Does using one offer to "pressure" another school actually work?

Simply say that you are writing to let them know that you have received an offer from institution X. If there is a deadline for you to answer the offer, tell them what it is. This may be helpful for the department chair to use in pressuring their administration or other involved parties to make a decision sooner than they would have otherwise - yes, people can often "hurry along" when the circumstances warrant it. It may also have a psychological effect of making you look more attractive and desirable, especially if institution X is a prestigious one. But let them be impressed by the news itself; keep the tone of the email neutral and informative and avoid coming across as smug or entitled-sounding.

As for what to expect, that seems beside the point. Just like you would update the places you've applied to if you had a paper accepted to Nature since that would make you a more attractive candidate, you want to let them know about a job offer from another institution. It may or may not have any positive effect, but it sure can't hurt.

If it matters (I don't think it does, but you asked), I'm in the US. Good luck!


Since you say you like the research where you are and you are fairly productive there, you can probably successfully get a PhD there. It sounds like your advisor is not perfect (busy, etc) but few advisors are "perfect" from their students' perspectives. And if you stay, you won't have to interrupt your research to apply to other schools and transition to a new group. Staying where you are is a "safe" choice.

If you go somewhere else, some of your weaknesses (which you are able to ignore in your current position) may be exposed, and you'll have to work on improving them. And you will probably meet new collaborators (especially if you go to anther country) and be exposed to new ideas and techniques that will be difficult to learn, but will make you a better and more capable researcher.

So the answer to your question depends on what you want to gain from your PhD: Do you want to get a degree and some nice publications? Then staying where you are sounds like the easiest way. Or do you want to improve yourself and broaden yourself as a researcher? Then you might be better off leaving.

Having said that - of course, even if you stay, you can still challenge yourself and improve yourself and your capabilities. But since you don't have to "prove yourself" in your current position, there's nothing forcing you to do so - you'd have to be exceptionally self-motivated and disciplined.


What title to put on a professional business card, for a person with a PhD

"Dr Name, PhD" is redundant, so this usage is often discouraged.  If you are going to indicate the degree, I'd recommend "Name, PhD" rather than "Dr Name" since it's more informative (at the very least it will keep anyone from thinking you are a medical doctor).  In the U.S. it's not common to indicate the university, but I think I've seen it more often in other countries.

I'd suggest thinking carefully before indicating your degree on a business card.  Some people without PhDs may respond bitterly, like you are bragging about your accomplishments or implying that your expertise is more valuable than theirs.  At the same time, some people with PhDs will look down on it as well, in a status hierarchy:

Some insecure people without PhDs feel resentful and don't want to be distinguished from PhD holders.
Some insecure people with PhDs try hard not to be confused with group 1, thereby irritating those people all the more.
Some better-established PhD holders aren't worried about being confused with group 1, but now they don't want to be confused with group 2, so they pointedly denounce emphasizing your degree as being tacky and in poor taste.

As a rule of thumb, I would omit the degree from your business card unless it's important for your credibility (i.e., the skills from your PhD are professionally important and people would otherwise assume you don't have them).

The one situation in which you should absolutely not indicate a degree is if it's irrelevant.  For example, if you're an accountant with a PhD in literature, then your business card should not read "Name, PhD."


Small bugs during review in software tool paper

You should submit the bugs with your review, not through Github.


Is conducting research in the field of evolutionary computing/genetic algorithms considered inferior within the CS community?

When applying to a school you should be aware of the faculty at that school and the research they perform. Take a look at their research papers. If nobody at the school does work in genetic algorithms, then it probably isn't going to help you to mention your interest in the area.

If you have a sincere interest in genetic algorithms, then you need to find a school with researchers that are doing work in that area. If there is a prominent researcher at a school working on genetic algorithms, then you really want to mention your interest. If the researcher is accepting new students it might improve your chances of acceptance.

There are always hot areas in a field, and machine learning is currently hot, and genetic algorithms aren't as hot. But, there is good work being done in both fields. (There is also bad work being done in both fields.) I would advise you to find someone doing excellent work, and then the field that you are in will not matter as much.


Who is a "Vowel" in a panel of Jury for a Master's Defense?

"Vowel" is likely a translation error from Portuguese, Spanish or another Romance language - probably caused by Google Translate.

In a committee or a board, a "vogal" or "vocal" is a member without a specific role. For example, in a committee I was recently to grade end-of-degree dissertations, the three members were the president (tasked with chairing the committee), the secretary (tasked with writing grades down) and one "vocal", with no specific task besides deciding grades with the other two members.

Another meaning of "vogal" or "vocal" is vowel. Both meanings come from the Latin word for voice or speak, because a "vocal" is a person who just speaks in a committee and vowels are sounds or letters that can be pronounced alone.

I tried to find a translation into English but no dictionary gave me a suitable one. Then, I would translate "vocal" to "board/committee/jury member". Maybe boards are organized in a different way in English speaking countries.

Just for reference, definition of vogal in Portuguese (see meanings 3 and 4), and vocal in Spanish (meaning 5) and Catalan (meaning 2).


I have just come back to my home country after an intense experience in Asia, as a postdoc in China. I will give you some advice, and what I heard about India. I had originally considered India as a possible destination as well.

I do not understand much of high-school teaching, and cannot help you there.

The best scenario Asia has to offer at the moment is a combination of personal safety, delicious exotic food, and ample job opportunities. You can expect to be mesmerised daily by traditions and sudden twist in lifestyle, while enjoying an absence of violence and threats; you will get as many interesting job offers as you keep on asking.

However I recommend you to be extremely careful. I was scammed on my salary and welfare conditions by reputed Chinese institutions, as partially discussed in the link below:
Persistent issues with salary pay as a postdoc in China: What can I do?

From what I discussed with many colleagues, similar issues are common in Chinese academia, but are just not openly discussed. And a solid resistance to exposing and discussing problems is a mark of Asian culture, be it in China, Pakistan, India, Japan, which you will be quick to bump into. I heard from Indian nationals that salary scams are not common, but other issues with administration and workmates are routine. (For instance postdoc salaries in India can apparently get delayed for 2-3 months, but eventually they will come; you may expect "informal fees & favours" to get procedures done). I think most of the difficulties I've faced in China would have driven an European nuts, as the cultural impact is so deep. In short, expect to attract a lot of interests in Asia.

Furthermore I recommend you study the destination country you choose very carefully as well, in deciding the region you'll be focusing on. Like China India is such a huge and heterogeneous nation; surely your experience will heavily rely on how you adapt to local standards of where you land. I left Asia with the impression that in the long run it pays better if you focus on 2nd-tier cities instead of heading straight to the more international 1st-tier megalopolises. Expect to learn the local language from start, and complete deprivation from your comfort zone in different spheres.

Finally I warn you about the food and a different concept of hygiene. I am sure you may have heard that some regions in India have a problem with urban chaos and water safety. Almost all foreigners I have known who lived in India for more than a brief stay got seriously sick, typically from some kind of food poisoning. Many could not finally adapt to consistently spicy cuisine. I was never sick in China, and I loved the food.

I believe it will be a great, memorable experience, but I recommend all preparation and precaution you can muster beforehand.


Former PhD supervisor faked results and submitted a corrigendum two years after publication

If you have incontrovertible, hard evidence that the adviser is falsifying data for personal gain, and can demonstrate as such beyond any reasonable doubt, you may have an ethical obligation "to science" to pursue this.

Outside of this, it is probably best to walk away. You already stated that you 'don't care' and even sent his emails to spam. Do you even want to be associated with this work (assuming he wants to re-do things and give you credit)? It sounds like the work would be significant and the rewards fairly minimal. Besides, based on your description, if he 'cannot implement' this commercialization attempt, there's little to gain.


Does Mathematics research in proven problems have any importance?

It is not going look bad at all. It sounds like the Professor has given you a project that is achievable in the time frame, and satisfies your goals of improving your math and getting some experience in research. It should have a positive effect both on your CV and on your understanding of the research process.

In my PhD experience, much of the beginning was is exploring the topic, reading the literature, and trying to figure out a new direction. This can take many months, and can even change as your understanding improves or new information comes to light.

I don't think people will expect to see original research on new problems until the latter stages of your PhD.


Is it OK to edit my undergraduate thesis results?

I am really stressed up and conceived the notation of modifying my lab results so that it is more presentable for my thesis since time is running out.

No, no, no

Never do this - it is highly unethical. If your deceit is discovered, you are likely to lose your degree, and may possibly face other consequences. (For example, if you have a job based on that degree, you may lose the job when the degree is revoked.)

