How to deal with my PhD supervisors rudely critiquing all my draft papers?

There needs to be a little bit of context in this situation...

Incoming Masters and PhD students often come in thinking that they are going to write one draft of a paper and submit it. The thinking is that writing a scientific paper is no different than writing a paper for one of their previous class assignments, and that they did well on all of those, so their writing must be impeccable... English is their first language after all...

To the contrary, I have never had either a masters student or PhD candidate who went through less than 10 revisions on their first paper before we submitted to a conference (let alone a journal). In all likelihood, this number is closer to 25. Even toward the end of their PhD, this often still involves about 5 revisions.

Everybody hates the advisor after the first few revisions (I hated mine), and does not see the point. However, I feel that if I have not taught you to write an impeccable scientific article by the end of your PhD, then I will have failed as your advisor. And in fact, everybody who completes a  PhD seems to be grateful for the struggle.

Typically, I tell students that they must "finish" a paper 2 weeks before the conference deadline. Then we do one revision every single day until the deadline. I mean no malice in the corrections. But there are some common mistakes that need to be refined and refined. Furthermore, everybody asks, "Why can't we just do one revision?"

The answer is simply that often the writing in the first few papers is too ambiguous and vague for me to infer how the rest of the paper should be written. For example, "Are you stating A or B as your hypothesis? Are you stating C or D as your takeaway from the plot you are showing?" These lead to further questions like... how did you come to that conclusion? These things cascade, and the process ends up taking several iterations, particularly at the beginning of a PhD.

With that out of the way... let's address your case...

  you didn't explain how you mixed this solution

This is a legitimate point. A scientific paper must detail every minute detail in the most unambiguous way possible. If the paper is at all ambiguous, then the results cannot be reproduced, and the work is not science!

  what are you doing here

This is a comment that I would write when I believe that you have not unambiguously explained your procedure. Or perhaps you added a plot, without explaining why it is relevant.

  don't send us manuscripts with errors, next time they'll be sent back to you

This is a bit cheeky I think. I wouldn't write this, but I can imagine that the advisors are perceiving that you are not trying hard enough in your edits. When I make edits, there are often errors that are repeated over and over again. If I correct 2 or 3 instances, I expect you to spot this pattern and propagate the corrections to the rest of the paper. If you aren't doing that, I would get very annoyed. The reason is simply that it may take you 30 minutes to apply all of the changes I suggest. However, on my end, I will spend hours going over your paper. Literally I can be spending 2 to 3 times as long reviewing your paper as you are taking to write it. If I don't feel that you are pulling your weight, then I will let you know.

  EDIT: They also rewrite almost everything I write. None of my writing ever makes it to the final cut.

Quite common for the first paper a student writes.

The final point I want to make is concerning why we do this? Why do we go through the trouble?

The most obvious answer is that if a paper is not clear, concise, and unambiguous, then the work is not reproduceable, and hence not science.

However, as you will no doubt have seen, there ARE many papers in very well respected journals that are extremely poorly written. These are the ones that you and your advisor will debate for weeks on end... I think they are doing this! I think that their results show that!

Those are bad papers. If I was reviewing them, I would reject them.

By going through this process with you in writing your paper, I am not only helping future scientists (by making your work more clear), but I am putting you in the best possible position to get your paper accepted into the conference or journal. The worst reason to get your paper rejected is because, "I could not understand what the authors are trying to accomplish", or a review which suggests a misunderstanding as to what the paper is trying to accomplish. That is just a waste and completely avoidable.

The papers that have been rejected by my group will often start with, " This paper was extremely clear and well written. However..."

EDIT:

I think that in general, it sounds like the PIs may be going a little bit too far in your case, but it is really hard to tell without knowing your research topic, the scope of the revisions, and your conversations with the PIs. So the following are some more takes on the things you wrote which I did not initially address:

  "you didn't explain how you mixed this solution," so I will write, "I mixed the solution by adding XXg of XX to XX." Then they have the nerve to tell me, "you're not doing a good job, you add useless details about adding XXg of XX to XX."

I can see 3 plausible explanations for this:

The PIs simply changed their minds about whether this information was relevant. People make mistakes, and opinions change...
They meant something different when they asked for "how you mixed this solution". I am not a chemist, but perhaps technique or something else matters and they wanted you to describe that???
Perhaps over the course of several revisions, this information got included earlier in the paper, in which case, you should avoid writing this info again at this specific point in the paper.

In any case, the statement "you're not doing a good job" is a bit  aggressive from my point of view. My guess is that they are getting really stressed about reviewing this paper. Perhaps they have been putting in a lot of work doing revisions and don't think you are "getting it" yet, or aren't trying hard enough. Whatever the case, they snapped at you here when they probably shouldn't have. In cases like this, you should have a sitdown meeting with them to understand why they do not think you are doing a good job. Did they sincerely mean it? And if so, how can you improve? If they really meant it, then this needs to be clarified in person.

  Really?! They also make jokes about my writing, like "impossible [to test mice immediately upon birth] unless you're a mouse midwife.

Probably they are trying to show that your logic is flawed, and simply giving you a counterexample. It probably isn't meant to be funny, it probably was just the first thing that came to their mind which conclusively showed the logical error in your writing. Scientific writing needs to be extremely precise, leaving no room for doubt. If there is an easy counterexample, then the writing is not precise enough.


How do I read a textbook or monograph with good comprehension?

You are not alone. Even highly educated native speakers find academic books hard. For the reasons for that see Michael Billig's book Learn to Write Badly (Cambridge University Press, 2013). It might amuse and comfort you.

Assuming you have to read a whole book, the strategy I suggest is to go through the thought process that the author should have gone through before putting pen to paper by asking yourself the following questions in the order given:

What single big question is the book trying to answer?
You would hope to find that stated very early on in the book, in an introduction or preface. Sometimes that may not be clear: that is not your fault.
What is the answer?
Sometimes considerate authors tell you the answer just after they have told you the question. Frequently authors are not considerate in that way. A good place to look is any chapter headed "Conclusions".
What in outline are the author's reasons for that answer?
Chapter headings might provide an answer to that, but sometimes you will have to dig a little deeper, skimming the beginnings and ends of the chapters themselves.

Don't be afraid of skimming the book to try to find the answers to these questions. Until you can answer them, simply ploughing through the book will be hard and unrewarding work.
 4. How does the author support each of the reasons given?
To answer that you will probably need to do a bit of ploughing, but don't expect to understand all the detail first time through. Keep constantly in your mind where the book is going, that is Questions 1-3 above.

When you have done all the above you can go into as much detail as you  need to master the author's whole approach.


Where can I see the standard salary range for California State University Assistant Professor?

I'm just assuming you mean California State University since it's the largest system among the states starting with "C", which can be found here:

https://transparentcalifornia.com/salaries/california-state-university/

You can search individuals by name. If the university or university system is public, then the information for faculty/staff salaries is usually posted on some government or independent auditing site.


