Will I need to retake my written qualifying exams?

I don't think this is a matter of finding the right argument.  If the rules of the specific department in question explicitly allow you to keep your old exam results upon readmission to the program after any length of time, then if you are readmitted to the program then you get to keep your old exam results.  If they explicitly say the contrary, then you can't.

More likely there are no explicit rules which address what happens when a student leaves the program and then is later readmitted to it: there are no such rules in my program, for instance.  In this case it is really up to the discretion of the faculty in the department.  Moreover, since this issue will probably be bound up with your admission decision, being too pushy or argumentative about it could really backfire.  I would say that it is certainly fair to explicitly mention that you passed the written qualifying exams in the same department at such and such a time, that you are excited to pick up where you left off, and that you are wondering whether this will be possible.

I do not advise that you say more than that or that you give detailed arguments.  It is also not a matter of "equitability": they are not obligated to admit you at all, so they cannot be obligated to admit you with certain additional constraints.  To be honest, the harder you argue about this the more strongly I suspect that you should take the exams again.  Nine years is more than long enough to forget everything that you learned as a master's student.  Indeed you write

  While I couldn't pass the present day equivalent versions of these exams (without much study).

Since you have said this, I would seriously consider removing the identifying information from your account!  Your own confidence that you could not pass the current versions of the exams is rather strong evidence that you should take them again.

  neither could many graduate students like me who are further along in their study.

There are almost certainly no other students in the program who passed their exams nine years ago.  Many PhD programs have total time limitations for exactly this reason.  (There was a student in my program who had done everything but his thesis, and he eventually got timed out because he had taken too long: I believe, after nine years.)  Moreover the other students in the program have spent the time since the exam pursuing their studies and going on to fulfill other programmatic requirements.  You left the program.  It is really not an equivalent situation.

Note also that although the mathematical knowledge tested on qualifying exams is not really time-dependent, nine years is long enough for the structure of the exams to have changed: if e.g. the syllabi are different or if the faculty know that the standards have been raised, then it is probably inappropriate to hold a newly admitted student to different requirements than other newly admitted students.  To be fair, it is probably more likely that there has not been significant change.

Finally, let me note that you haven't mentioned why you are not willing to take the exams again.  According to the structure you described, if you retook all the coursework it would take only one more year.  One year in an American PhD program is not a long time at all.  Taking one year to solidify your foundations before proceeding could actually allow you to graduate in less time than if you dive into something headfirst and then only after months or years realize that you need to backtrack to learn the basics.  Please think carefully about whether getting excused from the exams is really in your long term best interest.

Good luck.


What to do for letters of reference if you want to apply to grad school but you've been self employed?

The source of the letters matters less than what they can convincingly say about your chances of success in the program you are applying to.
So choose referees who can write such letters. They might be clients, or managers, or former professors, or people you consulted professionally while self employed. People who know your work and your work ethic.


I'm about to tell my advisor I want to leave my PhD. Do I mention this when scheduling a meeting or do I drop a bombshell while there in person?

If you think that there is any possibility that the advisor can adjust your working arrangement enough to let you continue, then it would be better to give him/her a heads up before the meeting. That way thought can be given before the meeting and so it needn't be so ad-hoc.

But have an idea of what you would need for yourself going in to such a meeting so you have some basis for discussing options.

Leaving a degree is a big step, make sure it is the right one. And make sure that others have a chance to try to work it out with you if there is any way possible. But for that, they, themselves, need a time for reflection.

And, as per your final thoughts in the question, have an idea about what you want the alternative to be. Ending with nothing isn't a very happy outcome.

But the goal isn't to get you to change your mind. Rather it is to find a way so that the conditions are appropriate and the future is clearer.


Citing a book vs citing the original paper

I think it can be appropriate to cite a book, exactly because they can provide a great overview of a topic. I can think of a some cases in which you can cite a book. First of all, you may want to point the reader to further background material of your field of research (say, in the introduction of a paper).

Another example: Say you are in -some research area- and you want to use something that is common knowledge in -other research area- citing a book may be helpful because they can contain more background and better explanations.

Finally as you already mention, if the result is very old finding the original paper may be hard (for both you and the reader). Furthermore the exact phrasing of a results changes somewhat over time, so it may be more difficult to read.


graduate student credit for work on a paper

Any significant words that you wrote which go uncredited constitute plagiarism, full stop. Your contribution may not rise to the level of authorship, but it deserves an acknowledgement at the very least. The editor of the journal where the article is submitted should be quite interested in this at the very least. If you have draft text saved that can demonstrate your contribution to the paper, that may be strong and convincing evidence. Git/SVN commits to a LaTeX version of the paper would be best, but any evidence of work in progress is good. Contacting the editor is the nuclear option, but if you feel strongly and have proof, you may be able to make a case for killing the article.

The real question for me is whether the PI is your PhD supervisor or not. Your graduation hinges on your relationship with your PI, and if you destroy that relationship by exposing their misconduct, you may do more harm to yourself than the publication is worth. What does your supervisor say? Are they the same person?

I cannot understand why a professor would exclude any contributor who appears to have done as much as you have from authorship for any reason. Are we missing something here? What argument does this PI make that you shouldn't be included?


Applying for postdoc position in UK - Physics

Well I am studying for a PhD at Cambridge and most of the post-docs that I have met are not from the UK. I personally know at least 3 post-docs from Germany and a large proportion (24%) of the graduate students are from Europe (39% are non-UK/Europe). So from my experience Cambridge doesn't seem to preferentially hire UK post-docs.


How ethical is the practice of including spouses as co-authors when they are in the same field?

Your question is based on one assumption (that you spell out):  "the barrier for co-author contribution is far more easily passed [for spouses], compared to two regular collaborating PIs.".

"Yeah, well, you know, that’s just, like, your opinion, man." -- The Dude

As pointed out in a comment, ethical people don't draw the line in different places depending on the situation (at least for the case in question). The line is already drawn by the ethics principles they follow.

So, to answer your question, it is ethical to include spouses when the spouses contributed to the paper, it is not when they didn't. Exactly like including anyone else.


Why is having multiple PhDs frowned upon?

I think your assertion really is an overgeneralization, but there are some negative points to pursuing more than one PhD.

It's the same concern as it would be for pouring an inordinate amount of resources into the wrong pursuit.  It might indicate something about the recipients decision-making abilities, or "perpetual student syndrome".

That said, if that's what one needs to do to pursue the career one wants, that's what one needs to do.

Let's look at two distinct situations.  A college junior starts thinking about her career path, and thinks"

  I want a very specific, highly specialized pursuit.  I believe that I
  will need two PhD's to establish my credibility and skill set for this
  path.  I am setting out to get two PhD's, and have a good plan for
  doing so.  I've already considered whether I can acquire the skills
  and knowledge by doing one PhD, and then endeavoring to cover the
  shortfall by some other means, and I don't think I can.  I'm well
  aware that some of the skills I learn during one PhD will be redundant
  with what I learn in the second, but there's absolutely no way around
  it.

Contrast this with a senior, who doesn't manage to get a job, so enters graduate school -- gets one PhD, doesn't see the career prospects, then gets another PhD to fix things.

Clearly, the first situation is better (though, I'd argue, exceedingly rare, and often unnecessary).  The second situation is much more problematic, likely more common than the first, and arguably, what some people tend to think the path was when told someone has two PhDs.


How to respond the reviewer who reject my paper but editor ask to revise

The same way you respond to the reviewers who didn't reject your article: you take the reviewer's criticism and argue why it's irrelevant, inappropriate, unfair, has been fixed in the revision, and so on. If the reviewer rejected your article without giving reasons, then you can safely ignore the reviewer (since the editor decided on revise, he/she clearly already disregards the reviewer's report).

There's no need to email the editor.


Flying with a poster tube as a hand luggage

There are a couple solutions to the "transporting a poster tube on a plane" problem:

Most flights allow a second piece of hand-luggage, so that bit is fine. And while it is larger in the length dimension than is usually allowed, I've never had this be a problem. In not-very-full flights, it can be stored on top or behind other bags. On fuller flights, I usually just ask a flight attendant for help. So far the tubes have ended up behind the seats in the last row against the bulk head, and in the coat closet usually reserved for first class. Generally, I find they give you "credit" for trying not to be a problem.
As has been mentioned, you can get your poster printed or shipped to the conference location.
Cloth posters. These are becoming more easily accessible. While more expensive than paper posters, if carrying a poster on forces you to check a bag, and your airline charges fees for those, the cost difference vanishes swiftly. These can be folded and stored flat in a shipping envelop or bag. Just make sure to take them out and iron them on a very low setting to get the creases out before you hang them.


Is it possible for a high school student to conduct research into computer science?

To answer the first part of your question, it is definitely possible for high school students to perform research in computer science.

But let's look at the broader picture here first. Computer science spans a lot of sub-areas, which have very different flavors and require different sets of knowledge in order for you to be able to perform research in it. Being able to program is good, as this is needed in some of these areas, while there are some in which programming knowledge is normally not needed.