It is always disappointing when a project doesn't work out the way you hope it will, but there is always that risk when you set out to do something that isn't completely straightforward.  See, for example, this related question: What to do when research leads to poor results?

Even experiments that are "known" to work (in the sense that someone claims to have previously achieved "good results" with that experiment) can't always be repeated reliably. See Estimating the reproducibility of psychological science, in which the authors attempt to repeat 100 published psychology experiments, and "replicated the original result" in fewer than half of them.

The correct response is to
write your thesis giving all the details of your work as it happened: the background, the experiment design, and the results. This serves to document your efforts, and may prove to be useful to other people who might try the same experiment in the future. You may also explain why you think the experiment may not have yielded the results you expect, and possibly propose a new experiment (if you have any ideas for improving your work).

Note that even when scientific findings do not match our expectations, the study is still considered a success (of sorts) if we can learn something from it. Even if what we learn is "this experiment does not yield consistent results in many cases." In contrast, false results might look nice, but are worse than worthless.

A lack of "good results" does not necessarily doom your thesis. To quote another answer:

  My PhD thesis was trying to demonstrate the nature of the relationship between stress and psoriasis symptoms (many people say "stress worsens psoriasis" - it's taken as a given truth, but it's never been empirically demonstrated). I was trying to answer things like what kind of stress, how long does it take, does it differ between people? I never found any evidence that stress did worsen psoriasis. Nor that psoriasis worsened stress (or any other psychological symptom).

  A PhD is an educational process. One should demonstrate that one has learned. The most important thing about a PhD is showing what you know, what you have learned, and what you understand. If anyone gets to the end of a PhD and says "Well, those results were all positive, just as I expected", they've learned little. At the end of your PhD (or any research project) you should want to start again, and this time do it properly.

The excerpt above is about a PhD, but applies at all levels of study.

  If I report my original results that didn't look appealing for my supervisor, I'm also afraid and doubt that she would require me to redo my whole experiment and delay my graduation date.

You should talk to your supervisor now - don't surprise her the week before your submission date and tell her that the experiment failed! Talk to your supervisor and ask for her advice on how to proceed with your experiment. Presumably she has more experience than you in this area and may be able to suggest a solution you haven't thought of. (And she probably does not want to delay your graduation any more than you do...)


Is it a bad idea to point out flaws/weaknesses of your model in your paper?

Science is not about getting papers published; it's about writing papers that move a field forward. So don't let worries about reviewers prevent you from adding content that you feel should be there. Indeed, modeling papers that hide their limitations are much less effective at advancing a field than those that clearly explain them.

Good reviewers recognize this and often look in the Discussion for a clear exposition of the model's limitations as well as its strengths. That said, to be worth anything a model must make useful contributions despite these limitations, and it's your job to explain how your model does that.


One option I can think of is in engaging in writing open source software related to such fields. You can gather experience in setting up goals and realizing them and you will work together with academics, students and hobby enthusiasts in the open source community.

A scientific/research project is often not very different to a open source software project with a experienced PI/group leader and PhD students, undergraduate students.

Github or scicomp/datascience/stats.stackexchange could be a good starting point or this citizen science register.


First published date vs Issue date: Which do I cite?

This journal (like many if not most journals) publishes articles online before formally assigning them to issues. Cite the issue date.
Prior to most journals moving completely online, journals would formally accept articles and then take weeks to months before publishing articles.
As online access became more common, journals would publish articles as "online early access" or similar terminology during this wait.
One warning, sometimes these online early access articles are not completely proof read (e.g., there may be small copy edits or changes to the final version of the paper). This usually does not occur until the issue date.
Last, you can also find older articles that have were published online after their paper print date (e.g.,  https://doi.org/10.2193/2005-680).


There is some research on this, with inconclusive results. Some problems with the existing literature:

These studies typically rely on student reports of cheating (i.e. students fill out an anonymous survey asking if they have cheated and if they have observed cheating)
The effectiveness of such a pledge seems to vary tremendously with context (big school vs small school, online vs traditional class, field of study, how much emphasis is placed on the honor code), and it is difficult or impossible to control for all of this
Many of these studies compare schools with a pledge and unproctored exams to schools with no such pledge and regular exams, which is not exactly the comparison you ask about.

See:

McCabe, Donald L., and Linda Klebe Trevino. "Academic dishonesty: Honor codes and other contextual influences." Journal of higher education (1993): 522-538.

Hall, Teresa L., and George D. Kuh. "Honor among students: Academic integrity and honor codes at state-assisted universities." NASPA Journal 36.1 (1998): 2-18.

McCabe, Donald L., Linda Klebe Trevino, and Kenneth D. Butterfield. "Academic integrity in honor code and non-honor code environments: A qualitative investigation." Journal of Higher Education (1999): 211-234.

McCabe, Donald L., Linda Klebe Trevino, and Kenneth D. Butterfield. "Honor codes and other contextual influences on academic integrity: A replication and extension to modified honor code settings." Research in higher Education 43.3 (2002): 357-378.

Roig, Miguel, and Amanda Marks. "Attitudes toward cheating before and after the implementation of a modified honor code: A case study." Ethics & Behavior 16.2 (2006): 163-171.

Vandehey, Michael, George Diekhoff, and Emily LaBeff. "College cheating: A twenty-year follow-up and the addition of an honor code." Journal of College Student Development 48.4 (2007): 468-480.

Konheim-Kalkstein, Yasmine L., Mark A. Stellmack, and Margaret L. Shilkey. "Comparison of honor code and non-honor code classrooms at a non-honor code university." Journal of College and Character 9.3 (2008).

LoSchiavo, Frank M., and Mark A. Shatz. "The impact of an honor code on cheating in online courses." Journal of Online Learning and Teaching 7.2 (2011): 179.


Research Scientist vs Staff Scientist in US academia

They could be anything and it will vary widely between institution. They may or may not be "academic" positions. They may or may not be "senior" positions. They may or may not involve advising/mentoring students, especially graduate students. They may or may not be open to tenure. A given institution might use either of the terms for something essentially the same as the other at a different institution.
If an institution uses both terms, you will have to ask them about the difference.
Of all the above only "tenurable" is unlikely, though a long term contract or an open ended contract is probably available. That would make it unlike a postdoc position.


What is expected in my academic CV as a new PhD student?

Write your CV as-if you hadn't started your PhD. As such, list the educational institutes you've attended, e.g.,

2015 -- 2017 Distinction, Master of science, University II
2010 -- 2015 Grade, Bachelor of science, University I
2002 -- 2010 High School qualification, School

And list what subjects you studied underneath at least the first two. (It's  probably no longer relevant what you studied at school.)

Mention your current position too. E.g.,

2017 -- present Doctor of philosophy, University III

And give a compressed summary of your research objectives underneath. (It should appear above the other institutes.)


Why do academics write/publish book reviews for journals?

In my experience, reviews are written at the request of journal editors and are typically not initiated by the person writing them.  My colleagues and I usually write several book reviews every year because our supervisor is on the editorial board of the journal and tells us to write them.  As reviewers, we do receive a free copy of the book, if you consider that an incentive. There is no prestige associated with writing one, and they don't count as publications in our annual performance reviews.


Should an undergraduate writing an article for a semi-academic magazine list a university affiliation?

Grad students often write "PhD candidate" on their websites, etc., so you might consider "Yuhao Dong, BSc candidate, School of Computer Science (or whatever your department is), University of Waterloo".

Edited to add: I was curious, so I checked the author guidelines.  They don't indicate how to specify your affiliation, so I would either ask the editor or look at some articles from the most recent issue and copy their style.


Academic Journal Article Peer-Review Feedback Tips

Submit your work to high-quality journals.  Those journals (usually) make sure to get high-quality reviews for submitted papers.  In my own experience, the quality of the reviews is strongly correlated with the quality of the journal.


What the benefits of summer school when working on masters degree?

The trouble with "what you're supposed to do" is that it often applies to some imaginary archetypal student or, worse, students of a very specific class and privilege. Not all students have the means to go without working, to help pay their own way through school. Academia is just starting to wake up to this fact, thanks to the consciousness raising of folks like Sarah Kendzior.

If you can find a part-job related to your field of study, then it's definitely OK for you to work over summer break. I was able to do this while in my MLS program.

If you are unable to find work related to your field of study--and if you aren't involved in student organizations or showing that you're otherwise productive in your "non-school" hours by starting to attend conferences, write papers, etc--then I could see it being a drawback to have a job in your "off" time.


