Can I say no when my principal investigator asks me to help cover lectures next semester?

I don't think a flat "no" would go over very well.  Covering classes is something that colleagues are expected to do for one another, within reason.  Yes, everyone has their own projects that this takes time away from.  But it's really the only way that faculty are able to travel during the school term, which most find essential to keeping an active research program.  Saying "I don't want to do any lecturing" will come across as unreasonable and possibly selfish.  Keep in mind that "focusing solely on research" is a luxury that basically nobody ever has.

However, you can certainly negotiate, and maybe reduce the amount, while still showing that you're willing to help.  Keep in mind that the PI presumably has an interest in your research success, so if the teaching would impact this in specific negative ways, beyond a generic "this is an hour of my time that I could be spending on research", you can point this out and suggest a compromise.

"I'm happy to help out, but seven classes over the semester is kind of a lot.  I am going to need to [achieve specific research goals] next semester and I think this might start to get in the way.  Maybe you can find another person who can cover some of them, and we'll split them up?"
"I can do January 18, but on March 7 there is a conference that I was really hoping to attend.  Perhaps someone else could cover that date?"
"February 10 would be fine.  April 3 is the week before [important deadline] and it might be kind of a crunch, so maybe someone else could teach on that day."

You can also ask for materials or other help that will lessen the amount of work for you.

"Sure, I can teach on January 30.  Can you point out the specific sections in the book that I should cover?  Will you be preparing notes for me to follow, or do you have notes from a previous semester?  Can you suggest any particular examples that I should present?  [etc...]"

With such assistance, covering a lecture should not end up taking an excessive amount of time away from your research.  You really should only need to prepare and deliver the lecture - you likely won't have to deal with creating assignments, grading exams, supervising TAs, holding office hours, answering emails from students, or the other things that end up taking the majority of time when teaching.


Why is the prospect of external funding driving hiring?

I agree that there is more pressure nowadays to get funding in areas like pure math in which it's valuable but not mandatory for doing great work.  It's still entirely possible to make an argument along the lines of "Sure, Alice doesn't get much funding, but look how wonderful her papers are," but it's slowly getting harder.

The short answer as to why this is happening is World War II plus inertia.  Here's a longer answer:

The first thing to keep in mind is that grant funding is on average genuinely good for universities, because the overhead rate paid to the university is often higher than any extra costs imposed on the university.  All other things being equal, it makes sense to prefer to hire faculty who can get funding, because they are subsidizing the infrastructure for everyone else (e.g., libraries and internet access).  Of course, all other things are rarely truly equal, and I wouldn't advocate for giving grant funding much weight, but there's a reasonable argument for giving it nonzero weight.

There's also a temptation to use funding as a simple numerical measure of popularity.  Universities should serve the public, and it's clear that people are much more eager to fund work in some topics than others.  It's not crazy to take that into account in university decisions.  However, if taken too far I feel it's an abdication of our responsibility for intellectual leadership.

But why do these things seem to be changing in recent decades?  Universities are generally conservative and slow to change, so it's always worth looking for an explanation of any movement, and in this case I think it's World War II.

Most funding agencies were set up in the aftermath of the war (e.g., the U.S. National Science Foundation dates back to 1950), and the whole tradition of large-scale government funding of research didn't even exist until then.  How academic leaders reacted to it was based on their personal history, and academic inertia meant the changes were slow in coming.  Some of the effects are still surfacing now.

Let's divide things up into academic generations since World War II, giving each generation a twenty year time span to displace the previous one.  Here are my impressions of what happened for cheap or theoretical areas in which funding is not essential to do good work (I'm sure things were very different in big science):

The senior faculty of Generation 1 (1945-1965) were strongly influenced by pre-war traditions.  They had never dreamt of making hiring decisions based on external funding and weren't about to start doing so now.  They were suspicious of how wisely the funding would be allocated, and they saw no reason to think these agencies were even going to continue indefinitely in their present form.
Those in Generation 2 (1965-1985) had still been brought up to be skeptical of paying more attention to funding track records than necessary.  However, they were getting more comfortable with the funding agencies and starting to wonder about how grants could or should be taken into account.  I believe this is the point at which listing grant funding on your CV became mainstream in pure mathematics.
The senior faculty in Generation 3 (1985-2005) went further and began taking funding information into account in ways that would have scandalized Generation 1.  If you didn't list grants on your CV, the dean might now complain about it.  But there was still a sense that this was somehow shallow and historically new.
Generation 4 seems to be taking the trend still further and normalizing it.

Of course this is all vastly oversimplified, and no serious history can be conveyed in a few paragraph-long sketches (even if I were an expert).  However, the key phenomenon is real: the funding landscape was revolutionized after World War II, and academic traditions have slowly been adapting to this fact.


Is a newspaper/magazine editor considered an author or an editor in terms of referencing?

Usually, magazine and news articles include the author name at the beginning or the end of the article, or at least some short form like an abbreviation that denotes the relevant author that you could look up. This is the person you ought to refer to as 'author'.

If you're not sure about the author, it would be better denote the editor as the 'editor' not as an author. It would be best to contact the editor to know the identity of the author if possible. But this would not always apply since a few authors prefer anonymity in certain articles.


What questions to prepare for PhD defense?

Generally speaking, PhD defenses come in two flavors, and it is not possible to say a priori which one yours will fall into:

A real thesis "defense" focuses on the thesis, and all questions will relate to the scope of the research work. In this case, knowing your own work and its context well enough should be sufficient, but it is of course possible that somebody asks you why you used method A rather than B. In this case, saying that you don't know B may not fly as an answer. However, you should not get a completely disconnected question just to test your general subject area knowledge.
A "Rigorosum" (dict.leo translated this for me to "doctoral viva", no idea if this is a well-known term) is a general final exam for a doctoral candidate. Typically, this will also include questions about the disseration, but anybody in the exam commission is free to ask about other topics in the field as well. Typically, the questions are getting "easier" (more high-level) the farther they are away from the topic of the dissertation. The claim here is that a fresh PhD should have both, depth and breadth in her/his knowledge.

There are a number of ways to figure out which class your defense will fall into:

Attend other defenses. Typically, PhD defenses are public, and it is highly recommended that any PhD candidate should visit a few before her/his own, to get to know the procedure and get a feel for what the defense talk is supposed to look like.
Ask your advisor. The advisor should obviously know what the requirements of the defense are, exactly.
Look it up in the programme description. Usually, the programme description will contain exam regulations for the defense, and this should describe the exam procedure and who is supposed to ask what kind of questions. This approach has two dangers: (1) you may misunderstand what the exam regulations are saying - as they are more legalese text, you may misunderstand the gist of it, and (2) the actual exam may happen differently than specified - there is no telling whether the exam regulation exactly captures the real spirit of the defense. Hence, you should really also talk to your advisor and/or attend other defenses as well.


Faculty interview: 15 min. PPT explaining Teaching philosophy and Research Vision

On the first point, there are some questions you should consider.

how do you lead students to have insights? Through in-class activities, assignments, projects, reading, essays, test taking? How much emphasis is placed on each aspect?
are your assignments/projects/tests creative? Or merely regurgitation of the material?
how do you account for the (expected) differences in learning style? Do you adapt your style to fit theirs?
how much work outside of class is expected?
how do you detect and respond to plagiarism?
how do you deal with disruptive students?

Regarding research, what is the reputation of the school? of the department?

What is their faculty known for? Theory vs lab vs simulation-based?
Can you find collaborators? (on campus and elsewhere)
Do you have collaborators outside of academia (National Labs, industry)?
How much money do you need?
Do you have special requirements?
How much staffing is required?
Can you use undergrads or grads or postdocs in your research?


Posting a (non-original research) Masters thesis on arXiv?

In my field (cosmology), plenty of researchers and professors post lecture notes on arXiv, and of course many people write and publish review articles which don't contain any new results. So there's no requirement of novelty to post on arXiv.
Whether it looks immature largely depends on the quality of your writing. A poorly written review will not be read, and could reflect badly on you if you continue in academia (employers and grant reviewers will look at your Inspire and/or ADS profile). Bear in mind that you can't remove things from arXiv.
I would highly recommend asking your supervisor about this. They are best placed to tell you whether it's appropriate or not, according to the quality of your work and the conventions in your field. If you don't post on arXiv, you could consider uploading the pdf to your own website, a public github repository, google drive or similar. Then you can still share the link with interested people.


How to proceed when a professor is not answering emails requesting for a grade? and not awarding bonus points as he said?

Yes, contact the ombudsperson, student office or office of graduate studies about this. If several of you do so then it’ll probably make the department push the Professor to do their job. Professors often see their teaching duties as secondary but this seems particularly egregious.

Hope it gets straightened out. I had a professor who failed to submit grades for nearly a year, eventually the entire class got an A- blanket grade which was infuriating.