Timeline for late tenure track positions

After the last interview, the committee will have to come up with a ranked list of candidates. Then this is forwarded to the department head for approval. Then this goes to the dean for approval. Then an offer letter will have to be drawn up. This has to be approved by the Office of Equal Opportunity. This process can easily take 2 or more weeks, and this is particularly true at places where final exams are running at the same time.
In other words, have patience!


Is a professor who's never had to write a grant application disadvantaged in the job market?

No, this is not a concern.

Typically individuals who receive endowed professorships already have a long record of applying for grants.  You could, as the donor, attempt to negotiate some other situation if you wished.
Typically endowed professors only leave their job due to retirement or death.  If you have really endowed the professorship with enough money, there will be no desire to leave for another endowed professorship, if one could be found.  An endowed professorship does not make the holder uncompetitive on the job market.  It makes employers uncompetative to hire the professor.
Most endowed professors do apply for grants.

Assuming you really have that much money to give, my advice would be: Require the holder of the professorship to refrain from applying for grants.  This will free up a lot of their time to do something more productive.
If you want to make a positive impact on academia, you can achieve more for your dollar by endowing (or just spending all the money immediately on) scholarships at institutions that charge low tuition, like community colleges.


I'm going to assume the US and the National Science Foundation for the purposes of this answer because it's the main thing I have experience with. Also, "IT DEPENDS":

If the research question needs to change a bit because the research isn't going exactly where you thought it would, the Principal Investigator should have a discussion with the Program Officer/Manager assigned to them by NSF. There's some slop in the system. They'll probably want you to follow the science. Biology awards probably can't be turned into pure theoretical Mathematics ones, but the PO will be able to guide the PI.
NSF money can't be used to pay a foreign national to work in their home country (nor an American in a foreign one) except under extreme circumstances or ones required by the science (think Large Hadron Collider or the Antarctic Program). The grant is to the institution under the direction of the PI, not directly to the PI and other named people. And, if the postdoc decides to go back to their home country, they just go home and don't get to work on the project anymore unless another source of funding with different rules comes along. If the PI decides to move from Harvard to Yale and wants to take the grant with them, then they can ask Harvard to release it to Yale and NSF for their permission, and maybe it'll all work out. Happens all the time. There were certain advantages at review-time for awarding the grant to the PI when they were at Harvard (Facilities document), now NSF has to decide if Yale is a good enough substitute. I've never heard of it not working out, but it might if the PI was taking a big step down (Harvard to a community college, maybe?). If the PI were trying to take an Engineering Research Center (ERC) or telescope or supercomputer with them, then everyone would probably say "no."


Discipline clarification or field of study

I have been in similar experiences with some friends, and I'm willing to share:

Here in Japan the programs usually have the weirdest possible names, even in the University of Tokyo they have the "PhD on Creative Informatics" (What's that supposed to mean?), when is nothing but a good ol' PhD on Computer Science. Or the "PhD on Frontier Sciences".

I asked my adviser and he told me that those names are usually for the sake of attracting more students. But he also told me something I've been seeing in the Industry looking for a job (Academic/Industry): No one really cares that much about the title in your PhD, but rather on your specialization topic. Usually questions will be directed towards: "What did you do on your PhD" rather than "What's the name of your PhD"

I advise you to create a brand around this concept of "Social Economics", if you know different people doing that, try to be in contact with them (Twitter/Mail/Conference) so you'll get recognized in the field later and when you get interviewed you don't have to explain it all over again.


How do the committees think of an international student who is exempt from the English admission requirement(TOEFL) but has poor GRE verbal score?

If you meet the requirements of a TOEFL waiver it would be a waste of your time to take this test. I would only worry about the GRE score if there is some sort of minimum admission score for the school you are applying too.

It's better to make sure that your statement of purpose is written in excellent English and that you provide other evidence of academic and research potential. Committees are used to dealing with international students and the challenges of English.


How important is specialisation in a master's degree?

I can just answer your question from the industry side:

I know enough people that don't even work in the field where they studied. Here in my department (in a well known company) we have guys from computer science, engineering and electrical engineering working on the same tasks. It's more important to have a technical degree than have a good specialization. Most of the hard skills you need for your work aren't taught in university. The important skills are the soft skills that the job will give you (to complete in stem fields with good grades will show them that you are not totally dumb and have the stamina for hard tasks).

Visit the courses that sound useful to you. I did it that way and am completely happy with my decision.


How to assess an unknown journal's quality?

When 95% is junk and the other 5% is sufficiently irrelevant that neither you or your supervisor and colleagues know about them, a safe and efficient strategy is to ignore all journals that actively request contributions.

I have also never heard of a legitimate journal using mass emailing to recrute editors (this is more a habit of author-pay open access journals that are looking to increase their market share).

Yes this strategy, if adopted broadly, would prevent some new journals from being known. The good news is: we already have way more journals than we could possibly wish for. It's good content and quality curation we're short of.


Including in progress but invited publications in resume and/or CV

I have seen people mentioning the 'under review' and 'in preparation' papers in their CV in the following way.

A. Author1, B. Author2, "The preparation of CV for a job" (under review)

A. Author1, B. Author2, "The preparation of CV for a job" (In preparation)

However, it does not add much value it the quantitative weight of CV except that people would know that your are active in your research.

If you are invited to submit an article, then you could mention like this:

A. Author1, B. Author2, "The preparation of CV for a job" (In preparation; invited for
special issue on Imagination)


How to deal with bad smelling (smoking) co-student

I believe the best thing to do is to be honest and tell him that the smell is very strong.

Engage him in a discussion about smoking and ask him whether he has any plans to quit. From my experience every smoker wishes to quit. Then tell him that the smell is strong and sometimes you can't focus because of it. Take into account that this is maybe the first experience for him to work in a lab. Later on, he would definitely be aware of this, such as a non-academic workplace.

Things you can do:

Try not to discuss or meet right after smoking.
Share gum with him.
Bringing air freshener to your office

In the end, there is nothing you can do if he's not willing to cooperate.

There are related questions discussing the same issue on Workplace.SE containing additional advice.


What is the likelihood of a PhD admission if a professor agrees to supervise?

Your odds are better than they might be otherwise, but they're not necessarily 100%, either.

Part of the issue is that some schools may not recognize or honor such "claims" or "gentlemen's agreements" to fund people after they are accepted. More importantly, the issue is that US admissions are typically done at the departmental level, not the faculty member level. That means that a professor telling you that you'll be admitted is not necessarily a guarantee, because the admissions committee has to make that call. (On the other hand, if the advisor in question chairs or is a powerful member of the admissions committee, that changes things substantially!)


How does one go about finding out who the good instructors are?

At most US institutions (and perhaps in other countries as well), the first week or two of classes are what's known as an "add/drop" period, in which you can switch from one class to another before you're "locked in" to the classes you're going to take for the semester.  This means that if there's a professor you're not sure about, you can attend a class or two with them and get a feel for whether their classroom style and their personality are compatible with your preferences.

