Peer reviewing process in top math journals

The biggest difference between top level journals and others is the care taken in the reviewing process. Four months doesn't sound especially long.

Perhaps the journal publishes definitions of its terms such as "reviewing" which might give you an idea. But likely, it is being looked at by other mathematicians with knowledge and interest in your area. If the paper is straightforward it might get reviewed quickly, but be rejected for lack of impact. If it is not straightforward it will take longer to asses.

It is also possible that delays can occur if a reviewer decides after an initial look that he/she can't give the editor proper advice and passes it back with another reviewer then needing to be found. This could occur for many reasons, not all related to the paper itself. Some of the time delay is also likely due to the normal end/beginning of year academic scheduling with holidays occurring in most places.


Giving students a complete set of study resources

It sounds helpful, not detrimental. NB, whatever materials you curate and provide will never be "complete" by any objective standard. Consider a textbook: it may be written to address a particular course design, and focus on the main topics relevant to that course, but it cannot make other study resources useless.

The major factor here is how much work you want to put into creating those resources, not what their easy availability would do to impressionable students.


What kind of audience can I expect for a scientific talk at University?

The answer to this question will vary from school to school. Typically speaking, you could expect faculty, staff scientists, post-docs, and graduate students at a generic guest speaker's presentation. As such, you might aim your talk for an audience of educated scientists with familiarity to your field (but not experts of the field).

If you want more certainty, you could ask the organizer who invited you what audience you can expect.

If you are comfortable adapting to your audience on the spot, and you are comfortable being somewhat informal, you could ask for a show-of-hands at the beginning of your talk. E.g.: "Show of hands, how many post-docs are there in the audience? ... Graduate students? ... any undergraduates?"


I want to participate in a summer research program, but my GPA is not high enough. Should I still apply?

I think you should. If you don't meet the requirement which you get the same result with "not applying". It wouldn't hurt to try, so I think you should totally give it a try. Good luck.


What advantage is there to getting a PhD in the life sciences when you can do research with only an MD?

The trick, actually, is to get that job. Without a PhD or other demonstrated research experience it might be harder most places. Most MD programs are focused more on patient outcomes than on science per se.

But yes, if you can convince someone to hire you then you can probably learn research methodology along the way. This will include a lot of things, including something of statistics and more on lab process than is probably normal in the MD program itself. Publishing in the scientific literature is also something to be learned along the way and isn't especially typical in the training of an MD.

The advantage of the PhD on top of an MD is that the focus is precisely on the scientific (rather than clinical) aspects of medicine. You learn to do science under the direction of scientists who also have some expertise in biology and other aspects of the wider medical area.

Note, of course, that Dr Fauci is 79 years old. He has had a lot of time to learn the craft and has been positioned in places where it is well practiced.

Note that in some places, an MD is, in fact, a research degree and requires an earlier degree in medicine. But this isn't the case in the US or Canada. See: https://en.wikipedia.org/wiki/Doctor_of_Medicine


Most schools don't actually give you a choice: they simply set you up with a standard email address following their standard format.  Often this is some combination of first name or first initial plus last name, though I've even seen some schools give everybody a horrible alphanumerical mess as their official email address.  Many places will then also give you an option of setting up one or more email aliases, which you can use to modify the default.

Personally, I think that anything that includes your last name (and nothing else bizarre) is pretty reasonable and professional.  For my own case, for example, one can reach me in various locations with various forms of "beal", "jbeal", "jakebeal", "jacobbeal", and "jacob.beal", all of which convey the same basic information of "yes, this is who you think it is."

It is worth noting that, in some circles, being the one to get your first name or your initials on a system can be considered particularly special.  This is because it can indicate that you had been a very early adopter and/or involved in the system's development.  That's unlikely to be the case for most RAs at a university, however.


I haven't heard of such a thing, which suggests a simple answer: an oral tenure defense is not necessary.  But regardless of whether it's necessary in some abstract sense, it might be a requirement wherever you end up.

It's possible that your tenure defense would be a grueling affair, with the audience trying to poke holes in your research or dispute its significance, but I very much doubt it.  At worst you could expect the same treatment as an outside candidate giving an interview talk.

The tenure defense is presumably intended to give you a chance to explain your research program, specifically what you have done and why it matters.  This is in principle redundant (your tenure file should already do this), but adding an oral presentation could help.  It's often inspiring to see someone present their own work, and it can be valuable to have a chance to ask questions.  In cases where tenure seems likely, the presentation could also play the role of an inaugural lecture, highlighting for the department the work of someone who is about to become a permanent colleague.

This practice seems uncommon enough that I doubt there's a clear standard for exactly what it means.  Anyone considering taking a tenure-track job with a tenure defense presentation at the end should ask how it works at that particular institution.

  I imagine their publication/teaching/grant record should pretty much speak for itself to a tenure committee.

Publication records can speak surprisingly unclearly.  A non-expert reading through someone's papers won't necessarily appreciate their novelty or how they contribute to the big picture, and may not even understand clearly how they fit together into a coherent research program.  Keep in mind that most people evaluating a tenure case will be non-experts: even other department members will typically have different specialties, and that's not counting university-wide committees or administrators.

One crucial part of preparing a compelling tenure case is sorting out these issues and framing everything appropriately.  This is done partly by the candidate, partly by whoever is overseeing the case (typically the department head), and partly by the letter writers.

So from this perspective, something more than just a binder full of papers is definitely necessary.  However, the added context is typically supplied through written documents; if there is an oral presentation, then it is just to supplement the written file.


Why have lectures in the information age?

Inertia/tradition accounts for many things. "Doing things they way they've always been done" [sic] is usually considered defensible, too. Also, people have already-existing mental models for what a lecture should be like, often including specifics about the subject matter.

The fact that information is available on-line is not wildly different from the fact that information was available in universities' libraries. Yes, a sufficiently motivated person can simply go to the internet/library and find lots of information. A potential problem is that there is too much information, that it is fundamentally chaotic (despite our attempts to impose order or develop "search engines"), and fundamentally hard for a non-expert to evaluate. Even worse, a non-expert may fail to realize that they are failing to correctly evaluate information. :)

Still, yes, very many classes/lectures are boring, and attendance is often easily replaced by reading the designated textbook or other sources. However, in several decades of observation, many students (at all levels) either prefer or have become accustomed to a kind of passivity, so that they'd rather show up somewhere at a regularly scheduled time, see their fellow students, and have the pace and content dictated to them by even a fairly boring lecturer.

In my own student days, I did not like going to classes, for the obvious sorts of reasons: for one thing, if one had read the book, a slo-mo flawed, re-recital of it seems pointless in comparison to just re-reading at one's own speed. Second, if one found the material interesting, why stop? Why not read ahead? Why not look at other sources, too, for complementary viewpoints? Why not look at related stuff? (This was as feasible in libraries as it is on the internet, with perhaps two added advantages: there really was not much junk in libraries, since it was filtered, and, second, the chances of serendipitous discoveries in libraries was larger than on the internet.) Such a process inevitably makes the "canned" lectures seem crazily irrelevant.

(Also, years ago, libraries were some of the few reliably air-conditioned places!)

But let's ignore the problem of student passivity, and ask why/how a lecture _could_be_ better than just reading a book or searching on the internet. Arguably, a lecture is not better if it just amounts to reading from the book, copying from it onto a blackboard, etc. I would claim that trying to make lectures simply present text-book material is a big mis-use of the medium! That is, systematic presentation of all the details belongs in a book or on-line, but not in a lecture. Oppositely, what could be in a lecture that could not be in a book or notes? "Affect", meaning intonation, gestures, facial expressions, theatrical effects, and so on, are hard to put into writing, but (by "lecturers" capable of it) can be put into a lecture. This includes reaction to facial expressions and body language of the audience/students, and conversational interaction if the group isn't too large. For example, lectures can include "pep talks" that would be hard to fit into writing. "Reassurance" can be done live better than in writing, I think.

Another feature is the "live/real-time" aspect: a lecturer (in mathematics, my field, for example) can literally do things in the lecture room, live, in real time, with voice-over narrative, in effect. That is, the audience can witness the genuine activity as exercised by an expert practitioner, with accompanying critical and methodological comments. Yes, up to a point, textbooks and monographs could be written in such a fashion, but it seems that stylistic pressures move them in the opposite direction, aiming for a sort of artificial perfection that can only be achieved by much editing! Too often it seems that writing aims to create impressive edifices rather than be accessible, helpful ... and a live lecturer can easily do better, if they try.

So, for my own lecturing, I definitely do think in terms of "adding value" beyond what students could derive from written sources, and in terms of using the medium in ways that distinguish it from static written sources (and not having a lecture be a bad re-copying of those written sources).


It probably means the background relating to your proposed work. You need to explain what's been done in the field and how it's been done. Ideally you'll also show how your work will build off of previous work and advance the field.

The point of this is twofold. First, to put your work in context for the readers of the proposal. Second, to show that you've done your due-diligence in understanding the field and won't be wasting the money in pointless or already explored directions.


How do I distribute a survey questionnaire to obtain a reasonable response rate?