I can understand your embarrassment, but you may have to overcome it and just ask for an accommodation. A reasonable person should agree.
But many colleges and universities have some sort of office of student assistance for making such requests and passing them on. If that is available it would free you from having to discuss your situation over and over. See if that is a possibility.
And, for what it is worth, I find such requirements to be offensive. Instructors need to find a better way to evaluate students than to intrude on their homes and families. Few students have the capability of setting up a secure testing space and finding others to manage their children, etc.


Professional goals in pursuing a doctoral degree - Statement of Purpose

Your SOP as a whole should cover your professional background in terms of classes, research, former professional experience, and your goals going forward. It sounds like you're asking about the last part of this.

Yes, your goals going forward are to do a good PhD and to get a job at a start-up. Those are reasonable goals, so it's reasonable to list them.

To the extent possible, you should be specific: what kind of research, which core skills, what types of jobs, etc. Obviously you want to leave yourself enough room so that your interests can evolve, but if you can articulate a well-thought-out, realistic plan for what you're going to do with this PhD after you get it, that will put you heads-and-shoulders above most applicants, who will be focusing on the PhD as an end in itself, or haven't considered jobs other than hyper-competitive faculty positions.


Probability of acceptance when editor requests "major revisions" but one reviewer recommended "full rejection"

I have successfully revised a paper with a reject from one reviewer, through a major revision, into an accepted article. It is definitely possible. I would write your best revision and include a very strongly (but politely and professionally) constructed and worded cover letter directly addressing the reviewer's points including the fact that using blog posts as counter evidence is outside the norms of the field. If the reviewer can point to peer-reviewed academic publications that support their negative points, then that might be sufficient evidence to reject the article, but otherwise, that evidence isn't very strong.


More co-authored than solo papers in the Humanities

In the UK, up until last year, hiring for lectureships was all about the Research Excellence Framework (REF). Going forward, hiring will likely be all about the REF. We just made two hires in my department and the keys questions were what did the applicants look like for the last REF and what might they look like for the next REF.

Co-authorship in my field is the norm and for the last REF where on the authorship list you were did not matter. I am pretty sure this was true across all assessment units, but you should check with someone in your department. For REF 2014, the same paper could be returned multiple times if the authors were spread across multiple universities (and possibly even multiple units of assessment). For REF 2020, we do not know what the rules will be. Potentially, they will attempt to assign partial credit to publications or only allow a paper to be returned once, but this would be hugely messy.

If REF 2020 devalues co-authored papers in History, and by 2020 you won't have N (last time N was 4, but could be reduced for new lecturers) single authored publications, then the joint publications will be looked at unfavourably.


Should I use a pen name or pseudonym on my papers as a form of semi-anonymity?

So your question is "am I being irrational in wanting to remain somewhat anonymous on the internet?" The answer is that in the end it is your trade-off. There is benefit to keeping private and professional live separate, but I have been able to so to my satisfaction while not hiding from Google & Co. To me the effort I would have had to put into this (for me it is too late now) was not worth the benefit, but preferences differ between individuals.

When you make this decision try to get an idea of what kind of effort you will have to maintain in order to maintain your online cover and what the potential downsides are if people find it hard to find you. Also try to get a list of all the bad things that can happen if your cover is blown, i.e. what horrible things will happen if Google knows who you are. If you have those two list you can decide for yourself if the benefits outweigh the costs.


Is scientific misconduct relatively normalised in some countries or academic cultures?

To answer directly, yes, but this needs to be detailed for a complete understanding. In my opinion, there are two aspects that must be considered

Lax view on dishonesty
what counts as dishonesty

There are some countries that have a more lazed view on dishonesty, one is my home country.

Cheating in an exam is always punished (not harshly though), but rarely looked upon by colleagues. Moreover, you usually have options to retake the exam if you were caught cheating and if you pass, you're at par with everyone else. But to really understand the phenomena, you need a little bit more context.

Where I come from, I had university classes where we had to memorize full lectures and all you had to do at the exam was to write the full lecture on paper. The whole exam was pointless, you didn't learn anything anyway, so if you could bypass the exam, it would mean that you managed to save some time that nobody gives you back. I even had a senile (literally, it's sad) professor who was giving sort of random grades, barely correlated with the number of pages you wrote and the graphs you made, without even reading what you wrote. Moreover, the study material was about techniques not in use for the past 20 years at least. If you take what I just said for granted, I think everyone would reach the conclusion that studying for this class in order to pass the exam is not only pointless, but the wrong approach, since the goal is to write as much as possible and draw some pretty, barely related graphs.

By now you probably think that the university I'm talking about must be some fake/scam university in an underdeveloped country. Again, you have to trust me, and I see how I am very hard to trust, but this university is considered a respectable university in a EU country.

To conclude this point, some countries have a more relaxed view on academic dishonesty, but things still go on, because the academic is pulled by other aspects of the society that work better. For example, I went through all this classes of this university and graduated, and this granted me a diploma that allowed me to join a masters programme at a world TOP 50 university, in another EU country. So basically, the good politics were good enough to join the Bologna system and EU, which allowed this backwards university to exist in order to provide diplomas for people for which diplomas are vital for their future. Even though I had such a horrific background, I performed well on my masters, at least at par and sometimes even better than students with good backgrounds.

Now going to the second point. Not everything that would be considered academic dishonesty in western countries is considered dishonesty in other countries. For example, a failure to cite half a page of verbatim copy in a PhD thesis in a western countries would be academically fatal. Where I come from, these things get relativized to other issues that there are in the countries, and I would add, for a good reason. It's easy to see plagiarism as the worst sin ever if in your bubble it is indeed  the worst sin ever. But when one public person is accused of embezzling millions or even tens of millions of dollars, and then the accused accuses the accuser that he copied some paragraphs in his PhD thesis, it is easy to see how the public opinion doesn't care about, literally, some copied words on a piece of paper. Then these things work as examples for the public, and the conclusion is: it is fine to plagiarize, but it is not fine to steal millions of dollars from public money. Both are bad, but at scale, the first is negligible and can be approximated with "not bad".

I don't want my examples to be used as some sort of reasoning to discriminate people that come from countries with different ethical standards, because everything that someone from these countries does, because he developed different cultural ethical standards, a person from a western country can do as well, just because he doesn't hold to his cultural ethical standards.

Considering the original question, and my cultural background, I think it might be valuable for the answer of this question, my answer to the original question.

I personally consider that it is not unethical if, the person that was asked to write a recommendation letter (the professor), does not mention the incident, if he truly recommends the student for the PhD position. Moreover, I consider it unethical to include negative comments in a recommendation letter. My reasoning for this is that a recommendation letter is just that, a recommendation letter. It should only include why you recommend someone, the fact that you recommend that person is already clear from the existence of the letter. A recommendation letter is not a summary report on previous activity. The moment you include negative comments in a recommendation letter, you start being deceiving towards the person that you are recommending, by giving false hopes, and also towards the committee to which the letter is addressed, by recommending someone you do not truly believe it should be recommended.

In my opinion, if someone writes a negative recommendation letter (logically broken expression), the letter says more about the writer, than its subject.


How to obtain the h-index or number of publications for a given academic as a function of time?

Scopus has an author search option. You can then examine a range of graphs that show academic output over time. Many universities have a subscription to Scopus.

As with any citation and  publication based metrics, the values are contingent on the citations and publications included in the underlying database. Scopus is fairly broad, but there is quite a lot of quality control. So the numbers will be quite a bit smaller than for example Google Scholar. Another option might be PublishOrPerish which is a downloadable free program which uses Google Scholar as the underlying data source.

Below I show an example for Albert Bandura (one of the most highly cited psychology researchers) using Scopus.

Citations per year

Documents by year

h-index by year

I could not see any easy way to just get the h-index by year. However, the h-index tab, does allow you to filter on different years. So you could manually, change the end year and repeatedly obtain the h-index to see how it went up each year.


Is it necessary to obtain permissions for copying figures from published articles in your proposal/dissertation?

For figures from your own papers, it would depend on the copyright transfer agreement you (or the corresponding author) signed upon publication. However, all copyright agreements I know explicitly authorize reuse of content for academic theses.

As an example: the American Chemical Society, which does not leave the authors too many rights, includes this wording:

  Authors may reuse all or part of the Submitted, Accepted or Published Work in a thesis or dissertation that the Author writes and is required to submit to satisfy the criteria of degree-granting institutions. Such reuse is permitted subject to the ACS’ “Ethical Guidelines to Publication of Chemical Research"

For figures from others’ papers, a thesis is not very different from any other publication (see the related question about blogging). Unless your institution has a specific agreement with publishers (as MIT seems to have), you have to either:

ask for permission; these days, it's all done online and once you have located the appropriate form for a publisher, you can make your requests and get all the answers the next day
rely on fair use in the US, or similar law in other countries; around me, most people actually do that, either knowingly or just out of ignorance :)


Is it a bad idea not to use slides in my Ph.D. oral defense?

