How does one assess one's chances of getting accepted into a PhD program in philosophy?

As everybody in the comments are saying, this is a very individualized thing. However, to get a good grasp of your standing relative to other students, I would check out thegradcafe.com.

Yeah, thegradcafe is an especially anxious and paranoid subset of grad school applicants, but you can see what kinds of applicants got accepted or rejected by checking the app board or skimming the forums. There's a dedicated Philosophy forum.


Why would a prospective advisor ask if I'm meeting other advisors?

One reason an advisor might ask this question is to know how time-sensitive the decision process is. If you're not considering other advisors at the same time, there is no competition and the potential advisor can spend some more time making her decision.

Another reason might be to gauge your interest in her research activities based on the other people to whom you're talking. Are you looking only at her field or are you looking more widely? Since you're coming from someone else at the same university, she'd likely be using such choices as a means of determining your level of interest in what she's doing. In other words, she probably wants to know if you're just looking for any advisor, and she happens to be someone you're talking to, or looking at her as a serious option.


Should I mention my blog in a postdoc application?

tl;dr-  While a good blog could be a professional asset, the given description sounds like something that probably wouldn't enhance an application.

Blogs can be professional assets, even with political content

A good blog can be a professional asset.  Such a blog could even touch on topics that others might consider politically sensitive; for example, it's entirely respectable to write a technical piece on forecasting climate change using data science techniques.

You can even write a heavily political blog in a professional way.  FiveThirtyEight's a great example of this: they're heavily involved in political analysis, but they're quite professional about it.  I'd imagine that its writers would generally do well to include a reference to it in their future job applications.

Then there's a grey area when it comes to the interfacing with politics in one's own field of expertise.  For example, if a climate scientist were to maintain a blog devoted to their research on climate change, then it wouldn't seem like the worst thing in the world if they occasionally included a political perspective piece in which they maintained an objective tone while expressing personal political opinions.  However, it'd be important for such opinion pieces to be substantial in terms of content and analysis.

Political rants tend to come off poorly

Political rants can cause the reader to think less of the writer.  This can be true even if a reader shares some of the same opinions.

I suspect that a lot of factors go into this.  As a partial list, in no particular order:

Readers get into the habit of filtering content from politically charged sources, so if the writer starts to sound like a source of politically charged content, it makes sense to put less trust into their assertions.
Strong political positions can reflect on a lack of political knowledge (Dunning–Kruger effect), professional focus, emotional inclination toward objectivity (stability), or/and reasoning skills.

  The whole problem with the world is that fools and fanatics are always so certain of themselves, and wiser people so full of doubts.

  -Bertrand Russell, on BrainyQuote

The willingness to engage in political rhetoric in professional venues (e.g., a job application) negatively reflects on one's general professionalism.

As a consequence of factors like these, many'll tend to respect a writer less for their political rantings even if they would tend to agree with the opinions expressed in those rants.

Overall, probably best to not share this blog

For the reasons given above, sharing a "partisan blog" that has "some strongly worded opinions" would seem like a bad idea.  While it's not impossible that a reviewer might actually enjoy it, I'd expect it to generally have a negative impact if anyone takes the time to check it out.

In general, folks'll be more likely to think well of your ability to operate in other venues if you're able to conduct yourself with the same sort of professionalism that you'd approach Physics with, keeping a level and objective perspective throughout.


Acknowledge receipt of email or answer it?

Probably best to acknowledge first anyway, since there is inevitably some risk that "instantly" becomes less instant...


Accepting organizing duties in a year...but waiting for a new position

It's not so uncommon for a "local" conference organizer to have moved to another institution by the time of the conference, but it's good if there are some actual local conference organizers.  Since you are part of a research group, it seems reasonable that you will not need to be a sole organizer (this wasn't 100% clear from your question).  If you are being asked to be the "primary" organizer, you can still do that remotely, but it also makes sense to ask to instead co-organize it with other people.

So I think the main thing you should consider is: how much do you want to be involved with such a conference, regardless of where you'll be?

Note organizing duties usually count as "professional service" rather than "university service," and organizing conferences can have positive benefits for your career.  If you are doing this as "professional service" rather than as part of your job duties (and it sounds like this is the case since you are getting asked to do it, rather than told to do it), once you make a committment, you should typically follow through.  However, if you do move, then co-organizers are generally pretty understanding that certain aspects are harder for you to do remotely.


Placement of illustration: before/after text?

Figures always go after the first reference to that figure.
Figures always have a caption. In almost all styles captions go after the figure, but before tables.
Having a figure as the last thing in a section looks a bit odd and you might want to stick in an extra sentence just so it doesn't look odd. Having said that- you can avoid this by not dividing the text very finely (that is, no sub-sub-sections).


Is a PhD degree from a European university considered equally valuable as one from the US?

One simple answer is no, the two aren't equally valued, because the two are also not even regarded as equal.  As a trite example, consider that many European countries (especially the German-influenced ones) are very picky about which letters you can put before or after your name.  I have a dual-degree, so I am "allowed" to use Dr. as a legal part of my name in Germany; but my officemate with a solely American Ph.D. cannot.  The way in which doctorates are made is also vastly different-- the U.S. requires coursework and then research, (often) mixed with lots of (often underpaid) teaching duties, while European doctorates typically frontload on the research and are light on teaching responsibilities.  Those different experiences produce different palettes of qualificiations and skill sets.  It's no wonder that if you're primarily paid to do research, you'll probably produce a better thesis than someone who had to perform teaching duties 20 hours a week.

However, there's also the danger of regarding "Europe" as a monolith.  I've heard anecdotes from some Italians who struggled to get funding to finish their degrees without taking on big teaching duties. (But see comments by @MassimoOrtolano.)  Croatia, Romania, and Bulgaria all suffer from "brain-drain" as young folk go west for education.  And I get the sense that when people say "Europe" in the context of academia, they're almost always, knowingly or unknowingly, referring to Germany, France, and the UK.  Few other European entities have as much economic, political, or historical influence as those three.

Along the same lines, Europe comprises dozens of different languages and cultures.  Asian students are more likely to already know English than French or German (or Dutch or Polish or Finnish...) and therefore will seek a degree in an English-speaking country.  American culture and accents are more familiar to the world than, say, British or Australian, because of the movie and music industries.  (The UK is also not super stable in terms of immigration standards at the moment.)  Seeking a degree in the U.S. is then just plain easier-- you don't have to spend time learning a new language or adjusting to a new culture.  For these students, it may be that because English is the de facto language of science, the notion of what's considered "prestigious" just followed blindly.


Don't overthink this. Tell the truth! "Your group is the best!" (... and I want to be with the best)...
Yes, if you can make some incidental remarks about how/why you know that their group is "the best"... and in what field, precisely... that would be good. Not just "gee whiz! Gosh!", but something a bit substantive.
I'd think departments/groups would want to hear from prospects that those prospects appreciate the expertise of the group/department/whatever. Otherwise it's really silly cold-calling. (When I (in the U.S., in math) get cold-call emails from people who're manifestly using a uniform template about "Dear Sir, I've studied and admire your research", with no details pertaining to me (either in the form-of-address or anything else) it's easy to hit "delete".


How to structure a theorem with dependencies on lemmata in following sections

In general, it is a good idea to give your reader a "roadmap" of the approach that you will take early on.  You might even introduce the theorem itself early on, but leave the proof for later.

Once you have established your roadmap, then you can proceed in order, building up to the theorem that the reader knows is coming (referencing you plan in the narrative that connects the mathematics).

Finally, when you have all three lemmas in place, you can return to the theorem, restate it, and state the simple proof drawing on all three lemmas.


Does one have the right or just the privilege to extend the PhD study period due to parental leave?

The word 'may' does not preclude refusal. It means, it is possible to extend.

In academia, in general, if there is good reason for extension of PhD, it is always allowed. Pregnancy is a good ground for extension and it would be very rare for a student to be penalised for getting pregnant.


Does being an older PhD applicant for U.S. universities mean there is less chance to be accepted with funding?

In my experience as a grad program director, there is zero truth to this rumor. Funding decisions have nothing to do with the applicant's age. Nor is having worked outside of academia for years a disadvantage -- we often look very favorably at students who bring with them substantial life experience beyond a college education.


Is it worth writing and publishing a survey paper while a PhD student

A survey almost certainly would count towards your paper count requirement.
A proof based on common sense is that surveys can generally be hard to distinguish from research papers: there exist review papers that have notable amount of novel work added but are still called reviews. Thus it is very unlikely for your department to put such a distinction.
Publishing your (already finished) survey is worth it.
Your original question states that you have to produce a survey of defendable quality. Then, the effort required is just polishing the survey further to publishable quality and handling the communication with a journal. The reward will be getting a publication, with all its formal (increasing your paper count, see previous paragraph) and informal (getting recognised) positive consequences. Surely worth it!
The proof is again based on common sense: if the pros did not outweigh the effort in your local environment, no work would have made its way further than internal discussions within your department.


Should I mention a part-time job that may have affected my undergraduate grades in my PhD application?