The University you are affiliated with likely has a 'behavioural research ethics board' or some similar title as was pointed out by @GEdgar. Such surveys constitute behavioural research and require approval by an ethics committee. The ethics application will usually require that you provide information about how participant anonymity will be maintained (YES -- even if that's a 'given'), how/where you will store the data and for how long, and what you will do with the data. The application, in most cases, can be completed online. If you are not the PI, bring your PI in the loop and get them on board. If applicable, you will LIKELY -- not necessarily -- need them to 'sponsor' your endeavour.
Edit
It is okay once 'ethics' says it's okay, which it likely will. This is minimal risk behavioural research that will likely see a quick turn around time. Also, the ethics application will require that you share with them the survey you are distributing. As you likely know, if you are using Qualtrics (or equivalent), it should be straightforward to download the questionnaire/survey. Search "YOUR INSTITUTION" AND "ETHICS" on Google. No doubt, you will find the right contacts, and I'm sure they'd be delighted to provide you with additional information, such as sample applications.


Still waiting for comments on my draft - what to do?

After 5 weeks, I think you can safely assume that she has forgotten about it. You can either accept that you will not hear back from her, or send a polite reminder.

Most people do not mind a friendly reminder about tasks that they have committed to but forgotten about. It is definitely not inappropriate. However, it is of course possible that she simply has no time after all, but then the right thing for her to do is to just tell you.


100% opinion-based and anecdotal.

I (and I am intentionally not saying "People" here though I do not think that would be an overstatement) will feel very weird if a student refers to a teacher with whom he/she has a professional relationship using only last name. So, I agree with Jonas's comment that you should use "Prof." all the way through.

In general social settings, I have only seen last name-based communication in sport teams (my coach called us by last name, and more than usual we teammates referred to each other with last name), and when someone particularly requested me to do so (e.g. "Nice to meet you, I'm Bruce Wayne; I go by Wayne.")

In academia, referring to someone with last name usually implies you do not personally know that person, not even by the 2nd degree. If I were to refer to a teacher in my school whom I do not know, I'd still say something like, "Hi, this is my friend John, he studies with Prof. Buddy" even I don't know the professor personally. One of the exceptions would be when a possessive is involved, like "Buddy's laboratory" or "The Dumbledore's Army."

When I refer to someone more remote, the last name method is usually used, e.g. "Have you read that paper by Kardashian? Sick stuff." Or, the full name method: "John Tukey introduces box plot in his book Exploratory Data Analysis." I wouldn't call them Prof. Kardashian or Dr. John Tukey. And yet, if I get to speak to a former student of John Tukey's, I would perhaps ask "So, how was it like studying with Dr. Tukey?"

As for worrying about repetition, out of all possible grammatically annoying repetitions, this is nothing worth concerning. In fact, it's more annoying to read a letter from a student who sometimes refers to the same person as "Prof. Y" and then flips to "Y." That sounds mildly psychotic.

I'd conclude that, yes, it is a big mess. English itself comes with plenty of odd rules and exceptions. Compounded with cultural practices and manners it can be confusing. It's not my primary language and the only way to get around it would be to listen and read more. And if you need to pick one in a pinch, err on the more polite and formal expression.


Publishing Valuable but Incremental Result

My interpretation is that the reviewer(s) consider that solving the specific problem is not a particularly significant outcome. Assuming that they are right in this judgement (they may not be), the paper must distinguish itself in other ways.
Maybe the problem/solution is shown to have parallels with some other problem/solution. Maybe the solution is radically different. Or maybe, as in your stated case, the solution is simpler than expected. You must identify which of these is most correct and focus on presenting that as the centerpiece of your work. If the simplicity/elegance is what stands out most, find a way to validate and quantify the simplicity, and use that as the central theme.
If, on the other hand, you are convinced that the solving the problem is an important outcome by itself, then stick with the paper and submit it elsewhere. It is very common that reviewer assessments of relevance/novelty vary widely.
Onto the larger point of incremental improvement being generally given less respect; this is the reality with most products, research output being one. The current model of scholarly publication favours work that will get more attention and generate more downloads/citations. This certainly has demerits, but it is the norm and it's best to live with it. This doesn't necessarily mean you should not pursue this line of enquiry, but you should assess what and why it can be more appealing to the readership. (A demonstrably simple, reproducible solution to a problem of my interest would definitely appeal to me).


Can I publish a critique of an experiment in a field in which I am not an expert?

In order for this to happen, you need two things:

You need to communicate with specialists and convince them that you have identified a logical flaw.  You might worry that they will take your idea without giving you credit, but you shouldn't worry too much about that: the more worrisome scenario is that neither of you will be able to convince the other and it will end with a stalemate.  Without expert advice, it's unlikely that you can present your idea in a way that would be publishable, so talking with experts should be the first step.  (Of course unlikely is different from impossible, but it's best to plan on getting advice.)
Once they understand you, the experts need to care.  Many experiments have loopholes and caveats that are well known to experts but not described in popular accounts or even introductory college courses.  You may end up hearing "Yes, that's logically possible, but it's not a possibility we think is important."  Or "Yes, Jones and Smith pointed that out in a paper last year, but I still think the conclusions are true and the experiment is illuminating."  Using an argument that is not 100% logically air-tight is not in itself a problem outside of pure mathematics.

I'd suggest starting by talking with someone from the course you took (the professor or a teaching assistant).  If all goes well, either you'll convince them that this is new and serious, or they'll convince you that it isn't.


What is the best way to design a paper questionnaire to support scanning and converting to raw data?

I can offer some help with scanning paper questionnaires as this is something I've done in a previous job. But, first, I would suggest it's quite involved so you may want to at least revisit improving your 'digital' response rate first.

Audience response devices

One option may be to allow the students to use 'clickers' to respond to questions. I would recommend having no more than 10 questions that can be answered on a multiple choice or Likert scale, which fits your requirements. Our department use something like this: http://en.wikipedia.org/wiki/Audience_response
We've found that about 10 questions can be answered in about 10 minutes.

Re-consider your online/digital surveys

If clickers aren't suitable - for example because the students are not physically situated together - you could consider reviewing your digital survey, purely because it's significantly easier to obtain data from responses. To improve response rates, I tried to follow these rules of thumb:

No matrices, ever.
No more than three questions per page.
No more than six pages.

Obviously this is going to vary depending on how much detail you need, but these reminded me to keep the questions light.

Scanning paper surveys

So, with all that in mind if you still need the paper copy route, here goes. To make it worthwhile you need:

a scanner designed for automatic throughput. That is, a single sheet personal/small office scanner is not going to speed things up for you if you have to manually change ~200 sheets. Something like this Fujitsu ScanSnap might do the trick.
Software that recognises marks. I used Eyes and Hands, which is deprecated and has been superceded by ReadSoft as far as I can tell. ReadSoft can recommend a compatible scanner.
There are some requirements about how you set your paper questionnaire up, and this needs to be precise. Therefore I recommend something like QuarkXPress or Adobe InDesign.
You need four recognition marks for each page, one for each corner. I often found a character from the header or text ok for the left hand side, but on the right hand side if text wasn't justified I needed to manually add some marks.
You need to lay our tick or text boxes quite clearly. For example, it's quite common to see tables without any padding used for response boxes on paper surveys but you need a gap between them for the scanning software to recognise them unambiguously.

With these basic requirements you can set up a survey to be automatically scanned and entered in to a spreadsheet or database.

Clearly this is quite involved so you may be able to find a company who can do this for your commercially. Some market research or survey companies might be able to do the heavy lifting for you.


Is it appropriate for reviewer to offer cooperation on a reviewed paper?

Since this is your first review, you probably ought to keep the following in mind:
It is not the job of the referee to fix the paper, it is the job of the referee to provide grounds for the editor to decide whether to accept or reject it. Presumably you have research of your own, and while it is no doubt very kind of you to offer very detailed instructions for how to carry out a new analysis, this is ultimately not what you are tasked to do.
What you can do in your review (which is to be addressed to the editor), is to point out that their current analysis has a flaw, and whether or not you think the paper is publishable with this flaw. If not, then you can suggest that the authors (and not you!) revise the paper using a better method. Here you can give a comment stating your suggestion, and point them to a reference.
And to answer your question concretely: No, it is not appropriate. It would place you in a double role, where the authors might feel pressured into accepting you, to have their paper accepted. If you are very keen on publishing your method under your own name (provided that it is, in fact, novel), you have to wait until their paper is published, and then write a paper of your own. Note that you cannot use privileged information obtained as a referee.
Finally, don't sign your reviews. I would hope that the editor removed your signature. If you don't like giving blind reviews, you should abstain from accepting them, and provide reviews on open platforms which allows this. Like it or not, blind reviews is the name of the game.


BibTeX knows how to deal with this, using the entry type @manual:

@manual{abc,
    organization = {University of Neverland},
    author = {John Doe},
    title = {Manual for ABC123},
    year = {2012},
}

If you don't know the author because it is not listed in the document, you can omit the field. The name of the university will be used instead.


Is it okay to clarify to a PhD interviewer about a question that I was hesitant to answer then, but am not now?