I have seen plenty of thesis defenses that use blackboards (the boards in our department are black- rather than white-, but I don't see that it makes a difference) and also plenty that have used slides.  You should ask around -- or remember from previous thesis defenses you have attended; these are almost always open to all interested parties -- to see whether there is any local preference between slides and writing on the board.  Ask your advisor too.

I suspect that you will find that it is up to you.  In that case: do what makes you feel comfortable.

  Is it a bad idea to use whiteboard and markers instead of slides in my Ph.D. oral defense?

No, if you know it will make you more comfortable and more able to present well, it's a good idea.

  If I use whiteboard, what if the committee have questions about the contents that I have already erased in my presentation?

I don't see any fundamental difference between a thesis defense and any other math presentation.  In general people can ask questions at any time; if the speaker indicates that she would rather address them later, then they get addressed later, in which case it's up to both the speaker and the questioner to remember the question (e.g. someone could write it down).  A question which is specifically pertinent to something complicated you wrote on the board is probably better addressed then rather than later.  If you get a later question about something that's not on the board anymore, your options are to answer the question verbally, to rewrite something on the board, or to pass out some other written materials which address it.

I will mention in passing that mathematical culture seems to prefer "chalk talks" more than general academic culture at this point.  I have absolutely never used slides / powerpoint / whatever in any class I've taught.  I do it only at large conferences where I can't be confident in advance that the board will be available and easily visible to all and/or that I've been given such a short amount of time that I feel that I have to whip through slides at top speed in order to "cover" what I want to.  Writing mathematics on the board takes time.  But so does understanding mathematics, and it feels a bit dishonest to need to present material faster than you can write it on the board.  Moreover, if you're writing then you can adapt your presentation to the audience on the fly (which for a thesis can be important, so that e.g. having a thesis defense in a room with nothing to write on at all would seem weird to me).

Good luck.

Further Thoughts: Many thesis defenses have two very distinct parts, and the first part really is a lot like a conference talk in that you have a set amount of material to "cover" and the general expectation that you will get through that "coverage" with little distraction.  So doing slides for that part of the defense makes perfectly good sense to me: a thesis defense is not a lecture, and the goal of that part of the defense is not to impart the maximal possible understanding to everyone in the room.  You want to get through that first part with little fuss, and you don't want it to drag out.  So for instance if you are the type of person that prepares much more to write on the board than turns out to be realistic (as I often am), then preparing slides could be a good strategy to stay on track.  Still, if you want to write on the board during this part of the defense: go for it.


Is paying someone to fix LaTeX issues in one's thesis ethical?

I do not see any unethical point in this.
You were supposed to make an original contribution to your thesis in terms of your research. With respect to writing, you can take help from your friends, supervisor, or anyone else (free or paid).

In our university in New Zealand, there was a dept. which used to charge a small fee to fix language issues for students with English as a second language. I suppose this should also work for the images/pictures thing as you are not an artist but an expert in your particular field.

Cutting it short, I do not see anything unethical in it.


What to do about past errors or inconsistencies in assignments I graded?

I could not follow a proper rubric to the bone.

That's not unusual.  Following a rubric is indeed difficult, even for people who have had many years of experience in teaching.  And the rubrics supplied by professors to TAs are often not very good.

Most often I'd have to make a rubric myself,

That's a good thing - you found something that helped you get your work done in a more consistent manner.

often I'd find myself grading differently towards the end of the pile as opposed to when I started grading.

This happens to everybody.  It's not desirable, and we try to find ways to avoid it, but a certain amount of inconsistency is inevitable when grading is done by humans.

Do I confess, and get terminated from my PhD

Nothing you've described sounds like cause to terminate a grad student from a PhD program.  TA performance is usually evaluated independently from academic performance, and staying in a graduate program is based on the latter.  The only exceptions I would expect would be something that went beyond poor performance into the realm of blatant dishonesty: taking bribes from students, etc.
If you were to "confess", I think the likely reaction would be something like "Well yeah, it was clear you weren't doing a very good job as a TA, and that's why we're not hiring you as a TA anymore.  So that's the end of that. Why are we still talking about this?"

is it technically possible to roll back grades like that en masse?

It would depend on your university's rules, but it's probably unlikely.  The standards for changing grades are usually if there was a clerical error (e.g. incorrect addition of scores) or "arbitrary and capricious" grading (e.g. grades that had absolutely nothing to do with the course material).  Just being somewhat inconsistent wouldn't rise to that level.  Moreover, there's usually a limited time period in which this is possible at all - after a year or so, the students' original assignments have usually been discarded and it isn't possible to regrade their work even if one wanted to.

If I think about how many students got,say, a C+ instead of a B- because of MY negligence and irresponsibility, I start feeling like the worst human being on planet earth.

So, a few students have a GPA that's 0.01 points lower than it otherwise would have been.  It's not exactly on par with mass murder.

Should I quit graduate school myself?

I certainly do not see any cause for that.

What would you do if you were in a similar situation,hypothetically?

If I found that I wasn't able to meet the standards of a job, and I didn't feel able or willing to put in the effort to get better - I would try to find a way not to have to do that job anymore.  And that's exactly what you have done, by finding a source of support that doesn't require you to work as a TA.  Again, problem solved.


Three papers came out on new technique at almost the same time. What order do I cite?

This could be a very delicate diplomatic issue. There might be three groups arguing over the paternity of the original idea. I strongly suggest citing all three.

As for the order, first of all check the journal guidelines. In my field, typically citations are numbered in alphabetical order in the bibliography; if it's the same in yours, then I suggest you to cite them ordered by their citation number (thus alphabetically), i.e., put them in the same bracketed list [a,b,c], with a<b<c.

Ordering the references like this is a good habit to adopt exactly because of these attribution issues.


Does building an app or software system count as computer science research?

What counts as research is a matter of opinion, and ultimately, up to the community of researchers who do research in that area.  It will depend on the novelty of the work, what we learn from it, and what has previously been done.  Generally, just building software usually isn't considered research if no new generalizable knowledge is created; but it can be considered research if it is aimed at developing new knowledge (e.g., evaluating a new technique for solving some problem we previously didn't know how to solve).

You are right: just building a useful app isn't normally considered research.  However, this can be tricky to tell from the outside, because developing a new technique to solve some problem can be research, and if you have a new idea that you think might solve some problem, often the way you to evaluate that idea is to implement it and see whether it does indeed lead to the claimed improvements -- which from the outside can look like you're "just" building a useful app.

So, telling research apart from engineering can sometimes be a bit tricky, especially for someone new to research.  Also, understand that this is somewhat subjective.  One person's research can be another person's "mere engineering"; the community doesn't always agree on what ought to be publishable.  Ultimately, this comes down to a judgement call, one that has to be informed by deep knowledge of the area and also by a sense of "taste" that is developed through experience.  We're unlikely to be able to answer whether a specific project of yours counts as research, because we lack that deep domain knowledge of the area, and because the description in the question is too shallow to tell.  If you're new to research, you might also have a hard time judging this.

If you're new to research, this is why you work with an advisor who is experienced in research.  Identifying useful problems to work on that are research-oriented and likely to lead to publishable results is one of the primary roles of your advisor/mentor.

Of course, if you don't know whether you can trust your advisor, and you don't know how to make those judgements yourself (because you are new to research and not an expert in that area), then you have a more basic problem.
Therefore, let me suggest a useful proxy.  Is the professor's work getting published in reputable peer-reviewed forums?  If it is, then at least that research community considers it research, which is good enough.  If it isn't, then you have reason to be wary.  Thus, with this idea, you can look at the publication record from that group over the past 3 years or so and see what their track record is.

You might also find it interesting to read a few of their past papers.  Often, published research papers try to identify what their novel research contribution is (either explicitly in the introduction, or implicitly when they discuss related work and compare to it).


Reverse-engineering results in a published research paper

Reimplementing published methods is a perfectly valid and common thing to do. Research papers should describe the utilized methods to enable other people to reperform the experiments and verify the results, so I don't see a reason not to speak publicly about what you're doing.


Using typographical variants of the same letter as mathematical symbols in a paper

Just an opinion: I think four variants of the same letter in one section is probably too much. In particular, I think (non-bolded) upright letters don’t work well for typesetting mathematics.