If you mention it, don't try to overemphasize it. Many students need to (or choose to) work part time. And if you try to use it as an excuse for poor performance it will not help you. But, I wouldn't really worry about it for several reasons.
You don't say where you got the "low" grades, though B's would be good by many standards. If they are in your major courses it has a different meaning than if they are in general education courses.
Your overall average seems quite high to me. There are, of course, lots of "perfect" students, but they don't always do well in graduate study as it is possible they have never been challenged and fall apart when things get hard and they aren't prepared for it.
Also, a grad school application in the US depends on many things, not just GPA. Decisions are made by people, not computers looking at numbers. What courses have you taken? Any research experience? Can you write? What do your letters of recommendation say? Any standardized testing evidence? People will be looking to make a prediction about your future success. Make sure that you provide plenty of that. A few "lower" grades won't be a deciding factor.
But to say that you worked your way through school financially does say that you work hard. That can be a point in your favor. But don't make it an excuse.


Asking PI I barely interacted with for letter of rec?

I've said it before, I'll say it again: writing a letter of recommendation for a student you know well is easy, it's a treat, and the letter you write can be GOOD. Writing a letter for a student you barely know is difficult, time consuming, and ends up sounding generic and forced. As someone who reads recommendation letters, it is very clear when the writer doesn't know the student.

I don't think them saying "no" is your problem here. See, even if they say yes, if you have this person who doesn't know you write your letter of recommendation you risk it sounding like a form letter which, in turn, won't distinguish you from the pile of other applicants. Unless the underling that they have write the letter really knows you and your potential, the letter is unlikely to be great. The box will be ticked but it won't be a meaningful tick.


How to proceed after academic dismissal from PhD program (plagiarism) and successful completion of master's?

As mentioned in the comments, I do not think that you will be able to find a supervisor who does not know you well already if you have a record of dismissal for plagiarism.

You could try:

Telling the truth about your dismissal (lying or omitting that you were dismissed would likely be grounds for getting dismissed again).
Explaining, with evidence, why it will not happen again.
Do not mention the nature of the trauma you experienced.  Academics are not likely to consider any kind of trauma to be an excuse for plagiarism.  And they are likely to have strong opinions about how children are raised.
There is no need to give the details of the process leading to your dismissal.


Algorithms, Combinatorics and Optimization graduate programs

You should consider applying to "Operations Research", "Computer science", and "Applied Math" programs (note applied math and not math), all of which can potentially have concentrations in your desired field of study. Make sure the schools have professors publishing in the journals and conferences that interest you. Courses you tend to take in these programs include. Every course below can be used towards a degree in applied math at Cornell (not sure about other places).

Analysis of Algorithms - CS

Simulation - OR

Machine Learning - CS

Combinatorial Optimization - OR

Algorithmic Game Theory - CS

Optimal Learning - OR

Theory of Computing - CS (complexity theory)

Stochastic Dynamic Programming - OR

Networks - CS

Mathematical Programming - code word for analysis with an eye towards optimization and algorithms

Nonlinear Programming - OR

I know that Cornell has a very strong theory component to both their OR and CS programs and you should probably look into them. No matter which program you choose at Cornell, you can bet that you will be able to take a lot of OR,CS and math courses and count most of them towards your PhD requirements (this may not be true at all other universities, you'll have to check). The above list is just a sampling of some of the courses offered at Cornell in OR and CS. Combinatorics is offered in the math department. The difference between all these programs will be in the required courses you have to take, for example OR requires stats, CS requires the theory of programming languages etc., but no one likes every single course they take in their PhD.

Edit: Actually at Cornell, Applied Math has the most flexibility of any program. As long as you have some background in undergrad algebra and analysis (which you can make up during grad school) You can affectively create your own curriculum, with very few requirements. Its very easy to focus on ACO there. Note that many applied math programs are not so flexible, so you really have to look around.


How to put in acknowledgments a research department of a university or an internship?

You can simply write

this work has been conducted while Alex was visiting XXXXXX


Is it common for college students to drop a year or 2 between UG and graduate studies?

I can't say if it's the norm, but I don't expect that working for a year or two after undergrad would be frowned upon by graduate admissions committees. So long as your job is related to your field of study, you'll be augmenting your academic studies with real-world experience, which can indeed be valuable in preparation for a graduate curriculum.

Personally, I applied for grad school straight out of undergrad, but didn't find the funding I was hoping for, so I worked for a year and then tried again. I received more and better offers the second time around.


How do departments evaluate and update their course requirements?

Departments ought to be concerned about their graduation rates. If the rates are low, it is a good idea to find out why and make changes. This could be changes to the curriculum, it could be changes to the admissions policy, or any number of other things.

Benchmarking is certainly a reasonable approach to review the current rules, although niche marketing often gives incentives to introduce distinguishing features that are consciously pitched against the prevailing practices.

I presume your department has a curriculum committee. Request a meeting and see where that leads.


Introduction to Programming with Pseudocode

This is exactly the approach taken by the Introduction to Algorithms course at MIT—or at least it was the case back in the early 2000's. The book by Cormen et al. takes a decidedly agnostic approach to programming, and presents everything in terms of pseudocode, rather than adopting any particular programming language.


Why does an "external member" of a thesis defense committee come to your defense?

Some external professors are in the same field and others are not. They serve different purposes. They might be paid a small stipend, but it is usually (as far as I know) just an honorarium. The receiving institution probably also pays for travel and lodging if the person is from away.

For the professor it is just a part of service to the profession. Their own institution may provide some recognition for it or not. Often annual evaluations are on research, teaching, and service.

However, the purpose of an in-field visitor is, at least partly, to give some external validation to the program that is visited. I've been asked if I think the entire program is up to the standards I would expect. This help prevent academic incest where a department only speaks among its own members and loses connection to the larger goals. "Would you give a doctorate to this candidate based on the thesis and overall program?" Here the visitor is from a different university for this to make sense. Sometimes from a different country.

The purpose of an external member of an examination committee, however, is quite different and may even come from the same university. In mathematics, the visitor might come from philosophy or a language department. They are normally not expected to read the dissertation and couldn't be expected to understand it. But they are expected to ask a question or two of the candidate and the quality of the answer can be heavily weighted in the evaluation of the student. Sometimes it is just a request to explain to the visitor some terminology used in the defense talk. A layperson's explanation is expected, and the candidate normally is expected to do a good job with the answer. Advanced students who can't intelligently discuss elementary things in their field are at a handicap. I've heard of situations in which the examination was failed for this reason alone.


Most published math papers are answers to open questions posed by the authors of the papers, right?

Most math papers are proofs of theorems. For instance, "I" might prove the following theorem:

  Let m>n>0 be integers. Then for a=m^2-n^2, b=2mn, c=m^2+n^2 it holds that a^2+b^2=c^2.

"Open questions" usually refers to problems left open by someone else in another paper (or sometimes, left open by the authors in a previous paper). Now, "me" proving this theorem is probably in response to a question I had: for instance, I might have wondered which integers satisfy a^2+b^2=c^2. However, if no one else had previously considered this problem, it doesn't count as an "open problem".

Typically, in the conclusions sections of a paper, the authors might mention several problems that they consider interesting but didn't manage to solve. For instance, in my paper I might mention the question:

  Are there any strictly positive integers satisfying a^3+b^3=c^3?

If someone subsequently were to solve this problem (whether in the margin of their paper or not) they would almost certainly write something to the effect of:

  We solve an open problem due to van der Zanden [2017], showing that there are no integers satisfying [...].

The point of mentioning that a question is "open" is to:

Credit the ones that formulated the problem (formulating a "good" problem can be as hard as solving it).
Demonstrate the significance of the problem (they considered it interesting enough to mention as an open problem).
Show that the problem is not trivial (they tried solving it but couldn't).

If I am solving an "open question" that I posed myself then none of these points apply (I could prove an utterly trivial, uninteresting theorem and then invent an equally uninteresting "open question" question that it answers) and so it doesn't make much sense to state an "open question" if there was no open question to begin with. Sometimes people answer their own open questions, but only if they previously stated them in another paper. If I just prove an interesting theorem (e.g.: "All swans are white") then reformulating the theorem as a question (e.g.: "We answer the question of whether all swans are white") doesn't add anything to the paper - especially if no one previously considered that question.


Why is bad behavior more tolerated in academia compared to the rest of the industry?

I suppose I disagree with the comparison between Academia.SE and Workplace.SE and your three points in general, but there's an answerable question here. I also agree with cag51's points that we (and at Workplace) always only get one side and that perhaps a bit of devil's advocacy is alright. Here I am writing from the perspective of US/Canadian academia.

But to get to the main issue:

[On Workplace,] most answers (rightly) point out that nobody should be the target of abuse and there's a general consensus to direct people to leave abusive situations as soon as there's a clear indication that they cannot be resolved properly. There is no merit in staying in a terrible workplace and fighting through it, sometimes it is just better to leave and find a better place.

As I mentioned in a comment, Workplace is full of software engineers, who tend to enjoy a favorable market in terms of employment. This means that for them, it's often very easy to apply for jobs and find a new one in weeks.
Why doesn't this work in academia?