My supervisor spells my name incorrectly

Mis-citing articles (and worse, removing authors) is one of those crimes that academics take very seriously (and no one else really understands). If you were a collaborator, then repeated behavior of this kind would get your advisor in trouble not just with you, but with editors at the journals, reviewers, and so on.

So you really should bring it up.

How do you go about doing it ? Because it's your advisor, you have to be a little more gentle: some options:

keeping it specific to each mis-cite: "I noticed you cited my work, but you omitted my name: can you please fix it". It sounds like you've been doing this already though.
the technical solution: "Here's a BibTeX file containing all my papers: you can use that for citing" - this works only if your advisor uses some kind of citation manager to cite papers.
the direct solution: "I noticed that in this, this and this paper, you omitted my name from the citation. I'd really appreciate it if you could contact the editors and submit a correction: I'd like to get credit for my work".

In other words, keep the discussion focused on outcomes and actions, rather than intent (because a) it's hard to argue intent, and b) you're in a position of weakness)


What should I do with a master student's online report that made my work look like his?

Ignore it. There are lots of bad papers out there that will never be noticed and/or cited -- and given the title, everyone who happens to come across it will realize that the original source is your paper.

Spare your worries for the important questions in life, for example on writing the follow-up paper that clearly explains why the original paper you wrote is so important!


Does working in a project without being a first author of any of its papers help my career path in academia

Yes, it helps, but first-author publications help more. Find a way to leverage your work on this project towards a first-author publication, talk to your advisor about switching projects, or find a new advisor.


I am not sure how you are using the term unemployed. Clearly someone with a paid academic position (e.g., adjunct teaching or lab tech) would not be considered unemployed. I am not sure if you consider an unpaid lab tech or a paid burger flipper as being employed. To me the real issue is being out of the field.

If you cannot get a relevant paid position and but can afford to be without income for a few months, then a year gap, and probably longer, isn't problematic. In fact many labs will hire unpaid researchers. In this case you could continue to conduct new research, publish, apply for grants, and gain new contacts. You could likely stay in an unpaid position as long as you could afford it without any affects on future job prospects. If you cannot get an unpaid research position then it really depends on how long you can milk publications from your past research and produce new research without any affiliation to a research group.

If you cannot get a relevant paid position and cannot afford to be without income for a few months you can sometimes find paid work in a related field. Working as a paid lab tech (e.g., washing test tubes) or adjunct teaching. These types of jobs won't help you publish more or get grants and in fact take time away from publishing, research, and getting grants. That said they can provide a limited set of new skills and cotnacts so are probably sustainable for a year or so.

In the absence of getting even a peripherally related job taking an unrelated job (e.g., burger flipper) even for a short period (i.e., months) gap can be problematic. Not only will it slow down publishing, research, and grants it may make you less flexible about being able to take up a new related position (e.g., how much notice would you have to give). You are also not building new skills or contacts.

A lot of the impact will depend on how important publication speed is in your field. If a few month delay in publishing will result in you being scooped, any gap is probably bad. Similarly the ability to do research without any resources will help you weather a gap. Similarly, if your field has new instigator grants with a clock that starts ticking upon graduation then gaps are bad.


If it is between 2 possible courses, its better to check what is different and what is the same, then join what it is the same and if there are not that many differences then add them all in the same course, if there are many, then you can either give one course with extra set of classes for each course (which is a bit of an administrative nightmare), or you can give 2 courses with shared classes of those that are the same.

As an example, in my university there are 2 extremely similar careers. 1 in the Licencee in Informatic sciences, and the other is the Licencee in Enginery of Informatic sciences. They are basically the same in most courses with same professors teaching in both, however, the first one has administration courses and the second has instead physics and chemistry. The other difference is that one has 1 semester of probability and another of statistics, and the other has both probability and statistics on the same semester. Who decides this? the direction of the school and the heads of careers/departments. they revise and update curriculum plans and then send them for approval/registration to the national education department, which might not be needed in your case.

My suggestion regarding the courses is in sum to check what is different between the proposed courses and see if it's worth A)to make them separate, B)Mash them together into 1 course, or C) Make 1 course with 'optional' extra classes needed for the student to Attain the credits to the different subjects.

Who needs to be consulted? All your stake-holders, meaning all the professors, chairs and  such that would participate in the definition of the curricula.


Getting into a PhD program with a low gpa but good profile

Given your other accomplishments I don't think the GPA will be disqualifying, and normally I would say don't worry about it, but in your case it's more of an issue. Your accomplishments are exceptionally strong for a rising senior in microbiology and are out of line with your weaker GPA, which will raise the obvious red flag that either your CV or your application are fraudulent.
You should address this in your applications. Specifically detailing your role in your major accomplishments and when you did the work would be a good way to head off any concerns from an admissions committee. You should also try to have your letters of recommendation be as specific as possible about exactly what you have contributed to the respective publications, which is another good way of keeping admissions from worrying too much.
I would also discourage you from applying to MS programs - most in microbiology are unfunded now and applying to a program you cant afford is pointless.


Doing a masters degree level research without following a Master Course

I don't know that there's going to be a single book that describes what you want, however, I'm going to make some suggestions which may help you on your way. I'm a little biased towards CS and research-heavy MSc, so I think I can be of some help here.

Topic

A master's degree typically is going to consist of two phases: One of breadth: where you try to find what you're interested in enough to specialize, and one of depth: Where you start to push towards the edge of human knowledge on that subject.

If you're already reading papers, then you should be finding the kind of papers that hold your interest the most, those which have you tracking down their references.

Once you've already got a topic, start to find the papers from the best conferences and journals (in CS, good conferences are often as good or better than Journal papers) in the area. Creative use of Google can often track down full-text even of papers which are officially 'paywalled'.

The goal of your reading here is to identify a gap in the understanding. This might be as simple as working on comparative evaluations of techniques, or as complicated as trying to create a new technique for yourself. What you'd like to do is answer a question the community is interested in.

Background

While you're doing your reading and trying to find your topic or get up to speed on the state-of-the-art, you should also be building up your background. There's always room to grow your background to support research. In CS, there are certain foundational topics which are (almost) always going to pay dividends when doing research: Algorithms and algorithmic analysis, statistics and probability, and utility programming (Data munging, shell-scriptng, etc.).

As you get further into a specialization you'll notice more techniques being deployed which will require more background --- i.e. your specialization might require more calculus than you know, which then will involve learning the calculus required.

Research

I know you asked for a methodology, but in my experience, research is a process of creativity and perseverance. At the highest of levels, you're going to come up with an idea, work on it, and find out it doesn't work. Rinse and repeat until you find out something that works --- in a special case. If the special case is interesting or common, you might be able to publish it! Otherwise, you'll work on generalizing the idea until you can.

Communication

To be recognized as a member of the research community, eventually you'll have to publish. This means learning to write.

I'd suggest learning to write informally first -- Start a blog, and document your learning. If you're not a native English speaker, use this time to practice writing in English. Get everyone and anyone you can to read your blog, and tear it apart on style, grammar, content, concision.

After your confident in informal English, start to transition into Academic writing. Read good papers. Take notes on what makes them good in your mind. Read about writing good papers. Write papers. Take previous projects, and start writing them up like you would submit them. As you write, you'll find the holes and flaws. Finish it anyhow, then sit down, and edit them: Why wouldn't they be accepted. Keep doing this! As far as format and outline, it's going to vary from field to field, and even venue to venue to some extent.

A Caveat:

This is going to be a very difficult process to do alone, with little guidance. Ideally you'll seek out and find a mentor. This might involve actually signing up with a school for a Master's program.

Most of the pieces I wrote about above will be an order of magnitude easier with an academic guide.


Why are recommendation letters highly relied upon?

In a typical example, if someone has three socially close friends (including current colleagues, coworkers, past professors), then, his applications are always supported by strong recommendation letters.

No, that's not what "strong recommendation letter" means.

First, strong recommendation letters do not simply state the author's high personal regard for the student, but provide specific, personal, and credible detail supporting the applicant's potential for excellence.  I don't just want to know that someone thinks you'll succeed—I assume they wouldn't write you a letter if they thought otherwise.  I want to know why.  I want compelling evidence, not mere opinion.

Second, recommendation letters have more weight if they come from credible sources.  At a minimum, the author should work at a credible academic institution.  The best letter writers are themselves experienced, visible, active researchers, with documented experience mentoring and/or selecting candidates for admission/hiring/promotion at departments similar to the candidate's target.  For faculty promotion in my department, letters are essentially required to be from full professors, preferably in named/endowed positions, in top-10 computer science departments, and there is a strong preference for ACM/IEEE Fellows, NAE or NAS members, and major award winners (Turing, Gödel, Dijkstra, Gordon Bell, etc.).