A lot of professors don't particularly care for this approach from their students—a student who comes into the class a week late will be substantially behind, and may require special attention to get them caught up.  But it may reassure you to know that you have this option in your back pocket should you discover that one of your professors is truly awful.


When applying for a PhD is it worth mentioning awards received for achievement in final year high school exams?

High school awards are unlikely to help much but they probably won't hurt you either. I think it's fine to include them on a short "early-career" CV but move them to the very end to signal that you understand that these are not important measures of your current qualifications.

Who knows, if they are really awesome, they might might even help. I saw a graduate student CV once that listed being ranked first on a province-level college admissions exam that included many tens of thousands of students. Sure, it was a long time ago, but I was still impressed enough that I remember this now. I think I kept my high school awards on my CV until I started thinking about going on the faculty job market as a PhD student. At point, they just seemed completely irrelevant.


Here are some answers to your questions:  Yes, MathSciNet is behind a paywall.  Yes, we ask reviewers to give us copyright to their reviews.  Yes, you can post your reviews elsewhere.
 In return, for each review, we put US$12 on account at the AMS (up from the US$8 it was a few years ago) for the reviewer to use to buy AMS books, to pay (part of) your AMS membership, or to pay for other things (such as t-shirts).  The credit is in the form of "AMS Points".

Why the copyright?  This helps us to copyright the whole database.  Copyrighting a database is rather different from copyrighting a journal or a conference proceedings volume.

Can you post the reviews?  The reviewer letter says, "You may post your reviews on your website, circulate them to colleagues, distribute copies to your students, and make other customary scholarly uses. You may even include your reviews in journals, books, and databases in the particular field(s) of mathematics to which they relate, provided that first publication credit is given to the AMS."

Why the paywall?  Creating and maintaining MathSciNet is expensive.  It costs millions of dollars per year to run it.  The subscription model allows us to cover the costs.  It would take a lot of donations or ads to make up for that.

Why so expensive? We work hard to make sure that we get things right. In order to do this, Mathematical Reviews has a staff of 80 people.  That includes 18 PhD mathematicians who serve as editors.  We also have people with advanced library degrees and experience that ensure that our bibliographic data is complete and correct.  We have cataloguers who ensure that we correctly identify authors.  We have copy editors who help out with the reviews and check references.  We have a whole department who work with the reviewers (and their reviews).  We have an IT department.

I hope this is helpful.  If not, post a comment!

--
Edward Dunne
Executive Editor
Mathematical Reviews


Chances are, if they are not answering their university mail address, they are either busy or can't be bothered. They are retired, so both is completetly ok (it is sort of the point of retirement that you do not have an obligation to react to work mail anymore). Trying to get in touch with them over different media is probably fruitless, and somewhat obnoxious. Besides, I would really hope that the university administration does not give out private addresses to the request of random people.

Edit: an almost completely unrelated side notice: emeritus profs can be insanely busy in some cases. There is a famous austrian physics emeritus who is now writing popular science books, breeding alpacas (!), touring Austria with a science-based stand-up comedy show (!!), producing and starring a TV programme, and waging an ever-lasting war against the catholic church (as head of Austria's atheist movement).


Suitable avenues (repositories) for self-publishing own figures (illustrations) under CC-BY-NC-ND prior to journal's final acceptance

I have yet to use either myself, but here are two sites to look into. Both allow publishing images/figures, and can assign them DOIs.

Zenodo seems like a good option, associated with CERN and the OpenAIRE project, and open to all fields. It also supports a wide range of licenses. Indeed, when uploading a figure under Open Access, there is a search field to pick a license. One choice is "Creative Commons Attribution-NonCommercial-NoDerivatives", but it's not clear if this is the 4.0 version or not, as other licenses have 4.0 as part of their name (e.g. "Creative Commons Attribution-NonCommercial 4.0)".
Figshare is the more well known option, but it has only limited options when it comes to licensing. When I try uploading a figure on a personal account, the only Creative Commons license available is CC BY 4.0. An institutional user can also use the CC BY-NC-ND 4.0 license, however.


How does it look if I finish my PhD in five years instead of four?

The quality of your thesis overshadows the length/duration of your PhD.

Having said that, it depends on your goals. If you clearly think (and your adviser as well) that another year would make a big impact on the quality of your thesis and, consequently, on your CV, and is not too risky to pursue extra work (i.e., the questions you want to tackle are not too ambitious and you have a good possibility of enhancing your CV) then go for it. Otherwise, I am not sure you would want to stay at PhD while you could be looking for your next (PostDoc or industry) jobs.


How to increase my chance for being admitted to a PhD if my MSc is in a different topic?

The change of topic should not be a serious problem as long as you have a solid CS background.  What is more likely the problem is your choice of new topic, and whether the schools where you are applying have faculty working in green computing.

For PhD programs, your best bet is to send a targeted and well-informed letter to professors working in the field that interests you.  I cannot stress the well-informed part enough - this is more than just looking at the faculty member's web page.  Read some of his/her papers, think up of suggested research directions or potential improvements of the research.  Demonstrate an ability to understand the professor's research and provide novel and meaningful ideas.


Can a university restrict publication of students' work due to plagiarism fears?

My former department had such restrictions in place prohibiting the dissemination of course work, although very little of the course work involved programming. Students signed an agreement at the beginning of every year. Further, every piece of course work required a signed cover sheet that stated that the students would not share the course work. Sharing course work was treated as academic misconduct and results in either a reduction in the students grade if the offense is discovered while the student is taking the class, a fine (talk about unethical) if the offense is discovered after the student finishes the class, or possible revocation of the degree if the offense is discovered after the student graduates.

While serving on the my department's academic misconduct committee I over saw incidents of all three types. The one case of misconduct after graduation was settled by asking the student to remove the content from the web and the student agreeing. Had they not agreed, it would have gone to a university committee. The couple of cases involving distribution after the class, but prior to graduation, were resolved with fines. In some cases the students paid, in other cases they appealed to the university committee. The university committee sometimes kept the fine and sometimes repealed the fine. The "in class" cases were sometimes appealed to the university committee, but were rarely (if ever) over turned.

As to the ethical question, our policy was reviewed annual at both the departmental level annual and the university level. It was also reviewed every couple of years by the legal department. We often discussed why the policy was so broad. In the end, we always decided that it was easier to make a broad rule and allow students to request exceptions than to try and cover all the creative ways students can cheat.


Where to put explanation of figures, in caption or in text?

Somewhere during my studies I have learnt that a figure and its caption should form a self-contained element. That means, if I isolated a single figure together with its caption from a random publication and gave it to you, you should from those bits of information be able to deduce what this figure is about and what you see there. That does of course not mean, that a physicist must be able to understand the full implications contained in a figure drawn by a chemist or vice versa, but they should be able to understand that "fancy stuff" is in the top left, "other fancy stuff" in the center is indicated with some arrow annotations and a drawn overlay indicates the mechanism that makes them do whatever is interesting.