If you want to stay in research, it's really hard to move at almost every stage of your career.

Academia is still heavily invested in the school calendar. If I was unsatisfied with my program, I would have to wait until the next fall to start somewhere. That's if I decided to leave in time to apply for another program (typically almost a year before starting; contrast this with employment). Even if I short-circuited the application cycle, I would still start in the fall.

And the chance of transferring to a school nearby - so as not to disrupt your life incredibly - is close to zero, unless you live in Boston, maybe. Most people, upwards of 90% have already relocated for grad school, so doing that again is a hard-to-overcome stressor.

Finally, PhD-to-PhD transfers are very rare and tend to make people suspect a problem.

Leaving a studentship is much harder on your career than a job.

As cag points out, changing could mean delaying by a year (which is costly), but most importantly, people select programs based on their fit for their dream project. I'm speaking generally, but I came to my program because of the resources. Finding the same resources elsewhere is not the same as finding a more-enjoyable 9-to-5.

Do I fully support this model of academia? No, but you can see why someone would tolerate more to study something they're passionate about instead of deciding to quit running networks for Company A and instead run networks for Company B.

If I left my lab on bad terms, I would likely lose access to the data I have spent years building on. So poof goes a whole pile of projects. Whereas when you leave a job, those projects are someone else's problem. My career would be affected by leaving a bad situation much more than a random HR person's (just to pick on a different job).

Lots of people are passionate about their jobs, sure, and they would likely tolerate a crappier boss compared to someone who just sees their job as a 9-to-5 (which is totally OK). It's that in academia, everyone is expected to be that person, and so you can see what it may seem that what's easy to quit over in industry is harder in academia.
Finally, I haven't even touched on the hierarchical nature of academia. If you want to work in some field, probably your professor knows all the other professors in the same field. Upsetting them could - or feel like it could - basically get you excluded from the field of your dreams. Whereas employment networks are much larger and your line manager has much less sway over where you end up next.


Does submitting an enrollment intent mean that I am commiting?

Universities typically consider such intent statements to be binding.

If you submit these statements to multiple universities, they will all hold seats for you, seats which could otherwise go to someone from their waiting list.  This hurts those other applicants.  It is also a serious inconvenience to the department's admissions committee, as they need to meet their enrollment targets as closely as possible; failure to do so can affect their funding, and in extreme cases, the survival of the graduate program.  So this is at least inconsiderate on your part, and arguably unethical.

If the institutions find out that you have done this, it is possible that they may rescind their acceptances; this is uncommon but has been known to happen.  In addition, you would certainly forfeit any deposits that you paid.

At the undergraduate level, where deposits are almost always required (in the US), this practice is called "double depositing".  The National Association for College Admission Counseling, in their "Guide to the College Admission Process", says:

  Colleges view dual or multiple deposits by students
  as serious violations of trust and may revoke a previous
  offer of admission from any student who is found to have
  sent tuition deposits to more than one college.

My advice is this: at this point, you should plan on attending the university X to which you've announced your intent.  However, if you are absolutely convinced that doing so would be a huge mistake (not merely that you think Y is a little bit better), then you could contact the admissions committee at X, explain your reasons, apologize, and ask to be released from your agreement.  If you do this, you should do it as soon as possible (ideally within days - don't stew about it for two weeks), and know that it will probably burn your bridges with X, as well as forfeiting your deposit.  If X says it's all right (they probably will - if you don't want to be there, they don't want you there), then you could send your intent to Y.

Some people might argue that you are also ethically obligated to inform Y of the situation.  I think it's kind of a gray area, myself.

You might also discuss the matter with an advisor or other professor at your current institution.  They might offer some perspective on X that would help reassure you.  In general, most people say that it isn't so crucial which institution you attend, within reason - your own skills and motivation are a much greater factor in your success.


Shall I include a list of workshops and conferences attended during my UG in my 4 page CV?

You should definitely mention that you attended conferences. How much detail to include depends on how much space you have left after you included all of the more important information on your CV. I cannot tell what is more or less important. You have to figure it out yourself. Here is what I usually do in such situations:

Make a CV listing everything you have that is even slightly relevant to what you are applying for. If you went over the page limit proceed to step 2.
Divide your CV into absolutely necessary/required info and 'other stuff'.
Rank the 'other stuff' from very important to barely relevant on some continuous scale, say 1 to 10.
Delete the least relevant info until you reach the page limit of your CV.

You can apply the same procedure to your conference list. I would say it is important, but not 100% of it if you don't have enough room. Rank the conferences you attended from the most prestigious/impressive to the least impressive. Start listing them from the most prestigious until you hit the page limit. Leave one sentence to mention the conferences you omitted, generalizing them in some way to underline their relevance: "... and other (number) conferences on topics related to molecular biology.


Asking a Professor to sign me to a group

Send another email stating that you have been unable to find anyone and have been refused by a few teams. You will try to "catch" him before class.

Then (choose one) if you don't get a suitable reply:

(a) Show up at his office in the morning before class and present the problem. Ask for a solution. I.e. "How should I proceed?"

(b) Catch the prof in the hall just before class and ask for a solution.

(c) When class is about to begin, raise your hand and ask for a solution.

(d) After class catch the prof and ask for a solution.

There isn't really much else you can do. Prefer a to b to c to d, I think. But, I assume the prof has seen this before. You might not be the only one with the problem so a group might be formed immediately.


Refusing the postdoc offer (email acceptance of the offer only)

Officially, you're always allowed to walk out. Particularly before signing any papers. Just make sure you let everyone know as soon as possible to avoid creating expectations and preparations.

Now, you're probably asking whether your peers will be happy if you walk out. Usually they will not appreciate anyone dropping a postdoctoral offer. If you understand exactly why they're pushy about you taking the offer, you will be in a better position to take this decision.

Don't worry about making others happy. Do what you must.

Good luck!


Getting in touch with a professor who has no longer an e-mail address... how to?

Do you have any suggestions?

My suggestion is for you to get some perspective. If the person you are referring to is who I (and everyone else here) think it is, you need to understand that this is a person who has reached an extraordinary level of celebrity in the scientific community. Saying he is "quite famous" doesn't begin to describe the situation accurately -- I'm talking about a level of fame where (I have seen this with my own eyes) when he gives a talk at another institution, star-struck graduate students and postdocs approach him one after the other asking to have their pictures taken with him. Moreover, this person famously dedicates his life to thinking, writing, and speaking at public events in various places. Being in close touch with his very large fan base is quite at odds with his lifestyle and his legendary dedication to his work.

In other words, there is a very good reason why he does not have a publicly listed email address.

For the same reason, I expect that even if you go to the small trouble of writing him a letter (which, amusingly and for a reason I can't quite understand, you seem to think is an incredibly onerous thing to do), the chances that you will get a reply seem rather low -- I wouldn't expect that he can spare the time to explain long division algorithms to random people asking for more details than he already put into his books. But in any case do give it a shot, in the event that you do get a reply you will have something to brag about to your friends. And maybe it will help free you from your psychological inhibition against writing old-fashioned letters, which is something that could be of independent benefit.


Examples/anatomy of good tenure track recommendation letters

While I do have sample TT recommendation letters, I'm not at liberty to share them, even anonymized (sorry!).  However, I've just re-read a few, and there are a couple commonalities I'll share below.

First, all made a strong case for the applicant having already impacted their field (for the record, all applicants completed a post-doc; none were straight out of graduate school).  This is noteworthy, because recommendation letters for tenure seek to establish that person's real, significant contribution to the field.  It is perhaps not surprising that the letter for a TT position has a similar flavour.

Second, all made a case that the work was likely to be funded. One of these had never previously received funding, the others were supported by post-doctoral fellowship or as some kind of co-PI on larger grant.

Third, all but one seemed to make an effort to highlight the 'departmental fit' in terms of research interest, both directly and complimentary.

I'm not sure how to answer your question about a 'great' letter vs a 'mediocre' one, but I did get the sense that the most compelling letters, in my opinion, had an air of 'obviousness'. What I mean by this is that the authors wrote as if 'obviously you must know this work' or 'undoubtedly you're familiar with...'.  I can't be sure if that was actually true or whether it was a marketing ploy, but it seems to have worked.

Hope that helps, and good luck!


Who can submit papers to peer-reviewed journals?

Anyone can submit a manuscript to a peer reviewed journal. The challenge that face persons without training in scientific writing through, for example, a PhD, is that the manuscript is probably far more likely to be rejected because of poor writing or other mistakes. The key issues for authoring a good paper is to have a good grip on the literature in the field, knowing the sources that should be referenced to provide the basis for the own work, to know how to write clearly, concisely and precisely, and to understand any specific publishing aspects of the field.

It is not rocket science but usually requires both good coaching and training. Approaching the authoring with care is therefore a good strategy.


What does "thanks x-institute for hospitality" mean in an acknowledgement?

Usually it means that, during at least part of the preparation of the paper, the author was on an extended visit to Institute X, and X provided something that was helpful.  It could be as little as an office or a library card, or as much as free housing, use of expensive equipment, travel support, etc.  However, this phrase wouldn't normally be used if the author was actually a paid employee of X during that time, even if temporarily.