Also you say ”for four different variables”; this suggests that maybe you want to denote four of the same kind of thing in four different variants. (If I'm wrong, ignore the rest.) That is definitely to be avoided. As @Wrzlprmft says, the variant should reflect the kind of object you’re talking about, and related objects of different kinds should be denoted by the different variants of the same letter. The first example that comes to mind is a Lie group G and its Lie algebra  (blackletter g).

Here’s an apposite quote from Littlewood’s Miscellany, via Milne:

  It is said of Jordan's writings that if he had 4 things on the same footing (as a, b, c, d ) they would appear as a, M3', ε2, ∏"1,2.

Bad Jordan!


Is it possible for a grad school applicant to cancel a letter of recommendation once it is submitted?

It probably is not possible.  If it were possible, you should not do it because making such a request will imply the letter is negative.


Can I work on old manuscripts using personal time?

Let's address your questions one by one.

  I am wondering is it ethical to spend some time to make revision of my old manuscripts in holidays/weekends in my house without using any resources from Institute?

What you do on your free time is entirely up to you: no job, boss, or conditions, can take that away from you...

(Well, almost… as noted in comments, there can be clauses that limit your abilities to work on other projects, but I would think that the principal case in which it causes problem / conflicts of interest, is when that "side activity" is paid, which, I assume, is not your case.)

  Should I need to discuss this matter to my present supervisor or Institute?

...yet, depending on the sensibilities and particular conditions of your employment, you may want to tell your supervisor. You don't have to make it super formal, as it is rather usual for a young post-doc to have ongoing work that follows publications made during the Ph.D. Just mention that you'll be working on some revisions on your free time, and that should be fine.

If your supervisor shows interest ("Great, you should make a presentation", "Tell me more", "What are the connections with our current project?"), you can try to make fruitful connections, but that may not arise.

  Should I acknowledge my present Institute? Is it also necessary to change my affiliation?

I would think that this will depends on the country, institute, kind of supervisor, and many other aspects. Listing your former institution as the "main institute", and your current institute as your current address would probably be the safest option.


Is arXiv a good path for very young researchers?

Reading just arXiv or even some top journal is not likely to be very helpful.

It used to be that subscribing to a journal (or ten) was the best way to keep up.

But the subscription model is dead, few academics subscribe to journals, few publisher retain print as their primary mode of distribution, and open access publications tend to get 5 or 6 times as many citations as papers that require purchase or subscription.  I presume you read arXiv primarily because it is free.

I presume you are still at high school but finding that not sufficiently challenging.
I presume you have read what you school library has to offer, and need to go beyond.
I presume you have looked at what's available from your local community/university.

Been there done that... I spent my high school years doing my own physics and chemistry experiments, extracting my own reagents and building my own equipment, building electronic devices and computers, programming unbeatable AI games/programs, programs to solve problems in mathematics, joining maths clubs and winning prizes in competitions, making use of university programs designed to encourage budding scientists and mathematicians... exploring my interests in the broadest possible way!

Contact the local university and talk to people there. E.g. I'm happy to take on high school students, and indeed at Flinders University we have the Australian Science and Mathematics School (years 10-12 only) on campus to facilitate just this encouragement of gifted students - but students need to be reasonably local.  Even without a formal program or relationship, academics are happy to talk to high school students, and I've run courses and competitions for high school students, given work experience opportunities and summer scholarships (not exactly restricted to local, but focussed in the state and the surrounding regions that the university draws from).  Sometimes I've just responded to high school kids contacting me out the blue, by working out a program for them. My university actually has a bit of a history of this, with Terry Tao being the most famous example.

What kind of program would I recommend for someone like you... I'd start out by recommending some of the classic papers, introducing you to the originators of the seminal ideas of the field, making sure you had the basics first hand - not via the Chinese whispers of arXiv, review papers or textbooks.  Review papers are often written by PhD students as part of the process of organizing their ideas - it gives them a free publication before they done any significant work on their own.  It also gets them lots of citations, and some people have an h-index that is mainly about their ability to write review papers or text books.  But yes, if there was a particularly good review paper or text book, I'd recommend it - unfortunately for my research area there are no good text books I can use, although I do encourage students to dip into some of those that are around - but my research oriented courses would have at least a dozen original sources of information, and perhaps half a dozen texts or reviews. This leads to an idea from Information Retrieval... Hubs and Authorities.

You've probably heard of Brin & Page's PageRank, which became the basis of Google's ranking based on how much pages linked to each other - it is closely related to singular values/vectors, looking at relatedness of pages in a symmetric way.  But an earlier approach (Kleinberger's HITS/CLEVER) developed around the same time distinguished between the source and target of links, distinguishing hubs (sources of lots of links) and authorities (targets of lots of links) - these relate to the left and right eigenvectors.

What you need to find for your field is the hubs and authorities.  A hub might be a review paper, or a website or society that coordinates the research area.  The authorities are the people/papers that developed the seminal ideas and everyone cites.  Always go to the source, cite the earliest and latest works in their developmental path.  Look for the citations of that work (on Google and Google scholar, concentrating on relevant papers with hints like filetype:pdf and/or site:edu.* | site:edu | site:ac.* to get the papers by academics and find where the open access versions are lurking).  A relationship with a university with relevant subscriptions would also allow you free access to IEEE, Springer etc. But all major publishers now allow people to archive preprints or postprints of their papers for free access - and this is what arXiv should be used for where allowed, but sometimes this permission is restricted to authors' own websites, or their employers'.

There are two ways to explore the field - and you can start from a single of interest.  You can try to go deep and specific (citations of and by that paper).  You can also go broad and applied (citations of the citations). Modern citation analysis is closely related to PageRank/HITS/CLEVER, and your library may have tools to help.


Can I start such a contact with one researcher that does not know me in one online conference?

Conferences, including online ones, are for liaising with people and talking to them. There is nothing wrong with what you suggest. There is always the chance the professor might ignore you, not be interested or not know, but that can happen anyway.
I do not know what functionalities the conference offers, but a brief text or email asking if the professor could spare the time for a chat on X and Y seems like a good way to start. Try not to ask during the questions after a paper presentation or, generally, the proceedings of the conference, but a workshop might be an alternative. Personally, I would just text or email him.


What email to use for corresponding author on publications when institution is not permanent?

It has become quite obvious by now that most researchers are on precarious employment for an extended period of time when starting their career.

As mentioned by Michael and Mark, it is very common to find gmail email addresses in scientific publications. I believe that nobody would find that objectionable.

Tips, anyway:

Do not use party.dinosaur@gmail.com but a variation on firstname.lastname@gmail.com.
The issue of perenniality remains: GMail deletes inactive accounts after some time. Check their tools to address this issue: https://support.google.com/accounts/answer/3036546?hl=en
Self-hosted email (i.e. firstname@lastname.tld) is also subject to cancellation if you don't renew your domain/email host.
If you maintain a web presence, your email will be easily findable in the future.

As a kind of "non-requested bonus", I would advise to register an ORCID and have your paper include it (most publishers will include it by now). The ORCID is a unique permanent researcher ID, see their website. On your profile, you can have a list of all your publications and also of your web page. You can include several URLs, meaning that you can list your current institution homepage, your personal hosted homepage, your google scholar account, etc. The ORCID page will be permanent, easily findable and you can update it.

EDIT: you can also list an email (at your preference) on your ORCID profile.


Is the knowledge gained from a masters conversion course suitable for pursuing a PhD?

I am in Psychology and not CS, but what we find is that students with a three year BSc are rarely competitive for a funded PhD and most must do a MSc course first in order to be competitive. We ran a MSc conversion course last year for the first time. These students faired better than undergrads, but not as well as the students on our straight MSc course. A number have continued on to the regular MSc course with the hopes of getting a funded PhD the next year. I think you would probably need a distinction on a conversion course in order to be really competitive for a PhD. That said, you can always apply and see what happens. Some places might offer you a 1+3 type program.


How can I study PhD in business after masters in physics?

It is very possible to switch majors. If possible, try to talk with a faculty member with whom you are interested in working. If they are willing to work with you then the admissions process is likely to be fairly simple.

With that said, a PhD in business is meant to prepare you for teaching or a career in academia, not in actual business. If you want business skills for work outside of academia, an MBA is the way to go. Considering this, an admissions board / faculty member is probably most interested in your aptitude to publish. Your masters shows strong quantitative skills and so if you have any publications, that will likely go a long way in helping you get started.