Research means to push forwards the frontier of mankind's knowledge. In CS, little effort is spent of replication experiments (i.e., when a finding by one group of researchers is tried to be replicated in their experimental setup). Rather, research is typically performed by trying out new ideas to solve problems that are considered to be interesting enough for research.

Now this is where the difficulty kicks in: in order to come up with a new approach for some problem of relevance, one needs to have a good overview of one area of research, which means to invest years in getting a good overview of the work performed in that area so far. Research students (e.g., PhD students) are expected to work on getting this overview themselves, while at the same time they also have an advisor at their disposal to guide them. Without an advisor that is already established in your sub-field of interest, there is a high probability that your research  efforts are spent in vain (e.g., because what you would be trying to do would not be novel enough).

Thus, it may make sense for you to find an advisor that can guide you in your research work. There are definitely sub-areas in computer science for which - with the proper guidance - high school students can make non-trivial contributions, while possibly also using programming knowledge.

So as a proposed course of action, look into which sub-areas there are in computer science, which one interest you, and read up a bit on the major results. Afterwards, you can check if you can make contact with possible advisors. As a high school student, you may want to aim a bit lower than at the professor level. E.g. a postdoc at the university closest to your home town working in your area of interest may be a good first point of contact.

Allow me to also add that learning to program in various languages is related to research only to a small extend. The scientific part of computing has a different flavor than most people outside CS would expect. It you haven't done so already, consider looking into the Wikipedia article on complexity theory, which gives you insight into a sub-area of computer science whose results are used in most other are sub-areas of CS as well.


Things to do before submitting a manuscript

Putting together also some advice from the previous answers, here is my suggested checklist:

Run a spellchecker :)
Prepare a cover letter. If the manuscript has a previous history (e.g., it is a modification of a rejected papers; overlaps partially with a conference proceeding), you should state it. Some may want to suggest possible referees in the cover letter; I find it ethically dubious, so I never do it. In case, you may want to suggest referees to avoid. (maybe we should have a separate question on this point).
submit a preprint, either at your institute or on arXiv, or at least think about it. Check the terms of the journal you are submitting to (this is a great resource) to make sure you can; often the submission is the best moment to do it, since the journal can have no reasonable copyright claim on what happened before it.
Even if you don't submit a preprint, make a backup copy of the .tex and .pdf files. If you use source control, tag the latest version as "submitted". This way it will be easier to recover that exact version when the referee report mentions "line 4 on page 2".
Send a copy to your co-authors, for backup and self-archiving.
Relax and celebrate.

You speak about applying the journal style in the manuscript; I suggest not to do it at this point. Referees won't care; it is really needed only after the manuscript is accepted, or if an over-zealous editor asks you to do it. You might spend lots of time without reason, resizing figures and line-breaking formulas that will be dropped after the referee comments.


Can the postdoc adviser withdraw our paper against my will?

Yes, an academic paper cannot be published without the consent of all its authors (as JeffE pointed out in the comments), so any one author can prevent publication for any reason, with no appeal or recourse.  Of course it would be unethical to do so for a bad reason, such as settling a personal grudge, but there's plenty of scope for good reasons.  For example, just feeling that it's not yet ready is a fine reason.

If your advisor withdraws the paper, then there's nothing you can do about it.  It can't be published in its current form with him as an author without his permission, and you can't remove him as an author if his contributions merit authorship.  (If they genuinely don't, then you can and should remove him, but you'll have to deal with serious questions about why he was listed in the first place.  Be very cautious with this, since if other people agree with him that he deserves authorship, then trying to remove him will be a disaster for you.)

In principle, you could try to extract your own contributions from the paper and publish them as a singly-authored paper without him.  However, this may be difficult, or even impossible if there was enough joint work that cannot solely be attributed to either author.

In practice, you'll probably have to work with your advisor to fix the paper, so that you are both happy to publish it.  He presumably feels it's worth publishing after some more work, since otherwise he would remove his own name from it and wouldn't care what happened to it after that.  Hopefully you are both reasonable people and can come to some agreement.

In the meantime, if you can't convince him to proceed with the submission, I'd recommend withdrawing it yourself, since it looks more awkward if he does.  (It can look like you screwed up and your advisor had to step in to fix it.)  If he withdraws it, then you shouldn't try to stop him, since there's nothing you can say to the program committee that would help.  All you can do at that point is to make it more awkward and embarrassing for everyone, without changing the outcome, and I don't think it's in your interest to make a fuss.

I'm sympathetic, since it sounds like your advisor has put you in a frustrating situation.  He should have reviewed the paper earlier, or asked you to hold off on submitting it because he needed more time to review it.  However, his failure to be a helpful coauthor doesn't justify publishing the paper without his consent.


What are ways for graduate students to make additional money?

Finish the PhD quickly.  People with PhDs are paid more than people without PhDs.  Becoming a PhD faster will get you to higher pay faster.  You will also keep that pay for longer, because you will work more years of your life if you finish your education sooner.  (note:  correlation between education and pay does not always imply causation; also in certain disciplines the pay is terrible both with and without a PhD)
Quitting the PhD to go into industry is a good choice if making money in the short term is the goal.
Switch to a university which provides decent funding.  This works best if you are early in your PhD.
Apply for outside fellowships.  However, keep in mind none of these pay that great.
Working a job unrelated to the PhD while enrolled will make the PhD take longer, delaying the time when you are paid more.  Do not do this if you can avoid it.


Advice for preparing a virtual presentation

First of all, you need to know the specific requirements from the conference host. Do they have a specific file format that they want you to use? Otherwise, you might want to do a screencast recording. There are free software available such OBS (Open Broadcaster Software) where you can record your screen and microphone at the same time. That way, you can go through your powerpoint presentation while recording both the screen and audio. Make sure you use a good microphone when recording and try to minimize as much background noise as possible.

Good luck with your presentation, I'm sure you'll nail it!

PS: Let me know if you're struggling with getting OBS to work, it's fairly easy and straightforward so there shouldn't be any issues (also many guides available on youtube).


Questionable content in student's theses

My recommendation is for the student to make it clear in the thesis that they know these are overly simple theoretical models. If the models don't significantly affect the main results, it is difficult to see how being honest can hurt. And trying to make it appear that the models are more significant than they actually are could definitely hurt.


How can I prove my self-studied knowledge?

One may prove their knowledge by these aspects.

They may have a certificate of the courses they have passed.
They may have a publication or patent registration in the field of their personal studies.
They may have worked in the field of their knowledge and their projects and portfolio is a proof of their knowledge.

A website designer may not have any certification of their design knowledge, but the websites they have designed are the proof of their knowledge.

You may have done voluntary/paid teaching at your undergraduate university or in an educational institute, so you have the certification of your teaching activity and that may be counted as a proof of your teaching and your knowledge. (Also teaching/research assistantships to a course which you have never passed but you did assistantship in that area.)
You may have some publications in the area of your knowledge, for instance, a published paper or book; or a contribution to a publication which is so related to your knowledge.
You may have done some jobs related to your knowledge. An engineering design, done some code-developing, etc.
You may have a recommendation letter from a professor in which has written that you have sit in their class for that course, but you have never registered for the course; so it proves that you have the knowledge of the course.

However, as far as you are registering for a graduate program, you must fulfill their requirements not what is generally/logically reasonable or what seems to be acceptable. So it is better to provide all your proofs in your CV or their application process website and let them ask you for more official documents. Also, you can email them and ask for your special issue.

P.S. It seems that your question indicates self-study knowledge, but some people may have done some non-degree programs and certificates of those courses may also prove their knowledge in the course.


Is it advisable to put entire source of my thesis up on GitHub?

I'm told for your field that the answer might be yes, because you're slightly less threatened in terms of being scooped than most, with physics (apparently) going largely by who submits first.

I would be extremely cautious publishing the source of my thesis in its entirety on a public repository. I'm all for repeatable science and open access, but the public should only have access to your code when this condition is met:

You have no further use of the exclusive access to your code. All the questions you've programmed have been answered, the papers and presentations that emerge from them are in press, and at this point, it is a question of reproducible research.

Once that's true, sure. Until that point? You're running the profound risk of your research being stolen.


On the use of hypocorisms on publications and university personnel list

Typically, you have full choice over which variant of your name you choose to publish under.

I know people who use a shortened version of their first name, substitute their (preferred) middle name, use their pre-marriage last name, etc. Publishers don't care and funding agencies use stronger unique identifiers.  I doubt that places like ResearchGate and Academia.edu constrain you either.

Just be sure to be consistent, and consider ORCID to help with disambiguation.


If you are a GRA are you consider fully funded?

Yes. I'm not aware of the term "funded" having a strict or legal definition. If you got paid every semester, then it sounds like you were fully-funded, and it's fine to say this.
As for what employers want, I'm sure this varies widely, but I doubt that being "fully funded" by itself will count for much. If you had to go through a competitive, merit-based process to "win" funding, it might be worth a bullet explaining this achievement.


First, congratulations! You've published papers, been cited, and gotten praise from colleagues! You've shown that you can publish, and I don't think your adviser and others would be pushing you if they thought you didn't have a shot at the top conferences and journals.