So in your special case, either make a legend containing the meaning of your different colored nodes or, if that is not possible, describe that in the caption. You can repeat that in the text if you feel it's necessary, but you're not obliged to do so in general. Also, it's no obligation to put into the figure caption the full interpretation of the implications you draw from this figure – this should go to the text. Hence the figure caption could be something like

  Figure 1: Process scheme of the process of doing fancy stuff. Yellow nodes indicate XX, red ones show YY and green ones TT.

In the text, there can then be the interpretation of the figure, for example:

  The process scheme of this is shown in Figure 1. As can be seen from the arrangement of the red, yellow and green nodes, everything is very colourful – which is very good in our case – and the guys at management would love it. However, a closer look at the connection between node "foo" and node "bar" reveals, that there could be some problem in [whatever fancy stuff you want to say]...

TL;DR: Put the stuff that is necessary to understand what's in the figure either directly into the figure (legend) or into the caption. The discussion of the figure can go to the text.


Since your supervisor thinks that everything is fine, you should not be ashamed of publishing your results.

If you are still unsure: You should talk about your concerns to your supervisor and request an honest opinion. Keep in mind, that he/she is also (partly) responsible for the quality of your results!


How do journals improve their impact factor?

I am an Associate Editor with a journal that has improved its IF from a little over 1 to more than 4.5 over the past decade. Some of the things that we have done to achieve this have been:

Better defining our unique niche within the field. Part of this has been placing an emphasis on publishing papers with finding that are generalisable across sub-fields, not specific only to a narrowly defined group of specialists.
Publishing Position Papers that help set the standards within the field. These Position Papers are designed to help scientists in our field improve their procedures, practises and assessment of their own work. They quickly become standard references, so they receive a lot of citations themselves, but are also something we can point authors to for guidance if their work needs improving to meet the standards of our journal.
When asking for revisions, working hard to make sure the feedback is as useful as possible and designed to help authors improve the impact of their papers. We try to get four reviews of each paper, usually including some comments from an editor about how to make the paper more impactful. The feedback that we have from authors is that, although our review process is longer than they'd like, they do find the extra feedback helps to make their papers better.
Inviting contributions from scientists who we feel can help us to improve the profile of our journal.
Changing the way we handle special issues. Like many journals, we used to let guest editors handle the review and acceptance of papers for special issues alone, with candidate papers taken from a group of invited authors after a workshop or major project. Now, guest editors must work with regular editors who know our standards and what we are looking for, and the opportunity to submit to the issue must be advertised generally, not just to workshop participants. We also make sure the special issue topics are broad enough to be of wide interest.

There are right ways and wrong ways to go about increasing a journal's IF. I think the above points are the right way. Some "wrong ways" that I have heard of include asking authors to cite more of the journal's previously published papers, and coming to agreements with related journals to encourage cross-citations between the two.


Most professors that I know in the US (in computer science) do not want to receive such emails and will ignore them. Many have a note on their website saying so. The expectation is that students should submit an application and only after they are admitted should they talk to faculty. If you are interested in a particular faculty member, you should note this in your application.
That said, norms vary greatly. In the UK, the expectation is the opposite in my experience -- you should only apply after contacting a potential supervisor.
You should look at the websites of faculty that you are interested in working with and see what they say about contacting them. If they do invite such inquiries, then you should contact them. In terms of timing, earlier is generally better, as long as you are at the stage of having reasonably concrete plans.


Should you cite a paper that clarifies the name of a mathematical object?

It is not wrong to cite the paper which clarified the term. In fact you must if you were to imply or use the definition that the paper provides.

A technical term may have multiple definitions in which some may even redefine it in different fields and aspects. It would be better to cite the one that connects to the most appropriate definition that connects to your use of the term.


Given a "Date Revision Due" for revised submission of a journal paper, am I required to submit before the beginning or the end of that date?

Unlike conferences, a journal's "date due" is rarely quite so precise a moment; this is because papers are all being dealt with asynchronously, on an as-arrived basis, rather than as a massive batch of hundreds all arriving near-simultaneously as for a big engineering conference.

Most journals will be comfortable with you submitting a little late if necessary (though there are some that will automatically discard your paper if you don't hit their deadline).  Thus, rather than fretting about time-zones, I would recommend that if you are worried about a last-minute submission, you instead email the handling editor and ask for a short extension.


Bad Relationship with Master's Supervisor: Missing Reference

I was in a similar situation last semester. My advisor had me join a research project, but gave me little to no information regarding said project. He told me that I would be working with honeypots, and it wasn't until my first day that I realized he meant honeypots in the cybersecurity sense and not literal honeypots. Although I was relieved to find out that I wouldn't have any bee stings from my research I could tell that I wasn't going to get any help from my advisor. In fact, he was away attending conferences for most of the semester, and rarely responded to any of my emails.

Here's what worked for me that I think will help you. You need to post up outside your advisor's office. When he finally comes in, you need to talk to him about how you're feeling and your current situation. I don't want to say confront him because I think that's too strong of a word, but he needs to know that he is not pulling his end of the bargain. Or, if you can't switch advisors, just ask him if there is anyone other resource that you can talk to, to gain more knowledge about the project (but on the low make this your "advisor").

As for the references, I would talk to the other people that you are collaborating with. See if they can help you with a reference letter. Or try to find other people who have worked with your advisor and see what they have done. I hope this helps and wish you well on your future endeavors.


If you want to be a computer scientist, can competitive programming be helpful early on in your career?

All types of practice are valuable, and if competition pleases you, go for it. However, programming quickly and under pressure is more akin to industry than to academia, and may leave little time for theory. Therefore I'd not call competition "important" for formation in CS, rather it's one of a number of forms of structured programming practice.


How can I get my name removed from the acknowledgments of a published paper?

You can't, and you shouldn't.

Authors are obliged to give proper credit to everyone who does work contributing to a paper. This is why papers must cite earlier relevant research.  By failing to acknowledge you, the authors would be falsely claiming credit for your work, just as if they had failed to cite a relevant paper in which you were an author.

Unless the acknowledgement is factually inaccurate, your disagreement with the authors is irrelevant.


If the editor handling my paper is a retired professor, then would it be fine for me to inquire about my paper status?

The time frame to a point where a question can or indeed should be sent varies depending on the typical time for that journal, or of similar journals in your field. To me 2.5 months does not sound too long, a decision after one month sounds very quick if I consider a normal set of reviewers also should make their evaluations in that period.

If you think sufficient (relative to what you perceive as "normal") time has passed you can certainly send a short e-mail asking for information. If you have an excuse for asking, in addition of just wanting to know, your mail is far less likely to be perceived as "pushy". But, regardless, editors will get hit by such mails fairly regularly and despite some of them or the bulk of them being a source of irritation at times, the question is not strange by any means. It is all down to the tone of the mail.

The fact that the editor is retired should not affect any aspect of the review procedure so I do not see any reason to take that fact into consideration. The journal must appreciate the work the editor is doing, otherwise the editor would likely not be there.