All of these are very general statements, if you are really serious about a PhD then you should definitely contact schools you are interested in and see if you can talk with faculty.


Does my supervisor want me to do my Ph.D. with him or elsewhere?

As Peter said in his comment, ask him.

However, having said that, and based on what you have said, it is very clear that he is not 'kicking you out' at all - on the contrary, he is demonstrating a very positive and constructive approach - by telling you that you have to pursue what is best for you.

Having said that, you need to consider a key question:

What is/are your goal(s) after you complete your research?

The professor is, as you say not an expert in the field you are interested in, and what he is suggesting is that, as this is the case then the internship may lead to opportunities that are more in line for your plans.

He is also seemingly suggesting is to pursue the internship and then decide where and what you want to study for your PhD.

Ultimately, the decision is yours to make - he is helping you to help yourself in this regards.

But, a piece of advice, do not assume to know the intentions of anyone - take his advice on face value and in the spirit that it has been given.


Are picture-perfect acknowledgement sections the norm in Academia?

You seem be concerned that people may judge the quality of your thesis in part based on the length of the acknowledgments section.  I don't think that anyone will do that.

You may be missing a required acknowledgment of one or more grants from a funding agency.

A separate question is whether you have overlooked people who could to be acknowledged in your thesis, or whether it would be appropriate to include a more specific and detailed acknowledgment of the individuals you are acknowledging.  As the Ph.D. is the culmination not only of years of research but of years of your life, it's not unusual to think more broadly regarding acknowledgments than you would for a paper.  You may want to include, for instance:

Faculty outside of your committee or university who also mentored you or gave helpful comments and suggestions;
Anyone who developed code that you used in your thesis;
People who helped you do a better job with the writing itself, e.g. through teaching you better grammar, better Latex skills, etc.;
Family members (particularly a spouse) who have supported you during your doctoral work or inspired you to be a scholar;
Fellow students who have given you encouragement or proofread or otherwise commented on your work.

I suppose you can go too far in being inclusive, and perhaps the example you linked does, though I doubt anyone will get very upset about that either.

In my own acknowledgments I tried to be rather specific about what each of these individuals did, or how I benefitted from their help.  For instance, I acknowledged my advisor

  ...not only for providing continual support and guidance, but especially for allowing (and even enthusiastically encouraging) me to pursue research that I found fascinating but that is only indirectly related to his own research program.

Some of these kinds of acknowledgments would be considered out of place in a journal article, so the thesis gives you an opportunity that you may never get again (unless you publish a book) to express gratitude to these individuals in a somewhat official way.  You have nothing to lose by being more inclusive in expressing your gratitude, and you may make someone who reads it very happy by including them.


Applying to Social Psych Programs: How important are grades in statistics?

Social psych is my field! (Well, one of them.) It's impossible to answer how much a specific grade in advanced stats will affect your application, but you can still get into some top programs with a B- in advanced stats. FWIW, I failed an important psych class one year in college and still got into top PhD programs before I retook the class, including the one I graduated from.

Do you understand stats well enough to take a graduate-level statistics course and do the kind of research you need to do for now? If so, don't retake the course, and focus on studying for the GRE and more importantly writing a great statement of purpose. One B- is unlikely to tank your chances if you are otherwise an outstanding student.


Is it common not be able to use tenured department colleagues to write letters of support for tenure?

Your department chair is 100% correct in asking you to remove letters from faculty internal to your university.  She is doing you a favor by mentioning this to you!

To be honest, that you think this might be appropriate makes me worry that you may have insufficient familiarity with how the tenure and promotion process works at American universities.  The whole purpose of these letters is to get a sense of your academic profile in the academic community at large (i.e., outside of your institution).  A good such letter is written by someone with a lot of status in the community and a good perspective...which includes a lack of involvement in local affairs and politics.  On the one hand, it is a waste to get a letter from faculty in your department, because faculty in your department already play a much larger role in the tenure and promotion process: they evaluate your entire dossier and vote up or down.  On the other hand, if you are asked for five letters of evaluation and you choose two of them from your own department, it will likely create a very strong negative impression: it looks like no one outside of your department has ever heard of you and your work.

I don't mean to be harsh or alarming, but: you need to get a clue pretty fast.  Calling attention to the fact that internal letters are not explicitly against the rules of tenure and promotion is absolutely the worst perspective you can have on the situation: in this regard just as is usually the case in life, not everything that is a prohibitively bad idea is explicitly prohibited.  I strongly recommend that you approach a trusted mentor (for this inside your department is probably better, although you should take whatever you can get) and say something like "I realize that I have relatively little knowledge of how the promotion and tenure process actually works beyond the formal rules, which I now have reason to believe do not tell the whole story.  Can you help me out?"

Good luck.


How to get the best of the last half of a PhD?

Postdocs are typically useful for two types of things:

They build experience as a (semi)independent researcher that is now typically required before you can be considered for a faculty post
They are a chance to broaden or shift focus of your research

For example, I know somebody working in robotics whose thesis worked was entirely in simulation due to grad school circumstances, and used the "focus shift" opportunity of a postdoc to get into hardware.  So a postdoc is worth considering if you feel that your current work is too narrow to be noticed by the type of organizations you might like to join.

As for where to go next: if you aren't absolutely driven to try to do a faculty job, don't try for it.  There is a huge world of non-traditional scientific opportunities out there, which are often hard to be aware of from inside traditional academia.  Some things to consider, with a lot of strange ecological niches that you can't even be aware of until you start talking to people in them.  Do note, however, that if you aren't a US citizen or permanent resident, then many of these opportunities may be harder for you get due to visa issues.

For pursuing all of these questions, however, the big thing you need to start doing is networking.  Get to know more professors in your department than your advisor, especially any ones who have had non-traditional career paths.  Go to conferences and meet people.  Look for events in your field that are also attended by non-academic researchers (this will likely be more in computer science or material science than physics), and look for the more informal and discussion-oriented attached events like Ph.D. symposia and workshops.  If your advisor can help you get introductions, that's the best help you can possibly get, but since you're interested in a non-standard path they might not be able to.

As you meet people, be honest about your situation.  There are always a lot of people trolling for good possible hires for non-faculty positions, both in academia and out of it, and there's a word of mouth network. If you've got good core computer science skills and don't come off as needy or desperate, there are a lot more possible matches out there than you might imagine.


What is the IEEE style for a translated quotation?

IEEE is based on the Chicago Style, so whenever you do not find any guidance directly from the IEEE, it is best to consult the Chicago Style Manual. In Chapter 11 of the Chicao Style Manual, titled "Quotations and Dialogue", you can find some relevant directives. For instance:

First, make sure your audience really needs a translation from
English sources; if you audience is an academic one consisting of
researchers who perhaps publish themselves in international journals,
then I am not sure whether translations are really necessary:
'Whether to provide translations of quoted passages depends on the
linguistic abilities of the likely readers' (11.86).

Second, you can simply quote the sentence in your translated version (in the usual form you use to quote another source), but consider putting the original text into a note
(11.88): 'In many works, quotations from a foreign-language source
need appear only in translation. Should the original be necessary, it
can be placed in a note.'

Third, credit the translation to a published source of the
translation with all bibliographical details. If such a source does
not exist, then the Chicago Manual (11.89) states: 'Authors providing
their own translations should so state, in parentheses following the
translation, in a note, or in the prefatory material—for example, “My
translation” or “Unless otherwise noted, all translations are my
own.”'


Three month delay in reviewing the revision of paper, Editor doesn't even answer the email

I agree that three months seem a little excessive for checking your revisions and providing a verdict. Since you received a minor revision on your first version, there does not seem to be any point of additional review so the manuscript must be with the editors still. Since the review process seems to have passed fairly quickly, there does not seem to be a general problem of a slow journal. Therefore, there can be a very reasonable explanation for the delay.

So, the only option forward is to contact the editors again. You should also check to see if there are more than only one "point of entrance" to the editors of the journal. If there are you may try another. Also, in case you have not done so, do check your junk mail folder to see if some form mail from the journal has been redirected by mistake. This occasionally happens if journals use such systems. Unfortunately there are no other routes to go other than to repeat the attempts to contact. A reasonable period is perhaps around three weeks between contact attempts.


Does everyone who is doing a PhD has to dabble in philosophy to a certain extent?

No. This is a misinterpretation of what “Ph.D.” means. The full title of the degree is Philosophiae doctor, technically a doctor “of philosophy.” However, this does not mean "philosophy" in the modern sense, but rather someone who pursues knowledge (“lover of wisdom”—the source of "philosophy"), not necessarily someone who studies philosophy.


Too many people writing a letter of recommendation

It's ruder to waste their time. Just send a simple email saying "Thank you for agreeing to write a letter for me, however I realised I accidentally asked too many people to write letters for me for this position, so you don't need to continue writing one for me. I would still like to ask you to write a letter for me in the future, if I decide to apply to other opportunities. Is that ok with you?".

Either they will agree, in which case great, or they'll say no, and eventually you will have to find someone else. My advice would be to ask your letter writers a long way in advance of the deadline, to avoid you having to rush around asking multiple people at the last minute. You will likely get a stronger letter that way too.


How to solicit funded research projects from industry to perform while in graduate school?

How would one go about this assuming no contacts are known a priori.

Likely you can't go for this without any contacts at all. You are thinking about this in the wrong order - you can't get money from industry first and use this to build up contacts to industry; rather, you would build up contacts to industry to achieve a level of trust so that you would be later on in a position to receive industry funding. This also means that getting direct industry sponsorship as a PhD student is at least uncommon - typically, companies are more interested in sponsoring a professor or chair that they have positively interacted with over a sustained period of time.

Slightly longish story short, your planned approach (acquiring industry funding) is not a suitable means to your stated goal (landing a job in industry).


Should I wait for the editor's response to my pre-submission inquiry or should I just submit the manuscript anyways?

You wrote the editor last Friday. The time that has passed since you asked that question is a whopping 1.5-2.5 working days, depending on the exact time at which you sent your message.
This is a tiny amount of time in the calendar of many academics. Buffy is right in suggesting waiting at least a week.


What is the name of the text that might exist after the chapter heading and before the first section?

Text between the chapter title and the first section heading is usually called the "lead paragraph" or "lede". Despite the name, this can be one ore more paragraphs of text.


What should I ask deans during my interview?

You want to be friendly, of course, and make a good impression. Depending on the school, these meetings are not usually too grueling; one purpose of the meetings is just to put a face with your name. There is a good chance these meetings will end up being shorter than the scheduled time.

Be prepared to give a very brief "elevator style" summary of your work.
The deans may ask you about grant funding. You may have a good sense, depending on your field, how important grants are to you getting the position. (Andy W mentioned this in the comments).

Some particular questions I would ask include:

I would ask all three: Where do you see the program/college/university going in another 10 years?  This can help you tell whether your vision for a school fits with theirs.
I would ask the Dean of Science about tenure practices in the college. Do your homework and read the tenure policies before you arrive, of course. As long as you are polite and non-pushy, you can ask for clarifications for anything that isn't clear. You can ask about tenure rates in general, but don't ask anything that would require talking about individual candidates.  If you are in a field where grants are important, you should also be sure you know the weight given to grants when they make tenure decisions.
If you will need anything unusual (e.g. large start-up equipment costs), you should mention that to a departmental representative first, and they can advise whether it needs to be mentioned to the dean.
If you are trying to arrange a second hire for a spouse, the dean may be able to discuss that. Again, you can talk with the department first.  CAUTION: This bullet only applies to applicants who are also interested in finding a job for their spouse, and who have decided to bring up their spouse before getting an offer. There isn't room in this answer to get into the debate about whether it is preferable to wait until you have an offer to mention that your spouse is looking for a job, which is another commonly advocated strategy for applicants looking to find a job for their spouse at the same institution.


What to add to paper where another team just beat you to the novelty

It seems you have answered yourself: you found different contributions between your paper and the other one. It's up to you to decide if those differences constitute publishable material and are worth submitting or not really.

The best recipe on how to handle it is, as usual, honesty. You can simply say something like "our findings are in good agreement with recent research...", "recent research came to the same conclusion using a different model...", cite the other paper, compare both and justify why your contributions are important.

This approach is perfectly common in research. Not everything is about novelty.

The reviewers will give you feedback that will provide some clarity and help you how to proceed from there.


Is it okay to work in different lab during Summer?

Ask your advisor.

Whether it is okay or not will depend entirely on him. He may have some reason why he wouldn't want you to (rational or not). It shouldn't come across as rude if you ask him openly and express your reasoning (have to go back home but would still like to be research productive and may be a good opportunity to network with the other lab).

Whether the other lab will let you, is a different question entirely. Another option is working remotely with your current lab.


What year to use when citing second editions of books

In this case I would say Be Honest: only cite the references that you have read. Even if you have read the "rev 1", you might be (wrongly) citing as "rev 2" a sentence from "rev 1" that was removed in "rev 2"...

It might be obvious, but sloppy mistakes like that happen


What is the status/reputation of the University of South Africa (UNISA)?

I offer the following evidence from credible and official sources against doing a PhD in Computer Science at UNISA:

Low graduation rates:  17 doctoral students graduated from the College of Science, Engineering, and Techonology (which includes the PhD in Computer Science degree) in 2010, 2011, and 2012 combined. Compare this to the 99 doctoral student enrollments five years earlier in 2005, 2006, and 2007 (combined). Graduation rates are expected to be somewhat low for distance learning students, but rates this low are a bad sign. (PDF source)
Inadequate supervisory capacity: The school admits that "many [research] areas in the School of Computing have reached supervisory capacity" and says that "long waiting lists started forming due to lack of supervisors," which is another worrying sign.  (Same source)
Very, very low research output: Research output is arguably the most important indicator of a reputable PhD program. On this page, 6 professors in the School of Computing (which offers the PhD in Computer Science degree) are listed as having openings for PhD students. I looked up the Google Scholar and/or DBLP profiles of these 6 (for those that had them) and consulted personal pages of the rest to get a sense of their research productivity.

Averages across two years (2012 and 2013), the number of publications per person per year was 0.58 on average (range of 0-1.5)
Of the 7 publications I found for these professors in 2012 and 2013, 3 were in conferences or journals with the name "Africa" in the title (i.e., not international venues). So the average publication rate per person per year in non-local venues was 0.33.


How do I find a collaborator for a social science research project if I'm not in school?

There are a lot of universities in and near Boston. They all have websites and the websites usually include lists of faculty and their specialties. Find someone that way and write to them with a proposal and offer to meet with them personally at their convenience. Introduce yourself and give a bit about your ideas, but don't make it too long.

Even if they don't want to work directly with you, many would be willing to give you advice about how to proceed once they know what your interests are. The larger institutions, with grad students, may even have a way for you to work with one of them. But academics are good at giving advice if nothing else.

But, your proposal will need to be pretty compelling, since such people are pretty busy with their normal tasks. Some people will just ignore you for that reason. Keep trying.


Is there any reason to get paper reprints of your articles?

I did it initially so that I would have a nice paper copy of my paper. In principle I could hand these out to my colleagues and other people who were interested in my work.

This is rather out-dated these days. You can just send interested parties a pdf and they can read it on their iPad. Save the trees.

I don't see any reason at all to actually pay for reprints. You have a copy already, right?


Translating academic CV - translate names of papers/thesis?

Things can be different in the humanities, but English is the language of science and, in a STEM field, you can reasonably expect whoever will read your CV to be able to understand the titles of your works (if they are in English).

However, if, as a courtesy to the reader, you wish to translate the titles anyway, don't eliminate the original titles, but put the two versions side-by-side.

Your last point is more critical:

  leave the names of the university and the qualification as-is per link 1, or put in parentheses the French name equivalent of my prior qualification?

The name of the university should be absolutely left as-is, unless
the university itself does not provide an official French
translation, which I doubt (on the other side, universities from non-English speaking countries sometimes issue statements about official English translations of their names or department names).
It's not always easy to find equivalences among qualifications in different countries, and it's almost impossible for grades. Thus, if you want to provide a translation, leave the original qualifications and grades too, so that the application committee can employ their equivalence rules, if they have any.


Peer-review: Reference to unpublished work

It seems highly unethical to disclose the work of Y. If no previous literature questions f=g, I don't see your role as the reviewer to question this. Hold your horses, review this in view of past literature, and wait until the work of Y is public.


Assistant Professor at my state university, Research Scientist at my Ivy League, or both?

There is nothing against having a joint appointment. I would take both! At 20%, you gain from networking at the Ivy, and show up once a week...or even half day to attend faculty meetings or seminars. However, focus your research at the State school. In return for 20% support, you must co-list the Ivy in pubs and seminars you give. I’ve done this before, and it’s not hard. Good luck!


How to stay in connection with a professor when you want to apply for the position in his group in next quarter?

You could contact him to ask for him to advise you on some papers for you to read that are related to the work for that position. This way you have a good excuse to contact him, you gain extra points for showing interest and getting prepared in advance, and also provides you with another excuse to contact him in the future to clarify questions you may have from reading those papers.


Is it OK to ask a school about average GRE scores and other admission information?

American grad schools generally run admissions through departments rather than the central administration. Ask the graduate student advisor (usually listed in the faculty web site) -- or your cognizant POI. They may not have a data about averages, though, as GREs tend to be deprecated except as a first-round screening mechanism.


Informing your advisor that you are changing disciplines

Directly.

"I've decided to pursue a PhD in statistics."

Then after the inevitable discussion:

"Can you write me a strong letter of recommendation?"


How should we approach the authors of a paper and ask them for their data?

It's very likely the publisher doesn't have the data if it wasn't published as an online supplement to the article.

You should start by contacting the authors (typically by email but perhaps by phone if email doesn't work) and asking for the data.  In my experience, many authors will happily give you access to the data, and if they are prepared to do this, a polite request will be the quickest and easiest way to get it.  Furthermore, it's most likely the case that you will need help from the authors in understanding details of the data.  If you've worked with them in a cooperative fashion, then there's a much better chance that you'll be able to get such questions answered.

There are various reasons why the authors might not be able to share their data with you.  For example, in research projects involving human subjects research the IRB approval for the study might not allow for such a release.  Another common situation is that a company has sponsored the research and considers the data to be proprietary and the researchers are contractual obligations that do not allow them to release the data.


What can be done when my assignment's requirements has been so vague that it is jeopardising the grade that can be achieved?

I am not versed in software writing assignment but there are a few things I can think of:

Submit your work with a memo, detailing how each of the assumptions was made to the assignment components that were not clearly specified. If you're so keen, list a couple alternatives you have thought about, with pros and cons, and why you made that choice. I have seen students sometimes do that in written tests and exams, and I often considered their point of view a bit differently.
For all the communications, if you have paper trail, keep the paper trail. If not, at the very least, have a log of meeting and discussion, jot down all main points. Any conversation about this project from now on, if possible, should have a paper trail, and if it's a face-to-face meeting, follow up with an e-mail detailing the main points covered in the meeting. If all go south, having this record to demonstrate i) your due diligence to clarify, and ii) the lack of clarity among the teaching staff would help you make the case if you decided to complain or grieve.

Good luck!


Writing bachelor's thesis as a front-end developer(computer science)

You could easily extend your possibilities by learning another programming language. Since you are already familiar with the underlying concepts, it should not take too much time to learn something like C, Java, or whatever is common in your field.

I would also do this apart from your thesis. This gives you a lot of new possibilities also after your thesis in your future career.

However, I recommend you to learn a new language before you start your thesis, otherwise you might run out of time or achieve only limited results. But that depends on your personal situation and how much time you have left.


How to correctly cite ASCII (Public table)? Do I need to cite it?

The ASCII standard is set out in this document, so you should cite it directly.


How tightly enforced are open-access embargoes?

One data point:

I am a mathematician, and I have never heard of this happening to anyone.

Many mathematicians post preprints on their website and to the arXiv, and it is somewhat common for mathematicians to also post scanned copies of the published journal versions of their older papers.

Ethical judgements may vary, but I am unaware of any authors who have suffered negative practical consequences for this, or even who have been asked to remove their papers.


How can I show which data I'm using in my paper?

Both the problems you state are significant, and (I think) very problematic to the further progression of computer science as an actual science. I work in services / software engineering, and quite honestly, reproducibility of results is very, very bad in my work as well as in the work of others.

I will comment on both of your issues, starting with the second one:

  The data is either not at all available or it is not clear which version of the data was used

In many cases, this is actually the easier-to-solve issue. I would assume your department has IT resources (e.g., a department web space) that you can use for such purposes. Additionally, there are other, more field-specific, repositories that you can upload data to (for instance, there is the UCI machine learning data set repository or the Grid workload traces archive). Making data available to the public is really only an issue if you are not allowed to do so because of commercial interests of your data provider. For instance, I have access to real traces of executions of business processes of a big german logistics provider, which I am not allowed to give out. This clearly limits the usefulness of these traces to me.

The second problem

  The source code that was used to generate the results is not (publicly) available

is sort of tricky in practice. Clearly, throwing your code to Github is easy, but this hardly solves the issue of reproducibility. You will still need to include pretty detailed usage instructions and documentation to make this code of any use to another researcher. This may seem trivial for a naive 1000 Lines-of-Code implementation of an algorithm, but, for instance, my current research prototype approaches 25.000 lines of Java code plus a bit of XML and Groovy. Just putting this up on a repository is not enough, if we consider that a paper can only be considered reproducible if it is possible to do so in reasonable time. An additional problem in my field is that often prototypes are built for a specific execution environment. For instance, my department has a small OpenStack based private cloud, and many demonstrators that our students build realistically only run in this environment without drastic modifications.

I am currently in the transition between a postdoc and a more independent research position, and one of my personal goals is to make all work that I and my students publish easier to reproduce. However, so far we are only making baby steps, but at least we are trying :D


Applicants who have already begun their undergraduate education at another institution and wish to transfer into this one.


Combining a conference with a personal vacation

Yes, it is typical to take personal time before or after a conference. Funding from your university would not usually mind.

Conference funds may be a little less flexible, so you should certainly check with them. With evidence in hand it will be cheaper for them, I find it unlikely they would decline.


How many different(but overlapping) master degree can one have?

There are no regulations preventing you from having as many as you like. But admissions committees will use the fact that you have a related degree and possibly downgrade the application so that the slot can be given to someone else. That isn't guaranteed, of course.
But at a certain point one wonders why you would want to do this. Lifelong perpetual students aren't looked at especially favorably. Especially when institutions are government funded to some extent.
And, if you want to continue your education, why not consider a doctorate in a related field instead. There is little benefit (some) if your CV shows multiple masters.
An exception might be if you were interested in industry and one of the masters program was very narrow and applied to the industry sector you want to work in.


Is it OK to decline a review request after multiple resubmissions?

That's a tough situation and not one I've run into, so I can't speak from experience.  In your place I think I'd decline to review, and directly contact the editor to explain your position. (If the review request doesn't have an explanatory text box associated with it, then email the editor directly.)  Something like "The authors have been cooperative but the paper quality has remained low for multiple revisions, and at this point I have no more constructive comments to give on this paper.  Unfortunately, my time doesn't permit another review" seems fair and clear enough.


How to cite a paragraph that is copy and pasted from another source?

You open with:

  In this section, I will briefly overview the Lipsum dummy texts and full details can be found in the source [1].

This suggests you are providing a brief overview, yet you follow with (what I presume is) a verbatim quote:

  Lorem Ipsum is simply dummy text of the printing and typesetting industry. Lorem Ipsum has been the industry's standard dummy text ever since the 1500s, when an unknown printer took a galley of type and scrambled it to make a type specimen book. It has survived not only five centuries, but also the leap into electronic typesetting, remaining essentially unchanged. It was popularised in the 1960s with the release of Letraset sheets containing Lorem Ipsum passages, and more recently with desktop publishing software like Aldus PageMaker including versions of Lorem Ipsum.

I suggest revising your opening sentence (perhaps provide context and set the scene, then introduce the verbatim quote)
 and indenting the quoted text, you can use  \begin{quote}...\end{quote} if you're using LaTeX.

Comment from the OP:

  So, as I see, using proper indentation and indexing to references is enough to quote a source?

Indentation is appropriate for long quotations, such as the example you provided. For shorter quotations, you can wrap a quote inside quotation marks (and follow with a citation), e.g., "Lorem Ipsum is simply dummy text of the printing and typesetting industry" [1]. In both cases, a reference to the original source must be provided.


Will a paper published in an unrelated/other sub-discipline matter for graduate admission?

Evidence that you can complete a research paper is a definite positive.  Many good students are not cut out for original research, so this should help make you an attractive candidate.  As you suggest, it is up to you to explain how the existing work does or does not relate to your intended research program as a graduate student.

NB: I am in the social sciences.


Reference to the unpublished lecture notes

In APA (6th) citation style, it would look like this:

Kanazawa, M. (2012). Context-free tree grammars. Lecture, Place/University. Retrieved 4 May 2017, from https://pdfs.semanticscholar.org/95a3/cb63b80c3416879d534f41eedcd174b40159.pdf

The Place/University should be corrected. Could be SemanticScholar.

Nevertheless, I'd check (before citing this lecture note) whether the information you want to cite is included in one of the given references.

Note: Since the desired citation style is not clear, I used APA as default. I can change the citation style, if the desired one is added to the question.