Are any of the people who have cited or praised you in a position that you could collaborate with them and/or pursue a postdoc? They have indicated that they know and value the quality of your work, and they might be able to help you raise your profile. That would be a promising path forward.

Academia is full of criticism and critics. It is easiest to give broad criticism, and it takes a lot of interpretation to make that constructive and to separate critical feedback on your work from your self worth.

One way to deal with the devaluation might be to try it your adviser's way. That is, since you know you can get your ideas published somewhere, see what it takes to aim at a higher publication. With your next research idea, plan to spend much more time on revision. Ask your adviser and anyone else who will comment what it would take to hone that into a top publication. Does it need a broader scope? Do you need to deal with more subcases? Is the idea itself too peripheral or incremental? Do you need to explicitly link it to more pressing issues in the field?
CS tends to have multiple-author papers. Can you collaborate on a paper that your adviser thinks has promise for getting into a top journal? (Either one that your adviser spearheads or one with a postdoc or fellow student?) You might learn more about the editing process they use, and the successful publication might help raise your profile.
Study how people present ideas in top proceedings and journals. You might not love their style--they may be more limited in length than in less selective venues, perhaps requiring them to be more opaque and more formulaic in order to pack in more results. But you, too, can write in that style if that's what it takes. What else do you see about the abstracts and papers that you can emulate?
Another way to survive is to think carefully about what you are proud of in your own work and what you value in others' work. This might give you a sense of who you want your closest colleagues and mentors to be.


What to list as affiliation when work spans multiple institutions?

Most journals understand that such complexities exist, and will allow you to list multiple institutions, so all four of your options are certainly viable.

That said, given that you have done much of your work on the paper while at your new institution, your new institution should certainly be listed as an affiliation, which means that you should be using either your option #2 (new only) or #3 (both institutions).

That leaves the question of whether the old institution should be listed or not.  From what I have seen, the customs on this tend to vary by field and also by institution: you can probably make a reasonable argument for either listing or not listing the old institution.  I would thus recommend talking with your co-authors to see what their feelings on the matter are, particularly if you have some co-authors from the old institution on the paper, who are the ones most likely to be upset if your judgement disagrees with theirs (in either direction).


Advisor manipulated/threatened me into sharing my first authorship

These are your options:

Focus on your new project in a new lab working with better colleagues.
Do the revisions yourself.
Let the former advisor do whatever they want.

I agreed to give X co-first authorship under the condition that major revisions will be done to address all ...

You agreed to the co-first authorship.  You should not break that agreement.  Unfortunately, revisions being "done" is subjective so you cannot punish the other party for breaking their part of the agreement.  Next time, only agree to someone's authorship after they have earned it.


Using a public GIT-Hub repository (that was a homework of my group) in my Bachelor thesis

Do I have to mention my colleagues, who implemented that homework with me, explicitly in my Bachelor Thesis?

Depends on what referencing system your given institute uses. Most likely, it would be a good idea to mention that in your reference. For example, if you are using the Harvard system:

[Surname], [First-name] et al [System (e.g. Github)] [Year of creation], [Repository Name], [Version #], [Type of 'thing'], accessed [Access date], [Repository URL]

  Do I need my colleagues agreement that I can use this project for my Bachelor Thesis?

As long as you correctly reference it, and that you don't use it commercially you should be fine, but just doing something like emailing them asking if you can use it as an example for your assignment would do no harm.

  Does it make any legal difference if I provide a link directly to this sample project or if the project is just visible in screenshots without showing an explicit URL?

Legal difference? Yes. If it would ever come to such, giving the actual URL would/could effectively protect you, as the opposition could claim that you edited the screenshots or that they weren't of the correct repository in the first place.

To be honest, I would prefer to have a few extra words in my bibliography rather than be taken to court and be prosecuted.


Is it an insult to my US university to not walk in graduation?

If attending a graduation ceremony is not your cup of tea, you don't need to go.  Better to stay away than to go and be uncomfortable!

It would be considerate to let your department know that you won't be attending.  Some universities make more of a thing of graduation than others, so depending on the vibes at your school, you might want to have some travel plans that conflict with graduation day.

By the way, congrats!


Should I be honest with postdoc candidate about awful lab working environment?

The general rule in these situations is that being honest is okay (though consider that it can be risky if word of your honesty makes it back to the boss), but it's important to stick to facts and to your opinions about your own situation/experience.
"The team is destructive" is not something you should say, nor is "the lab is mismanaged". Those are your opinions about other people: stay away. What you can say is "I feel like I've had trouble getting credit for my work", "I wish I had more freedom to choose the direction of my work", etc. Even better is to use specific factual information (note: opinions are not facts), like "I've only been able to get one first-author publication in the past three years."
That said, take care of yourself, too. If you need a recommendation for a future job, it might be necessary to bite your tongue a bit. It's good to want to warn a candidate off gently, but consider that once you are gone someone is going to get that position, and it's even possible that the person who does will have a different experience than you did.
Also related: https://workplace.stackexchange.com/questions/137037/can-i-tell-a-prospective-employee-that-everyone-in-the-team-is-leaving (not an identical situation but I think the advice there still applies).


How to answer question about funding a project

Some organizations require applicants to list alternate sources of potential funding in order to determine whether the applicant has sufficiently explored funding options and is expending effort to obtain funding. If other options are less likely to be funded (due to poorer fit) or are unavailable, you can highlight that to emphasize the importance of applying for this particular grant.


Is it okay to ask your professor about the final exam that I took 3 years ago?

It is completely fine for students to request to see their final exam scripts. As a lecturer, I am actually surprised and slightly frustrated that many students seem to be only interested in their mark, not the feedback.
However, asking for an exam dating back 3 years may be a bit more difficult. Exam papers are only kept for a particular amount of time, often ~3 years. So if you want to ask, do it as soon as possible before your exam paper is discarded.


I believe my PhD dissertation was unfairly graded too low (cum laude): what should I do?

Why it matters

In my field, cum laude or rite (the two worst German PhD grades) are rarely ever awarded and if they are, it’s usually a sign that there were major issues and a strong hint that the PhD should not consider any career aspirations in academia. Such PhDs often end in positions which mainly care about the title for its own sake (e.g., to impress customers). Your field may differ a bit, but even in law (which is known for using the entire spectrum of grades), such grades would not bode well on an academic career.

I would be careful with taking the position that the grade does not matter. As already said, the vast majority of PhDs that stay in academia have either summa cum laude or magna cum laude (the two best grades). Since getting a summa requires at least a bit of luck in many examination rules¹, many people do rightfully not care about the difference between the two. On the other hand, not having either is likely to raise some eyebrows and may prevent you from getting your desired position without you ever knowing why. Even if you find stories of people who had a successful academic career in your field with a cum laude, beware of survivor’s bias.

Moreover, many job offers in Germany (in particular at government agencies) explicitly require a very good PhD². This includes professorships to the extent that it is in the text of the respective laws (Landeshochschulgesetz), e.g., the one for Northrhine-Westphalia states (translation mine):

  Einstellungsvoraussetzungen für Hochschullehrerinnen und Hochschullehrer sind […]:
  […]
  besondere Befähigung zu wissenschaftlicher Arbeit, die in der Regel durch die Qualität einer Promotion nachgewiesen wird; […]

  Preconditions for being hired as a professor are […]:
  […]
  an outstanding qualification for scientific work, which usually is evidenced by the quality of the doctorate; […]

Now, this does say “usually”, which means it is technically not impossible to get a professorship with a bad PhD, only more difficult. But that already can be a severe disadvantage and may mean that you are ending up with a considerably worse position.

One function of such rules and phrases in job offers are things like avoiding nepotism or having to hire a bad candidate due to lack of better ones. Still if the criterion is phrased respectively, it may be legally impossible to hire you since you fail a hard criterion. If I found out that the successful candidate for a public job I failed to get only has a rite, I would certainly suspect foul play and consider legal action.

All in all, this grade may very well be career-ending.

¹ I know of cases where somebody did not get a summa only because they did not perform top-notch in a one-hour oral examination on their field of study that was unrelated to the topic of the PhD. Consider a theoretical cosmologist PhD being asked about lasers.
² Including your grades on your CV as well as providing a copy of the actual PhD certificate is the default in the hiring process, so you cannot really hide it.

What to be scared of

  I am now considering to appeal to the university. But, I am scared.

… of what?

It sounds like you have little left to lose here.
If your PhD gets re-evaluated from scratch, you are very unlikely to end up with a worse grade.
There is a small risk that you earn a reputation over making a fuss about this, but those who care about this will also likely care about your grade.
On the other hand, if I were to consider you for a position and asked you for the story behind your grade (and I probably would), I would rather be negatively surprised if you hadn’t made a fuss.

What to do

Now, every faculty in Germany has its own PhD rules and therefore it is difficult to make any general statement here.
However, there are several aspects of your story where my PhD rules could have kicked in:

There would be two further members of the committee who can intervene in case of major disputes or grades being given with questionable reason or an accusation of academic misconduct (using material without a reference) against which you could not defend yourself.
The entire committee (four professors) grades the defense.
If the two main examiners differ by more than one grade, a third examiner would have to be consulted.
If your thesis is deemed to have major flaws, you have to be given the opportunity to amend it.
Grades for the thesis have to be given independently and cannot be changed afterwards. (It sounds like the “bad” examiner wanted to give a cum laude, so it cannot be the middle, unless he changed it to a worse grade later.)
There is a written record of committee’s decisions.
Nobody else would have been admitted to attend the committee making the decision. It is particularly weird that students can attend, but you cannot.

I recommend that you thoroughly read your faculty’s PhD rules and consult with whoever oversees the process (usually the dean). Also talk to the “good” examiner (your supervisor, I presume) to get a more detailed story of what happened.

Note that most PhD rules also forbid you to just submit your thesis to another university.

Caveats

Beware that you very likely did not get the full story so far.
For example, attendees of the committee’s decision tend to primarily report the most egregious aspects even though other points had been made.


This is a manifestation of game-playing, and is completely understandable once one starts thinking in such terms.

For example, if a person is in an excellent situation to get tenure at their current institution, they are probably in an equally good position to get other jobs, perhaps with tenure.

Another feature: if a person has done good-enough work that they've got outside offers, this can set in motion the getting-tenure process at their current institution.

(Shallowly enough, the "best" certification of one's academic virtue is outside offers.)

At the same time, I think most up-for-tenure assistant profs in the U.S. are not really looking for outside offers as they come up for tenure, so even if they could generate them, they'd not try. For that matter, despite the "rewards", many people find this game-playing obnoxious so don't do it.

To answer another part of your question: yes, most formal job offers only arise after informal inquiries and back-and-forth, because... as with high-school dating... getting turned down is embarrassing. :)

The people who are interested in gaming the system continue to do so after tenure, typically...


What is the h-index exactly and how does it work?

The h-index is a measure of the impact of someone's publication list. An h-index of 10 for example means that the person has published 10 papers with at least 10 citations. The total number of papers published may be higher, but only 10 will have 10 or more citations.

Critics argue that this measure disadvantages young researchers who did not have time to publish a lot and whose work has not been published for long and thus may not have attracted many citations. Other criticisms include that it makes a researcher focus on how to increase the citation count for a paper that may be not that good but would increase the h-index.

For more explanation, see for example the Wikipedia article.


The low-tech way will be to check in google scholar who cites each of your papers. You list will be ranked by citations number, so you can immediately see which paper is more important.


Forced to Quit PhD although the hard and proved work

You describe a very difficult situation that has only difficult solutions. It seems pointless, even dangerous, to continue with this supervisor and, perhaps, even at this institution. It may be impossible to change the behavior of the supervisor, even if the department puts pressure on him to change.

However, though difficult and disruptive, you may be able to take the work you have done and use it as a firm basis for application elsewhere. I would normally just suggest changing supervisors at your current place, but it may not be possible and if the current supervisor is truly vindictive, then he might still be able to interfere.

But if your current and previous work is good, you can find an academic home somewhere. If you decide to move, investigate any future supervisor at least a bit so you don't get in to the same situation again.

You don't suggest that this could be a case of pure sexism. If it is, then in some places you can make a case for sanction of the professor, of course. Sadly, sexism is too accepted in too many places.

Let me add that I can't judge your work. It may be that your advisor thinks your work has less value than you do and that is his reason for his behavior. Of course, you have stated that others (reviewers, editors, etc., if that is the meaning of your second paragraph) have given validation to your work by publishing it.

But even if the professor is correct, it doesn't excuse bad behavior toward a student. If he thinks you are on the wrong path, his job is to guide you to a better path, not to disparage you.


Is it still possible to get a decent job in academia (specifically physics) nowadays?

I've heard from a couple physics professors and chairs that it's somewhat difficult to find a first position in physics in general

This is a dramatic understatement. I always recommend reading the first chapter of Karen Kelsky's book. She demonstrates that our universities are not in crisis -- that was 20 years ago. Rather, they are in decay. Most departments are not growing; they are shrinking and cutting back. Yet, graduate programs keep pumping out PhDs.
For physics in particular: APS reports that in 2012, 1800 physics PhDs were awarded. In contrast, there are 9400 physics faculty positions total -- about half of which are at institutions with no physics graduate program (i.e., schools that -- with a few exceptions -- focus on teaching rather than research). From this, you can estimate what fraction of physics PhDs end up with faculty research + teaching positions (see also here).
In short: saying you want a faculty position is like you saying you want to join the NBA -- of course you do! But even for the best students, it is a long shot.

I'm concerned I'd be left out without a job if I tried to do so

Now for some good news. 1-year post-PhD, only 4% of physicists are unemployed. The overall unemployment rate for those with a physics PhD may be around 1-2%. There are research positions outside of universities, and there are also non-research positions that are both intellectually engaging and financially remunerative. Further, you should not have to incur debt to attend graduate school. Thus, attending graduate school in physics might be a good choice (financially and otherwise) even without the allure of a faculty position. But it is certainly good to be realistic about the situation; indeed, you might consider subfields, projects, and skills that could lead to interesting work both inside and outside of the university.
Note: this answer, and the statistics therein, refer entirely to the situation in the US.


Publishing a result that is aesthetically pleasing, but has no practical value

Yes, this is fine.  Math papers very often contain results just because they are interesting or instructive, even if they do not seem to be "useful".

You could mention this when introducing the result, with something like "The following theorem may help to illustrate the connection between blah blah blah..."

Authors also sometimes signal this sort of thing by describing a result as "pleasant", "amusing", etc, though "elegant" is probably a little too egotistical.

If the referee feels it's too much of a digression, they might suggest you take it out.  But I don't think this would be the difference between acceptance and rejection.


I want to write a historical research paper

There is no requirement to be in academia in order to be able to publish. You need to find a "suitable" journal for your work and figure out how to submit to them. Now a days it is mostly via an online form. They may ask for some background on you, such as affiliation, but that is more for informational purposes than anything. Independent Researcher is a valid "affiliation", generally.

But you may want to get some advice from someone in the field if you have any doubts about the quality or relevance of your work. You may need to decide whether the academic or popular press is more appropriate for your work, and a pro may be able to help you with that.

But, hopefully, your research took you through papers written in reputable journals. Those are the ones to consider first.


What correspondance for corresponding author?

All correspondence regarding the paper should go to the corresponding author (with very few exceptions).

If you should contact them with requests for clarification is a judgment call. If you are a student not understanding it, you should probably first discuss it with your supervisor. If you are an experienced scientist and believe that there is insufficient information or even an error, asking them would be appropriate.

Me and my colleagues have also (successfully) contacted corresponding authors with requests for access to data for a meta analysis or to invite them to a workshop (all expenses paid).

So there are a number of legitimate reasons to contact a corresponding author. That's why the contact data is given in the manuscript.

However, from the perspective of a corresponding author, most correspondence you receive is usually with the journal (and spam from other journals and conferences).


Are you required to declare past conflicts of interest?

Usually the consideration is not about the funding received when the paper was published, but received while the work was being done. To illustrate: if a grant is won after a paper is submitted, but before it is published, it would be strange to see it declared as a conflict of interest.

But if a researcher persistently receives funding from a particular source, and then takes time off from that funding and uses those windows in funding to publish material in support of that source, then it would be inappropriate to stay silent about that funding: doing so would be against at least the spirit of the rules about declaring conflicts of interest; and may be explicity against the letter of the rules, when the papers contained work that was done during the funding period.


How shall we reply to an editor after a minor revision of a paper?

There’s nothing going on behind the scenes here. Just send it back and say “I’ve made the requested edits, I hope the manuscript is now satisfactory,” or whatever you would normally say to an editor when sending back a paper.

You seem to think that there’s some kind of implicit social dynamic going on with the editors comments. There isn’t.


Accepted in MSc program but not invited for a visit?

I was accepted into multiple MS programs in math. None of them invited me for a reimbursed visit. When I applied for a PhD, every program gave me an all expenses paid tour. It has been my experience that if you are an MS student, you are not going to be cared for much. If you are a PhD student you will get much more in terms of "acceptance perks."

That being said, they should at least be willing to guide you to the proper resources for learning more about their school. If it was me, I would not accept the offer from your first choice. They do not sound easy to work with.

I would reach out to a few people that you want to work with at your first choice school. If they also blow you off, that would be a bad sign. A really bad sign. A degree from a middle of the ranking program is worth more than five blown years on trying to get an MS at a high rank institution and banging your head on the wall. My experience is that it is much better to go to a school where they care about you and you will be happy than to go to a school where they do not even know you and are totally unwilling to help you.


Updating a review paper after several years by publishing a new review paper

Updated review papers are not particularly unusual, as a Google Scholar search readily demonstrates.  You should definitely explicitly declare the paper as an updated review, and it is probably best to send the paper to the same journal as before.  If you can get in touch with the journal editors, they may even be able to expedite the review process, since they already know and have accepted the first version.


Have there ever been any "Lebron James" of academia?

Stephen Wolfram self-published a physics book at age 12 and then 3 more by the age of 14 (a lot of people do this, but you can look at the PDFs by clicking on the links here and I think you'll find that these could compete in quality to the works of many adults at the time).

That same link will tell you that he did not finish high school, or undergrad, but received a PhD at age 20 from Caltech. On the recommendation of Richard Feynman and Gerald Freund, he joined Caltech's faculty at age 21.

  Have there ever been any academic researchers who showed so much
  promise at one stage (in undergrad or grad school maybe) that they
  were offered funding to set up their own research institution, or a
  high-ranking position they'd typically be unqualified for?

To qualify into the PhD program at Caltech, one typically needs at least an undergrad degree, and Stephen Wolfram did not have one. As user StrongBad points out, entering a PhD program at Caltech is far more exceptional than entering the NBA straight from high school, when you look at the percentage of people that have done either. Entering the faculty at a university like Caltech at age 21 and only 1 year after finishing the PhD, was also probably less common percentage-wise, than entering the NBA straight from high school.

You ask about "setting up their own research institution", at first I was going to tell you that including this in your question was a bit extreme, but after reading more about Wolfram I found out that he set up the Center for Complex Systems Research (CCSR).

However LeBron James stayed in the NBA for a fairly long career and has continued to be (arguably) the best player in the NBA. Wolfram "academic career" was short relative to most other academics, because he shifted to doing other things such as:
(1) making software for academics
(2) making educational resources and doing outreach
(3) managing businesses that help academics
He did continue to do academic work and published a book with academically original content, but it wasn't received as well as the mid- to late-career achievements of LeBron James. His success in (1), (2), and (3) though can definitely be compared to the mid- to late career achievements of LeBron James.


Can a graduate from university of applied science In Finland study higher degrees (Masters and PhD ) outside Finland?

Yes you can.
You would have to go through the application process of whichever university outside of Finland that you wanted to apply for. The university may have certain minimum requirements, and it would be a competitive process, with you competing with others trying to get into the university.
Depending on which country and university you choose, you may be counted as a EU student or as an international student, which usually has higher fees than domestic.


How random is the graduate admission process in the United States?

There is without a doubt some randomness in the process, but I find your question impossible to answer. In the question, you implicitly assume that the "quality" of an application is a well-defined concept that could be used to replicate an experiment.

But this isn't the case. The only way you could do this is by submitting N "equally good" applications to the same graduate programs in the same year, and expect the same outcome for all. But this is clearly not a workable concept. Rather, different graduate programs may look for different candidates (for example because they have different areas of strength), and possibly may want to balance areas in successive years. In other words, the "quality" of an application is a concept that can only be measured against the current needs of individual graduate programs. You can't repeat the experiment at a different place or different time and expect the same outcome.


What is a reasonable percentage salary increase for tenure and promotion

Data on faculty salaries is available from the AAUP survey:

http://chronicle.com/article/2013-14-AAUP-Faculty-Salary/145679/#id=table

Associate professors make, very roughly speaking, 10% more than assistant professors.  However, since professors get a few percent raise a year, you can estimate that the difference between the most experienced assistant professor and the least experienced associate professor is about the typical annual raise.  So, I think the answer is "not much."  However, it varies widely by institution, school, department, governance model, etc.


Is it okay to give link of my recent paper in the cover letter for a postdoc application?

While I've only been on the applicant side of things, I expect that it would be fine to include a link. Different PIs will react differently, of course, but it seems unlikely to ruin your application. Just make it clear from typesetting that it is a link. Given that the PI might only look at the printed version you should probably make the link text self-explanatory as well, e.g. using an arXiv identifier. However, depending on the method of submission you might be able to just attach the preprint of interest to your application. I expect that this is the ideal approach, when possible.

As support for using links, see this Nature Jobs blog post

  When you’re reading an article online you’ll often find links to relevant content that is outside the article. This technique can be used in your cover letter too. Use links to information such as your research lab website, or your online portfolio and research papers. You can even link to specific papers that have been highly cited or extra-curricular projects you’ve been a part of. Let the employer know that there is so much more to you that what appears on that flat piece of paper!


It happens quite often that you need abbreviations only within a figure. In this case, you will usually just note the abbreviations in the figure caption.

So you could caption your table something like "Table 4: Some data showing the influence of speed (S) on test (T)."


Why is there still so much academic gibberish?

There's one of my papers, much of which is couched in seriously obfuscated language: in places, even worse than the example linked by OP. (I won't say which paper, in case I embarrass my co-authors.)  In my case, I think the reasons were:

More than a decade elapsed between production of the first complete draft of the paper and its submission to the journal where it was eventually published.  During that period, we changed our minds several times about some of the core conclusions; but each time, some bits of explanatory text got left in the paper that were only really apposite in the context of now-obsolete conclusions.
During that period, my co-authors and I were not in very frequent contact, and we ended up using edits to the text of the paper to communicate with each other about the science in the paper; this produced text that was sub-optimal for communicating with readers.
Despite the long total drafting period, the submitted version was finalized in a tearing hurry to meet a deadline for a thematic issue of the journal, so there was no time for a thorough pass through the text for clarity and concision.
Perhaps most significantly of all: the referees let us get away with it.


Is someone who solely contributes negative feedback to a paper considered an author?

To moderate Yemon Choi's comment:  yes.  Your first assertion is that A and B are collaborating, which means they should be co-authors, unless one actively backs out.

For a mathematical project, it's easy to have lots of ideas but not enough time to pursue them all to see which (if any) work.  If someone can shoot down ideas and tell you they definitely (or with high likelihood) won't work, this can help put you on the right track.  So in your situation I would say B was instrumental in finding a correct solution.

(In a somewhat different abstract scenario where B dismisses some approaches to a problem that A suggests, and B does not otherwise actively work on the project, it may depends on the situation and they should have a discussion about whether B is a co-author or not.  And some people will have different opinions about the same situation, e.g. RS versus A in the RSA example.)

In general in a mathematical collaboration, if there's one key idea it's unlikely that both collaborators arrive at it together.  Maybe through discussion they enhance each other's understanding of the problem, and then one will have the key idea and the other will encourage/validate it.  That doesn't mean was the other person was unnecessary, even if you can't
pinpoint parts of the final paper as being "their contribution."

(And if collaborations became competitive to the point of dropping co-authors just because the didn't see the final solution first, who would want to collaborate?)


Filling in details from other papers, is it good or bad?

Let's call the other paper [A].

First of all, you might like to check whether a proof already appears in some other paper or book, [B].  You can search MathSciNet or other databases for papers which cite [A].  If so then you can cite both ("The following proposition was stated in [A]; see [B] for a proof.")

Otherwise, whether to give a proof is at your discretion.  If you think the reader would find it helpful to see the proof, and it doesn't distract from the main purpose of your paper, and it isn't excessively long, then sure, you can include it.  People often use phrasing like:

  We make use of the following proposition, which is stated in [A].  Since [A] does not include a proof, we give one here.

Another option is to put the proof in an appendix, or to write it up as a separate note which you post on arXiv or something.

The Perelman case is about something different - people disagreeing over whether the original paper actually solved the problem, and how much of the credit for the result is due to those who filled in whatever gaps there may have been.  In this case, you describe the proof of the proposition as "not particularly difficult", so it's likely that the authors of [A] did in fact know how to prove it, and so would most of their readers who took the time to do it.  It's reasonable to give all the credit for this proposition to the authors of [A].  There's nothing wrong with you including a proof, and as long as you don't try to take credit for the result, no controversy will result.


How to reference multiple authors of a chapter from a book [APA]?

From the APA blog this is what you need to site in APA

  Author, A. A. (Year). Title of chapter. In B. B. Editor (Ed.), Title
  of book [E-reader version, if applicable] (pp. xxx–xxx). Retrieved
  from http://xxxxx

You will see in the purdue OWL that you should only list seven authors. So your chapter citation should look like this. I'm assuming this is the chapter you are referring to at this link.

  De Groot, R, Ramakrishnan, P.S, Van De Berg, A,  Kulenthran,, T, Muller, S, Pitt, D, ... Rossler, M. (2005).
  Chapter 17 Cultural and Amenity Services (Xu Jianchu and Hebe
  Vessuri Ed.). In  Rashid Hassan, Robert Scholes, and Neville Ash (Ed.), Ecosystems and Human Well-being: Current State and Trends (Vol. 1, The Millennium Ecosystem Assessment, pp. 455-476). Washington: Island Press.

For in text citations use the following link

  Six or More Authors: Use the first author's name followed by et al. in the signal phrase or in parentheses.

  Harris et al. (2001) argued...

  (Harris et al., 2001)


My supervisor wants to put someone else as first author on one of two papers when I have done most of the work on both. What should I do?

Generally speaking, it is infeasible for us to judge whether authorship or the order of authors on any given project is "fair", as all of those depend a great deal on discipline and the particularities of any given project.

That being said, from the little text you provide the 1/1 split does sound fair. There are two papers coming out of the work, one experimental and the other theoretical. The person who did the experiments first-authors the experimental one, the "theory guy" leads the theory paper. So far, so good, I would say.

You say that there was "nothing new" in the theoretical work. This seems highly unlikely to me, what would even go into the theory paper if that was indeed the case? In general, providing a solid theoretical basis to experimentally observed results is a very valuable contribution, that you maybe need to learn to value higher. Sometimes the theoretical methods to achieve this are straight-forward, but this does not diminish their value for your project.


How to tell my adviser that I want to change our focus?

I'm a PhD student in pure mathematics, so I haven't been in your exact position, but perhaps something close to it.  Nonetheless, allow me to play devil's advocate for a moment.  (Feel free to take all of this with a grain of salt.)

  My approach has always been to understand a topic from the ground up...

I think this is a great attitude.  Being able to go from the foundations to the frontiers of research demonstrates a deep understanding of a subject.  However, I think this approach is also wildly impractical as a young researcher.  Ravi Vakil has written about a different strategy for learning, speaking of "tendrils of knowledge":

'Here's a phenomenon I was surprised to find: you'll go to talks, and hear various words, whose definitions you're not so sure about. At some point you'll be able to make a sentence using those words; you won't know what the words mean, but you'll know the sentence is correct. You'll also be able to ask a question using those words. You still won't know what the words mean, but you'll know the question is interesting, and you'll want to know the answer. Then later on, you'll learn what the words mean more precisely, and your sense of how they fit together will make that learning much easier. The reason for this phenomenon is that mathematics is so rich and infinite that it is impossible to learn it systematically, and if you wait to master one topic before moving on to the next, you'll never get anywhere. Instead, you'll have tendrils of knowledge extending far from your comfort zone. Then you can later backfill from these tendrils, and extend your comfort zone; this is much easier to do than learning "forwards".' (Emphasis mine.)

(You can find a similar message in cartoon form here.  Make sure to keep clicking on the images.)

Of course, there is a balance: if you really do not understand the basics of a subject, trying to dive into a research question will be fruitless.

  I know that publications are essential. I want to eventually publish something, but not before I have built my own essential knowledge foundation of our field. Learning the topics thoroughly is more important to me than making a publication, and it seems to me that if one strives to truly understand and advance their field, then publications will come much more easily.

Again, wanting to learn for learning's sake is admirable.  But remember this: You could spend your whole life (and probably more!) studying things that are already known without ever producing anything new.

All right, resigning my post as Lucifer's lawyer, I absolutely think you need to communicate your unhappiness with your advisor.  Just make sure that you aren't overly confrontational.  I think outlining your goals for your last semester and masters program is a great idea, but I'm not sure including a bullet-pointed "what I am looking for in the advisee-adviser relationship" is such a good idea.  Other than that, I am glad to hear that you're open to compromise.

Some advice/questions:

1) Have you ever previously mentioned to your advisor your discontent with your lack of background?  If you haven't said anything yet, for all they know, you're perfectly happy with everything, and this may blindside them a bit.

2) Ask your advisor if you can do a reading course on a topic related to your research.  This way, you will have time to ask questions about the more theoretical aspects of the subject while still moving forward on your research.

3) Does your professor have a research group, or other students working on similar topics?  If so, try turning to them for help when you have questions about fundamentals.  Your peers are sometimes your best resource, and discussing things with your colleagues is sometimes the most effective way to learn something.

4) At my university, students have both a primary and secondary advisor.  I think it's a great system: the secondary can provide another perspective, and can also mediate any potential advisor-advisee conflicts.  Does your university have anything similar?

5) If you're sick and tired of debugging others' code, why not write your own?  My own research is often very computational, and I honestly don't think I really understand an algorithm until I can implement it myself.  That said, there is value in accepting some "black boxes."


classifying work folders and data, any recommended structure?

There are other possibilities, I know, but most will fail at a certain level of complexity. Think instead about how the WWW (World Wide Web) is "organized". Basically it isn't we use search to find things. Google indexes things in complex ways to make search fast. But the MACOS (and I assume others) do something similar with files that it can reach. If you can keep a vast amount of information "online" search will find it.

You can aid search, of course, by "tagging" your files with one or more of several standard (to you) keywords, much as the tags on this site are used to help users find questions of interest.

Likewise, if an OS allows alias "files" you can also "file" aliases of important files in some complex directory structure, but it takes work to design it and to keep it rational over time.

And, of course, keep everything backed up.


How is on campus professional training named in US or Canada schools?

I don't think there's anything wrong with calling these "internships."  If you are concerned about the possibility of confusion, you may say "university internship."  As you will also be identifying the campus office you worked for, the situation should be clear.


Is it acceptable if an advisor does not include me as a co-author on presentation?

There are basically two schools of thought on who should be on the title slide of a presentation: (i) everyone who has contributed, (ii) the name of the person who is actually standing in front of the audience and giving the presentation.

There is no accepted standard for which is the "correct approach". I tend to think that fields where projects only comprise 2 or 3 people use method (i), whereas more collaborative fields use method (ii) -- and I tend to think that that makes sense, because otherwise one would have to list a dozen or more people on the title slide, which is simply not very practical, and also not useful to the audience.

So I don't think that taking your name off the title slide is unprofessional or unethical in itself, even if you were the one who prepared the slides -- your adviser was, after all, the one who presented the talk and the project.

That said, if the adviser had been me, I would have made sure that you would have been prominently mentioned in the talk (and made sure that your name is spelled correctly!) but in the beginning ("Before I go through the details, I do want to mention that most of the work I am presenting here today was actually done by my student rapidCascade, and I do want to make sure that he gets the credit he deserves!") and at the end ("Before I end, let me acknowledge that many people have contributed to the work I just presented. In particular, I'd like to single out rapidCascade who has done more than any of the others.") These words may not be reflected in any of the slides, and unless you were there in person, you'd never know that this much credit was given, but it is possible to highlight someone's contributions without making this explicit in the slides.


Are the peer-reviewers of papers submitted to a conference that took a place in location X from X too?

No, the reviewers could easily be from other countries and may, or even may not, be attending the conference.


A direct answer for your question would be that quality would be better than quantity in this case.

By a larger paper would not always be of a better quality than a smaller one. But if you mean a paper with more extensive research and collation of results obtained from rigorous time consuming experimentation, then yes. Such a paper would carry more positive impact than multiple smaller ones that you could use just for the count. This is from the viewpoint of your advisor.

Some may prefer increasing the number of publications, but it would only matter if they are published in reputable journals, in other words, if they all hold quality (at least in most cases).

So if you intend to sacrifice quality for quantity, my honest opinion would be the same as your advisor's.


Ethically, do I need to include as coauthor a person who provided basic knowledge to fill a gap in my research?

The International Council of Medical Journal Editors (ICMJE) has established four criteria for being considered an author. The person's contribution should fulfill all four criteria. If not, they need to be considered as a non-author contributor and their contribution acknowledged, such as in Acknowledgements section. You can read about the different criteria and designation here. To directly answer your question, the person would be a non-author contributor.


If undergraduate Honor's Thesis printed/shelved in Alma-metar's library & checked out a number of times -- does it count as "published" on a CV?

Any work that has been made publicly accessible in an archival manner can safely be considered published (along with some that are a bit more tenuous).  That includes all manner of theses, whether or not anybody is actually reading or citing them.  Thus, you should definitely list it in your CV as part of your publications.

In a typical academic CV, however, publications are separated into different categories.  How many categories depends on the particulars of one's field and record, but it typically at least divides into peer-reviewed (e.g., journal articles) and non-peer-reviewed (e.g., your thesis).  I would further recommend having a specific category for large non-peer-reviewed works like your thesis (on my own CV, it's "Book Chapters and Theses"), to distinguish them from smaller tech reports, abstracts, and the like.


Paper status with Associate editor after Under review

The editor has received the reviews and s/he is in the process of judging them (sometimes maybe s/he will decide on a new review, but not likely) and communicating the decision to you. Sometimes this can take few weeks for various personal reasons (for example heavy work load on the editor). I expect that very soon you will receive the answer.


How common is flipped classroom type teaching?

The question explicitly asked is not that suitable for this forum. There is a answerable question hidden however: How to encourage a specific teaching style in a university?

Just "giving feedback to the university" will achieve exactly nothing. Universities are huge bureaucratic monsters with immense inertia build in. What you can do depends on your role in the university:

If you are teaching, then lead by example. In the universities I have been at there always was a department aimed at improving the quality of university teaching, and these are your natural allies. Contact them. Maybe they can broker contact with other teachers who want to do this or are already doing this. If you reach a critical mass, beautiful things can happen.

If you are a student then your options are fairly limited.


What is a computer science conference, really?

Most computer science conferences expect that, except in extraordinary circumstances, at least one author will present the paper in person. The paper is also, in most cases, published in the proceedings, possibly on paper and distributed to some set of people, such as a special interest group.

The reason for this is that we highly value collaboration and face to face conferences give us a chance to sit and talk as well as interact with authors.

If you publish in a lot of conferences you need to plan for the travel. Grant funding is one source, as is university funding. I think that personally funding your travel is not especially common, but possible.

Note, also that many conferences attendees work in industry, not academia, where they do research of various kinds. It is common to see folks from IBM Research, or Microsoft Research, for example at many ACM conferences. They are funded by their companies.

One option for a prolific publisher (we should all be so lucky) is to do a lot of collaborative work so that if you can't attend, say, SIGPLAN POPL 2021, then one of your coauthors will be able to.

But no, it isn't just another way of saying "journal".

I should also note that quite a few people attend such conferences even when they have no part in the program. They are just there for the collaborative opportunities and for informal meetings.


Supervisor has suprevisees do peer reviews for them – what are the ethics of this?

It isn't inherently wrong to give younger members of a research group reviewing assignments (it's a legitimate and commonly used teaching tool when mentoring younger scientists), but there are two points that are definitely ethically questionable:

The review is in his name because the person quoted uploads it in his name. That's deception: The editor expects the review to be from him, in hopes of tapping his experience, but gets nothing of the sort. The younger scientist also doesn't get any credit.

There is no teaching element in all of this. Yes, there is trust, but if he never read these reviews, he can't give feedback to the younger scientist on what they could do better.

When letting younger scientists do these reviews, I often do take their (final) review after we talked about it in some detail, and prefix it by saying something along the lines

The following review was prepared by one of my graduate students. That said, we discussed it in detail, and while the words are those of the student, the conclusions are ones we share and that I believe appropriately reflect our views of the paper.

This way, the student gets to learn, and we together provide a review that meets the expectations.
In other words, I find the behavior exploitative and ethically questionable.


As @GEdgar said in comments, you should consult with your adviser. But in general, a paper should be about one thing. What you need to determine is whether that one thing is the method, whether it is the application of the method to a particular cause (then four related papers), or your other posited approach of two papers.


How to improve the language of my master thesis by myself?

My best tip for proof reading your own work is to have your computer read it back to you. We often notice how things sound weird when they are spoken compared to when they are written.

Microsoft word includes text-to-speech as part of the Word. I use it all the time. Stand alone text-to-speech software is available if you use something else for your writing.


arXiv preprint and final paper differing by sections and appendices

There doesn't need to be a strict correlation between an arXiv publication and an actual publication. It's actually common to use arXiv to publish extended/longer version of a published version (which seems exactly what you want to do). So

Yes, it's OK to have a final paper that differs from the arXiv version.
Yes, it's even encouraged to cite the arXiv version to point to appendices/extra material/proofs/detailed examples, etc.

However, the main rule is still that your journal paper must be self-contained, i.e., must be understandable without having to read the arXiv version. In other words, if removing the section implies to remove a definition (for instance), then you must put this definition somewhere else in the paper.


What to do about a student who missed multiple assignments and claims illness?

First, there may very well be policies in place to handle this, so I would check those first, in case your hands are tied in some way.

Generally speaking however, I'm fairly permissive with medical absences and helping students catch up, if (as it seems from your email) the desire is actually for them to catch up. In your case, for example, I'd schedule a meeting for the student to try and figure out a path forward.

I'm aware that this leaves me open to being exploited by the occasional student who has decided to fake an illness, but I'm far more concerned with make sure those students who do have major medical or life-related issues have the chance to do well in my classes, and I'd rather the occasional student get away with an undeserved extension than have someone who genuinely needed my help not get it.


Generally you would need to contact the university and/or some specific research group to see if they could accommodate you. I think that this is rare enough that you won't find a lot of places with policies designed for it, so you would need to work through individual contacts.

Some research groups may be able to hire outside researchers, but many have funds intended only for supporting students.

If you can go visit some nearby university and make contact with a researcher or department head you would learn more.

You might also need to worry about what your company permits you to do outside the company. Some will want to impose restrictions. Others not.

It would be different if you can bring research funding from your company with you. Universities are usually pretty happy about outside funding.


Is a GPA of 3+/ 3.3+ but below 3.5 considered good for scholarships in Europe and the U.S?

In the US it is probably sufficient for admission, but admission to graduate programs here depends on much more than just GPA. Some depends a bit on which courses you got full marks and which not. But even more will be the statements made in letters of recommendation, research you might have (not essential, but helpful), standardized exams (some places) and your Statement of Purpose.
Admissions are handled by people who want to be able to predict your future success. If the many pieces of an application point to that then you have a chance for admission.
However, the more competitive an institution is, the harder it is to "measure up". So applying to a wide range of graduate institutions is advised if you want to maximize your chances.
Getting a scholarship, however, is a much more difficult proposition. There are few of them (in the US) and may depend on the grant funding of the faculty. Most support for grad students goes to doctoral candidates. But it is possible, here, to apply for a doctoral position with only a bachelors, so you might consider that. It would likely come with support.


How long does it typically take for editor's final decision after reviews are completed?

Reviewers can only recommend a verdict so what they say is not necessarily the outcome, the editor has final say. Of course if two reviews agree then it is very likely the outcome will be what they suggest. In a normal review situation involving an editor, the reviewers provide their reviews to the editor who in turn will make a judgement and pass on comments and possible suggestions for improvements to you. If your manuscript is in an open review system (such as the discussion format of Copernicus Open Access journals), you  may see the reviews before final decisions are taken and in such a case, I would not trust reviewers opinions on the verdict until you also hear so from the editor.

As is pointed out in a comment, it is a bit intriguing that you seem to have the reviewers comments but not that from the editor. The time between completion of reviews and to a decision by an editor will vary depending on many factors. The editor has to read the reviews in light of the manuscript and then value the comments and provide a synthesis of the outcome for you. Obviously the editor will have other manuscripts to handle in parallel which influences the time a decision may take. To state a time that can be applied to any situation or journal is therefore pointless. I am, however, certain that any serious editor is not keen to hold on to a decision for any extended period. With the journals I have published and the one where I am Editor-in-Chief times from receipt of reviews to decision can vary from maybe days up to a month in rare cases. This seems reasonable for the field in which I work but I am sure that such times vary between both field and journals within a field.


If you have a few meetings with a professor to discuss a paper, but they do not do any actual writing, is this sufficient to justify authorship?

The content of those meetings is largely going to be the answer to your question, and we can't really know the content of those meetings. There's a case to be made that those discussions helped form things, and he doesn't sound otherwise problematic, so I think it's likely worth just making him an author and moving on.


In mathematics, is it a problem if all research is joint with senior co-authors?

It can be an issue, but it is doesn't have to be a large one.  If all of your work is joint with senior people, many people will wonder to what extent you contributed to these projects, and to what extent you were just following others.  Particularly at top schools, people want to hire leaders in their field, and certainly people who will be productive without mentors/advisors alongside them.

Who you're collaborating with (the very top people or virtually unknown people, just your grad school/postdoc advisors or people at other institutions, etc) and what the results are also play a role in how this is viewed.

However, this can definitely be addressed in letters, and thoughtful letter writers should address this issue.  Another thing that is helpful is if you go forth and talk to many people about math (at conferences etc) so that at many places where you are applying someone will be able to address how well you "know your stuff."


Been working towards undergrad degree on and off, now finally found my passion and want to go for a PhD. What should I do?

What matters most to be accepted into and succeed in a PhD program is an advisor who values you and your work and will vouch for you.  Grades only matter if you're applying through the front door in a pile of 1000 applications, which you want to avoid.

During your remaining years in undergrad, look up and seek out the Mathematics professors at the college or university you want to attend.  Read their research, journal publications, conference presentation, research agenda, etc. and figure out how you can contribute to that and build upon it.  Then reach out to a select couple of them and have coffee with them, discuss your plans, volunteer to join one of their research projects as an undergraduate research assistant (sometimes it's even paid), and so on.  If you demonstrate aptitude, particularly when it comes to novel research and deep understanding of the subject material AND you have found the right advisor who wants to work with you, that person will help you with the application process and take you on as their graduate student.

Good luck!


Referee wants me to add a plot – because the paper has none

While there may be a way to add a very cool and colorful plot to my paper, I don't think it is necessary, it would be complicated to read and so I should add more text to explain how to read it.

It doesn't seem to me that you have really considered the reviewer's request seriously. You seem to think they should just be able to follow the formulas without any visual, thus putting the onus on the readers to do the work of understanding your paper. The onus should be, instead, on you to explain your ideas in the clearest way possible -- and this will greatly improve the impact of your work, as the reviewer says.

I find it hard to believe that there isn't anything visual you can add that would be helpful, no charts, figures, or pictoral examples. When I read technical papers, I have found that visuals that go through an example in detail are almost always invaluable for understanding, regardless of the type of research (very applied or very theoretical, etc.) Are you sure that there is nothing you can add?

  The paper still does not contain a single plot. I encourage the author to present some of their results in graphical form, which will greatly enhance the impact of this paper.

You seem to have taken some offense that this was not a useful suggestion, but I find it very unlikely that this suggestion is not useful.


How does failing in a course during Master's studies in Germany affect job prospects?

In my experience, it will have minor to none implications.

Job interviews barely talk about failed exams, if they even pose a question about your studies at all, they focus on what you put your focus on.
You could check your Prüfungsordnung or get in touch with the Studienbüro, if they actually include the amount of failed attempts in your Abschlusszeugnis. If they don't, you could chose to lie about it.
Your final grade and internships plus work experience are far more important than a failed class. So even if you decide to tell them, it should have minor implications.
Nonetheless, I think if they have to pick between two equal applicants where one has no failed attempts, they will pick him/her.

Things that actually are part of job interviews/applications in germany (in my experience)

Hobbies you persue (as an opener for the interview)

Final Grade

Your Abschlussarbeit, if it's related to the field you want to work in

In Computer Science, they could ask algorithm questions, although this depends on if they have qualified personnel

Experience in the workfield (internships, experience during your studies)

Questions to check if you fit into the company and have the required competency to do the job.

In the job interviews I had, they never mentioned my transcript of records.


Funding in mathematics from large companies as undergraduate

Charitable funding from large companies seems unlikely
In the US, only about 4% of scholarship dollars come from private sources.

Here is the breakdown of sources of college grants: federal government (44 percent), colleges (36 percent), state governments (9 percent), employers (7 percent), and private scholarships (4 percent).
-"7 Things You Need to Know About Private Scholarships", U.S. News (2011-02-01)

So, you're in the UK and asking about summer research funding, but it seems likely that the same trend would apply: that not much of the funding would come from corporations.
The big problem's that there doesn't seem to be a reason why they'd do it.  Even if a company wants to give its money away to research, it seems like they'd target medical research or something else with near-term applications.
You may want to think out an argument for your research
In general, the problem's that capital's a finite resource; people could just as easily put their economic power toward medical research or their own interests.  So, why should anyone want to give you money?
This isn't rhetorical or to make you feel bad!  Rather, it's an important life question that we all have to ask.  And if you can find a good answer to it - one that isn't biased by your own personal wants, but rather is objectively compelling - then that'll give you a basis for pursuing sponsors.


Electrical Engineering freshman want to pursue PhD in Theoretical Computer Science

As Buffy commented, I would consider changing majors.

With that in my mind I can offer the following:

IMO the best place to start with theoretical computer science is with understanding the theory of computation and complexity.

Sipser has a wonderful book which is available online for free:

http://fuuu.be/polytech/INFOF408/Introduction-To-The-Theory-Of-Computation-Michael-Sipser.pdf

I would also recommend reading a book about discrete mathematics - specifically one that deals with graph theory. For an interesting, more modern connection between mathematics and computer science you can take a look at Expander graphs, which have applications in networking, and see whether the flavour of these notions is appealing to you.


Normal career path for lecturer in Computer Science

I think that would depend on where and what you teach.  I've been a "computer science" prof for years because at the beginning of my career while working for a "dot com" I was asked to substitute for a class at a very famous design school and the instructor never came back.  Then I went to the department chair with a bunch of suggestions for things I thought they could improve in the program and they made me an assistant professor.  Then they put me in charge of the technical faculty.  Then they let me expand "coding" classes out into things like physical computing and HCI.  And because of this experience (teaching, curricular development, faculty leadership, not to mention panels and publications) I've been hired at other places, and go back and forth between industry and teaching.

It does sound like you're in the UK but I know a lot (most) schools in the US will hire people with very strong industry experience even if they don't have a Ph. D.  So while having a Ph. D. might be a clearer path to some extent, teaching gigs are competitive no matter what you do.  Working in the industry might not necessarily work against you!


Why should I write a good undergraduate thesis?

The audience
The correct, but somewhat cynical answer is that the main audience for a thesis or dissertation is the examiners. They'll have to grade it (or at least sign off on it), so you want to convince them to give you the grade you want. The next audience you'll want to target is actually yourself.
Some years from now you'll have forgotten some of the details. You can try to track them down again, but if you've written stuff down in a format that's helpful to you it's going to be a lot quicker and less painful. Basically, if you write the document well it can be a great reference. (I admittedly haven't opened my bachelor thesis many times, but I looked something up in my Masters thesis just yesterday.) Sometimes the thesis can also be useful for students doing their projects on the same topic, in the same research group, etc.
The other big point is that writing the thesis is supposed to be practice for future writing of e.g. dissertations or papers.
What sections are most important?
From the practice angle, all of them. To convince your examiners, probably introduction, results and conclusions - but different people will have different priorities. However, it's a case where you have a few people who are supposed to read your thesis, so an excellent abstract is less important than in a research paper. Basically, you want to show that you understand the field, and have done good work.


Job market in academia: applied/computational math vs. pure math

Applied mathematics is looks great for research oriented schools, as it is great for connecting field like physics into calculus, it’s evidence that you are aware of the connections and potentially build on them; pure mathematics doesn’t look as good, unless the field you are looking to research in is mathematics itself, as schools in general will assume you are more focused arithmetic, rather than the actual application of your degree to your field of study.


As a lecturer, can I use the same problems used in another course in my own course?

Check if the MOOC has a license assigned to it. If it is for example Creative Commons Attribution (CC-BY) you are allowed to use the questions as long as you give a reference to the original creator. You don't need to ask the MOOC in this case. CC-BY-NC (non-commercial) might be a difficult case, because you teach this course as a business and earn money for it.
A second option is to directly ask the MOOC creators.
Adapting the question significantly is a third option, as long as you don't copy directly texts from the original question and just base it on the general idea this would be fine.


How to automatically retrieve journal ranking and quartile from article list

The typical place to obtain journal IF and ranking data in a searchable and sorted format is your institution's library. They usually subscribe to commercial ranking services that provide spreadsheets (typically Excel).

If you are a member of the institution (researcher, student) this should be made available to you. Depending on the type of subscription, the library might be reluctant to just share the file via email (in my experience, they are usually allowed to do so). In this case, ask if you can use one of the library's computers to extract the information you need.

Once you have the list of journals sorted, it'll be a bit of legwork to match articles to their respective journals, but a hundred should be doable in a few hours


Most recommended automated way for conduction university exams

Conducting assessments with larger and larger cohorts of students is an interesting problem and many possible approaches can be tried, but some are more suitable to some subject disciplines than others.

As already mentioned multiple choice tests are one such technology. They could be computerised quizzes using, perhaps, a VLE (Virtual Learning Environment) or even an online free survey tool. There is also optical scanning of answer sheets for computerised marking of paper quizzes, but my experience shows it has limitations. Writing good multiple choice questions is a skill that needs to be acquired.

There is also peer assessment: getting the students to mark each others papers. Often more effective that you'd expect. This can be done on paper or electronically. When done electronically it can handle anonymisation and also multiple moderation.

You also need to reflect on the goal of assessment. What is it trying to achieve? Are you measuring rote learning memory or understanding and application of knowledge? Sometimes group and team tasks which are assessed by portfolio or presentation can achieve the same goals and deliver less marking burden.

You mention mid-terms. One should also question what function they serve. In many places they are only part of a carrot-and-stick approach to motivate learning and not for the assessment result. In this case they can be substituted with other forms of task which perform the same motivation function in student engagement.


How can I find a PhD position to work on a highly specific idea of my own?

You should look for faculty working in the field that you are interested in researching, and then pitch your research idea directly to them.

Make sure that you do a good job with a preliminary review of the literature for your idea and understand the professor's specific research interests, so that your letter does not sound like any of the hundreds of mail-merge messages that professors get every week.

If your idea is really worthwhile and you do a good targeted job of pitching it, changes are that someone will agree to work with you on it.  However, the reality is that most students come into a PhD without a really good sense of existing literature or the feasibility of their ideas.  It is for this reason that there is great value in being open-minded about your PhD thesis.

Many students make the mistake of thinking that the PhD should be the pinnacle of their career, solving some grand problem in human existence.  This might happen for a few figures in history, but, more typically, the PhD is the start of a research career and not the end of it.


Statistical analysis plan giving away some of my results, Reviewer 2

This is a ridiculous request (edit: eh, maybe not quite so ridiculous; comments suggest that my 'however' paragraph below applies in this case, but I'll leave the rest of this answer as-is). For one, even before you have run any tests you should have a plan for post hoc testing.
I would respond that it's not possible to correct this without moving statistical methodology to the results, and that the authors feel strongly about keeping this methodology to one section. I can't imagine an editor having a problem with this response, and if the reviewer feels strongly that the boundaries between sections of a paper are sacred then this speaks to their preference directly as well.
However, make sure you aren't saying things you don't need to say if it will help please the reviewer. For example, if you write something equivalent to "we do ANOVA on apple oranges and banana models" and then say "for oranges, we then did post hoc test xyz corrected for multiple comparisons", you can drop oranges from the second section, writing "if significant, we then did post hoc test xyz corrected for multiple comparisons". It doesn't matter that you ran these tests on oranges, it matters that you planned to do this post hoc testing for any significant omnibus ANOVA results, no matter which class of fruit.