He is asking you why you need a PhD, he is not asking you why you want to sell your research. So, I think the focus of your response is misplaced; why does it have to be presented in a way that if you're not a CEO + PhD then you're a loser who will spend the life publishing shelf fillers?

Instead of comparing to (you + PhD + company) versus (other + PhD + no company), think (you + No PhD + company) versus (you + PhD + company.)

There are dozens of way you can cast this decision positively without dissing the interviewers:

The vigorous training in scientific thinking will enhance my credentials as a CEO.
I would love to work more closely with the R&D so that I can better tailor my company's strategy.
I love to challenge myself, PhD is a great milestone, a trial for me to hone my grit.
I would love to see my research idea turned into a product that people would love, it's always been my dream.
There is a lack of research perspective in the current industry, I wish to change that.

Generally, try to project the difference between the normal you and a better you, not a better you and the inferior you. Some of the negative comments, as you said, may be hurtful even it's not targeted at anyone but yourself.


When should I publish in interdisciplinary versus subject-specific scientific journals?

My opinion on this is as follows. If your research advances the state of the art of field X, either by adding new knowledge specifically to X or improving existing methods/knowledge in X, you should submit to an X-specific journal. If your paper improves knowledge in field Y using methods from field X, I would either publish in a journal specific to Y, or in an Y,X interdisciplinary journal.


I am going to teach a course, but the classes have already started with another professor. Any tips?

It's a hard situation. I hope the other teacher can update you on what was done. Preferably with a bit of lead time before you take over.

I would, myself, spend the first session back doing a review. Or at least the first hour if classes are long. Ask the students a lot of questions. "What was the most important thing you learned in the past weeks?" "Anyone else? What..."

Try to make a list of the things that they thought were important. Have them ask you a bunch of questions also. How can you help fill in as necessary? One way to get a lot of questions is to ask for them to be written out on index cards. They can be anonymous.

This session should be mostly the students talking and you listening and prompting. Don't try to cover new material. Another trick is to ask them to write out (and hand in) sample test questions based on the previous weeks. Read these aloud as time permits. Get feedback from them on the questions.

Your goal is twofold: "where are they" and "how can we make a smooth transition".

This should give you a good basis for understanding where you can start in the next session. It should also give you a certain rapport with them as someone who listens.

But you will need to be flexible about where and how you start so that the transition is smooth.


What is the role of research in liberal arts college faculty evaluation?

I believe your list implicitly says this, but I'll include an answer anyhow, because I think this is an excellent question and I am interested in hearing answers that supplement what I write below.

Teaching divorced from serious engagement with the subject matter taught is arguably a very suspicious activity. In principle, if someone is paying a large sum of money to be taught a subject, the teacher should not only be able to convey his subject clearly, but also should be a practitioner of that subject. The living content of a subject is found in the minds of its practitioners, and so attempts to teach even the ideas which are archaic without the living insight driving honest contemporary investigation of the topic is very much in danger of becoming stilted, sterile or, perhaps worst of all, too packaged or neat.

One might oppose this view by pointing out that most undergraduate students do not need to know what is going on at the front lines of any subject, and the historical efforts and ideas, presented clearly in an engaged way, are enough. For cultural purposes, this may be so. However, a passion for teaching at the highest level morally ought to be accompanied by a passion for learning at that level, which is what research or serious scholarly engagement is at its heart.

Another strong argument against requiring research is the following: students at an average primarily undergraduate institution are generally not going to be prepared for graduate study in certain fields, so why should time and energy of faculty be sunk into research in such fields. (Many good institutions with PhD programs also need to remediate entering PhD students, suggesting that this problem stretches beyond undergrad-only institutions.) Again, though, I answer that learning and teaching should, ideally, not be decoupled.

A third argument is that it is possible for an engaged teaching faculty member to learn for his own enrichment and that this does not need to happen at the level required for research or peer review. I can only answer this, unfortunately, by my personal experience and opinion. It bothers me that when a student enters university in order to learn a subject, he cannot tell the quality of knowledge he will receive (whether the community of peers of a student's professor regards the professor's ideas and approaches as relevant). It is our responsibility to ensure that students are exposed, to the best of our ability, to ideas that have impact. I cannot see how to do this without being able to point to peer-reviewed faculty contributions.


I think the main problem here is the use of the term "published" just because it is posted on the web page. If a report is under revision, it is strictly speaking not published. Once published it should be fixed in terms of its content or it should carry some form of revision marking such as "Second Edition" or "version 2" in which case the different editions or versions must be continually available.

If you find some information in the 2013 draft which is later dropped, it means the authors no longer support that point for one or another reason. Hence it would be potentially bad to attribute such a point the authors.

So from this perspective I do not support any of your forms for referencing. It appears you should view the work as unpublished and only rely on the latest version as a source for information.


How much novelty should I add to my previous paper to get it published in New journal?

This seems unlikely. I doubt that an editor of a reputable journal would accept it, knowing the details. And it would be an ethical lapse to obscure the details, of course.
You can, however, write an extension of the old work, citing it as usual. But the new results would have to stand on their own to pass review. If they don't, then an option is to continue work until you have something that editors and reviewers (not readers here) find sufficiently "interesting" and novel.


Is there anything I can do about a teacher who is rumored to be unreasonably severe and whose class I am about to take?

As a former college instructor myself, the number one thing that made me willing to work with students was a willingness on their part to form a mutual relationship of trust.

I was always much more willing and desirous to help a student out when they treated me respectfully and did not treat me like I was out to ruin their life.

Let me also add that it is always of benefit for the instructor to know who you are. This is especially true in a class that potentially could have 50+ students in it (like introductory English). Try to find a way to introduce yourself to the instructor by asking a meaningful and intelligent question after the first class. Even just introducing yourself can sometimes be of benefit.

In closing, may I also be generally blunt? College is an entirely different beast than high school. The standards are often much higher. The negative reviews of this teacher could be negative in part because he is handed a sloppy bunch of kids who just want an easy A. Not always is this the case, but it is sometimes the case.


What do profs actually think when writing a letter of recommendation for an average student for grad school

If you want to go to graduate school and think you will be successful, you should apply. Let the admissions committee decide your package.

I've written plenty of recommendation letters for more "average" students and I suspect most other faculty have too.

The only time I turn down a recommendation letter is if the student really did poorly (e.g., sub-3.0 GPA) in my classes. Then I gently suggest students find another letter-writer. This has only happened once.

Plenty of average students go to grad school and most of them get Ph.D.s. The degree is not necessarily an indication of exceptional brilliance. There are brilliant Ph.D. recipients, and there are less stellar Ph.D. recipients. Instead, the Ph.D. indicates a number of factors, including the ability to do independent research, a great deal of learning and advancement beyond a master's or bachelor's degree, and a huge amount of perseverance.

So I will write a letter appropriate to the student. I will indicate the grade they received in my class, or the research work they did in my group (e.g., "top third" or "top half of the graduating majors").

In terms of writing the recommendation letter, I try to stress positive points, but I am also honest to the admissions committee.

On the other side, the admissions committee knows how to read recommendation letters. There are many graduate programs, and not all programs expect the truly top students. So they can translate your application package into an evaluation of how likely you are to succeed in their program.


Gender transition as a starting faculty member: a terrible idea?

How infeasible is transitioning as an early-career faculty member?

I transitioned as a postdoc back in 2013, so I did it.  Whether or not it's a terrible idea depends on many factors, and just plain luck.  I don't have experience in industry, so I can't comment much on that.  But I'm sure it's the same situation: it depends on many factors, and plain luck.
Travel
One thing that would likely be distinct between academia and industry is traveling: conference travel is the norm in academia.  This has two important consequences:

Surgeries for transgender medical procedures are not performed in most places, e.g., in Canada, there's only one clinic that performs GRS (in Montreal).  Different surgeons have different styles, and have different levels of experience.  To be able to choose one's desired surgeon (and get the most suitable results), one needs to be able to travel, which I expect is far easier in academia than industry.
For surgery, I organized to attend conferences nearby, which helped ease the travel costs.  My hormones are prescription-free in Turkey, so I stock up when I'm there.

Traveling is more difficult for transgender people, including security inspections, applying for visas, carrying medicines, facial hair growing during long flights, dilation, shared accommodation, and so on.  In fact, some countries have anti-debauchery laws.