Can an author refer to work they did jointly using the first person?

In maths you never use the first person singular anyway, so they question as stated does not apply. Also, all work in a paper (in pure maths at least) is understood to be the work of all authors. In fact, it is common to refer to the other paper in the third person, even when the authors are the same.

In short: no, this is not acceptable.


How to do a good job of undergraduate advisement?

I've had some experience in running a training program for faculty advisors and working with new advsiors at my institution in the US (you haven't said so, but I'm guessing that you're at a US institution.) I've been asked a lot of very similar questions in recent years.  Your questions show that you care about doing a good job!

Your questions also seem to show that your university isn't providing enough support to faculty advisors.  I'd argue that having incorrect information on the web site and pushing new programs for undergraduates without providing relevant information to the advisors are signs of disfunction in the advising system at the university level.  You may be able to work around these issues, but a better long term solution is to encourage the administration to fix the system.

At a very low level, you can address systematic problems like this by being persistent but polite in reporting issues to the responsible authorities.  For example, emailing the registrar's office to tell them that information on one of their web pages is contradicted by the current catalog should probably result in the incorrect web page being updated.  Don't complain about these things in a very public way though.  Some administrators welcome this kind of assistance while others dislike "interference" and might ignore you.  If you run into that attitude, then your best approach may be to escalate to that person's boss.

At a higher level, issues like these can be addressed through faculty committees.  If you have a faculty committee that deals with advising issues (or more generally with academic procedures) then you can bring these issues to the attention of the committee.  Don't be surprised if you're recruited to work on the committee!

Here are some suggestions of things that you can do on your own to be a better advisor:

Learn as much as you can about the academic rules and keep up with changes.  In working with students, either be absolutely certain of the answer to a question or know who to ask to get an authoritative answer to that question.  The worst mistake that you can make is giving incorrect information to a student.  In comparison, "I'm not sure of the answer to this question" is much better.
Make sure that you have correct information about any student that you're advising.  Know how to use your Student Information System to look up a student's transcript, run a degree audit, etc. Many advising mistakes are the result of advisors not having complete and correct information about their advisees.
If a student is in danger of "flunking out" due to bad grades, it is important to intervene as early as possible.  If the problems are academic rather than personal than you should work with the student to come up with a realistic plan to address the student's bad grades.  Make sure that you know all of the rules about academic probation/suspension and that you're aware of the options that a student might have for withdrawing from classes.  Monitor your advisees' performance by checking their midterm and final grades each semester.  If your campus has an early alert system then respond to flags raised on your advisees.
Crisis management is important.  When a student who has been doing well suddenly starts doing poorly, this can very rapidly result in loss of financial aid, academic suspension, etc.  Often times these situations are the result of personal problems (health problems, psychiatric illness, drug abuse, death in the family, breakup with a boyfriend/girlfriend, etc.)  These kinds of personal problems are not things that you should address, but you should refer the student to offices that can help (a campus health center, counseling office, etc.)  In these situations it is often best for the student to cut back on their academic commitments by dropping courses or even withdrawing from an entire semester.
Academic decisions can affect financial aid, and the rules are so complicated that faculty advisors generally aren't in a good position to answer questions about them.  Check with your financial aid office on the consequences of any action that a student takes that changes their number of registered credit hours.
Advising students should ideally be more than just course selection.  The traditional "prescriptive advising" approach of simply telling students what courses to take should be replaced by a "developmental advising" approach in which the advisor's job is to help the student understand the choices available to them, clarify their goals, and then take responsibility for their educational path.  This kind of advising can be more rewarding for both students and advisors but it takes a lot of work.  Developmental advising can be particularly helpful for those students "of moderate ability and motivation" by helping them to figure out what they want to do in life and having that serve as motivation to do the hard work necessary to be more successful students.
The reality is that a BS/BA in mathematics is not by itself a qualification that is likely to lead to an exciting career in mathematics.  Most students are going to need to combine this with either a second major or a more advanced degree.  For example, there are lots of opportunities for students with MS degrees in applied math, statistics, OR, etc.  Some web sites that do provide useful information on careers for students majoring in mathematics include:

http://weusemath.org/

http://www.siam.org/careers/

http://www.amstat.org/careers/

http://www.ams.org/profession/career-info/career-index

http://www.beanactuary.org/

https://www.informs.org/Build-Your-Career/INFORMS-Student-Union/Career-Links-for-Students/Career-FAQs
You should get to know the "career services" office on your campus.  I encourage my undergraduate advisees to attend job fairs and look for internship opporunities starting very early in their undergraduate career.  Finding out that many employers have GPA cutoffs at 3.0 (or even 3.5) can have a powerful impact on a student who has been getting lower grades...


Is it normal for graduate tuition to be much cheaper than undergraduate tuition?

The standard full-time undergraduate course load is 16 credits per semester (32 credits per year). (See here: the four-year undergraduate degree requires 128 credits.) The flat-rate cost for the example you have cited comes out to $1539.375/credit.

The standard full-time graduate course load is 9 credits per semester (18 credits per year). The flat-rate cost for the example you have cited comes out to $1538/credit.

For the school you have used as your example, the per-credit fee for part-time students is $1538/credit in most cases.


How best to split up a comprehensive literature review

I would try to do 4* topic papers (one on on each subtopic within section 3).  Then do a wrapup.  I.e. 5 LPUs.

In the four topic papers you can be a skimpier on the methods (or perhaps go full bore on methods in first one and skimpy on others, but "referring" to the discussion in first one.)  The wrapup will "review" the previous 4 and make some general observations (cross-correlations, etc.).  I would be brief on definitions (less than currently in there) for the 4 topic papers.  Just basics with some footnotes (skip history entirely).  You can go more in depth on history in the wrapup self review paper.

*If a couple naturally combine, fine, do 2 or 3.  But 4 is fine too:

P.s.  I'm not an expert in your topic and I really just glanced at it.  But what I saw looked solid.

P.s.s.  Chopping into LPUs is not sleazy.  It's actually in some ways more efficient to process (at least for a reviewer!)


Mandatory army service in the middle of PhD, will it be possible to finish PhD under these conditions?

This is likely to depend strongly on the country, but in many country's militaries, technical expertise is highly valued.  I have known a number of people in the US, for example, whose official duty assignment was a Ph.D. program.  I do not know whether this is possible in Israel, but suspect your professors may know, and may be able to advise you.

I would thus advise you to investigate whether it is a possible to proactively reach out to the military people who you will need to deal with, and see if you can opt into a program or line of duty that might support this for you as well: it may require making a longer-term commitment to the military, but if it gets you the career you want, the tradeoff may be worth it for you.


Sharing with research team about being affected by a natural disaster

I would call it not only professional but close to mandatory. A supervisor has to be informed of special circumstances or reasons for specific behaviour in order to manage the team effectively, set realistic goals, assure the people are comfortable and to show basic human decency. You do not have to share something that makes you feel uncomfortable, and do not have to provide a lot of detail on personal circumstances. I think it is best to do so at an early stage, saying there is issue X and you would appreciate some consideration, rather than have to explain possible poor performance later after frictions have appeared.