Consulting gigs for quantitative sociologist

What you need to do is establish visibility, especially with those who might benefit from your services. Having an extensive and helpful web site can help, especially if it is, itself, visible, such as one hosted by the university. Perhaps a professional blog or such will give some people an idea of what you can offer. But make it helpful to readers, not just an ad for your services.

But that isn't enough.

One possibility is to make contacts through adult students (MS, and doctoral level). Some of them may be employed by firms that would be interested. But you need to meet the people responsible.

One way to meet people is to do a bit of research on the interests and expertise of people with some authority at local companies/agencies and invite them as guest speakers, either in your own classes or generally.

If you want to cast a wider net, you can use professional meetings to make contacts with others of similar skills and desires and find a way to share contacts. Not a quick process, but it can build visibility.

Another way, not especially lucrative, but possibly rewarding, is to volunteer your expertise to local non-profit or government agencies. I suspect a number of them would be interested in knowing more about their clients. You can also get some of your students involved in this work, to their advantage, perhaps. But this sort of thing will also raise your visibility once it becomes known what you can do.

You can also, of course, form a formal group with colleagues and advertise your services.


Who to ask about the update after a campus interview.

Most academic departments can't actually make hires for their university without higher university approval. This is because faculty hires are a long-term obligation for the university. Typically, it is a commitment of several years, at least until you get a third-year or tenure review.

Therefore, the process is that the university allocates the department a "line" which means they have permission to search for a candidate. Then the department interviews and chooses candidates. The final step is for the university to formally offer the position. However, if the university's priorities or budget changes during the hiring process, the department can lose its "line." This happened to some U.S. state universities recently because state legislatures cut budgets and made hiring "freezes" necessary.

What seems to be happening in your case is that the department has chosen you but the university is dragging its feet on making the decision final. This is likely because they are not sure of their budget or some other aspect that is out of your control. It is possible that the chair can continue to push for your candidacy a bit harder (making the case that even if some departments lose their line, her department should not), but there is little that you can do about this situation. I would continue to look for other positions.

In terms of who to ask, stay in contact with the chair as best you can, stressing your continued interest in the position.


How to write a math abstract for a conference in an experimentalist dominated field without "specific numerical results"

Writing as a mathematical modeler in Epidemiology, and a regular submitter to conferences with these types of requirements, which are dominated by empirical research findings, this is something that's hard, if you approach it from the direction you have - with the numerical results coming at the "end" of your research.

It would be good to have a numerical result, because as has been mentioned, while you might not view these as the crux of your research, it may very well be the crux of why someone is interested in your research. Even as someone who does appreciate the theory side of things, I'm often rather more interested in the numerical results.

That being said, these conferences are mostly looking to avoid "Will be discussed" results, where there's no means to evaluate if you've done anything, or if it will be interesting. The latter is especially hard for deciding whether a presentation becomes an oral or poster presentation, because giving one of the precious oral slots to someone whose going to largely be discussing a slew of null results is (often) irksome.

You do however have results, and that should be enough to make it past the bar. If X and Y are both possible within the parameter space, and that means something for the field, then that is a specific result, and you should expand on why that's interesting.


Is there a more gender-neutral and specific term for "Underclassman"?

Referring to years verbosely makes sense to me.

First-years and sophomores

First and second years

Or if you want a different meaning

First through third years


Why are most of the top universities American?

It started in the 1930s, when Nazi Germany started to fire Jewish professors and other people who opposed the regime. Many others left voluntarily as well. Germany had the best universities before this period. The United States ended out getting more of the refugees than any other country (e.g. Einstein) and this started the ascendancy of American universities.

Then World War II happened. Germany ended out with their universities basically obliterated, through the actions of the Nazis and also from the war itself. Japan's universities were also very damaged. The US on the other hand, not only benefited from the refugees but also from the war effort. A lot of money and effort was put into the Manhattan Project and so on, and this infrastructure was used after the war. Other European countries did not really gain as much... some suffered extensive war damage and others like France were at least occupied. Britain's academic institutions were (basically) intact but they were losing ground to the Americans.

After WWII the Cold War happened, and universities were highly supported by the US government during this period, building on the earlier growth. The US had a lot of financial resources and were willing to use them to help universities. Also, American universities in recent decades have been quite welcoming to foreigners, and the increasing prominence of US universities in turn attracts immigrants. So this has become a self-perpetuating phenomenon.


How to find less-competitive faculty positions in the US universities?

Although (see my comments), I cannot recommend this sort of career path, here are two ways for an outsider to determine which positions will be less competitive:

Teaching load and pay. If the pay is poor, and the teaching load is high (say, 4/4 or higher), then the position will be less competitive.
Look up the average SAT scores (easy to find via Google) of American schools to which you are applying. This is a reasonable (although not perfect) guide for the quality of the undergraduates that these schools enroll. Schools with lower averages will have less competition for faculty positions.

That said, all faculty jobs are highly competitive.


Putting link of full text of paper in Google Scholar

If the preprint version of the paper has been indexed by Google Scholar, then Scholar should show that version of the paper as well.  Assuming that it's permissable under the publisher's rules, you could post the paper on your personal web site and Scholar would eventually find and index it.  However, you can't explicitly add anything to Scholar's index.


What are the options for a drop out turned professional to return to academia?

I was in a similar situation about a decade ago. I just went ahead and got the BS degree. I was a systems admin for about 10 years prior. Here are my thoughts:

Of all the classes I only learned useful stuff from about 4 of them. Data structures, algorithms, signal processing (ironically in a brain device class where the equipment was garbage), and operating systems. Everything else was a complete waste of time including all the calculus' (more than 2 years worth of calc+ math)  and general ed.

Id say that if you already know algorithms and data structures real well along with memory management and signal processing then there is no point to either a BS or MS degree. You will learn nothing. But if you have not seen those subjects before, it might be worth it though I suppose, now that I fleshed out the entire thing for you, you could just get a few books (lol). By the way, I teach CS now at both undergrad and masters level even though I dont have a masters. That said...

I actually started a MS degree once and all I got was the same education but more specific to certain fields like signal processing sound waves for voice recognition. I learned nothing in that course but it did require a huge amount of my time which I didnt want to waste on such a trivial thing that I can figure out without instruction. I just dropped the program after that. If you want to go into education however, you really should get a masters which is the only reason I am currently considering doing an online program. But if youre already in the real world, id say time is better spent making a product.


Is it normal to interview for faculty positions in December-February and not hear back yet by the end of March?

Commiserations -- the job search is tough.

If they haven't gotten back to you by the time they said they would, it most likely means you are not their first preference candidate. They probably have already made an offer and are waiting to have that accepted or rejected. You could still get an offer as their second/third/fourth/etc. preference.


Do non-academic extra curricular activities matter for grad school applications?

In general. non-academic activities are not considered for admissions for schools and most fellowship programs in the US. The primary reason for this is that graduate programs are looking for people who will become excellent scholars and researchers (and sometimes even good teachers!). Success in sports and other highly non-academic activities is less likely to have significant influence in assessments of one's ability to do research, and therefore is not strongly considered.

However, there are exceptions. People can choose to fund activities however they choose, and can place whatever restrictions on the use of the money they donate. For instance, an alumnus could fund a fellowship for PhD students who play the tuba in a college marching band. While this doesn't happen often, it can be done. But typically admissions committees aren't concerned with such issues, and don't take them into account in making admissions decisions.


Financial aid sources for dependent, disabled student?

This response is US-centric.

It is most unfortunate that the local university was unwilling to provide any kind of financial aid except for loans. However, this need not spell the end of your academic journey. Here are several avenues you should explore before giving up.

Begin your higher education journey at a community college. They offer lower tuition rates than almost any other institution is able to do.
Apply for federal financial aid using the free FAFSA application.
Investigate other financial assistance and scholarship opportunities. As a disabled person, you should be eligible for various scholarships. There are various free scholarship websites which will permit you to find scholarships suited to your specific situation and interests. Scholarships.com and Scholarship Experts are among my favorites, but there are many other free services available, including this comprehensive list of external scholarships provided gratis by the University of Phoenix.
Make friends of the folks in the financial aid office. They are usually more than happy to walk you through the process of applying for federal, state, and local financial aid and may help you find other sources you hadn't considered or were unaware of.
Find out where the community college Foundation Office (or similar office) is located and make a special effort to meet these people. Their job is to match students with sponsors and the rewards for your efforts can be substantial. (For example, they once put in my application for a scholarship I didn't know existed, and gave me half-a-semester's worth of tuition without any effort on my part!)
Finally, contact a counsellor or other mental health professional. Depression is a serious illness. Get help!


You need to think longer term. Decades, and perhaps centuries. Research done today may seem to have little immediate impact, and that is true. But over time, it contributes to the general knowledge that makes things possible. Think of any scientist from the past whose name is known today, even, say, Euclid. Some of what they did may have had some immediate effect, but much of it laid the groundwork for later advances.
In pure mathematics and theoretical physics, for example, an interesting question today may be vital in the future. Isaac Newton's calculus work was so unimportant that he put it in a drawer for years. Leibniz did "interesting" things in understanding real functions, but without their work, and what came after, much of engineering in the past 150 or so years would be impossible.
Think Mendel or Darwin. They studied and thought because certain questions were "interesting" to them. They laid the foundation of modern understanding and that led to "useful" things.
Note that Einstein's work took years to be accepted because the "great minds" of the day were focused on a different theory that turned out to have no basis - the aether.
Moreover, many of the advances of the "great minds" of science were only possible because of a general advancement in understanding, much of which was contributed by those whose names we no longer remember. The current state of understanding the world can be thought of as an advancing front with many contributors, some of whose contributions we remember specifically, but it is the front itself that makes them possible. All of us push against that frontier in our small, perhaps, ways.


How much experience should a teaching letter writer have with my teaching?

In a situation where "teaching matters", there are two significantly different tangible assessment types: student evaluations, and peer (or supervisor) evaluations, not to mention the more extreme sort of commercial sites which have the systemic problem that the commenters self-select, typically with skewing to negative, even ranting reviews.

The aggregate response in university-organized end-of-term student reviews is useful, not necessarily as a gauge of whether you're a good/effective teacher, but whether the students are "happy". For that matter, successfully generating no "complaints" during a term is some kind of success. This does matter.

Peer-evaluation (occurring not at pre-arranged times, but unplanned, yes), or evaluation by your director of undergrad studies in your department, is the closest to what hiring committees might care about. In particular, if you are doing what your peers or "boss" think you should, it doesn't matter whether the students love you or not... as long as they're not actually unhappy.

(Indeed, our goal surely isn't so much to make students "happy" in a superficial way, as to achieve certain pedagogical goals.)

The attributes relevant to undergrad teaching, especially lower-division, are essentially unrelated to seminar talks and even to graduate-level teaching, since the objectives (and the frame of mind of the audience) are invariably very different.

Edit: a "teaching letter" that merely reports that the student evaluations were positive, or that there were no complaints, is positive, but cannot count as a "strong" teaching letter, I think. This is a special case of the weakness of recommendation letters of any sort that merely repeat facts not known first-hand to the writer. First-hand information is better, and, further, lack of a first-hand-information letter-writer is not a good thing...


University advocates for students facing academic misconduct charges

It seems to be that the overall process is working well. The problem is that Student B was denied the opportunity to have an advocate truly being a proper advocate.

In absence of any university regulations which require you to bump it up higher, I would recommend handling it locally if you can. There seems not benefit to engage higher ups if not needed.

I would, however, have someone examine the entire advocacy system used. The fact that two students were given the same advocate on a case where they are basically claimant and defendant comes off as wildly unfair. Of course, the advocate is not a lawyer but still, the system simply should never allow that to happen. When you saw it happened, it would have been better (if it is allowed) to stop the proceeding immediately and sort out the advocacy issue.

In short, the problem is with the advocacy system, perhaps not with the advocate. Someone should dig into and fix that so that such problems never happen in the future.

As for the current two students, if Student B (not the advocate) did admit, then it seems clear that blame should be shared (it was not theft but rather collusion).


Difficulty in thinking properly during exams

I find that doing strenuous exercise, like an hour-long swim, before an exam relaxes me and calms the nerves.


Do American Christian Universities and Colleges offer as high quality education as other countries?

Christian universities in the United States are tremendously diverse.  The fact that a particular university is "Christian" tells you only that it is not a government owned university.  Almost no other conclusions can be drawn from a Christian identity.

Each university makes its own curriculum.  A science department at one university may exclusively teach science based on religious beliefs.  A science department at another "christian" university might not employ anyone who knows anything about christianity.


Is having two MS degrees in the same subject, from different depts, useful?

I would be very confused about why somebody needed two degrees in the same field. If the fields were overlapping but distinct—mathematics and computational science, for instance—that would not be such a big deal. But somebody with two biology degrees or two mathematics degrees from different universities would be such an exceptional case that I would want to have some explanation for this in the statement of purpose. (Why did the applicant feel it necessary to have a second bachelor's or master's degree on the same topic?)


Creative Ways of Getting Teaching Experience

First of all, put down all of that experience on your CV, and when you apply for jobs, make sure you write a great teaching statement on some of these experiences.  Make sure to talk about any courses you designed (the LaTeX one, perhaps?), and don't disregard the high school teaching at all.  I was a high school teacher for seven years before I went to get my PhD, and when applying for college teaching positions, I played up the fact that teaching high school is (in some ways) more challenging and that it made me a better teacher.

I believe that with your current experience, you have a good chance at one of those community college adjunct positions (depending on your field), so don't sell yourself short yet.

One other option that might not sound so great but could at least get you into the classroom is to apply to adjunct positions with for-profit colleges (U. of Phoenix, etc.).  If you can disregard any problems you might have with that "type" of education and dedicate yourself to doing the best you can for the students, it would give you experience.  The problem may be that you're in the sticks.

Speaking of living in the sticks, are you able to move for a semester?  If you're flexible enough, you will be able to find that adjunct position (Alaska?  Kansas?  Puerto Rico?).

Let's say you can't find a teaching position.  What's stopping you from developing a full-up course, even if you won't teach it now (or ever)?  Be creative, and design the course you've always wanted to teach!  You can then put down, "designed xx undergraduate course, which included a unique assessment plan and a flipped classroom approach, blah, blah, blah."  A bit hokey, maybe, but it's something.

Depending on your field, you could branch out and apply for positions or volunteer to teach classes that aren't directly in your field.

The bottom line is (and you seem to already know this): you have to be as flexible as you can if your goal is simply to get college teaching experience.  But try to think if there are other ways you can be even more flexible, and something is likely to come your way.


I feel overwhelmed for the acceptance rate of some conferences

I know the feeling. I have just a few days ago received a reject (with mostly positive comments) from a conference with an acceptance rate of less than 14%. Happens to the best of us. (or more accurately, it mathematically has to happen to most people most of the time, otherwise you can't end up with such low acceptance rates)

  If I submit a "short paper" rather than a regular one, Will that make easier to get accepted?

Generally yes, but the "short paper" tracks at some conferences have in the mean time become viciously competitive as well. In one major conference in my field, the acceptance rate for work-in-progress papers is nowadays below 20% as well.

By and large, whether you should submit a short paper or a full paper (potentially at a weaker conference) depends on how mature your work is. A short paper at a strong conference has good chances if it is ongoing work with very high potential; mediocre finished work is likely to be rejected as a full or short paper at such venues. You have better chances if you submit a full paper to a weaker conference in this case.

  My research is a software artifact that has been tested (not only unit-tested, but integrated in a bigger architecture and proved to be compatible with external applications) but not evaluated by a broad audience of users.

In most fields, whether your component is "compatible with external applications" or whether it has been "evaluated by a broad audience of users" are not the core questions for scientific merit. There are almost infinite "software systems" out there for which both of these properties are true, and which are scientifically still entirely irrelevant (pretty much all standard software, for instance). More relevant is whether the research question underlying your work is interesting, and whether your work in its current stage is able to sufficiently and convincingly answer this research question.


Do Geophysical Research Letters (AGU) accept PhD thesis as reference?

Of course. At all universities I've ever heard of, the PhD thesis is public (potentially after a waiting period for intellectual property reasons), and consequently it can be cited.

It may of course be that these theses are not always easy to get -- they may not be on the internet, for example -- but they exist and are available to the public from the library, for example.


Why does the IPCC 1.5 degrees report say "Do not quote, cite or distribute" at the bottom of every page?

I just got this reply from one of the lead authors:
"The 1.5°C Special Report indeed still had a "do not cite/do not quote" label on it, but that is in the meantime removed. Important to note, however, is that the version of the report that is currently online will still be subject to copy-edits as well as consistency edits, which can be significant. By the time of the UNFCCC climate summit in Katowice in December of this year, this should all be updated."


How can I gracefully exit my current post-doc position for a new one?

I changed from one unfinished postdoc to start a new one.  In your list of reasons, there is one that easily trumps all others:

  the new position is in the same city that my partner lives in, and we will be able to live together.

Tell your current advisor that you are moving to another postdoc so you can live with your partner.  Any remotely humanoid advisor will understand and accept that.  The reason for my move was exactly this.

All your other reasons are less important, and may be interpreted as implicit criticism of your current place.  Since you have the two body problem, you can move without mentioning any other reason.


What can I do if a student in my lab threatens to tell lies about me, and my advisor doesn't want to fire her?

She has been mean to you, not the PI. He clearly signals that he likes you and your work. You say that he also realises she has an immature attitude. I think that you are in a good position here, unless you mess it up.

The superviser clearly sees the situation and - in veiled form - tells you to be the mature part of the interaction. When he tells you to forgive her, that's very clearly what he means. In short, at this stage, you have to show maturity. Clearly, you need to work on that (I quote your response: "Hahaha...." - SE is not the place for such formulations).

You should not worry too much to prove that she lies about you, as the superviser made very clear that he will not pay heed to her stories about you (why otherwise would he have emphasised that you are one of the brightest students he had?). He has sent you a clear message of confidence.