The intersection of these two aspects of strong letters is direct comparisons with the applicant's peers.  An ideal PhD recommendation letter for my department includes sentences like "Among the 13 undergraduates I have mentored who went on to top-10 PhD programs in computer science, I would rank [applicant] roughly 3rd, well below [famous person who proved P=NP], but on par with [successful person] at MIT, [successful person] at Stanford, and [successful person] at CMU."


Is it a good idea to connect data points on a plot to increase readability in slides?

Drawing the lines implies a continuous relationship between the parameters. So if you can expect continuity, then connecting the points is fine. A second point to make is to avoid colours that are as similar as the green and blue you have chosen. One reason the difference is hard to see in the first scatter plot is due to colour. Try to experiment with colours that contrast better and your problem may be solved by just altering colours for one or both of the data sets.


Received a book review request, how to know if publisher is credible?

Why do you care? Let them send you the book, if you are at all interested in the topic. (Free books! Yay!)

Then review it. If the book is obviously crap, then stop reading after page 15, write up how far you got and why you stopped reading, and submit the review. You may not get any more requests for reviewing from that particular publisher after that, but a one-paragraph review that warns people off a bad book is certainly helpful. And the entire process won't cost you more than half an hour.

And if the book is good, you can spend more time on it, write a thoughtful review and got a Free Book out of it.

EDIT: on second, third or more-th glance, I do see a way in which reviewing for a shady publisher can hurt you. Suppose an author plagiarizes a large amount of text for his book - but you don't notice (maybe because you are not familiar with the text that was plagiarized) and write a good review. Once this becomes known, of course people will wonder why you did not notice.

This really presupposes that something like this could more easily happen with a shady publisher, an assumption which may be open to question itself. I'd rather wonder about the author than the publisher here.

So I'd recommend something like this: google the author. Check his publications. Does he have a track record in the field? I'd be suspicious if someone with no scientific footprint suddenly were to write a book.

Check the publisher. What else have they published? Go by the publisher's website and by Amazon, especially if you don't trust them to be honest on the website. How are the reviews of their other books on Amazon? If you google their books' titles with "site:edu", does any educational institution set them as textbooks?

Finally, if the author has a website but does not mention the book you are supposed to review and the publisher looks extremely fishy to you, write him an email and ask about the book. It may be that an unethical publisher put his name on a plagiarized book that he never saw (however, I don't think that this is likely).


What can I do about newspaper with poor referencing?

Given that most newspapers don't have their own "on-staff" technical writers to handle such articles, I doubt that writing a newspaper and pleading with them to include more information about the publication will be very helpful. More importantly, providing large amounts of technical detail is frankly not what a newspaper is meant for. The best you could reasonably expect is that the web page for the article might include a link to the journal page. But you should probably not expect full details of the publication on the web page itself.

For sites and publications like Ars Technica, the situation is different, since they're much more science-oriented. Then it would be reasonable to politely email the author of the article you're interested and request that the additional information be added.


Does high school success in Math have a correlation with Undergrad success in Mathematics?

You are who you are. Don't be overly concerned about others. You will need to work very hard, of course, but the fact that others may be able to pick things up more quickly than you doesn't mean that you can't excel.

The fact that you were admitted suggests that others have faith in you. Have faith in yourself.

You can also try to find a study group with others at the new place so that you get additional exposure. Use good study techniques and never - never fall behind. Start early on assignments. Ask a lot of questions. I was once thought to be very smart because I asked a lot of questions in class. But in reality I just wanted answers that weren't apparent to me.

You might also try as much as possible to limit outside interests until you find your way in a new environment. However, agreeing with a comment by user aeismail, that doesn't mean to give up everything for academics. Spend several hours each week on something that contributes to your health, reduces stress, and engages your mind in a different way. I now use Taichi which does all of these things. As an undergraduate I practiced Judo several hours a week. I didn't get very good at it, but it was a great complement to studying. As a grad student I rode a bicycle with a local club - fast but not competitive. That was physically satisfying, but didn't have a mental element like Taichi does. But don't occupy yourself with trivia.

But yes, studying great books in advance ain't gonna hurt you any. I studied out of Rudin over 50 years ago and still have the book(s).

You might also find that some courses are more challenging than others Analysis v Algebra for example. That is natural as the core thinking processes and insights are just different enough that you can groove on some things and find others a bit more work. Put your best efforts where they do the most good.

Talk to your professors. Ask questions. Listen. Ask more questions. Correlation only matters for groups. You are who you are.

Why you ask questions:

Here is a story (real occurrence) from the University of Kansas about 50 or so years ago. A prof, quite well known and respected, was lecturing in Topology. This meant writing proofs on the board. Occasionally a step wouldn't be filled in with the statement "Of course it follows, trivially, that ...". On one such statement, a student didn't see the obvious connection and so asked. The prof looked at the board and the developing proof for a few minutes. Then walked over to the corner of the (chalk) board and started making notes to himself in a tiny script. He went into totally abstract thinking mode, ignoring the class. After a bit of writing and erasing, etc, he wandered out of the room toward his office. The students followed along, gathering outside the office. The prof started pulling books off of his shelf and consulting them - several books - several more minutes.

Then he seemed to find enlightenment and returned to the classroom. When everyone was again seated he announced. "Yes, of course. It's trivial."


Is it common for research disciplines to have a large gap between theory and practice?

Significant splits between theory and practice, such as you are describing, are not at all unusual.  What many people fail to recognize is that research spanning between theory and practice is effectively interdisciplinary research!

Moreover, what you call "theory" others may call "applied" and vice versa.  I have noticed that whether I feel like the "theory person" or the "applied person" in the room depends strongly on which community I am participating in at the time. In fact, what you are experiencing is only a small part of the theory/application spectrum.  Many funding organizations attempt to quantify the theory/application spectrum with some sort of technology readiness level rubric, and you are almost certainly experiencing only TRL 1-3 communities, as that is where almost all academic research lives.

Why this matters, and why there is a gap in communication between communities, is that the problems encountered and solutions required at different TRLs are often fundamentally different.  At one end of the spectrum is: "Might this be plausible?" and at the other end is "How much does it cost to get one shipped to me by Tuesday?"  All of the questions on this spectrum can be valuable, even if some seem "farfetched" and others "boring" to you based on where you personally happen to be sitting on the spectrum right now.

Spanning different levels is difficult, and to do so you will need to figure out how to speak the languages of the different communities.  If you are able to do so, however, it can be of great value both to your career and to the larger communities in which you live.


How can I get a paper if our library is not subscribed to the journal?

My university has an inter library loan system where I've been able to submit requests for copies of an article. It requires entering citation information about the article and I have seen requests returned in a week or so. Sometimes the requests are digital, sometimes they are physical.


Does a lecturer need to cite their teaching material?

As with writing, anything presented in a class without citation should be either the work of the presenter or common knowledge.  Your teachers are supposedly experts in the fields they teach, and so should have amassed quite a lot of the common knowledge in their fields.  For example, I'd happily describe the Bell-LaPadula model and its applications, mentioning Bell and LaPadula by naming the model, but without further citation.
For those courses I taught that had a textbook, I organized classes around the textbook, but certainly presented material not contained therein, often without citation, because, as Buffy has written in another answer, "It is known, even if not known to you and the other students."
If I had used only the textbook publisher's slides, I'd have felt I was cheating my students.  If a student had asked me the source of material in the lectures but not in the textbook, I'd have said, "Right out of my head unless specifically cited."  I expect your professor might answer the same way.
If the textbook were sufficient, professors could announce it on the first class, then say, "I'll see you in three months for the final exam."  The role of the professor is to explain, elaborate, and expand.  The latter two necessarily go beyond the content of the textbook.
With all of that said, I'm not sure I understand the goal of your question.  Do you believe there's a "secret source" that's somehow being hidden from you?  I doubt it.  More likely, there are many sources, accreted over years of study by the professor.
If you're looking for material to supplement the textbook, ask.  Professors want you to learn and if there are accessible supplemental resources, they should tell students about them.


Getting a letter of recommendation when the referee gave no indication about the strength of the letter

Two things.

First, he is demonstrating strong willingness to write a letter for you. Although you can't know for sure without asking directly, this is a good indication that his letter will be strong.

Second, ASK! In this situation, don't be afraid to ask him bluntly, as ff524 recommended.

Finally, in future, you can avoid some of this uncertainty by phrasing your request this way: "Are you willing to write a strong letter of recommendation for X application?" In this way you are asking not just for a letter, but for a strong letter, and their response will be more indicative of the strength of their letter.

And for this one, all indications point toward it being a risk worth taking. Best of luck on your application!


Disappointed about workshop, are all like that?

I understand your frustration, but workshops are not for seminal research. It is usually for hosting / presenting papers that cannot make it to major conferences or provide a venue for very small and specialized areas of research. This is not a bad thing. Especially in CS, papers that are technically correct and well-written sometimes get rejected in major conferences, due to the high rejection rates. In this cases, workshops provide a alternative venue to patent those results and lower the authors' sense of rejection.

Also, many research projects (in EU but maybe this applies to USA as well) have the obligation to organize workshops during the duration of the project. In those cases, it is normal that most of the submissions are from project partners. This explains the little "inbreeding" you encountered. Also, since each workshop has a minimal number of papers that should be presented, in cases of low number of submissions, it is inevitable that some less-good papers get accepted. Also, although peer review is still formal (and not blind to bad papers depending on their authors, as you imply) on those workshops, the requirements for presentation are less strict than major conferences and marginal papers might actually make it.

Are all workshops bad? No they are not. It is actually easy to tell them apart (most of the cases).

Are they co-hosted with major conferences
Do they take place for many years
Who are the PC chairs (this year and previous years)
How good are the papers that got accepted in the previous years?

All these four criteria are a strong indication of the quality of the workshop.

A general advice. Many researchers (not excluding myself) tend to overvalue their research in comparison to others. Since your paper also got rejected for the major conference, that also implies that it was not that seminal or exceptional (which is of course OK). To someone else's eyes the comments you make about the "other" papers might also apply to yours as well. So, talking about lame papers and workshops (especially if you express those ideas publicly) will not make you a lot of friends and academia is really a very small world.


What post PhD path alternatives are there?

Selling out?  Hardly!

I am a researcher in industry, and I love it. I get to work on important problems and my work is expected to translate into real products in roughly 5-10 years.

While working on my PhD, I felt that the academic mindset was overwhelming. I have never had any intention of doing anything but research in industry, but I was certainly in the minority.

Some of my reasons for choosing my career path were/are:

Many people in academia seem to be overly focused on publishing, even before they can make reasonable and meaningful conclusions (which can contribute to a mass of conflicting literature). To me, conferences are for discussing interesting work, but publishing is for disseminating conclusions (& supporting data) that can have a meaningful impact on a field of knowledge. In industry, I have to write up reports all the time, but only the important stuff gets published.
I am a scientist, which is just the modern term for a "natural philosopher." I take my role as a philosopher very seriously, but as much as I love knowledge, I believe it is irresponsible to use other people's money to pursue research that is unlikely to benefit those people in a timely manner. Pure research is a hobby; Applied research is a job. In industry, I am free to pursue pure research when I have spare time, but I get paid to work on real problems.
In an academic setting, it is far too easy to pursue research in a very narrow field in which everybody knows everyone else. No thanks! I love that my job forces me to work outside my comfort zone, with a wide variety of people that I would never interact with in an academic setting. I have grown personally and professionally from these interactions.
Working for a company, I am usually guaranteed funding for something... but not necessarily things I think are important or interesting. As with any funding agency, I have to propose research projects that the company is willing to pay for. I have some early-stage projects that require minimal funding, but also others that require huge investments and therefore must offer much in return. However, I can also apply for funding through both private and government agencies. We often do this when we want to pursue a new area of research and/or collaborate with other organizations.  (Note that we also fund grants for others too, so some of my work involves reviewing those proposals.)

Granted, very few people can actually get a job doing research in industry. It is highly competitive, and you often need far more than just a PhD. I worked in industry for 2 years before starting my PhD, but internships can also be great experience.  (Unfortunately, most PhD programs frown on internships or other outside jobs... which is very disappointing!)  Of course, networking also helps.  I have found that most research jobs are not advertised, so you have to actually talk to people.  In my case, I asked the VP of research for some career advice and ended up with a job offer.

I hope this helps.  Doing research in industry is very different in some ways, but similar in others.


Do's and don'ts when writing an academic book

There are many books and online resources on mathematical writing.  These range from style guides that deal with issues from type setting to copy editing to books that talk about mathematical writing at a somewhat higher level.   Here are a few of my favorite sources:

Nicholas J. Higham.  Handbook of Writing for the Mathematical Sciences.  SIAM 1998.  http://www.worldcat.org/title/handbook-of-writing-for-the-mathematical-sciences/oclc/697886419

Steven G. Krantz.  A primer of mathematical writing : being a disquisition on having your ideas recorded, typeset, published, read, and appreciated.  American Mathematical Society, 1997.   http://www.worldcat.org/title/primer-of-mathematical-writing-being-a-disquisition-on-having-your-ideas-recorded-typeset-published-read-and-appreciated/oclc/797735421

SIAM Style Manual for Journals and Books.  http://www.siam.org/journals/pdf/stylemanual.pdf


Should a research presentation make use of suspense to engage the audience?

I believe that using suspense in a talk is a terrible idea on any but the shortest rhetorical time scales.

The reason is that, at any given time, a significant fraction of your audience will not be paying attention.  It doesn't matter whether they're twiddling with their phone or just thinking about what you said two slides ago: the point is, it's terribly easy for people to miss bits of a talk.  As a result, if you build your talk as a suspenseful mystery where somebody has to be paying attention at the right times, then you'll probably fail to convey key information to a significant fraction of your audience.

Now, there's nothing wrong with using it in the short range as a bit of rhetorical flourish, e.g., "And what did we find? The wires were covered with purple spots!"  Once you start putting long-range dependencies in your talk, however, you're gambling with attention.  Likewise, even without putting in a dependency, if you say your key idea only once in your talk, you're decreasing the number of people who will hear and remember it, compared to if you say it in "preview" and again when you get to it in detail.

In short: don't hide information from your audience.  There's plenty of other, more effective ways to make a scientific presentation interesting.


Do degrees from the ETH of Zurich value the same as 'normal degrees'?

are candidates with a Msc ETH or Dr. sc. ETH considered too?

Of course, yes.

The reason for the presence of the ETH qualifier is well explained in this answer, and the (possible legal) validity of a certain degree can be established regardless of any qualifier attached to the degree.

Moreover, if you look at the position of ETH Zurich in international rankings, you will see that it can be certainly classified among the top universities. Whatever one can say about the real validity of such rankings, a university would probably not be able to stand in top positions if its graduates were systematically ignored in other university selections. And if this were the case just for the presence of the ETH qualifier, I'm sure they would have already removed it.

  do they think that Bsc ETH = Bsc?

Given the prestige of the ETH Zurich, I'm sure that several if not many selection committees would think Bsc ETH > Bsc.


Is it okay for professors to completely copy another professors' notes, assignments, and exam questions word for word from another university?

If 1st professor published his/her notes and question with a license which allows that, it's almost ok.  If 1st professor published questions without anything which looks like a license, the 2nd professor should ask permission.

The main pros of using notes and questions made by somebody  - optimization of work. Why should anybody invent a bicycle if we can get already invented bicycle and use it?


Teaching load in New Zealand research universities

The standard load will generally be around 3 courses per year or equivalent, with 2-3 hours of delivered lectures per week per course. It is common to teach only subparts of courses and distribute the load over the year in that way. Usually there is a notional "student workload" by university policy for a course worth a given number of points, and working backwards from there determines the notional staff workload, but there can be some flexibility in structuring a course within that. The number of points per course can differ between departments.

Terms are generally twelve weeks long for the two main semesters, with the summer programmes and often summer courses themselves having idiosyncratic layouts (particularly because "summer" in New Zealand includes Christmas & New Year's). Many departments do not offer summer courses at all. The main semesters run approximately March-June and July-October.

There are generally tutors hired to run tutorials or labs and grade assignments and tests for all but very small or specialised courses. Those may be undergraduate students, graduate students, or full-time employees, depending on the department and course. In general exams are marked by the course lecturers themselves.

All of this can vary between institutions. In addition, there are certain parts of some universities that operate on a different model of courses, often with a larger number of shorter terms, and those will be different in numeric terms but likely broadly similar in actual workload.


Should I put job talks on my vita for positions I didn't get?

Edit:  From the perspective of applied social sciences (e.g., social welfare / social work)

No, a job talk is not the same thing as what is considered an invited presentation and should NOT be added to your CV. An invited presentation is connotes something much different -- that is, something that is akin to a keynote or a presentation at a formal conference / meeting.  Keep your CV clean and don't reach for things that don't belong.  I see lots of recently minted PhD's trying to work things into their CV to make it appear weightier than it really is.  Don't water down your CV with activities or products that don't belong.


Do case reports require ethical approvals?

From a legal point of view, in the United States, preparation of a case report for publication does not require review by the ethics board because case reports do not meet the legal definition of "research" (according to most interpretations):

  Case reports submitted for publication do not strictly meet the criteria of research. Although a case report (defined as a retrospective analysis of one (1), two (2), or three (3) clinical cases) may be illustrative, it does not meet the Federal Policy for the Protection of Human Subjects definition of Research, which requires an investigation that contributes to generalizable knowledge about a disease or condition. Instead, a case report is intended to develop information to be shared for medical or educational purposes.