I highlight some other important factors below.
1. Transitioning is personalized.
Everyone's transition is different.  For many people, transitioning is essential: they choose between transitioning or killing themselves.  Other people find it suitable to not transition full time.  Many people are between these two extremes.
Whether or not what you have in mind is "a terrible idea" depends on you: (a) how critical it is to transition, (b) your financial situation, and (c) your family situation.  And many other factors: religion, friends, disability, race, local laws, and so on.
2. At no point is transitioning convenient.
I doubt there will ever be a point where you feel now is the optimum time to transition.  At the very least, a huge amount of time gets eaten up with updating one's documents and medical care, along with simply learning how to dress and behave.
One point: If you wait, are you going to publish under your dead name?
My experience is that students mostly don't get involved in the transition.  If you stay focused on the material, so will they.  I would say family is probably of greater concern than students.  However, there's inevitably some complications: your reputation (good or bad) rubs off onto your students, and writing letters of recommendation can be a bit awkward.
Some people take medical steps (such as sperm donations, hormones, facial hair removal, etc.) prior to socially transitioning.  However, WPATH standards of care for various medical treatments have real life tests, which is relevant if you're intending to seek medical treatment down the line.  You need to establish yourself as your gender to get medical referrals.
When I've asked older transgender people, they only ever say they regret not transitioning earlier.  In your case, if you end up losing your hair, it could have significant and irreversible negative impact on your quality of life; you may want to consider starting medical treatment soon.
3. Transitioning takes place with incomplete information.
Whatever decision you make, you're going to make it without all the information.  You won't know how people will react in advance.  You'll make a decision without knowing which path is best.  And, regardless of what you do, you'll probably spend a fair chunk of your life thinking you made the wrong decision.
4. Don't overvalue being passable.
Being passable helps everyday activities proceed smoothly.  However, my impression is that if someone is making an effortful attempt to present and behave as a certain gender, one's gender will almost uniformly be respected (despite not being passable).
Setting a goal of being passable is risky; it is often not achievable, and it can be devastating to accept that oneself is not passable.
I'm mostly passable nowadays, but people still find out about my past through my prior publications.  Generally even if they find out, they act like they don't know.
Hormones make a big difference to passability (but they take time).  There's also surgery, such as facial feminization surgery, which is a major improvement, but it's expensive and a referral may be required, depending on the surgeon(s).
5. Unpredictability.
Transitioning takes time, and over time people's values change.  There's also a roller-coaster of emotions, a "second puberty" when one undergoes hormone therapy, and often dieting becomes important (which may mean a lack of energy to be productive).
Particularly difficult for me was belonging to a "boys club" (mathematics/computer science) while I was desperate to establish and assert my femininity.
People are unpredictable.  Just because someone has liberal values, and so on, doesn't mean they're going to be accepting.  Likewise, just because someone is conservative, doesn't mean they're going to be hostile.  The people you work with make a difference to your quality of life in general, and it's impossible to predict.
Task difficulty is unpredictable.  There's going to be things that turn out far easier than expected, and things that should be simple which are complicated.
Mental health is unpredictable.  It's difficult to maintain mental health as a transgender person.  It's possible to end up with depression and/or anxiety, eating disorders, and engaging in self-harm or suicide attempts.  (Every transgender person I've asked has a clear plan on how they would kill themselves.)  And even without being transgender, academia can be a rough ride mentally.
Relationships are unpredictable.  In addition to transitioning having unpredictable effects on your current relationships, hormones (if you choose to go down that road) are known to affect people's sexuality, which may impact if and who you marry, which may impact your career options.  Moreover, if you end up marrying a man, by default a husband's career is socially considered more important than the wife's, and it's considered the wife's responsibility to look after children (perhaps through adoption).
6. Other points.

Don't get lost in your transition.  It's common for transgender people to end up only thinking about their transition, and that becomes who they are as a person.  My impression is that this causes others to perceive you as "a transgender" rather than "a woman".  I feel it's best to develop non-transgender-related interests.

Work harder than expected.  Job security is a big deal for mental health, but on top of this, medical treatment is expensive.  So I encourage you to make sure your colleagues have instances in their mind where you have gone beyond what's expected.

Have ambitions beyond merely surviving.  It is hard to have goals when you feel like you're merely surviving on a day to day basis, but it's good for one's mental health.  Don't just constantly perceive yourself as a victim, but do something with your life.

Expect hiccups.  While deeply hurtful, you're inevitably going to be misgendered and deadnamed, have people comment on your appearance, have people scheming behind your back, and so on.  When this happens, it makes me paranoid (Is this what people truly think of me?).  Somehow, you need to continue to be productive despite this.  As you become more established, these hiccups become less frequent.


Why might my tutors from several years ago not respond to my email request for a meeting?

The absence of a response can be because of several reasons. Your mail can indeed end up as spam but it is usually the e-mail system that sorts it there automatically, not the person. Sending additional mails will then be pointless unless the recipient actually goes through the spam folder to look for erroneously sorted mails.

A more likely reason for the lack of response is a matter of priority. I think etiquette would dictate at least a brief answer to the effect that the mail was received but cannot be followed up. You are requesting something that is a personal favour to you. As such, and as has been commented, it is only fair and indeed professional to provide a short and clear statement of the purpose of the meeting. After all to meet someone during work hours better be about something work related.

The tutors have probably also tutored many others. From their perspective, you, without any derogatory intent, will be one of many. I often get requests from students who apparently think that because they are out of the program they should be "friends" with me. I would end up with many such "friends" but none that would have any significance either professionally not privately. Hence there is an unbalance between how your tutor has meant something for you and what you have meant to the tutor. This is built into this sort of relationship. Hence, you need to look at the formal role of both parties and evaluate if your reason for contacting the tutors is mostly a professional issue or a private issue. In the latter case, the response may be less than what you would wish for. If your cause is professional, you are far more likely to get a timely and satisfactory reply.


I discovered a new analytical integral. How should I present this knowledge?

You actually have three choices: physics, pure math, and applied math. It might be useful in any of those domains.
But there are two questions to ask, and they are related.

In which domain is this result most useful?
How is it connected to other things within each of those domains?

A pure mathematician will find the result most interesting if you have strong connections. A physicist or applied mathematician will find it most interesting if it is useful outside its original application.
That's not to say, of course, that any of them would find it uninteresting. But they are all looking for things that can be used to extend their own work.
So, I would try to figure out where it fits most naturally and write it up accordingly, focusing on either the connections or the usefulness. Then send it to any good journal in that domain and listen to the feedback you get. Reviewers may agree that you have chosen correctly or not.


Does submitting TeX sources to arXiv increase risk of plagiarism?

is it really true that this does not make plagiarizing data easier than the simple PDF submission?

The Arxiv doesn’t claim this. All they claim is that plagiarism is pretty easy anyway. The respective Arxiv text reads:

  There is no file format or other technological device that can protect you from [plagiarism]. At the very least, unscrupulous re-typers would always remain a threat. Postscript does not provide a barrier in any event: it is quite simple for someone with a little knowledge to extract any text from a Postscript file. Moreover a plagiarist who cuts-and-pastes directly from your TeX source is all the more easily detected, since the source is easily identified. We archive all versions of papers so that we can assist in any priority or plagiarism disputes.

  So, how safe is it to submit (La)TeX source files to arXiv?

For all practical purposes I would say it is as safe as any other type of Arxiv submission. I concur with the Arxiv that making a technical copy of your article is pretty easy anyway. Even re-typing the entire article and using screenshots of your graphics is a comparably easy task. Yes, the quality may suck, but that wouldn’t bother the plagiarist.

The main challenge to successfully plagiarise is to use the plagiarised article and remain undetected – not making a technical copy.


How to supply proof that you are a reviewer for a journal?

You don't need to prove it. If someone thinks you're lying, they can just contact the journal editor and check. Reviewers aren't supposed be completely anonymous, anyway. It's just that no one outside of the editors should know who reviewed which articles.


"Please enter any comments you would like to send to the Journal Office"

This kind of question is a "catch all" in case there is something you wanted to add that did not fit in any of the other questions in the submission.  If there's nothing you can think of that was not already covered in the rest of the submission, just leave it blank.  I have now submitted a number of papers on submission sites that use a question like this, and I have never had anything to add.


When and why did journal article titles become descriptive, rather than creatively allusive?

There's an interesting discussion of this in the introduction to Titles are "serious stuff": a historical study of academic titles by Salager-Meyer and Alcaraz Ariza (link). One point they argue is that titles (as well as abstracts) increasingly need to be more informative given the growing production of papers, in order for readers to make quick decisions on whether to read them or not. If this is the main factor, the information content would be expected to increase similarly to the size of the relevant academic community.
However, there's something I find much more interesting hidden in the introduction:

Other scholars have stressed that titles should be as informative as possible in order to facilitate the process of storing, searching and retrieving the information (Black 1962; Mitchell 1968; Tocatlian 1970; Feinberg 1973; Manten and Greenhalgh
1977; Hodges 1983; Diodato and Pearson 1985).

The paper by J. D. Black (IBM British Laboratories) is titled The Keyword: Its Use in Abstracting, Indexing and Retrieving Information and discusses how

Librarians have been accustomed to using systems, schedules, thesauri, lists of headings, etc., to define and classify the literature which comes into their keeping. They use these same methods to retrieve and disseminate this literature. However, within recent years these methods have begun to show signs of strain, and in some cases breakdown, due to the tremendous increase in the volume and complexity of technical literature.

Specifically, Black showed that a 1960s era (punch card) computer can be used to extract keywords from a title to achieve a similar efficiency as manual classification, but for significantly cheaper cost, and allowing better scalability. Black also writes

While the index may be practical and usable, we still do not know precisely how efficient it is. In its present form, the efficiency is dependent on the author's choice of title. <...> before long the engineer, scientist, or mathematician will realize that if his title is not descriptive enough his paper will not be used as much as it might be.