Whether he likes her or not, you do not know, but it seems very clear, even through your report, that he takes pity on her. He will not fire her; it is not your job to make him do so. He also will not remove you, unless you decide to go. He seems a very reasonable person.

As for her using threatening language, you have a number of options: when she does that, you ignore it. Or else, you find a reason for yourself to go away, without responding, to some made-up excuse (for yourself), such as the bathroom. Or else, you respond: "This is not the place for threatening language. Please refrain from such language, it is inappropriate to talk like that to your colleagues." - or something along those lines. In a cool, calm, and collected manner. If she indeed has the maturity of a 12-year old, she may not absorb the words, but she will absorb the tone.

She presses the buttons where she sees an effect in. If you signal to her that you have no business with her, and that you are unaffected by her threats, you will become an uninteresting target.

Forget about winning/losing. You just do not have to play her game, you decide which games you play, and which ones you don't.

Bottom line: stay away from her; relax, the PI trusts you; and follow your maturity level and do not let yourself be dragged down to hers. She is not the one to set the agenda, your PI is, and he unambiguously signalled his trust in you. When he sets the meeting, if she apologises, graciously accept the apology (even if you do not believe in it, take it at face value), but still stay away. Her safety procedures are not your business anymore - you have made your case.


Is it unethical to expect one's PhD students to work after graduation without compensation? Should graduates ask for compensation for work?

You are thinking about this like an industry employee (which you are, so that's a reasonable stance).

Your advisor is thinking about this like an academic (which they are, so that's a reasonable stance).

Some perspectives:

Academic work is personal work and community work

You don't work for someone in academia as much as you work with someone. It seems like you are feeling a lot of conflict with your advisor right now, but I'd step back a bit and think about whose research this is. Certainly at some level your work benefits your advisor, but isn't it your own work, too? Do you not want to see your results published?

Is your advisor making decisions about suggesting further experiments that pushed your timeline beyond what you hoped because they are getting free work out of you, or are these steps to make the paper better and importantly to make it publishable (see below)?

In academia, it is normal to work on projects from a previous position; in industry it is not

Almost every academic will, at any time they move positions (including graduating as an undergraduate/graduate student, between temporary positions like post docs, and when getting hired as a professor and any moves afterwards) have some unfinished business at their previous place of work.

It's not reasonable to expect every research project to fall neatly into the academic calendar, conveniently finishing right at the conclusion, especially given the unplanned timelines surrounding peer review. Therefore, people tend to spend part of their time in their new position finishing up things from their past one, while being paid only by the new institution.

This gets "paid forward" in the future when the same happens during the next transition. A frequently asked question here at Academia.SE is some version of "which institution/affiliation should I list on this paper, new or old?" because of how often this happens.

Unpublished work is worthless to you and the academic community

Maybe your work is in a thesis in some draft form already, but all of the work you've done that isn't published is doing nothing for you or for academia. Maybe you're fine with that, because you aren't an academic anymore, but ultimately whatever funding agency funded your research and the university you worked for did so because they wanted you to produce published results, not just to give you the PhD title. If you think there is value in the work you've done, then that should be an incentive to get it into a form that can be shared.

On the other hand, you may decide that publishing is not actually of any benefit to you. If you don't feel intrinsic worth in the project, and if you don't plan any return to academia, then probably one more published paper won't mean anything tangible for your CV.

Given these differing perspectives...

I don't think there is any fixed answer. Should you do work for a past advisor without compensation? No. Should you collaborate with people you've worked with in the past to share your research with the broader academic community? Probably yes.

Ultimately it's up to you to define where those boundaries are. Personally, I would think it to be irresponsible to fail to follow up on basic authorship duties like responding to reviewer comments, editing manuscripts for submission, etc. These activities shouldn't replace paid employment, but they can be completed in a few free hours during a transition period. Coming in on several weekends to run experiments sounds like a bit much - maybe there is a compromise solution where you can train a new student to run those experiments, add them as a coauthor to the paper, and continue helping with the manuscript(s)?


Whether to include a middle initial in author name on academic publications?

It's a matter of author's own preferences whether to include the middle initial or not. It's better to be consistent from the beginning, and do not use different styles in different papers, although the author might be able to "glue" together their records in some bibliographical services if they treat different spellings of their name as different persons (I have managed to do this on Scopus for myself, but there may be other databases which I don't know).

This, however, does not solve the main problem - it only reduces the chance that two authors will have the same name or initials, but it does not eliminate it completely. This is why authors are advised to establish ORCID:

Quoting http://orcid.org/, this is "a persistent digital identifier that distinguishes you from every other researcher and, through integration in key research workflows such as manuscript and grant submission, supports automated linkages between you and your professional activities ensuring that your work is recognized".

Some publishers already allow the author to specify their ORCID during submission, and some others already require it, for example PLOS One and the Royal Society.

Another useful feature of ORCID is that it allows the author to keep a public profile with a list of their publications (and other optional details). Even more, one could link their ORCID profile to Impactstory (https://impactstory.org/) and track online impact of their research. As an example, by now I've already stopped maintaining a list of publications on my personal homepage since I can just put there links to several databases, ORCID being one of them, and most of them (as reported by Impactstory) are in open access anyway.


In addition to making changes according to the reviewers' comments, you may also make other corrections and changes that improve the quality of the paper. However, you should indicate to both the editors and the reviewers that you have made such changes, and explain why they have been made. Given that it's a major revision, the paper would go back to the reviewers anyway, so it makes sense to correct everything possible.

As a caveat, however, such corrections should not be made in an attempt to skirt around flaws raised by the reviewers. I recently reviewed a manuscript where there were several anomalies in the data, and I mentioned these in my review. The authors completely removed the offending data, and replaced them with new results that better "fit" their conclusions. Such behavior is not acceptable, as they did not explain why the previous results were wrong; they just replaced them.


How much feedback to give for an undergraduate / master's thesis?

As noted in a comment, this is probably highly dependent on the university culture and field. My answer is based on my impressions from CS in Germany.

In my subfield (HCI-related), it was most usual for doctoral candidates to supervise between one and four Bachelor/Master theses a year, maybe a bit less for post-docs (each of which took exactly 6 months). (Depending on the topic, supervision occasionally took place in groups - i.e. two or three supervisors for one student, taking turns at supervision tasks or focusing different aspects of the work.)

As a rough guideline, the "amount" of supervision provided was usually a weekly meeting (typically, between 10 and 60 minutes in length) with the student to give them advice and answer questions. And, realistically, in some phases and for some students, to remind them that they should get some work done because they cannot work on their Bachelor/Master thesis forever. As a secondary channel of supervision, students were free to ask urgent questions whenever they came up, via e-mail or by just dropping by in the supervisor's office whenever it was convenient.

The kind of supervision covered a wide spectrum - essentially, everything from high-level advice (decisions about the content and how to proceed, developing some basic ideas for solutions together, scientific best practices, ...) to low-level operational details (technical issues in the code and in the LaTeX document, stylistic writing and layouting questions in the document, ...) could come up.1

As for looking at drafts, I agree with semi-extrinsic's answer in that it's likely too late if the thesis is almost due. Personally, when I knew the student was in the phase in which they had already scheduled some writing, I would ask my students on almost every meeting whether there's a new or revised section that I can read and comment on (not necessarily because I was so keen on commenting, but first and foremost as another means of urging students to do the part of the task that most liked the least - writing the thesis document). Moreover, at least at my home department, we usually required students to use the department's Subversion version control system, which was another way how supervisors could look at the students' progress and the current state of their thesis when they had a feeling progress wasn't as smooth as it should be.

Lastly, concerning fairness, I must admit the thought that there could be anything unfair (in a way that should be avoided) in this never crossed my mind. Of course, supervisors in different institutes may hold very different opinions as to what amount and kind of effort is optimal and feasible in their supervision. But then, students are not assigned to supervisors in my place; they usually pick a topic they like and they know beforehand who is going to be the supervisor for that topic. Anyway, as a result of the different opinions, supervision between institutes differed. Students could have bad luck with their supervisor, or with the typical style of supervision in the institute that focuses on the subfield they like. But the question is: Should you do anything about it? I'd say no. First, because I consider it part of a university graduate's skills to also get along with supervision that does not ideally suit their personal preferences. And moreover, because I firmly believe that unfairness should not be countered by removing any advantages until every option is as bad as the original quality minimum.

1: This does not mean that students would have supervisors do all their work. The goal was rather guiding the students towards a balance between working out problems autonomously and not being shy to actively contact the supervisor about any current roadblocks.


I have been to seminars like that, including ones where large numbers of my colleagues are present.

So long as you have meaningful and productive questions (i.e. don't ask a question for the sake of asking one) and ask them as respectfully as you would any other topic, there isn't a problem.

I will note that choosing not to attend is also sending a message, and in the seminar I was in, a number of colleagues expressed disappointment that the room was nearly entirely women (in this case it was about the status of women in the field).


Speaking to experience in a statement of purpose for a PhD program.

I'm not sure that the statement of purpose is the right place to try to address deficiencies in your CV. Instead, let me suggest a different strategy. (I'll note in passing that I'm in Philosophy, in the USA--so take this with a grain of sand since you're in a different field. A second grain of sand if you are applying to programs in other countries.)