(Source: Tufts)

Many institutions therefore do not require any kind of review for publishing case reports. For example:

  Q:  Do faculty who prepare a  case report as an article for submission to a journal require IRB approval prior to preparation?

  No.  A case report is a medical/educational activity that does not meet the DHHS definition of “research”, which is: "a systematic investigation, including research development, testing and evaluation, designed to develop or contribute to generalizable knowledge."  Therefore, the activity does not have to be reviewed by a JHM IRB.

(Source: John Hopkins Medicine)

(Another example: University of Wisconsin - Madison)

(Another example: Columbia)

As pointed out by Fomite, some institutions have an IRB make the determination that a study is "not human subjects research" even for a case study. For example:

  A number of studies submitted to the UNC-Chapel Hill IRB are deemed “not human subjects” research which means, once reviewed and so designated, no further involvement with the IRB is needed unless a change in the study might alter that decision. This designation can be given to studies that involve human beings but are not considered to be research in the federal regulations (e.g., not systematic, as in single subject case studies and/or are not designed to contribute to generalizeable knowledge, as in program evaluation or quality improvement projects) or when information is collected from humans but is not about them (e.g, a survey of public health department directors about the content of programs offered).  When a student has a study that might qualify for a “not human subjects research” designation from the IRB, the online IRB application will be shortened considerably.  Once submitted, the IRB will review the application and let the student know if it agrees with the “not human subjects research” determination. If it does not agree, then a longer IRB application will be necessary.

(Source: UNC Nursing)


How many applications are usually received for a given PhD position?

There was over 80 for the position I applied for a few years ago, at a Dutch neuroscience institute with a good reputation. I imagine there would be more at world famous universities in the US. I hear that most of the time, most applicants aren't that good, even the top 10% who make it to the interview. In my case the best candidate got the position, and the one ranked second (me) got an offer for a position later on... so in the end it was one out of 40.


'leadership' quality

The achievements and skills that you describe are more capabilities of an independent and respected researcher in your field.

Evidence of leadership usually pertains to roles at different groups.
The more traditional "leadership" activities are usually representative or publicity roles for your department or college. Committees, uni groups, local community groups that reflect your research area and you are able to represent your uni/college.
Representative roles at your professional association, invited government roles, leadership roles at conferences or journals, etc.
This university gives some examples of the expected evidence for each academic level - James Cook University Academic Promotion Evidence

There are "non-traditional" activities that has done well for other professors that I know.
One professor's blog became a world leader in the field with a great list of contributors and research stemming from her blog which supported her academic promotion.
Another professor runs a great Facebook group that has become a defacto society/research group for her small field.
Anything that points to respect and trust from a group seems to be good indicators for leadership.


What is the difference between "enabling", "remedial", and "developmental" courses?

My impression is that there's a large element of euphemism and trendiness: "remedial" can sound off-putting or condescending, while "developmental" has fewer bad associations, but they really mean exactly the same thing (namely, a low-level course designed to build skills and fill in missing background in preparation for successfully taking the standard introductory course).

In my experience in the U.S., "remedial" used to be the standard term, but "developmental" has almost completely taken over.  Nowadays, anything described as "remedial" sounds worrisomely old-fashioned.  I haven't run across the term "enabling" in this context, but some quick web searches suggest it is popular in Australia.

There may be differences on average in how remedial or developmental courses are taught, but they reflect how pedagogy changes over time, correlated with but not caused by the change in terminology.  Any previously remedial course could be relabeled developmental without making any further changes.


What are acceptable citations within a research paper for a peer-review journal?

The general rule is that the reference you cite must be authoritative and provide strong evidence for the claim that you are making based on it. Readers should be able to follow the citation and see for themselves the evidence supporting the claim.

For example, if the claim is "80% of basket weavers prefer to work with Australian reeds", then the citation should be to an article which describes a rigorous survey of basket weavers, including the details of the methodology and statistical analysis. Such a study would most likely be published in a peer-reviewed journal.

Suppose you read an article in Basket Weaving Weekly Magazine that makes the same claim. Can you cite it as the source of the claim? Well, there are a few possibilities:

The article got this claim from study in the peer-reviewed journal. In this case, you should cite the original study (not the magazine article), crediting the authors who actually did the study. (You should also read the study and make sure it actually makes that claim, and that it provides strong evidence for it!)
Basket Weaving Weekly Magazine did a survey of its own readers, and the claim is based on the results of that survey. In this case, the article may or may not describe the methodology and details of the statistical analysis, and those may or may not be sound (up to the standards of rigorous scientific research). In this case, you'll have to determine whether the claim is even supported by strong evidence - but if it is, and the evidence and supporting details are in the magazine article, you can cite it.
Basket Weaving Weekly Online makes the claim, but doesn't give any details about where it came from. In this case, you are lacking strong evidence for the claim and you should not state this claim as fact in your paper.

Citations are most often to peer-reviewed research articles, because most of the time, these are authoritative and include strong evidence to support whatever is being cited. But there are certainly occasions where it may be appropriate to cite something that isn't a peer-reviewed research article. (See for example this answer, or this answer.)

This is just a general rule - specific fields and specific publication venues may have written or unwritten conventions, which you should learn and follow.


Corrigendum to correct formatting/aesthetic errors previously brought up during proofing process

How cut and dry is the rule of not being able to correct articles once they are published?

While nearly all journals are inclined not to make any changes to the content after publication, they do encourage the use of corrigendum or errata (see AMS policy). However, some publishers allow minor changes to formatting with the version of the old publication archived. This can be acceptable as long as the change does not affect the result or conclusion in any way. In your case its just minor formatting changes and it seems fine in this case.

There are some bureaucratic publishers (such as the one you've encountered) who disallow this feature. This would be especially in the case where print versions are involved to preserve the integrity of the article. Or, just to save the time and effort involved in the process. Hence, it is up to the author to make sure that formatting errors are minimized before making the final camera-ready copy of the manuscript before publication.

  Is it worth publishing a corrigendum?

In your case, no. Corrigendum is useful for minor content changes, error and grammatical corrections but I haven't yet come across one for defining formatting errors in tables and uniformity in capitalization.


How can I politely tell a student that I already support him several times and that is enough?

I'll assume you already have language that indicates your support. Don't give up on that.
But, ask him for two things. First, that he only asks for feedback once a week (or whatever you are comfortable with) and add a report on changes and why they were made.
Second, ask him to specify in the report things he is unsure about and to detail why he is unsure.
The goal is to get him to think more deeply about why he is doing things and to separate the simpler from the deeper things.


Is it fine to post my paper's preprint both on my blog and on arXiv?

If my paper is already on my blog, isn't it more likely to be flagged as plagiarized by any average plagiarism software?

This won't be a problem, unless you do something really weird, like post your paper on the blog under a different name.  Lots of arXiv papers also appear elsewhere, and the arXiv couldn't function if this caused trouble.

  There have been evidences of proper articles being rejected. This being the case, how does it ensure security?

I'm not sure I understand what you mean by security.  Strictly speaking, nothing is ensured, but in practice I believe very few proper submissions are rejected (almost none).  Unless you are an amateur researcher or are working on something unconventional, I don't think you need to worry about rejection by the arXiv.

  The reason we post our papers first on arXiv is to prevent the content from being stolen by some anonymous person, who first rejects our paper upon submission and unlawfully uses the content elsewhere. How is arXiv different in this aspect?

It's not different in principle, but in practice I don't consider this a serious issue.  I doubt any arXiv moderator has ever stolen a submission, since the risk/reward ratio would be terrible.  (It makes little sense to try to steal a paper when the authors will presumably post it online somewhere else shortly, and when there's an electronic record that you rejected it from the arXiv.)

More generally, I disagree that this is a key reason to post to the arXiv, since theft by reviewers is rare.  When people talk about establishing credit by posting to the arXiv, they generally aren't talking about preventing theft, but rather publicizing the work enough that nobody else will independently make the same discovery and claim credit.


How can I withdraw my paper from a fake conference?

The fake conference is unlikely to co-operate – it's a fake conference operating for unscrupulous reasons. You can try, but I wouldn't expect them to play ball.

Your best chance of success is to clearly explain the situation to the organizers real conference, and hope that they understand your situation and accept your paper / talk request without problems.


The proper way here is to rearrange your paper so that this does not happen. It might be possible to put the theorem into the paper twice. Once in the introduction, possibly without some technical details but with more context and intuition around it and once after the required lemmata a proven with all the technical details.

The main reason is that the proofs of your various lemmata and theorems depend on one another but you want the dependence to form a tree and not have any loops. If you have a theorem that depends on a lemma proved later on, it could look like the proof of the lemma also depends on the theorem stated earlier on.