Of course, if this automation of title processing is the main factor, one would expect to see a significant increase in the information content of titles starting some point in the late 50s, or early 60s. A 1970 paper by Jacques J. Tocatlian called Are titles for chemical papers becoming more informative? looked at precisely this, by comparing measures of information content between papers published in 1948, 1958, and 1968. (1958 being the year the KWIC index, or Key Word in Context, was introduced.) As Fig. 1 below shows, they found no significant difference between 1948 and 1958, but very different results for 1968. Here the measure A, for example, is defined as the total number of substantive or informative words. On the other hand, Fig. 2 shows that titles with few substantive words might have started being eliminated before the introduction of the KWIC index.

I don't know if there is similar evidence from other fields that the introduction of automated indexing was an important development, but it strikes me as likely that the same mechanisms would apply elsewhere too. So, long story short, a growing number of publications and the introduction of computers may have driven a large part of the push towards more descriptive and informative titles.


Can a PhD student write recommendation letter for me under whom I worked?

Everyone can write a recommendation letter for you. So the answer is an absolute yes. Nevertheless, the question now becomes: how strong can a recommendation letter written by a Ph.D. student be in order to have a strong application in order to get accepted? But this is a different story.
You may want to send it in addition to the other recommendation letters.


Requiring student to participate in online challenges to complete coursework

This sounds like a great idea to me overall, but I can see a few potential issues:

It's possible that one or more of your students might already be a participant, which could raise issues of fairness.  (Other students may complain that he/she got a head start.)
Similarly, the fact that these problems are widely distributed on the web may make it easier to find solutions online.  I haven't looked at the Project Euler solutions online and don't know if they are any good, but it's not hard to find purported solutions.  This could also be a pain for you: if you make it easy to cheat, then you're more likely to have to figure out how to deal with cheaters.


Is it acceptable to paraphrase or include reviewer's comments in revised manuscript?

It would be acceptable to paraphrase the referee's comments, although if you do so, you should take care.  First, the paraphrasing should be thorough.  You cannot quote an anonymous* referee directly (since you do not know their identity to cite them), so what you put in your revised draft should not include any specific extended phrases used by the reviewer, of the kind that would normally need quotation makes.

Second, you should point out explicitly in your reply letter with the revised manuscript that you have followed the referee's way of describing the subject matter carefully.  Make it clear that you have done so because you though the explanation in the referee's report was exceptionally clear.  The referee is likely to be flattered, but in the unlikely event that they have some problem with your having done this, they have been warned and can ask you to make further changes.

Third, you should include an acknowledgement to the anonymous reviewer.  This person has made a minor but specific contribution to your paper and deserves credit at that level.

*I have assumed the reviewer is anonymous.  If not, things probably do not change very much, although you have the option of simply contacting the reviewer to ask whether they are okay with you paraphrasing them this way.


How do I cite a webpage with no author but a possible corporate author?

In Harvard style the Author is a Key to the bibliography, just as the index number (like [1] is a key in Chicago style). One has to disconnect this from the concept of a name. In particular, when citing a web page with no clear author name one has to find a similar keyword to use. The corporate name makes a good keyword. It better to remember it is only a keyword and not start to use full sentences. The full details of the reference will be shown in the bibliography. So the Title of web pages should almost never be used. Thus for your example I would cite like this: (WWE, 2002). The bibliographic entry would be:

  WWE (2002), "World Wrestling Federation Entertainment Drops the ‘F’", World Wresting Federation Corporate News, 6 May 2002.  [Online] Available at: http://corporate.wwe.com/news/2002/wwe-corporate-world-wrestling-federation-entertainment-drops-the-f [Accessed: 12 Apr 2016]


Is a research assistantship considered full-time employment?

I don't have citable information to give you but being a doctoral student and usually being on a research assistantship, anecdotally, I can tell you that in the United States, if you are a full time MS/PhD student and are on a research assistantship then it is not considered a full time job. Your full time job is that of a "student".

This was confirmed by an HR representative of my university because I asked her this exact question.


Should I complain to higher authorities about the incompetence of this teacher?

This is more of an extended comment, placing some guesses as to what's actually happened here. As an answer to the question it is the advice to consider which parts of the following applies to your situation, and adjusting any actions you may take accordingly.

Keep in mind that computer science is not programming. This instructor likely doesn't code much Python in their main job (CS research presumably), nor did they necessarily ask to teach Python. Rather, the departement decided to teach Python as a beginner language, and somebody needs to do that teaching – somebody who knows enough about programming to help actual beginners, which will be helpful to the course's intended audience, but not necessarily an actual Python expert.
You, apparently, are a Python expert, which is great – relax, this course is going to be easy for you, and if you can even contribute to making it better for your fellow students, awesome.
But don't let your superiority in Python fool you into thinking the instructor is inferior as a teacher of a beginner's programming course. You think their introduction to the language was bad... why?

Was it hard to understand? Well, that could mean they explained stuff badly, but surely you as an already-expert wouldn't have had problems regardless?Maybe they actually explained some aspects that really are more tricky than you ever considered.
Was it too shallow? Well, that may be exactly what's right for your fellows without earlier Python background.
Did it use outdated or unidiomatic code? This happens a lot in university courses, but it's not necessarily such a bad thing. Keep in mind that anyway today's up-to-date is just tomorrows outdated and one language's unidiomatic is another's bread&butter. General concepts are more important in a beginner's course than language-specific details.

Regarding your concrete statements,

doesn't know what a return statement does

I plainly refuse to believe that. I mean, if it's really that bad then forget all I wrote above... but almost sure there has just been a misunderstanding here.

or how to iterate over elements of a sequence

That too should certainly not be a problem to anybody teaching anything programming-related, however I would still remark that Python's iterators are somewhat idiosyncratic. It's true that for a Python course, they should have read up on this properly, but again make sure you're actually interpreting this properly. First teaching loops with indices before going to range- / iteratee based ones is a valid pedagogic decision, even if it doesn't make much sense as far as Python programming in particular is concerned.


Is it possible to do a text search just within the references of a paper?

I do not know of a tool with such functionality built in, but with automation (using a tool like iMacros or Selenium), you might be able to obtain the result you seek. (Unfortunately, it is beyond the scope of my answer to explain how to use such a tool, so I understand that my answer might not be useful if you do not already have such skills and are unwilling to learn them.) The procedure might be something like this:

Navigate to a web page with the full list of references of the article whose references you want to search. This should be in a full text database like EBSCO, ProQuest, etc.
For each listed reference, use the automation tool to copy the title, authors and date of the reference.
Use the automation tool to search for the referenced article in the database. If you enclose the title in quotation marks, the first article that comes up should usually be the referenced article that you want. But you should use the automation tool to record the full citation details of this first article so that you can manually verify later that it is indeed the article that you wanted. (This latter step is important!)
Use the automation tool to click on the first article that comes up, then search for the words you are looking for.
Use the automation tool to save whatever results you want.
Finally, double check the list of full citation details of the articles that the automation tool actually searched on (that is, the first one that came up for each search) to make sure that they are the correct articles you intended from the references list. Whenver you found that the automation tool guessed wrong, then manually search for those articles.

Again, this answer only helps if you know or are willing to learn automation tools. (If you do choose to learn a tool just for this project, you will probably find that it opens new opportunities for lots of projects in the future, so it might be worth your time.)


Should I submit a rejected paper as it is in some other place so that publication decision comes quickly?

Ignoring reviewers' comments and simply resubmitting to a different journal sounds like a bad idea to me, for a number of reasons,

While some institutions are obsessed by quantity of publications, quality is at least as important for building a reputation (not to mention more altruistically for actually improving the state of knowledge in the field). If the reviewers have advised you on how to improve it, and if they are not obviously talking rubbish, it seems unwise to discard this advice without a very good reason.
It's entirely possible that the new journal may send it to one or more of the same reviewers as the old one did. There are existing questions on this site from reviewers who this has happened to, and the results are unlikely to be good for you if you have not changed anything. The reviewers are unlikely to recommend acceptance, and the editor may be annoyed if advised of what has happened.
Even if it does get published without revisions in the new journal, the previous reviewers are likely to read it, and it won't do your reputation any good with them.


what happend status of the journal changed back to the under review from reviews completed?

After reviews are complete the editor has to make a decision about the paper. There are various possibilities between accept and reject including "seek more information". For some reason the reviews weren't sufficient for the editor to either accept or reject and so they sought more information - putting the paper back into review.

It might have been simple like seeking a clarification from one of the existing reviewers or it might have been asking someone new (or several someones) to take a fresh look.

It might even have been that the editor sent the paper originally to the wrong reviewers and so got back nothing useful.

It is possible that they will respond to a request from you for the reason. Your situation isn't unique.


Applying for another job within same department?

This seems to me to depend on personalities more than anything. You need to make a judgement about the reaction of your boss. Most people, IMO, would support you in any career advancement. Giving early notice, in most situations, is beneficial, as it lets them know that they may need to search for a replacement or otherwise arrange schedules, etc.

Putting your options out, as you have here (fantastic opportunity, career goals...) would probably be a good way to approach it. I don't think anyone expects you will remain a post-doc forever.

If your boss is a reasonable person, then it would seem to me that s/he would be happy for you, and happy that if you get the new position that you will still be available for consultation and that your expertise won't be lost.

There are exceptions, of course, even beyond personality. If one is working with highly sensitive information, for example, it might be necessary to escort them off premises immediately on hearing that they might be leaving. But the situations in which you would need to hide your application would, to me, be rare.

Finally, I think that the issue of same department has no real world meaning in such a decision. For example, most people would celebrate a move from post-doc to tenure track faculty.


Is it better to submit a paper to a journal "normal" issue, or wait 4 months and send it to a more focused "special section" of the same journal?

I would strongly recommend choosing the special issue unless you are studying something time sensitive due to competition (e.g., you have a known competitor who might publish tomorrow) or emergence (e.g. an ongoing natural disaster).

First, depending on how the journal works, you might not actually have any delay in publication.  Check and see whether the journal has a "just accepted" or "online first" section.  If so, then your article will not have to wait for a special issue package to become available and citable.  Instead, special issue articles will become available asynchronously as they are processed, and then packaged later.

Second, special issues, while they are reviewed no less tightly, have a specified audience that improves your chance of acceptance.  You can much more readily pass the "audience interest" bar that many high-profile journals apply, since somebody else has already made the case that work in this area is of broad interest. Also, because reviewers are picked with expertise in the subject, you are less likely to get a bad match with a reviewer who knows little of your subject.

Third, you are likely to have a higher long-term impact from the publication, as it is grouped in a package with others like it, where it will be easier for people to discover or seek it out.

Finally, in most fields, four months is just not a long time.  Finish your paper now, send it to the journal special issue before the deadline, and move on with your work.


MBA with a BS in Comp Sci, pros and cons?

When you say you are interested in business, do you mean you want to be a manager? Or in finance? Or are you "academically" interested and you simply want to learn about things like OB, finance, accounting or Ops?

If the latter, then I suggest online personal enrichment programs (like coursera, etc.).

If the former, then an MBA may be worth the time and money; many companies want people with an MBA for certain positions (this is especially true of consultancies). Other companies view MBAs as a cliched, cookie-cutter education and avoid them.

You need to figure out what kind of career path you want and do some research regarding the benefits of having an MBA for that path.

As a datapoint: I am a programmer with an MBA (from a top 40 US university). It was not worth it.


How to get permission from Google to use Google Scholar Data, if needed?

Google Scholar, as you said, does not provide API, nor a complete documentation.
In the comment Davidmh cites this question, and I think that settles everything:

Google Scholar robot.txt disallows bots
Google service Terms of Service says

  Don’t misuse our Services. For example, don’t interfere with our Services or try to access them using a method other than the interface and the instructions that we provide.

  So, in the end, you don't have permission for a script that fetches multiple pages at a time.

Following this Quora question, I found scholar.py, that is not an answer to your question but could be of use (I have not tried it).

Furthermore, I also asked the developer of the H-Index GS Calculator, to get another opinion, but I'm sure the "one-click" nature of the plugin complies with the ToS. A bot does not. Maybe you can change your system in this direction.

UPDATE: the developer says the in the past he wrote the GS team the same questions, and they replied

  you can do stuff, respecting the ToS (so, no bot)
  they will not provide an API, for legal constraints with affiliated digital libraries (ex. Scopus, WoS, etc.).

Also, his calculator has a throttler that reduces the number of queries per minute, to mitigate the issue. There are few simple techniques to "cheat", but, we are at the boundaries of the ToS :-).


How to cite a journal paper which do not have a page number?

Officially that number seems to be called Article Number (see the Table of Contents of Vol. 176 of that journal; the journal seems to have switched from 'page numbers' to 'article numbers' with Vol. 166).
It nevertheless seems safe to call it the page number. The reason is that Elsevier itself deposited that 'article number' as the 'page'-metadata in CrossRef (a depository for research papers' metadata).
See here: http://api.crossref.org/works/10.1016/j.sigpro.2020.107674, where it says:
"page":"107674"


I think that there are a lot of different variations, between continents, countries, and even individual universities. It is definitely true that pretty much every school in the US will have its own policy (since there are no national policies regarding registration in the US—although there are some rules that apply to financial aid obtained from federal sources). In Europe, things can also vary greatly between countries and schools (although they're trying to standardize things, this is still very much a work in progress).

Your best bet is to contact officials at the international office of whatever institutions you're interested in attending, and asking them directly.


Can I have both my supervisors write reference letters?

I've sat on my department's graduate studies committee during application season, and so I can provide at least one point of anecdata for how PhD application recommendation letters are used, at least in my tiny corner of the academy. YMMV.

First, These letters are among the last things that are looked at. We don't have rigorous thresholds for grades, GRE scores, subject GRE scores, publications, etc. But all of those things are used to "objectively" sort the pool. First the obvious admits are skimmed off the top, and fellowship offers are made to some of them. This is the first place where letters are important, since quotes are mined from those letters to try and win funding for these students from the University (i.e., we entice the student with a prestigious award, and the department doesn't even have to pay for her!) The money quote is usually a ranking and/or direct comparison -- "In my twenty years at Giant State University, I've seen no more than 5 students of X's caliber. I would say her talents remind me of Y's at that age, who is now a professor at Prestigious U" -- and this is why even a mediocre teaching letter is more useful for this purpose than a nice letter from a PhD student (who can not be counted on to have a reasonable intuition for another's future potential).

Second, we work our way down to the marginal cases; this is much more difficult since the marginal cases require a more holistic take on the application package. No one gets immediately thrown out just for bad grades or a bad subject GRE score, but we expect some explanation of a mitigating circumstance (not an excuse!) in the personal statement, and hopefully reflected in the letters as well. For example, if you were dinged in the first pass for a low GPA, we would like to see that it was a bad first year (and not a bad fifth...); that you are on an upswing. If you think you might be a marginal case for whatever reason, the letter from the PhD student might be helpful -- perhaps you don't have any publications, but the PhD student can vouch for your work and verify that you have something in preparation, or explain why your project failed (projects often fail!) but that nonetheless you mastered some state-of-the-art technique on the way.

On the other hand it is a big waving red flag if those things are then not pointed out by your actual boss (the PhD holding supervisor). If you think the student will write a better letter, then you're probably best off having that student lobby on your behalf with the professor, to make sure the professor's letter is strong, and then get a second letter from someone else.

I would strongly recommend you do not ask for a letter from a non-academic unless it was an actual research position (and even then, these can be iffy if the supervisor has no letter-writing experience). On occasion we see glowing letters from a student's supervisor at their summer construction job, or a call center for a political campaign. Well-rounded students are great, but such letters are almost useless.


Can a PhD student who preps animals for study, but didn't collect data, claim co-authorship?

I think there are two ethical issues here:

1) Authorship. By most definitions, the work you did does not qualify you for authorship, because you did not have a significant hand in drafting/designing the research or the manuscript (that doesn't mean some labs wouldn't assign authorship in this case, but that if you read the fine print for authorship requirements for journals or professional societies, animal husbandry would not be sufficient). It seems clear you did not have a role in the manuscript because you didn't even realize your name was not included in the authors list or acknowledgments until now.

It would generally be good practice for the authors to at least include in acknowledgements somebody who did as much technical support as you did, and it would also be good practice for you to be offered to contribute to the manuscript and analysis to attain authorship privileges. You should not have been offered authorship as an incentive if the PI and other student did not intend to allow you to earn it.

2) Research ethics and appropriate use of graduate students. I think this area is where you have a greater case. It sounds like you were made to do way more work on another project than should be typical for a graduate student. A technician, sure, because your primary position would be as a paid assistant in the lab, but as a student, your primary position is as a student.

I am unclear why your PI thought this other student should not learn to work with the animals when their project was so dependent on animal work - that doesn't seem to be full training, how is the student going to start an independent research career if they have not learned the basic techniques of their field?

By no means should you expect to always work solely on your own project, but, unless you are overstating your contributions, which I understand is certainly possible, it seems like you were made to go beyond the normal level of assistance. I would consider carefully the technical contributions the primary author made to the project, and weigh how your efforts compared in terms of total hours.

Have you also had time to work on your own independent project, and is that work progressing to your satisfaction? If yes, then maybe there isn't a major issue, and this is just an unfortunate situation you will learn from in the future and you certainly now have a good reason to stop doing this work for other students. If no, then you certainly need to address this with your supervisor, and if you can not reach an arrangement that is suitable to you, you may need to talk to your program or department to get further guidance.


Changing Phd topic in between because of lack of 'usefulness' of current research

First of all: talk to your supervisor! what does he expect as results? What does he think? does he really want to leave you for the rest of the time doing nothing?

I think, to say that a technique B is not useful to solve A can be a PhD alone. Are you really sure that it is not? Did you exploit EVERY possibility? Or are you just not interested in finding the right way but are more interested to do something that works?

Even dough in the end, Einstein, Newton, Gauss and Shannon are the ones who were right, but never forget about the hundreds and thousands of people, that tried another approach/theory but found out it was a dead end! This is research. Writing that and why some approach not works is as valuable as finding the right path. Mostly regarding such a big field as you mentioned.

If you can really state that there is no way to use this technique (and propose other/ use similar techniques like ANN or ML in general), that's already good research. I really think, you just don't like to do a PhD at all?

  I do not wish to be an academician and investing my time on training myself in such a work is not in sync with my aspirations

Three possibilities:

give up the PhD and go into industry. There are a lot of companies which do research, mostly in the field I assume you are working on (machine learning, big data?)
Ask your supervisor what you should do next and stick with this PhD
if you really find another topic, which you find very interesting (even if it may fails! that's academic research, stick with it...), you may start a new PhD. But I would only suggest that if you do it for the fun of research and not as training. What you actually train as a PhD is doing research on your own. So don't expect the same experience and usefulness for the industry you would earn in the industry.


what happens to the grant I wrote with my PI if I switch institutions

If your name does not explicitly appear in the proposal as an investigator, then the funding, if the grant is awarded, is not committed to you in any way, shape, or form. The PI could in principle take your ideas and use it to fund another student to work on your project!

Unfortunately, most universities will not let grad students serve as PI’s, with the exception of some programs that are specifically aimed at graduate students, such as the Kirschstein Fellowship at the NIH. So you are definitely running the risk of writing your idea up as a proposal and ending up with absolutely nothing to show for it.


Is it polite to ask for acknowledgement of transcript received at university

Since you are already accepted and they are asking you for materials, it is perfectly acceptable to correspond with them quite regularly to follow up and ensure everything goes smoothly. In fact, I would very strongly encourage you to do so, because paperwork is easily lost, misplaced, or delayed until it creates quite the inconvenience for you!

A script such as this would be quite fine:

email them that you have sent the transcripts and they are supposed to arrive by X date (you are past this point, but it is good to know for the future)
email them 1-3 days latter (depending on the urgency of any deadlines), and tell them you were told the transcripts would arrive by X date, and would you kindly confirm if you have received them?

If 3-5 days pass without confirmation or other reply, feel free to politely follow up and ping them again. Something of the general form "don't want to be a bother, but I know how bad international mail can be [you are giving them a polite 'out' so it isn't them being slow, it's probably someone else's fault], but have my required transcripts been received?"

If another 3-5 days pass and you still haven't heard anything - or sooner if you are running against any kind of important deadlines that you are aware of - feel free to escalate the issue with a call to the office, contacting someone else in the hierarchy (director of the grad program, for instance), etc.

None of this is impolite - it's just how things work. You are ultimately responsible for not falling through the cracks, because you are the one who pays the greatest cost of things get lost in the shuffle. You can be polite in your phrasing (but at least in the US no need to be excessively deferential - just clear, to the point, but with a touch of politeness and please and thank you), but following up and making sure things are received and acceptable with reasonable time to process inbetween is both fine and highly suggested!


License and attribution of images in compiled work for public outreach

There's a lot of confusion around this sort of thing in academic circles, because academics have been trained heavily about attribution, but attribution is mostly orthogonal to copyright. There is no general right to use things for academic/non-profit purposes, unless copyright law in your country happens to include "fair use" or similar provisions. They vary from country to country so I can't advise on them.

Some specifics, based on what you asked:

Something in the public domain can be used however you like, as the author has relinquished all copyright claims and "gifted" the work to the public.  Thus you can use it, modify it, etc. However, do not assume (as some do) that anything you see online is public domain. It's probably best to assume that something isn't unless you see a statement to that effect.
Something with a creative commons licence can be used according to the terms of that licence. The various varieties are quite self-explanatory. All will allow you to reuse the work for non-commercial purposes, but not all allow you to modify it (the "no derivatives" variants).
Something without any stated licence or that expressly reserves rights should not be used without permission - except possibly as provided for by any "fair use" style provisions that your country may have.

Generally the licence for your work need not be controlled by the works that it contains - "viral" or "copyleft" terms such as those of the GPL are not common outside of software licencing. However, if you choose a licence more permissive than that of works that your document contains, you should make it clear that it does not apply to (eg) those figures.

Disclaimer: I am not a lawyer, and this is not legal advice; any of the above may be wrong in your, or any other, jurisdiction!


What is the code of ethics and citation in course development

This depends on your definition of a "course". Is it an online course? Do you earn money with it or is it available for free? Or do you actually mean an old-school course taught at a school somewhere to a small group of people?

If it is a free online course, you should at least mention somewhere where you got some of your ideas from, as a courtesy to the other authors. The course they made might be part of their portfolio with which they apply for jobs, if your course then raises doubts concerning the originality of their work because you did not reference them properly, that would be bad. (You should also double-check whether they have written something about this topic somewhere, maybe they released their course under a Creative Commons license, for example.)

If it is an online course that you earn money with (Udemy or some other e-learning portal comes to mind), the situation is probably more complicated and there would be some legal issues that I don't know anything about. In this case you probably have to mention your sources and also ask for permission.

Finally, if it is simply a course taught in a classroom, I think it does not really matter. Your students will not care where you got your ideas for the design of the course from as long as the course is good and helps them to understand the topic.


We want to start working in a new research direction. How to proceed as the first student in the group?

For your question from the research groups perspective there is no definitive answer. Many things are possible and it depends on the group, the students, the field and whatnot. However, if you plan to enter such endeavor, you should discuss plans and responsibilities.

For a personal perspective: It is a lot of work to go into a new field. Read basics, but stay up to date. Talk a lot to people who work in the field to get a better sense, what the pressing questions, the important goals are and learn the jargon. Listen to talks on the topic, prepare well ad ask questions to get in discussion.

The bad news is, that nobody can guarantee any short-term outcome (unless you can somehow figure out some low-hanging fruits in the new field)…


Peer review - discussing paper with the author

The benefits of peer review are first to detect and prevent fraud and ridiculous claims, and second to improve the clarity of the published record. So, in general terms, if your conversation furthers these objectives, it's a beautiful thing.

On the other hand, if formally reviewing the paper comes with a commitment to maintain confidentiality, you will want to reconsider, and think carefully about how you back out of either the conversation or the formal review.

Confidentiality has benefits, like allowing reviewers to be critically honest without fear of retribution. It also has problems, like the inability to have an efficient conversation about honest disagreements and misunderstandings. This handicap is why some journals (along with the preprint system) are starting to allow for conversation without the blinds of confidentiality. If your journal-specific reviewer expectations do not prevent an open conversation, it may be the best approach.


Is it acceptable to contact the PI for a research position, in addition to applying through the careers site?

Unless this is an extremely high-profile position likely to get thousands of applicants, I don't think there is any harm in dropping the PI a brief email (3 sentences!) informing them you've applied for their position, telling them how much you respect their work, and letting them know they can contact you if they need any additional information.  If their HR department is useless, the PI may ask you to send your cover letter & CV.  But write the letter in such a way that the PI can easily ignore the letter (doesn't feel obliged to respond) if their HR department functions well.


When lecturers mark the worksheets / assignments, they try to assess student's knowledge and understanding of the subject. Of course, they can not look inside the student's head, so they have to make judgement based on what they see. Mark schemes and rubrics are introduced for the sake of objectivity and consistency, particularly when several lecturers share the marking. However, we have to accept that no mark scheme and rubric can cover absolutely everything. There are always some distinctions between students' works which are not accounted for in the mark scheme, but still (by a lecturer's judgement) should be accounted in the grade. That's what she probably tried to explain to you when you asked.

It is impossible to tell from the fragments you show if your work is really of the same quality as you peer's or not. We can't tell by just looking on your graphs --- something essential may be written in the comments above and below. To me it looks like these two papers are both wrong in some aspect, but I am not sure these errors are "equivalent".

You professor backed up a little by offering you an extra mark. It is hard to tell, if you really convinced you that she's been unfair, or she just don't want to spend her life arguing about it. It may well be that she deviated from the rigid set of criteria prescribed by the mark scheme, but I would not blame this on her personally. The mark scheme is not the law, in a sense that it is probably not more important than your professor's expert academic judgement. I can see a point in your frustration, but it really looks to me just as a manifestation of the complex nature of academic assessments in general, not as her bias against you.


My paper is accepted for a presentation in a conference; but I can not attend. Now what?

You'd have to ask the conference organization. You should try to get somebody to present the work for you, or (just out of courtesy) tell them it won't be presented (so they can schedule talks correctly).

What will happen is up to the conference. Some I've attended just did not publish papers which weren't presented, others did publish in their proceedings regardless (you had to pay any attendance fees, at the very least). What happens with "selected papers" also varies, one conference I went to selected papers only among those presented, including in their selection the presentation and questions and answers, asking selected authors for a revision based on the above.


Realistic time frame for GRE scores to appear in My GRE account

I believe, 3-4 years ago (woah...) when I took the test, it took approximately a month for the scores to appear. When you leave the test they will give you a score right there for the math and reading portions of the exam-- they state that these may change, but from what I've heard, and my own experience, they don't.

Things may have changed since I took it, however. Although, since human graders are still required for the writing portion, I doubt it.


What questions should I ask to find out originality of students’ work?

Asking alot of questions can generally rack out the ones who did the projects themselves and ones who didn’t.

Questions can be just simple ones like “how did you this?” or you can ask further questions based on their replies, e.g., if they answer with “Using technique A”, you reply with, "Oh I see, how do you use technique A?” or “How does it work?”


Your paragraph is less informative than, perhaps, it should be. If you give citations for each claim then it becomes clear. Give a reference after "previous work" and "paper Z", etc. Then the I and we is obvious.

I think that readers of a grant application will want those citations, actually. "What previous work...?"

But an "Royal we" is often used as you say, but it would be a consistent usage. And it could sometimes be interpreted as "we = researchers in the field generally"


How to find out if my specific idea is really new, or if someone has already worked on it?

What I find most critical: figure out the nomenclature. Look for articles about your research question in your own words and create a list of keywords that are frequently used. There is usually no consensus, so you will end up with synonyms.

Once you know the words used by the community in your field to describe the concepts and problems, literature searches get a lot easier. My usual approach is to use a large database of publications (in my field Medline is good, I guess your field has its equivalent) and look for the few keywords I listed. Now, don't read all articles of course, do a selection based on the title first, then on the abstract. There is a lot of redundancy in published papers so you will be able to weed out a majority of the papers at this point.

In some fields, senior researchers sometimes write review articles that list the 'open problems' in the field. Even if they don't give such a list, good review papers give an overview of the state of the art and are a great source of secondary citations.

Of course, discuss the matter with your colleagues and adviser, read prominent blogs and if possible go to (a) good conference(s). Conferences are great to grasp what others do and don't, and they help to make sure you don't reinvent the wheel.

Finally, I think you shouldn't worry too much at this point, here are a few words form my answer to this question Is there any research on the prevalence of academic theft?

  The chances that your idea is absolutely original is close to zero. Concepts, ideas and theories are almost always due to an
  intellectual environment in which many researchers are present. Even
  theories traditionally attributed to a single individual [...] were the result of
  inputs from several individuals over several years.

  The chances that your state of research, access to resources and previous intellectual work is similar for someone else is very small.
  Research breakthrough are a result of the right coincidence of
  opportunity, resources and intellectual maturity.


Are there any great researchers who are terrible teachers?

If you ask are there "any" then the answer is clearly yes. But, like anything else, skills are learned. I turned out to be a good teacher, beloved by my students (mostly - some exceptions). But I started out as a terrible teacher with really poor ideas about how people learn.

If you don't do something (a lot) you aren't going to get very good at it. Being a "natural" researcher doesn't just happen either. But if you are allowed to spend all of your time on research and no one ever requires that you do any effective teaching, then you probably won't get good at it.

Some brilliant people make too many assumptions about others. If I have deep insight into some topic, I might, falsely, assume that my students do too. In particular, I might forget how long and hard it was for me to develop that insight.

But if your students turn out to be "just like you" then you can probably reach them ok. If you learned easily thorough lecture and you can lecture with some logic and completeness, then people like you will probably do ok. But, not all students are the same.

Your experience of hearing "good" lectures in public settings is, a lot, due to the fact that your general educational experiences are probably a lot like those of the speaker. And if they are established and experienced, then they probably have a lot of experience getting through to  people like you. But maybe not so much in a class of beginning undergraduates.


Is there (or should there be) a website to record errors in papers

A site which has some ambitions and potential in this direction is PubPeer, which aims to be a general "online journal club", but which has also become a place to dissect papers for errors and possible fraud, particularly in biomedical areas.  It is thus one clearing house for discussing errors in papers.

Interestingly, they also have apparently set up a system that allows you to use a browser plugin to easily dual-post your comments on PubPeer to comments on the paper at the corresponding journal's site, which may also help with putting pressure on editors to actually make corrections...


strategy of a maths/science chalk talk interview

If you already know which topic is the most desirable one to the selection committee (perhaps, it's a subject they are not offering right now or willing to commit to a full-time instructor instead of a part-time one), I suggest choosing that topic. Also, if you know that your teaching material and/or approach for a specific topic is relatively unique and could be of interest to students (e.g., applied discussion of theories or real-world case studies), you might go that way. Other than those, I suggest sticking to the topic with which you're most comfortable.
I think Observing time limits during interviews is important and neglecting them could make you nervous. So engaging with the audience is OK as long as you don't waste time or enter into a heated discussion.

Good luck with your interview.


Is it ethical to get participants' consent for the inclusion of their data in the research after data collection?

As long as the study is IRB approved and the approved procedures are followed, then publication should not be a problem. It seems a little strange, but reasonable, that an IRB would aprove a protocol where minimal risk data collection was kept secret, but require informed consent prior to data analysis. I would have expected consent and debriefing to happen immediately following data collection, but again, if there is a reason to delay it, that seems fine.


Is it ethical to profit by trading on information in a research paper before it is published?

I can think of several different cases:

Case #1: I do research based on interviews that shows fanny packs are going to come back in style. I buy a few stocks in addition to publishing my paper.

Case #2: I do research by mining a publicly available non-restricted social sciences data set that shows people will start drinking R.C. Cola more than Coca Cola. I buy a 10% interest in the company based on my research.

Case #3: As an unemployed geologist, I discover that there are major, high quality, and easily accessible oil reserves under west virginia and buy a large number of shorts on oil stocks before the research goes public.

Case #4: I work for a natural gas company and do research on their behalf and discover that their wells contain far less natural gas than previously thought. I short their stock and profit.

Case #5: I have access to private algorithms that can predict anything. I use these to figure out who the next Justin Timberlake will be and invest heavily in his company.

Case #6: I discover a tree found only in a small forest in France can cure cancer. I buy the entire forest (to monopolize the resource and get rich).

I don't see anything wrong with cases #1-#3. Trying to work our criteria without availing to ethical theories, I'd suggest the following questions to evaluate any hypothetical profit:

How much profit are we talking about? (a $20 bet? several millions dollars?) The smaller the less meaningful the simultaneously benefit.
Who was the research done for? If I have no obligations to others based on my research, then it's more likely to be in the clear. If I was employed or working on a grant, then I have obligations to my employer which may obligate me to act or not act in certain ways. Is my profit in conflict with these obligations?
Did my research depend on resources that I don't own or have the right to use?
Does my profiteering involve something that might otherwise be immoral?

And of course, on the research side, you have an obligation to disclose any material conflicts (but again, the size of investment matters -- we don't need to know about $100 bets, but we do need to know you have a controlling interest in a blimp company for your paper on the future of air transportation).

tl;dr if it's merely your research will impact some companies, then assuming we're not talking George Soros level amounts of money, there's no obvious reason why it would be unethical to benefit financially from your research.


How to reply this mail from potential PhD professor?

I doubt that any reply is expected. It seems to be a general response and may not have actually come from the professor, but from his/her office, instead.

I wouldn't expect much of any response until the deadline for application has passed. I suspect that viable candidates will then get further information about what else might be needed.

But if you haven't completed your application by submitting required materials, it would probably be good to do that soon.


The referee says that I did not attempt to "reject" my model – what does this mean?

Of course, it’s hard to be any certain without intimately knowing your work and you have to judge whether the referee’s request is any reasonable, but:
This sounds like a request for Popperian falsifiability: The referee wants you to perform an experiment, analysis, or similar that – given your a priori knowledge – could reject the model.

Obviously my null hypothesis is that my model is wrong […]

I do not find this so obvious. In many cases, a model being wrong does not pose a feasible null hypothesis, because it would have to include every alternative model. There are exceptions to this such as when your claim is that some model has predictive power and you can investigate the null hypothesis that its predictions are as good as chance. But even then, your null hypothesis is something different from “my model is wrong”.

Details: the null hypothesis is that the model does not significantly explain the data.

That does not sound like a null hypothesis. First, the word significant (in the sense of statistical testing) does not make sense within the hypothesis as it is a property of the data with respect to the null hypothesis. Second, what does your null population look like? For any given model, there is an infinity of models that are an even worse description of the data. Are they present in your null population?


PhD admissions: Overlap between B.Sc. and M.Sc. transcripts

Your two degrees sound reminiscent of the "3-2 combined" programs that are common in the U.S.  Read up on a couple of those and I think you'll start to relax.

Please do let the admissions committee know what you're doing this year.  Perhaps that information can be fit into one of the standard documents -- perhaps your CV, perhaps a cover letter or the statement of purpose.

No matter how streamlined an online application process is, I would think you could contact the department and ask them what email address to use for submitting an additional document that didn't fit into any of the pigeonholes provided.


Should I use both surnames when addressing a Spanish professor as 'Dr' in an email?

Mexican here!!

We also have two surnames, and to be perfectly honest we do not mind if you use both or only one of our last names.

People call me Dr Palafox and my former advisor (Who is the head of the CS department) Dr Benitez. We are talking people from all the spectrum of workers, from administrative and cleaning staff to general directors. So is perfectly fine to use only one last name.

Actually is going to sound weird if you end up using both names, because we rarely do. Even the President is rarely called by his 2 last names, unless is a very specific situation.