Use the Statement of Purpose to show the committee what you are going to do in the future, not to tell them why what you've done in the past isn't bad.

Here's what I mean by the past/future comparison.

Bad: "I did a lot of work that is relevant, even though I know my CV didn't look like it." or "At my current lab job, I was taught techniques x, y, and z." Bad because it sounds like you are apologizing. It comes off weak, passive and submissive. You want to project confidence and competence, but not arrogance. Successful PhD students are people who are able to be self-motivated and don't have to have their hands held all the time.

Better: "I plan to apply my experience in techniques x and y, to problem z because . . . " This is better because it is active--it says what you are going to do rather than what has happened to you.

The second distinction that is important is the distinction between showing and telling.

Telling: "While working on this project, I acquired knowledge of techniques x, y, and z." This is weak because it just sounds like a list of things. There's no story--I don't get anything about your personality or your interests or what is special or unique about you as a candidate.
Showing: "We were interested in p, so I suggested we use technique x and we discovered r. A colleague who works in r suggested that we also apply technique y, which turned out to be the crucial step . . ." Now there's kind of a story that I care about a little bit. And I've learned more than just that you know x and y. I've learned that you know how to suggest techniques, and you're not afraid to tell the PI what you think, and that you know how to collaborate, etc. These are all good things. The committee gets a more complete, detailed idea of who you are as a candidate if you can show who you are and what you are interested in than if you just tell them.

Most aspiring grad students (and newly minted PhDs!) are going to fall into the trap of telling rather than showing, so this is a good place for you to stick your neck out ahead of the pack.

Another example: Instead of using the SOP to say why you don't suck, use it to say why you want to go to this specific PhD program. Don't say, "I am interested in Neuroscience." That's telling. Instead: "I became particularly interested in question X after reading "X: an intriguing problem" by Prof Y." (where Y is somebody on faculty). You want to be specific about the strengths of each program.


What is some pre-requisite information one should know before applying to a CS grad school in the US?

I will give some guidance for the US only.

Here, you apply to a school or to a department. There is no need to contact professors beforehand. I would do so only if you have already set a research agenda and only a few professors would qualify to guide it. Most "blind" contacts are treated as noise by professors until you formally apply and are at least close to acceptance.

Funding in CS in the US is most likely to be from a TA position. One gets a very modest salary and (normally) waiver of tuition fees. It is enough to live on in most places (harder around Silicon Valley, where housing is outrageous). The tasks are helping professors with their courses, such as leading smaller question-answer sessions and grading. Those with more experience might get to teach intro courses. Normally you would apply for a TA position when you apply for admission. Ask each institution about the possibilities. In some subfields, in might be possible to get a research assistant position funded through a professor's grant. This might be good, but if the funding ends, so does the job.

You can always ask for fee waiver and probably should. It may be possible or not.  Things are very variable in the US as there is no national system of universities.


What are the downsides of publishing your statement of purpose on the Internet after you've already been admitted to a PhD program?

In general, I think this sounds like a great idea.  I would further say that the same essential content is often a good starting point for your personal professional website.

The only potential downside that I see is that in the future you might look back with embarrassment on naive ideas in your statement where your feelings have evolved over time.  If you have enough self-confidence to be OK with with that, it's fine: nobody will expect a mature researcher to believe all of the same things they did when just starting grad school.


Is there an API to obtain article information via DOI?

You are looking for https://doi2bib.org . It shouldn't be very hard to extract the actual bibtex entry from the html you get from that page.

If you want to see how it works under the hood, take a look at the sources here: https://github.com/davidagraf/doi2bib2/ .


Realised afterwards that I committed mild plagiarism in a paper I wrote as an undergraduate, what should I do?

but sometimes I would quote single sentences or parts of them directly from my sources without indicating that they were direct quotes (even if these unmarked quotes were always followed by a citation to the original source).

"You didn't use quotation marks where you should have in a paper you wrote as an undergrad? My god, you are despicable human being."

Nobody reading your question here will think this.

Rather they will think something like:

"Wow, you wrote a journal paper on your own as an undergrad and it's still being cited?"

I would imagine that the vast majority of readers of your paper, even if they notice, would think likewise.

Though it's technically plagarism, I think it would be quite obvious to a reasonable reader that if your intent was to plagarise, you would not immediately cite the plagarised document you stole the quote from. Omitting quotation marks sounds like a minor transgression to me, particularly if your area is STEM where the (natural) language of the text is a means not an end. (If you did not have the citation(s) at all, I think it would be a different matter.)

Mistakes happen and this was clearly just a mistake.

(I would also add that I think it's pretty common for researchers to be somewhat embarrassed by earlier papers that they wrote when they were more junior. At least I am. But that's just a sign of improving.)

  I also don’t know what I could do about it. I have thought of putting something like a public admission and apology on my website (from which the paper can also be downloaded)

I would suggest two things:

Update the preprint on your homepage.
Keep a list of errata on your homepage.

In my area (CS) people mostly read the preprints (found through Google or Google Scholar).

  public admission and apology

I don't think there's a need to apologise. I think you just need to admit your mistake and move on. Again, mistakes happen!


Is it possible for research paper to have a similarity of 2 out of 100 using iThenticate?

I don't think I've ever seen an iThenticate paper with 2% similarity. Less than 10% is rare enough.

However: so what? Low similarity isn't a problem, only high similarity is. The latter implies plagiarism, but the former ... I can't think of any way the authors can cheat by having low similarity. If it's a fake paper generated by SciGen then perhaps it would have abnormally low similarity, but you've already ruled that out since you understood the paper. It's also presumably possible to force a paper to have low similarity as well, simply by continuously rewriting the parts that iThenticate flags.

I'd assess the paper on its content and not worry about the similarity.


I get overwhelmed while self studying courses. What can I do when I can't sit in classes anymore?

Reading and watching videos is not a substitute for learning. Treat the material like you would if you were in a class. Find exercises that you can do to assure that you have "mastered" the material. Take notes. Make checkpoints at which you can assess your progress. You learn from reinforcement and feedback. The latter is hard in online learning. Find someone who can give you some feedback and answer questions. Find a working group if possible and learn it as a group, reinforcing one another.
I wonder, also, whether you can informally sit in on a course while not taking it. A friendly professor might permit it and even let you take exams informally. I've done this as a professor, actually, when wanting to learn the basics of a new field.


Framework Analysis: Can framework analysis (Ritchie, Spencer & O'Connor) be applied to open-ended survey question responses?

Yes it can. If you need to provide justification on the method that you used it would be helpful I'm sure. However like you say this method is used for interview data.

I'd guess (but obviously don't know for sure) that your survey data might be quite minimal/basic if it features at the end of a more structured questionnaire and although there are similarities with many qualitative data analysis techniques, I'd imagine you'd be looking to organise your open-ended responses into something more manageable, perhaps grouping together responses reflecting a particular view.

The following article may be of help:

Hsieh, H.F., Shannon, S. E.; Three Approaches to Qualitative Content Analysis, Qual Health Res November 2005 vol. 15 no. 9 1277-1288. doi: 10.1177/1049732305276687


How reasonable is it to ask my referees to send their recommendation letters to me?

You should ask your references to send the letters directly to the hiring committee.  Your references will be more candid in letters that you have not seen and this will increase the credibility of the letters in the eyes of committee members.


How to delay a potential advisor without burning bridge?

There shouldn't be any guilt involved since you don't seem to have made any commitment. I think there are some important points to be made in a note totem.

Thank you for your interest and support
I'm feeling a bit overwhelmed right now and need a bit of time to explore my options and further directions.
I'll be more than happy to meet with you when the term starts for additional advice.

If he has already said that he wants you to be his student then it is a bit tricky, of course.

I'm delighted that you would consider me as your student, but ... (point 2 above)

If he has not been explicit about taking you on, then don't be presumptuous, of course.

I'm currently trying to decide on an advisor, but (point 2, again)

Then, find out some more about this professor and the other. If they are, in fact, not tenured but about to be evaluated then you need to know that. It can get in the way. Look at a few papers by each potential advisor. Talk to a few other grad students if possible. The department might be able to put you in touch with a few.
Let the wording be your own, but you haven't walked through the door and you aren't closing the door.
If you want to prime the pump a bit, ask for recommendations for a paper or two that you might explore now to help you make a decision.


What does it mean to go directly from "under review" to "decision in process"?

Manuscripts move from "Under review" to "Required Reviews Complete" when all the necessary reviews to make a decision have arrived. This is usually journal-dependent, e.g. some journals can move the status when one review has been submitted, while others might ask for 2 or 3 or more. Manuscripts move from "Required Reviews Complete" to "Decision in Progress" when the editor's ready to make a decision.
In this case you didn't see "Required Reviews Complete", which could mean:

Editor decided to make a decision before all the reviews have arrived. This could be for all sorts of reasons, e.g. the status moves when 2 reviews have arrived, but only one reviewer submitted a review and the editor's making a decision anyway. Or the editor decided to terminate the review process on the strength of that one review. Etc.
Editor "got to" the manuscript before you did. In other words, there really was a "required reviews complete" status, but the editor was monitoring the journal at the time and moved the manuscript along before you saw the status change.

In all cases there's nothing to do except wait.


Former professor wants an update to write a recommendation letter, should I include a bad grade?

I would err on the side of being honest, as you have a legitimate reason for why one specific class was an issue. Whereas that is explainable, it would be a mark against your character if he discovers that you did not give him a complete list of a classes after he requested it.


To what extent similar remarks from the same author can appear in different papers?

To some extent plagiarism isn't charged when there is essentially only one way to say something. But this rule mostly applies to things that are widely known, not research results. This may be the case here or not.

But it is better to cite the other (first) work in subsequent work (or cross cite if appropriate). One of the purposes of avoiding plagiarism is to allow readers to have access to the complete context of an idea. This might be especially useful in the case at hand, since the "similarity" itself may provide context that would be helpful.

When in doubt, cite it.


How to get feedback on unfinished research papers if I don't have any direct contact with people qualified in my field?

How can I get feedback on unpublished scientific articles if I have no direct connection with anyone qualified in my field?

Make contact with those qualified in your field.
As an undergraduate, without a reputation, don't expect top-professors to be interested. Aim lower. Personally, I'd suggest a top PhD student or a top postdoc. Someone who's work you have studied and are interested by.
Offer co-authorship.
Don't ask for help, make a mutually beneficial offer: Many researchers are willing to help (this forum is an example), but, everyone is busy, make an attractive offer when contacting researchers. For instance, you could offer your services to help-out on their work, or you could offer co-authorship of your work (in exchange for guidance), or ... Explain your short- and medium-term goals, e.g., publishing your work, developing your profile, getting a post graduate degree, and pursuing a PhD.


"Breaking in" to reading papers in an unfamiliar field?

You could use a database, thorough your university library for example, to search for papers in your area of interest (with keywords or author names etc). This will help you see what others are researching and publishing and to determine if that is what you want to do too.

Reading relevant blogs and forums (that deal with same or similar topics as the one/s you're interested in) may also give you some ideas.

Similarly, talking to academics you may wish to work with is a good idea, as already suggested to you by others.

I would also make sure that the academic I am working with is someone who is going to be supportive (and have time for me) to make sure that I get some help (rather than being completely on my own). If this relationship doesn't work, your job is going to be much harder. You can change direction of your research later in the degree or post graduation.


Do my publications help my department/university?

(Although OP is in the US, the question doesn't have a "united-states" tag, so...)
In England and Wales, there's a pot of government money called "QR funding", which is allocated to universities in proportion to the quality and quantity of their faculty members' research publications, as measured in an episodic exercise called "REF".


On the possible obsolescence of research paper titles starting with "On the ..."

As I always understood it, a paper called Zero-dimensional vector spaces claims to be an exhaustive overview of the topic, while On zero-dimensional vector spaces would be merely a contribution to the study of those spaces. So it is humility on the part of the authors.


How often should an editor ask for reviews from the same referee?

From my experience as an editor, it is not unusual for referees to ask for "time off" from being assigned reviews and give bounds for the frequency of requests.  As Buffy suggested, some editorial systems allow referees to enter this information and the editor sees it before sending out review invitations.  I was glad to honor such requests from reviewers---I wanted them to feel satisfied & respected so that they would write more helpful reports in the future.
Similar to Fred Douglis, I tried not to ask anyone (other than editorial board members!) to review more than twice a year.  However, we aren't mind readers.  If your pattern is to submit a helpful report and then say yes to another request soon afterwards, then maybe you have the time, really enjoy reviewing, etc.  What editor wouldn't follow up on such enthusiasm?  My advice is that it's up to you to speak up about what you have time for, how often you're comfortable reviewing, etc.  I think there's very little risk of getting on the editor's bad side by setting up those kind of parameters.


If you want to do a PhD in mathematics, how important is it to start immediately after finishing undergraduate studies?

But I've been told by a few people that if you want to do a PhD in mathematics, you have to go pretty much right after undergrad, mainly because recent letters of recommendation are so important, and professors forget you after a time.

You do not have to start a PhD program "pretty much right after undergrad".  It is most common to do so, but there is a substantial minority of students who are older and/or spent several years out of school.  In (American, at least) academia, your age counts for nothing; the ticking clock in the sky keeps track of the number of years since your PhD.  I know several people who spent years off from undergrad in the sense of leaving school but clearly kept up with their mathematical reading and learning -- while in the Israeli army, culinary school, creative writing programs... -- and started grad school with skills at least at good as those around them and a maturity that most 22 year-olds lack.  I've looked through hundreds verging on thousands of job applicants' CVs, and I am struck by how often the stronger candidates were in their 30's rather than their 20's when they got their PhD.

Of course the biggest risk in taking time off between undergrad and grad is that you will get distracted by the rest of the world and not come back for graduate study.  But that's only a risk in the context of your original plan: if you found something else that you like better than being a graduate student, good for you.  It is also relatively common that after a fairly small time away -- one or two years -- people realize that they really do prefer an academic career.  (For some reason this seems to be most common among high school teachers.  Isn't that a bit sad?)  If you're not totally committed to a PhD program, taking time off and seeing whether your desire waxes or wanes is a pretty smart idea.

Of all things in your decision, I don't think that going straight to a PhD program because you're worried that your professors will forget about you is a good strategy.  Professors don't forget about students that quickly, but after a few years, they may.  To combat this, I would say: if you are not sure whether you want to do a PhD right away, why not apply right away to PhD programs?  Certainly knowing where you can get in and seeing the programs that admitted you are all factors in your decision.  If you apply right away, professors will write letters for you, and if you go away even for a long time, those letters should still be equally usable afterwards: your past undergraduate performance is not a function of time.


How to cite papers where the names are sorted?

If the authors are listed as Adams, Brown, Clinton, Dylan, you cannot cite it as Brown et al. The standard thing is to simply cite Adams et al.

If you are one of the authors and you cite it.
Let's say that you are Brown and you now have an article with Eldridge. Then you can write the following:

  ... as was shown by the first author in collaboration with Adams et al. [ABCD14].

This way you cite the paper properly and at the same time, you make it clear that you are one of its authors.


Travel grant for undergraduate researcher for attending conference

There are several strategies for this in addition to the usual ones outlined previously. I assume you are in CS/IS/IT from your profile. Your primary costs are conference registration fees, air fare and living expenses.

If its a top conference, it will have student volunteer positions. For instance, this and this. This defrays cost of registration (free) and some of your living expenses (food and some cost of living). Apply for it immediately.
You mention that you are getting some travel grant from the conference. Thats a good thing. Keep it for airfare.
If its a ACM/IEEE conference, it will be sponsored by a SIG. SIGs have their own funding. For instance, see this and this. If you are an ACM/IEEE member then you can apply for these funds which are independent of conferences.
Sometimes, in limited ways, industrial research labs and other government labs have funding. Search for and apply for these. For instance, see this , this and especially this.

I was once a poor student and had to make use of multiple sources of funding to go to conferences. You can also do it ! Basically, apply for everything that you find and see. Of course, the best way is to simply ask another co-author or someone actually visiting the conference to present the paper.

Another way is to just pay the registration fee (which is comparatively less). That way your paper is still indexed in the ACM DL or IEEE Xplore etc.


Should I explain how I identified a relevant supervisor in my SOP?

I don't know if adding this information is a good idea, but I think your current text is not.
In the draft, as it stands, you are just pointing out highlights, that proofs that you have skimmed through two papers. You are not showing any hard work because you don't even need to understand the papers to say that the method is interesting and to quote limitations they themselves described. I am not saying you haven't worked hard, or that you don't understand the paper, but just that it doesn't show all that. So, it risks backfiring at you because it sounds sort of pretentious.

If you want to show deep understanding, you would need to "cook" some new knowledge, like relating several papers, or relating their work to other people's. Mind that it will be read by people not familiar with the paper, and they may not know what is your own work, and what is just regurgitating.

One tip I can give you is to try to give it a focus from some other field you are an expert in. For example, sketch out how you would like to introduce a different mathematical modelling technique (like, instead of solving a single differential equation, you model your system as a network of interacting differential equations, where the topology comes from blablabla). This will give them a reason to hire you specifically: you are not just another mini Prof. X, but someone that would be bringing in new knowledge to the group.

Just make sure you run this through your local expert, to make sure you aren't saying anything silly, or that has actually been done before.

If after doing this you believe you are adding new useful information that would make you look better in the face of the admission committee, include it; otherwise, don't.


Has it become harder for Chinese students to be accepted into graduate programs in the US?

US universities have always taken country of origin into account during admissions. I don't think there will be a major difference on the University side for admissions moving forward.
The visa situation is something else though. DHS is sitting on J1s, won't process H1Bs at all, but is still approving F1s and OPTs. This is likely to have a substantial chilling effect as it makes it much harder to do post completion training in the US.
I'm not sure they're going after china more than any other country - had a Singapore national just say forget it and walk away from a job offer over visa issues.