Suffice to say that many academics have friends and family outside their country of work and are personally aware of what it means to be away from them in a time of need. I cannot imagine many supervisors who would not be sympathetic to such a discussion, or would not appreciate the honesty. In practice this may not mean more than a pat on the shoulder and some more relaxed time, but even that can be important. If the conditions allow, a leave or temporary interruption of studies can also be warranted.


Uppercase/lowercase paper titles on a CV

Formatting of titles in citations is specified by citation style guides, APA, for example and depends on the context. If you are formatting your CV in APA style, you would use the link I provided and use "sentence case" for both titles (capitalize first word only) in your CV.

Note that this does not depend on the capitalization of the title in the original source; you should consider the title capitalization to be a formatting issue which will vary across formatting schemes but should be standardized when you bring the works together, like in a references list or CV.

This goes for English capitalization rules; I am not aware of APA guidelines for citations in other languages, such as German, which use different capitalization. Without further guidance, I would just suggest to be consistent.


Some journals are known for rapid publications, e.g. PeerJ (30 days to first decision). Some publishers offer various venues for "accelerated publications", e.g. this list at Taylor & Francis. There is another list here.
In general, you could simply ask the editor of any journal from your domain beforehand whether they would grant you an exceptionally speedy submission process for reasons pertaining to an emergency issue. It is possible that they will consider such a request.


Does completing research ethics / compliance training courses reduce the incidence of ethics or compliance breaches?

Most studies have focused on the effectiveness of training programmes in impacting surrogate outcomes such as the knowledge and attitudes of participants after compared to before attendance at the said programme. Study designs are generally weak, as is usually the case in education research in general, I suppose.

I am aware of a single study conducted in Nigeria that attempted to answer the question you posed, but only secondarily. In their amazing study, Okonta and Rossouw [1] managed to survey 133 Nigerian researchers, 91 (69%) of whom admitted to have ever committed scientific misconduct. When they cross-classified whether these respondents had "education in ethics" in the past, they found no statistical significant association. Furthermore, prior education in ethics was not associated with having had committed the following specific actions:

plagiarism
falsifying data
intentional protocol violation related to subject enrollment
intentional protocol violations related to procedures
selective dropping of data from 'outlier' cases
falsification of biosketch, resume, reference list
disagreements about authorship
Pressure from study sponsor to engage in unethical practices

Take from it what you will.

Reference:
[1] Okonta P, Rossouw T. Prevalence of scientific misconduct among a group of researchers in Nigeria. Dev World Bioeth. 2013 Dec;13(3):149-57. doi: 10.1111/j.1471-8847.2012.00339.x.


What form should evidence of a directed study take on a graduate application?

I think you should ask your mentors to discuss your research in detail in recommendation letters. Provide them with the language to discuss your research. I would also include it in personal statements and course work.


Should an undergraduate answer a call for reviewers?

Normally a PhD (in my experience) will conduct their first peer-reviews with their supervisor or another academic. An undergraduate may (rarely) have the technical expertise, but reviewing is also a skill (that doesn't take long to pick up, but requires a bit of guidance). Poor reviews can waste time of committee members or, worse, harm scientific and academic output, and even harm your own reputation. On the other hand, if you contact a member of staff that would be an opportunity to learn how to do it properly and maintain or even advance your reputation at a very early stage in your career.


Can I request to see a reference about me?

As a general rule, institutions are very reluctant to give access to letters of reference to anyone and candidates in particular. That's because they know that if they regularly shared these letters with the people being written about, letter writers would stop giving honest assessments.
As a consequence, regardless of matters of law or regulation, you should expect that universities will not give you the letter. You may have a legal way to obtain such a letter, but you will likely have to sue the university to obtain it. Whether that's worth your time or money is a case you need to evaluate for yourself -- taking into account that knowing what is in the letter does not actually change anything. It's not like the university will offer you the position you were seeking just because you know what was in the letter.


PhD interview question when you don't know the answer

In most cases, the interviewer does not care about the "answer", but rather about how you answer. I would answer honestly with something like "I do not know, would you like me to try and work it out?"


Is it okay for a professor to leave the classroom only 5 min past the class start if nobody has shown up?

I think this is less about regulations and more about respect and conditioning the students. Also, don't feel offended, you are not the (primary) reason for what happened.
Legitimate Reasons for Leaving
Respect
The fact that 0% of the students arrived shows the professor an

immense lack of interest in his teaching subject ("I disdain the subject that you spend years researching and thus I disdain you.")
OR complete disregard of his didactic skills ("You are so bad at teaching, that I don't think I can gain anything from your lecture.")
OR disregard of his personal status ("You are such an unimportant person and your status is so much below me, that you will have to adjust your life to mine and wait for my arrival.")

Even if the class only consists of 5 students, he might extrapolate that everyone has one or more of these convictions. If he waits for students to arrive, he accepts his lower status and/or personal offense.
Operant Conditioning
If the professor waits for students to arrive, they will be conditioned that coming late  has no negative consequences. Canceling the class will incur a penalty to students and might force them to take arrival times more serious in order to gain the advantage of having the course material explained to them.
Recommendation
Communicate (in person or via e-mail) to the professor

that you are very sorry for your absence
state your reasons (should be severe enough)
and make sure to allude to one more of the three points mentioned in the respect section.

If he feels that you have legitimate reasons for being late and that your absence was not a sign of disrespect, I am sure that he will be more inclined to wait longer next time you are late or might even offer you to come by his office to "pick him up" for the lecture.

OP's Update
(This should probably be a new question, since the update significantly changes the circumstances.)
I am very sorry that the professor refused to give a lecture for you alone.
It is not your fault that you were the only present and thus it is imho unfair that you have to bear the consequences.
Updated Recommendation
I would approach him again

start with how unsatisfactory the situation for him and you is

again alluding to the respect section and

then ask him: Why do I have to bear the consequences for the action of other students? hoping that he is rational enough to realize his mistake. Basically you should try to make him understand that he does the same to you that other students are doing to him.

Maybe he was just disappointed about the low presence again and is an overly emotional person. Unfortunately that is not something you will be able to change.
If this does not resolve the situation I would ask around the department for existing regulations regarding this.


How much time should you spend on reviewing a paper?

I take it you are asking how much time a reviewer should spend on reviewing an individual paper.*

You should spend as much time as it takes to ensure that the paper satisfies the fundamental criteria for scientific inquiry that apply in your field. This is the minimum. Some journals or conferences also ask their reviewers to assess the novelty of the contribution and its topical fit with the venue. Personally, I believe a reviewer should go beyond a pure quality check and make constructive suggestions for improvement, if the paper has potential.

How much time is "as much as it takes"? This varies depending on your practice, on the paper, and on the discipline. From what I hear, reviewing math papers can take many working days. In political science, which is my own discipline, a thorough review takes me the better part of one working day. This is a mean with a large dispersion around it.

15 minutes are not enough time to read a paper, let alone to apply even a basic quality check, unless the paper is very obviously insufficient. Rubber-stamping every paper is not enough; arguably, it is even worse, because you don't even pretend to do your job. Both "approaches" simply bypass and sabotage the peer reviewing process.

The editors and readers, i.e. the scientific community, entrusts you, as reviewer, with the task of upholding the scientific validity of the research that is being published and disseminated. You and your colleague are breaking this trust. You are doing the community a big disservice. Please stop immediately to take on any more reviewing tasks.

If you are concerned about the time reviewing takes away from your own research, do less reviews rather than more superficial ones. Peer reviewing builds on reciprocity. If you want to publish in a refereed journal, you should "give back" and review. Since most journals require two reports, reciprocate by writing at least two thorough reviews for every paper that you publish in a peer reviewed venue.

If you are concerned that you lack the expertise to write a review, tell the editor that you aren't qualified, and they will find someone more suitable.

*An earlier version of the question asked how much time do you spend. Nobody is interested in how much time I or any one individual spends on reviewing a paper. Perhaps you're interested in some general patterns across many individuals, but I'm not aware of any research on this.


How can I publish my independent research?

Find a suitable journal and submit the paper.


Easy subjects with high grade vs tough subject with lower grade

Should I risk it?

That depends on the particulars: how useful are the easy courses, how hard are the hard courses, ...

  Will anyone really acknowledge this risk I am taking?

Yes, the admissions committee will certainly consider what subjects you studied.


Quick publication in a good journal VS long fight to publish in a very prestigious journal. What's more impactful at the beginning of a career?

Given that you aren't yet in a doctoral program and so have some time left in your student career, a long review process doesn't seem like a huge issue. Normally I'd give the old advice "Don't let the perfect be the enemy of the good."
Even being under a long review by a top journal is a plus and you can point to it for most purposes.
No one can predict however and you take some chances either way. Nobody guarantees quick review or eventual success. Nobody serious or honest, anyway.
If your advisor thinks it is a top quality article, then that is probably good advice.


How should I describe my country's volatile situation in a letter for a scholarship application?

Something along the lines that you persisted and managed to graduate despite that the life as you know it was being destroyed in a war-torn county. The hardships of war, hunger, constant fear for safety (or whatever you feel like sharing) gave priority to the survival. As the result your grades in the final years suffered. You are eager to continue your education in the safety of whereever you are applying, and ready to give it your all without the distractions of the war.

The point you want to make is that you graduated during the whole crisis, which is truly impressive. Congratulations on that. It shows the character and persistence. Grades you can fix.


Sending a thank you letter to a research professor?

Is it too late or "awkward" to send him a handwritten thank you note now that it's been about two months since I've last contacted him?

Nope.
Two months is not so long in the academic sense at all. Whether or not it's handwritten shouldn't matter as much, either. Typing it up is perfectly acceptable, readable, and much easier to correct if you make an error.


Is Mozilla Developer Network a valid source to cite?

If that's where you got information you used then that is what you cite. Whether it's a reliable source of information is a question you should probably take up with your advisor.
Sometimes you can trace information found on a secondary source back to primary sources. That's often the case with wikipedia. When that's possible it's preferred.


I've seen it done by some students at Utrecht University, while I was a fellow student, and as Master/PhD teaching assistent. I think this was never frowned upon, and personally I'd have a slight preference even for LateX-ed homework, because it is guaranteed to be legible (although I've also seen homework that was poorly LaTeX typeset).


Can I contact the author of a paper for questions, even if I've never studied over high school?

About your questions:

1) If you want you can link the Wikipedia article or make a small summary explaining your thoughts, usually Professors or researchers do not have too much time to read long emails; so try to keep it up simply

2) explained before

3) It is nothing bad that you point to the other papers of consequence Z, if he knows about them he will tell it straightforward

In conclusion, do not feel bad that you did not have any formal education. Just address to the researcher in a respectful manner and tell him/her that you are interested about his job. You do not need to send your CV or a motivation letter just for asking something, but beware, you can or you cannot get an answer (usually depends how much interested of free time the researcher you are appointing has)

Good luck!


Why does academia still use scientific journals and not peer-reviewed government funded alternatives?

There are many businesses which are inefficient in the sense that you judge publishing by. There is nothing requiring markets to accomplish some collective endeavor efficiently. Instead, markets are only efficient in terms of people being able to pay for things they want. For example, whether avocado toast is good nutrition is irrelevant to the market. But if you want to pay $15 for it, and if there is someone else willing to give you an avocado toast for $15, the market will certainly provide for that exchange.
Likewise, your arguments about how the current publishing system is inefficient are tangential at best. It so happens that a lot of people (in the current world, not in some fantasy post-journal world) want to publish in journals, and read what is published in journals, which is why the journals exist. You point out some important reasons for this and say you understand this, but

would it not make much more sense to have tax-money funded web-portals

Well, no, it wouldn't. If there is demand for service A, why would the market fail to supply A and instead supply only service B which doesn't fill the same needs? The answer is that a free market wouldn't. You could have government force the market to not provide service A and only service B, but then you have a non-free market. Which isn't the end of the world, but it so happens that most people in charge of government these days favor free markets, barring corruption.
That's the most direct answer to your question: The current publishing system is in place because that's what the free market came up with, and implementing your system would require government interference in the market. It is not politically expedient to implement such interference. This is all for today, mind. 20 years ago open access was a pipe dream, perhaps 20 years later publishing will change completely. But we can only speculate about the attitudes of the future.

I'd also like to point out some inaccuracies in your question.

Scientists act as editors and reviewers check the quality (while paid with more tax money)

Actually editors often get paid by journals. Also, not all research is publicly funded.

Now universities have to pay the journal huge amounts of money (exact numbers are usually not available due to NDAs) to access the paper to which the journal did not contribute anything (apart from minor formatting issues and putting a pdf on a webpage maybe)

These days, a lot of research is made freely available after a few years, the university is really paying for quick access (and also access to very old papers).

Here 60-100 USD would be more appropriate than 6000 USD.

No, it wouldn't be, because no journal would bother. $60-100 USD would buy you maybe 1-2 hours of work from a single skilled person in which they must:

Read the manuscript
Finding reviewers and keep bugging them to submit reviews on time
Read reviews and decide if they make sense, then pass them on to the author
When revised MS is in, work with reviewers to decide if the revisions address the initial concerns
Work with authors to get it formatted and proofread

It is not realistic for a single person to do a single one of these in a few hours, much less all of them.

Is this not fundamentally wrong that scientists do the work and journals skim off the profit?

There's nothing more wrong than any other for-profit enterprise. The only thing you can criticize here is the entire concept of seeking profit, but I don't believe there are currently significant contributors to science that are opposed to profit seeking. The closest thing that comes to mind is China, but they have for profit journals also, and a lot of Chinese research is published in western, evil capitalist, journals anyway. Now that you mention it, when the USSR was around I think they did have government run, non-profit journals.  But it is not considered "fundamentally wrong" by most governments today.

make them accessible to everybody and layouting might have been something non-trivial but nowadays this is not the case any-more.

No, it is easier, but still non-trivial. Even just writing a manuscript purely for yourself takes some work to get all the equations, figures, citations and so on to display correctly. But if you had a journal where you want a uniform formatting from many articles by many different authors, it is a lot of work to come up with a system that works for everybody and also get the authors to follow it.

That would cost a fraction of the paywall and open access fees that journals make money from at the moment.

Government can be notoriously wasteful, so it's not a given that it would be cheaper. Perhaps the cost might be spread out over everyone via taxes, instead of being born by individual universities, researchers and those poor souls who actually pay $30 to download a PDF. But then the first two are already covered by tax money.
You have to also consider quality of service and not just cost. The classic US example of government-provided service is the DMV. It doesn't make sense to be a realist on private publishing and an optimist on public publishing.

My feeling is that the field of science does not need the journals at all anymore - what am I missing here?

Well, I suppose we can say you are missing the trees for the forest. Science is not a single person. Individual scientists obviously do need journals. Nowadays, thanks to the internet, they don't need them to publish - but they still need the credibility of being peer-reviewed and the visibility of being in a highly-read journal. They also need them for the mundane reasons of justifying job and grant applications.


What are the benefits of organizing a conference?

If everyone refused to organize conferences, we would have no conferences.

Yes, it's that obvious.  The same goes for editing journals, refereeing papers, and most other service activities.

The main result of a research conference is that it helps attendees do better research, to find and understand new ideas, and to disseminate their own research, etc.  By organizing the conference, you are the facilitator of all that.  Furthermore, you get to influence the direction of the conference -- what it will focus on, who the invited speakers will be, how it will be run, and so forth.

Additionally, I would argue that academics are paid to organize conferences in the same way that we are paid to referee papers.

Finally, there are fringe benefits to you personally, including the prestige mentioned by @user3209815 -- you can list it on your CV under service activities.  Frankly, this is not going to make or break your career, and you probably shouldn't be doing it early in your career, since (as you point out) it takes time away from things that may be more essential.


Can an unsuccessful grade appeal hurt an academic career?

Can a grade appeal that is not granted affect a person's transcript,
  reputation and/or perception throughout their academic career?

I have never heard of a school that lists grade appeals on a student's transcript, and to me that sounds about as logical as listing on your transcript that you wore the wrong shirt color. But that doesn't prove that such a school doesn't exist, so only a professor or staff member at your school can give an authoritative answer to that question. Why don't you ask them?

As for affecting your reputation or people's perception of you: well, any interaction we have with other people has some potential to affect our reputation or people's perception of us, so the literal answer to your question is "yes." It's reasonable to worry about that a little bit, but on the other hand if we all spent too much time worrying about such things, we'd never get very much done. In your case, what I suggest is that you go to your professor (or email him) and explain that you are surprised by your grade and would like to understand why you got an F, among other reasons so that you can learn from the experience and do better next time. Ask if you can review your final exam and possibly go over it with him to understand what you got wrong. Don't sound like you are assuming that you deserve a better grade or that the F grade couldn't possibly be correct, since that could come across as entitled, arrogant, and possibly delusional. If you ask the question in such a way, I don't see how you can possibly leave a bad impression with the professor -- this is a reasonable request that most professors hear all the time and are usually happy to help with.


when a PhD position is re-posted after I had an interview

It could have a lot of reason why a position is reposted. Computer mistake, additional position, confusion with another position, people not talking properly to each other, fraud, rejection, ...
Don't do anything at least until the end of this week (which is near)! Do not look at their homepages if this makes you nervous.

In the meantime, live your life as if you did not get this position. Apply for other jobs etc.
If you really want to get a definite answer from them and they do not call you, I would give it two more weeks (could vary by locale) until you call them. Do ask for feedback and do not call your rejection a "failure". In most interviews, people do not fail (except there is a special test) but it comes out that they don't fit the position well enough because of other interests.


I do not think it is reasonable. If you are mentioning you won at a competition, you must also mention what was your place or in what capacity you won an award. There are good reasons for this in my opinion. First, it is possible the reader is aware of the competition and finds it misleading of you. Second, if you clearly mention the details of the award, it is possible you might rise in the eyes of reader for your integrity and honesty.


Have a job, but might not finish Ph.D. on time.

If this were a full-time tenure-track position, the answer would likely be different, because in many fields (particularly STEM fields) you'd probably be able to request a "gap year" that you could use to finish up your work and do a short postdoc stint somewhere before beginning your full-time position.

However, as a lecturer or instructor, you don't have nearly enough leverage. You may ask if it's possible to start the position if, for instance, the thesis has been submitted but not defended by your planned start date. But I would get in touch with them as quickly as possible and ask what would be the latest you could get your degree before starting. Then, if you feel you can't make that deadline, try to negotiate (but be aware that it might not work!).


Consequences of submitting a job application close to the deadline

I would say this depends on the department and their hiring practices, but in my department (math at a public US research university) applying early can definitely give you a leg up. In math in the US, there is a centralized application system (mathjobs.org) that most places use, and in my department all faculty get access to start looking at applications well before the deadline.  Many of us do start looking at applications early, partly out of interest, and partly so we can take our time.

The advantage of applying early is that faculty may start talking about some candidates before any search committee meetings and people have the chance to get excited about your file early, which would give you some early momentum to help you stand out when we officially have meetings and rank candidates.

That being said, in other departments, faculty might not look at applications at all before the deadline, in which case there is no real affect.  I do not know how common our approach is, but at least a few of my colleagues agree with me that it is better to apply early.  I have also heard of departments that have somewhat misleading deadlines (they start officially reviewing files before the deadline, which might be in fine-print in the ad), so my advice is to try to prepare you application a bit early, and then submit application when your portion (i.e., excluding the references) is ready.

Incidentally, in mathjobs, the candidates submission date is readily visible, though it is not something that we focus on or analyze.  (Though often we'll sort by submission date to see what files came in since last we looked.)


What if I may not have research experience for math PhD application?

Firstly, I should mention that I am a 3rd year math PhD student at Brown. So I have a hint of knowledge, but not as much as a professor who has been to more institutions, and certainly not as much as someone who has been  on an admissions committee.

Firstly, many starting PhD mathematicians have no real research experience. The reason is simply that research mathematics is so far from most undergraduate mathematics. This is also why doing research is so hard without a supervisor (for that matter, it's hard with a supervisor). Many candidates have done REUs, which look generically good but often don't usually result in a publication or anything.

What I recommend to you is that you:

Identify what you're interested in and pursue it. You say you maybe like applied analysis or PDE. Maybe see what some people are doing, read some of their stuff, backtrack if you need to. In this sense, you can just do research without waiting for someone else's permission. I'd like to mention that there is a polymath project you might be interested in, