Seriously, it's okay!

6) Steal shamelessly from others in your field. Read popular accounts of your area, or ask other people how they try to describe things. If you work in the Langlands program, read Ed Frenkel's book and see how he tackles this challenge. Look at the "What is a..." series in Notices of the AMS. In general, people seem averse to doing this across academia, but everyone benefits if you can use the best exposition, regardless of whether or not it is original to you.


Prolonging a PhD to improve research CV, is this good ?

As Irwin suggests, prolonging the PhD to improve your research track record is a standard strategy, especially for students who are interested in pursuing an academic career.

The minimal requirements to get a PhD are fundamentally weaker than the minimal requirements to get an academic job.  Despite all high-falutin' talk to the contrary, the only real requirement for completing a PhD is convincing your thesis committee to sign the requisite paperwork.  Most faculty have an image in their heads of the necessary work; for example, in computer science, a minimal PhD thesis is roughly equivalent to two solid conference papers.

On the other hand, the academic job market is a true competition.  Only people with truly outstanding research records (and strong recommendation letters) get invited to interview for faculty positions, or accepted for research postdoc positions.  It doesn't matter whether you're "good enough"; lots of people are "good enough". What matters is how you compare against other people on the market.  So it's actually quite rational to delay completing the PhD past the point where you have a viable thesis, in order to improve your research record.

That said, phrasing the delay in terms of "making your thesis stronger" is totally missing the point.  Your PhD thesis is an administrative hurdle.  At least in computer science, if you're lucky, three people will ever read your thesis, including you and your advisor.  (The standard joke ends "...and your mom.")  Your colleagues will see and judge your track record through your peer-reviewed publications in conferences and journals.

So, the short answer is: Do more original publishable research, and then publish it.  And then I guess you could show off to your committee by including those results in your thesis, but whatever.

Also, please slap your advisor for me.


Financial resources for M.Sc. students in the U.S. universities

This depends a lot on the university, the discipline, and the individual department.

A key factor is that many universities have "terminal masters" programs that are not research oriented.  Students in these programs typically complete an MS degree by coursework only, and don't complete a thesis.  Students in such programs almost never receive financial aid in the form of fellowships or teaching or research assistantships.  Other MS programs are research oriented and include a thesis or significant master's project.  Some departments have two different MS programs, one with thesis and one without.

Even if the MS program is research oriented, departments with strong PhD programs tend to focus on supporting PhD students and MS students may either not be eligible at all for assistantships or they may be given lower priority than PhD students.

Some departments that do not have PhD programs do have research oriented MS programs and will provide financial support to MS students.  This is one option, although these departments are not going to be as highly regarded as the departments with strong PHD programs.


Are you allowed to copy text from your Master's thesis into your PhD thesis?

No. It's called self-plagiarism. You can of course cite results from your Master's thesis, and even quote it, but only if you clearly indicate the source. That it wasn't published doesn't make a difference.


How to deal with a procrastinating (student) collaborator?

There are a couple of options that you could consider:

You may have to put your foot down (in a nice way), and gently remind her that it was her idea to collaborate and that such collaboration is difficult unless you both adhere to the deadlines set.  If it still persists, tell her that the procrastination, particularly with the tasks are making the collaboration untenable.
If this is not a critical aspect of your work, take a more relaxed attitude yourself to it - in terms of punctuality and task-completion.  The rationale for this is that if she does not place the collaboration as a high priority, then why should you?  This second one you would need to be careful about, the approach would be to put your other work before it.