I will give two answers, you are welcome to choose which one to pay attention to ;)

Short answer: If you can change to full time without negative consequences, then I don't see why not. It might look a little 'cleaner' on the diploma and might prevent some biases or questions that part-time doctoral work might arouse in your country (assuming you want to remain in your country, here you are a better judge, since our countries are probably not the same as 3-yr PhDs are definitely not the norm in the U.S.). So if the benefits outweigh the effort, go for it!

Long answer: I realize everyone's circumstances are different and there may be reasons to rush a PhD for the sake of the diploma and a brighter future with higher salary. With this disclaimer, to me, any (part or full time) PhD done in 3 years by design of the program (rather than special case as with some highly talented students) raises suspicion about the quality of the PhD program.  However, from your comment it sounds like it's not that the program is designed to be have 3 year typical duration; it's that you have 3 years of funding on your job contract. That changes the situation, because it means that you are potentially rushing like crazy through a PhD program that is intended for a longer average completion period (e.g. 4-5 years).

This is important because regardless of what your transcript will say, it's what is left in your head that will ultimately determine your worth as a professional in your field.

Students who complete a PhD in 3 years are either highly talented and do so with no detriment to their knowledge - to say it different, they complete the PhD in 3 years because when they are done, their knowledge is at least equivalent to that of typical students who take longer. They are ahead from the start, hence the typical program is too slow for them. That's an OK situation. Different strokes for different folks.

Another situation is that students who complete a PhD in 3 years are in a big rush, the reason being that there are strings attached, and a longer term carries a higher cost either in money, or time (e.g. fellowships that require a student to return for home country for a minimum of 2x the duration of PhD study).

This is problematic for the obvious reason that simply being in a hurry does not make one more qualified by the end of the 3rd year, i.e. more ready to graduate. The reason why this is problematic is the same as the reason why it is problematic if a medical student completes medical school in 2.5 years instead of the typical 5, or an attorney graduates from law school in 1.5 years instead of typical 3. Even if you study really hard, it raises eyebrows. To me personally, a PhD completed in 3 years raises eyebrows in the same way.

I offer this as something to think about because being in a hurry seems to be at least partly the case here. If I am wrong, please correct me. I might also be biased by my own graduate study, which I did not rush. As a result it took longer than average, but I did not see it as a race, and I honestly believe that I have gained more skills, knowledge and experience (and perhaps a little wisdom) than if I had rushed it.

Bottom line: If at all possible, I recommend to reconsider your plans, taking into account factors other than the contract duration of your job. So far it seems that this single factor is the main consideration. The assumption is that once 3 years is up, that's it, life is over, there is no money left in the universe to fund your study. Is that truly the case? Could it be possible to find fellowships, or part-time work with tuition waiver, to fund a continuation of the study for another year or two? Would this make you a better academic, with better skills under your belt? Or would it only make you look lazy and weird compared to all your peers? I hope you use long-term thinking and consider all options. Good luck!


How one legally can justify distance learning for on campus programs?

Edit: this answer is somewhat specific to the context of the COVID-19 health crisis and about legal justifications for various exceptional teaching strategies being adopted by many universities all over the world these days. It’s not clear if that’s what you meant to ask about exactly. If it’s not, please clarify.

The COVID-19 situation and the way universities are responding to it is an illustration of the adage that “it is easier to ask for forgiveness than for permission”. Basically the situation is so unprecedented that universities are doing whatever they can to stay operational, and leaving legal questions for later. My guess is that these will all be addressed by governments, legislatures, and regulatory bodies at a later time when the people in charge emerge out of panic mode and have time for dealing with such issues.

At the same time, the question of legality is indeed significant, and people are in fact paying attention. For example, in the US, I have heard that the visas of many foreign students explicitly forbid “online learning”. As a result, I have also heard (this is basically gossip and I can’t confirm it or cite a reference) that some institutions are referring to their current mode of operation as “remote learning” in a euphemistic attempt to pretend that that’s conceptually different from “online learning”. Silly? Perhaps, but that’s the kind of advice lawyers are giving apparently. Similar fig-leaf, CYA-style advice is being given about protecting your Zoom class meeting with a password to avoid being accused of compromising your students’ privacy. Does that mean using Zoom is technically legal in the sense of being fully FERPA-compliant? Who knows - probably not. But at least we make an effort to minimize whatever legal issues we have time to think about and energy to do something about.

But the short answer is, in the academic context as well as other contexts having to do with civil liberties, restrictions on people’s movements and many other aspects of our daily lives that are being disrupted, the law is lagging far behind. People in charge will do whatever they need to do without asking for permission, and ask for forgiveness later if they have to (they probably won’t).


Publishing: Is working at home perceived as unprofessional?

No one will know that you are unaffiliated since you are free to put your research institute as an affiliation. Your institute might even be upset if you don't since you did this work while in their employment even if your contract doesn't give them rights to it if done on your own time at home using equipment that does not belong to them. If you put them as your affiliation, someone will eventually notice and may come asking questions. As such, it would probably be best to show this work to your employer through your current line manager/PhD supervisor and ask for their advice. It's likely that with some help you and your advisor will be able to publish this article together. This is how it works in the "real" world.

My favorite publication of my own was mostly done at home and in notebooks I bought myself while a student. I eventually passed it by my PhD advisor, he made some edits and suggested some changes, helped rewrite the introduction and conclusions, checked the math, and we eventually published a paper together. It was a very satisfying way to bring my side-project to a close. The material never even appeared in my dissertation (as I didn't do a so-called stapler thesis).


Should I push for my paper to be published as an undergraduate?

Perhaps your advisor is worried about the depth or novelty of your work, suggesting that it might not be worthy of publication. s/he might be correct or not. But there is no reason to restrict yourself to an undergraduate journal. If the work has the right quality it can be published anywhere that the referees and editor will accept it. The fact that you are an undergraduate has no bearing on the issue of quality.

You can submit a paper, certainly, though whether as a sole or joint-author depends a bit on your field and location. It might be worth it just for the experience.

But speak again with your advisor/mentor to find out why they were originally a bit dismissive. And look at what appears in any journal you might submit to in order to judge your paper against what they normally accept.


Would taking an Editor-in-chief position at a mid-tier journal be good strategy for a tenure track professor?

Being an editor-in-chief is a rewarding position that most departments value on someone's CV.
So much for that. But I cannot stress enough how bad an idea it would be to take on such a role while being an assistant professor without tenure. As the EiC, your workload consists of 50% assigning papers to associate editors, and 50% dealing with the difficult papers where some bigshot's poorly written paper has been rejected and they complain/some associate editor not actually doing their work/other cases that are not of technical nature but involve people. You have to make judgment calls about these papers, decisions, people, and that's hard if you don't have the stature and independence that tenure gives you. That's because to get tenure (and, to a lesser degree, for promotion to full professor) you rely on the well-known people in your community that are exactly the ones who you might have to make decisions about. In other words, without the independence that tenure gives you, you will perpetually find yourself caught in conflicts of interest, and that's a really awkward position in which you can only choose between lose-lose options.
In other words, don't do it if you don't already have tenure or anticipate getting tenure shortly after taking on the role.


Paper submission: Major revision impossible to pull off

You have a number of options. Only you can decide which is the best in your case.

(1) You can withdraw the paper from the original journal and submit it elsewhere, in the hope that a different set of reviewers will be more enthusiastic or realistic.

(2) You can re-submit to the original journal and simply decline to do the reviewer's request.  This is perfectly reasonable, and editors will simply use their judgement as to whether the paper is still acceptable even without this revision.  If you do follow this route, be sure to make as many of the requested revisions as you possibly can, to show that you aren't simply being stubborn, and also explain professionally (clearly but politely) why you didn't do the other revision (it isn't practical) and why it isn't necessary (you already have strong statistical significance).

(3) You can request an extension from the editor.  The 2-month revision time is almost always negotiable, if you have a reasonable argument. I recently requested an extension from 2 months to 6 because a co-author had had a baby, and the editor was perfectly happy with that.  (I offered to include baby pictures, but even that was not necessary.)

My own preference would probably be, in order, (2), (1), and (3), but you will have to decide on your own.

Edit to add that, as @jakebeal says, you could just ask the editor if they feel the major revision is necessary.  I would be a little hesitant about that, because I think (without evidence) that editors would be inclined to say that everything the reviewers asked is required, and then you're stuck with it, while if you just send in your revision as in (2), the editor might see it differently.  In other words, it's often better to ask forgiveness rather than permission.


Should I address an EiC by his given name after he undersigned an email with it?

Dealing with a superior is always tricky. And I would say, replying with his first name does not give everyone a pass to just address him like this.

A few things to consider are:

How well do you know him
Have you done work with him
How does he addresses you in the reply
How do other people of your social status address him

My rule in a general business is to follow how the person is calling me. If they use my family name or first name, or even use my title or not. Copying this form of address is usually safe.

With a superior, my default would be to use at the very least his family name, and even throw the title in it if I want to show deference (especially if he's doing me a favour). Now, if you know that person and have a good working relationship with him, it might come a point where you want to just skip the formalities and be on first name basis. That's a judgement call and I don't think we can help you with this, as it comes with your personal experience with that particular person. Furthermore, some people are really tight on with being called by their full titles.

In the end, if you are unsure and it is expected that you will have an extended correspondance/work relationship with him in the future, I would just advise you to just ask him if he would be OK with it, and keep using the formal titles until then. The worst that could happen is you're gonna look stiff/strict/pedantic about etiquette maybe... it's not as bad as being painted disrespectful.


What is the maximum reviewer score for IEEE conference papers?

IEEE conferences are allowed to organize their own reviewing system, so there is no uniform system between them.


Should I cite sources about a technology description?

If something can be deemed common knowledge in your field there should be no need to cite it.

MIT define common knowledge as;

  Broadly speaking, common knowledge refers to information that the average, educated reader would accept as reliable without having to look it up.

There is further detail on that link about Common Knowledge and it's applications. They also say that there best advice is: 'When in doubt, cite your source.'

That said if you are taking something verbatim from a source you should cite it.

Just on your sources; in academia you tend to shy away from citing from wikipedia etc. You can see a discussion on that issue at this question


What does my colleagues' question really mean?

It is impossible to read their minds, of course, but I think that they are at least expressing surprise that you don't have doctoral students. There may be a (very) mild rebuke in it, especially if it is thought to be a necessary element of the work.

But, there may be an implied warning, that, although they can't sanction you for not having students, there might be long term negative consequences for your career if you get by without accepting students. You don't say whether you have been asked to be an advisor and you don't say whether you have turned people down. If either is true then the warning, as well as the rebuke, might be a bit stronger.

But whether there are consequences or not depends on local custom at your place of employment as well as your other contributions to the profession.


Expected size of search results for a meta-analysis?

The short answer to the last question is that yes, for some questions people do sift through tens of thousands of results to find a small yield of relevant studies. (And the pool becomes smaller when later screening for details like N and standard errors and adequate description of the population and intervention to allow for a technical meta-analysis.) But that may not be the ideal way for you to do this.

The Campbell Collaboration helps coordinate literature reviews and metaanalyses on many social issues, as the Cochrane Collaboration does for health. The Campbell Collaboration has a document on how to write a good protocol for such a review, including specifying your search strategy, and there's some longer guidance on search strategies and information retrieval here.

The latter document says:

  The decision as to how much to invest in the search process depends on the question a review addresses and the resources that are available. It should be noted, however, that article abstracts identified through a literature search can be ‘scan-read’ very quickly to ascertain potential relevance. The process can be facilitated by answering a few specific questions that relate to the inclusion criteria when scanning the abstracts, such as “Does this document report an empirical study?” or “Are children age 3-18 in the sample?”. If the answer to any question is No, then the reference is excluded. But any study that makes it through all of the questions answered either Yes or Can’t Tell, is retrieved. At an estimated reading rate of two abstracts per minute, the results of a database search can be ‘scan-read’ at the rate of 120 per hour (or approximately 1000 over an 8-hour period), so the high yield and low precision associated with systematic review searching is not as daunting as it might at first appear in comparison with the total time to be invested in the review. (p. 23)

Much of the work done by these collaborations involves large research groups and/or volunteer labor and/or automated screening. For your workflow, you would probably want to find a system that lets you view the title and full abstract without clicking through--easier in some databases, maybe a deep option somewhere in Google Scholar. This difference in the view may allow you to more efficiently screen the literature even if there are many potential results.

It seems to me that a good reason for using Google Scholar would be if you want to seek out "gray literature," technical reports, unpublished results, and results in multiple languages. However, Google Scholar will probably bring up more irrelevant studies than if you search databases. For your search terms, though, I'm not sure that you'll run into as many well-designed (RCT) studies on a novel technical infrastructure that would fall through the cracks like that.

Thus, I think your best bet might be doing your main search via PsycINFO or some other database, plus a dissertation database, and then look at Google Scholar a bit to see if anything was systematically missed.


How to write a teaching statement without any classroom teaching experience?

(1) What is a "statement of teaching interest?" How does it differ from a "teaching philosophy" or a "teaching statement"?

I would guess that all three quoted phrases mean the same thing.  The "teaching statement" is not as formalized a genre as the sonnet: there is a range of reasonable responses, and to my ear all three things are asking for the same range.

Of course, if one is especially interested in a specific teaching position it would be better not to guess but to inquire what they mean.  I don't see any reason to be shy about that: just ask politely.

  (2) How does one write this statement without any classroom teaching experience?

Others have given some advice on this.  It is certainly possible to literally write a teaching statement without any teaching experience -- one talks about one's teaching philosophy, teaching goals, and so forth, while not mentioning the experiences that one hasn't had.  It's not like they're asking for the secret masonic handshake: anyone who has gotten a PhD has certainly experienced enough teaching to be able to write about it intelligibly (let me assume that someone who has gotten a PhD has learned to write intelligibly on academic matters!).

However, isn't there another key question here?  Namely:

  (3) What are the chances that someone who has absolutely no teaching or TAing experience whatsoever will be seriously considered for a faculty position with emphasis on teaching?

I can answer this question from the perspective of a math department at a research university: it is very likely that I would not seriously consider any such candidate.  Let me explain.  "Even" at a research university, teaching is a big part of the job -- roughly half, according to university directives -- and someone who is a truly unsatisfactory teacher is going to be an eternal liability and problem.  Well, you say, what if they are a truly outstanding researcher -- can't they learn to teach?  It doesn't really work for me.  If by "truly outstanding researcher" you mean that they've proven the Weil Conjectures, then they deserve to be at a truly top place which can afford to have faculty who literally never teach, or who only teach graduate seminars to their own brilliant students.  Any candidate like that is not going to come to my public research university, and if anything still less is she going to go to a teaching college.  If someone is simply a strong enough researcher that I would otherwise be very pleased to hire her, then her complete lack of teaching experience creates an insurmountable fairness issue when one compares her to other candidates with similar or moderately worse research profiles but who have devoted a substantial amount of time and energy over the years to teaching.  Even serious research mathematicians work hard to be competent teachers: it takes time and energy.  Sometimes people have less than stellar teaching, and it really can ding them a bit even at a "serious research university".  Someone with no teaching has to get a zero averaged in to her total grade, so to speak.

I explained how it goes for mathematics at a research university.  The OP's candidate is changed twice: from mathematics to biochemistry, and from a research university to a teaching college.  From what I've heard on this site, teaching experience is valued significantly less in the non-mathematical sciences than in mathematics.  On the other hand, I happen to know that teaching experience and credentials are valued way more highly in teaching colleges than at research universities: though I think of myself as a "serious teaching guy", when I visit a colleague at such a place I feel like I am hiding in a foxhole doing math all day compared to them.  Moreover smaller places are smaller, so the "ethos of the college" is something which is more strongly felt by all, whereas being a scientist at a research university is almost a different job from being a humanities professor at a research university.  My best guess: there is little chance that someone without any teaching experience will get any real consideration at a reputable teaching college.

So I would say to the OP: if your friend wants this job, it's not about how to write the teaching statement, it's about how she can acquire some actual teaching experience.  One semester of good evaluations in any reputable post high school academic institution would make a world of difference.  If she's not willing to acquire that, is she really that serious about a teaching career?  Compared to the other candidates, I mean?

Two final points:

I. I do not want to leave the impression that one should write a "teaching statement" that hides the fact that someone has no teaching experience.  Although this should come out elsewhere in the application -- e.g. on the CV -- in my view it would be dishonest not to at least remark on this in the statement itself.

II. Others have counseled that a teaching statement should "[l]ook at what the professionals say about teaching" and "use pedagogy literature".  This is good advice, but it can be misapplied.  Namely, you need to have real understanding and ideally mastery of anything you talk about in these job applications.  Most people know not to talk about locally ringed topoi in their research statements if they do not want to get asked what a locally ringed topos is in an interview.  However, at least in my line of work, it is something of a cliche that young people "use pedagogy literature" to the extent of absorbing some trendy buzzwords, which they then misuse.  If you talk about flipped classrooms, IBL and so forth and reveal that you don't fully understand what these terms mean, that is so much worse than not using them at all.

In fact at my research university (it is a bit different at teaching colleges, I happen to know) most of the faculty are not familiar with the pedagogy literature, and if I'm honest, some people pride themselves on the conjunction of that ignorance and their superior teaching.  I don't think pedagogical literature is BS (or not all BS, anyway; every branch of academic literature has some BS), and I do believe that if you actually learn these ideas and articulate them properly and well it will be to your credit.  But be careful.  Also be aware that the trendy technique that one committee member might like might make another one roll her eyes.  So a good teaching statement succeeds independently of its use of this kind of terminology and ideas.


What should I do if my final year project supervisor does not answer my questions

Email is a terrible way to supervise work for both parties involved.  It's difficult to ask a good question over email and it's difficult to address a misconception over email.  From your question, there's no way of knowing which of several types of problems you are experiencing with your advisor.  The answer to all of them, however, is to have regularly scheduled meetings that are face-to-face if possible, or over a video link if you are doing distance learning.


Changing research disciplines during Graduate school

It's certainly possible, at least in the universities I'm acquainted with, to apply to a Ph.D. program in a field different from your masters degree. But to be accepted into such a program, you'll have to convince an admissions committee (or the professor with whom you want to work) that you have the necessary background. You mentioned that you have relevant background but not formal training, so this may present a problem. If you can take some relevant courses while you're in the masters program, or if you can get recommendation letters attesting to your background knowledge, that would help. If that's not possible, then you may need to take some classes after you get your masters degree and before you apply to Ph.D. programs.


What to write in appeal for a rejected PhD application?

You don't say why you are appealing the decision.  If only 9 out of 116 applicants got a scholarship, then it is overwhelmingly likely that they turned down many strong applicants.  Do you have a good reason to believe that your application is stronger than the 9 who received the scholarship?

I hope you're not under the impression that simply not having received an award is grounds for appealing the decision.  What if all 107 unsuccessful applicants appealed the decision?  The program would surely have to reconsider having an appeals process or perhaps even giving out the scholarships at all.


How to handle a PI who constantly threatens to kick me out of their lab?

Don't walk, run.

This kind of behaviour should be viewed as entirely unprofessional and unacceptable in any working environment; it astonishes me what gets politely overlooked in the academic world. What you describe is bullying. While the work may be exciting, it is doubtful that you will ever be able to flourish as an independent researcher facing daily abuse from your supervisor and suffering the toxic secondhand effect of your supervisor abusing your colleagues. I cannot imagine that after several years of that you will still be able to maintain the same level of enthusiasm for your work, and perhaps for academia altogether.


Paper submission with company affiliation

If I am understanding this correctly, the paper was submitted while the person was still working for the company.  If this is the case, then the affiliation should stay the same as it was at the time of submission, as it sounds as though the work was explicitly done as part of their responsibilities at the company.  A second affiliation might later be added, for the person's new position, if it is appropriate and the conference supports this, but the first should remain.

If the paper was submitted after the person was fired, that is a much bigger problem, and it is unclear from what you have written whether that would be appropriate, ethical, or even legal.


Would the professor be annoyed if I failed two grad school applications in previous year?

Two rejections are not so many, especially if you applied to highly competitive universities/departments. Some suggest applying to as many as 10 different places (of course, assuming you find so many research departments that interest you).

Just ask your professor again, I would not expect him to be annoyed. Even though we cannot know for sure how he will react, the uncertainty about his reaction should not block you from pursuing your academic goals.


Is it useful to include my teaching experience in primary school when applying for lecturer position

I'd say that if it's the (only) teaching experience you have, you should probably mention it. Teaching is teaching. Regardless of the level at which you teach there are some basic skills which are common to most, if not all, scenarios. For example one expects teachers at all levels to be pedagogical. Moreover you'll be telling the selection committee that you are familiar with the job type, albeit at a different level. Indeed you know how to prepare a lesson, you have an idea of how the marking process works, you know how to keep students interested, etc.

Another important point to note is that primary school teaching experience shows that you were deemed competent, and responsible, enough to be allowed to work with kids, which is something I believe can say a lot about you. We all know how protective parents are with their little ones. Allowing you to somewhat shape the initial part of their lives definitely implies trust and recognition.


How effective is it to fund a researcher as opposed to a research idea?

There are a few funding schemes which are working exactly in this direction, giving the researcher lots of freedom in their line of research. Sometimes, the funding comes in form of a "prize" and the prize may only be used for further research topics.

In a smaller scale (you were talking about a larger amount of money) each tenuring decision is such a grant: The university is investing a significant amount of money into a person without any further control about the future research directions (at least in Germany). There is just some hope that people will not stop doing interesting things. If you sum up the regular amount of money a professor recieves, plus the additional staff / expenses granted, you end up with large amounts of money. I must say this freedom is something I really enjoy, and for me it is my major motivation for staying in academia.

Of course, those professors still write grant applications...


Why are there no computer-friendly versions of papers?

Why don’t journals make alternative computer-friendly versions of the articles?

They already do. It’s usually called HTML version. I couldn’t find any statistics on how widely available this is, but as far as I know, all major journals in my field (physics), all mega-journals, and Elsevier offer this.


I can't access a reference of an article I am reviewing: what shall I do?

While online access is very useful, it is not the only access. Every university I have been affiliated has provided an ILL service either at no cost or a nominal charge (e.g., a $1 processing charge). US University libraries can make requests to both the Library of Congress and the National Library of Medicine. I am less familiar with the ILL system in the UK/Britain, but I believe ILL requests can be made, possibly through a university, to the British Library.

There are of course some articles/books that are truly hard to find (e.g., not held by the LoC with deceased authors). In these cases, it seems reasonable to request a copy through the handling editor. You should never contact the authors of a manuscript under review directly.


Putting class ranking in CV, but against dept guidelines

So, you put it on your CV, the future employer does what employers do and phones the institution to check details of awards, years etc.

BOOM - the institution does not confirm you were "top of the class" as that is just not done.

Now the future employer is confused - what else may be wrong on your CV AND your referee is pissed at you as well.

Do you really want to go there?


I suppose there is a difference in fields, but your research should be evaluated by a committee, and the level of research you have done is independent of where it was published. Even unpublished work can be part of the theses, so your argument of waiting for reviews is strange.

The committee should not really care where it was published or presented. They should evaluate your work - not the conferences/journals.


Is there any PhD program does not accept foreigners due to its strategic importance?

As ff524 mentioned. Prospect Iranian students at USA universities are not allowed to study nuclear or petroleum science.
If you apply for scholarship of Mexican government, you will not be awarded if you want to pursue degree in tourism, culinary study or plastic surgery!!!
Most countries, i think all of them, but I am not sure, dont permit law, police, national security, military,teaching positions, to citizens of other country. or if they permit, they will not give you right to work after finished studies.


Are there known cases of leaks in academia?

Academic publications are sometimes subject to an embargo, in which information about the publication is shared with the media, but they are restricted from publishing a news article using this information before a certain date.

In this context, leaks are not uncommon. Sometimes the author of the paper is responsible for the leak; on other occasions, the publisher or a news agency may be responsible.

Here are two examples in which the Associated Press broke an embargo:

AP technical glitch unintentionally breaks JAMA Avastin study embargo
AP breaks abortion data embargo

In both of these cases, there were no serious consequences for anybody involved.

In a case that did involve consequences, a researcher published a paper using data that was made available through the NIH, but was subject to a data embargo. The paper was retracted (see the story on RetractionWatch), and the researcher's access to the shared data was suspended:

  Upon learning of the violation, the investigator’s access to dbGaP [database of Genotypes and Phenotypes] was immediately suspended pending an investigation by the NIH Data Access Committee with responsibility for the dataset involved and a review by the GWAS Senior Oversight Committee (SOC). Information pertaining to the incident was requested from the investigator’s home institution through the Institutional Signing Official that approved the investigator’s original request to the NIH. After a thorough review of the circumstances pertaining to the violation, the SOC revoked access to all dbGaP data for a period of six months.

  All work with data downloaded before the date of the access suspension was expected to cease during the ban. This ban included the Primary Investigator as well as those individuals working with the individual-level GWAS data under his Data Access Request, because they also agreed to abide by the terms and conditions for data use within the Data Use Certification agreement. The period of the ban passed on March 4, 2010, and Dr. Zhang may now submit new requests for access to dbGaP data.

Another data leak scenario was mentioned by Stephan Kolassa in a comment: when a researcher uses private data that is leaked. Here is an example of a case where

  the world's largest futures exchange has accused the top U.S. derivatives regulator of illegally sharing sensitive market data with outside researchers who then used the information to publish academic papers about high-frequency trading

Possibly the most high-profile case of data leakage in the very recent past is Climategate, but that turned out to be more of a "hack" than a leak by someone who had legitimate access to the data. In 2009, a server at the University of East Anglia (UEA) was compromised, and material was leaked including more than 1,000 emails, 2,000 documents, and source code, pertaining to climate change research. Many of the emails concerned technical aspects of climate research, such as data analysis. In this case, climate change skeptics argued that the leaked materials showed that scientists engaged in a conspiracy to manipulate climate data. However, various investigative committees reported no evidence of fraud or scientific misconduct on the part of the scientists.

The individuals responsible for the breach were not identified. Police said said, however, that despite rumors to the contrary, the attack had been carried out "remotely via the internet" and that there was "no evidence to suggest that anyone working at or associated with the University of East Anglia was involved in the crime."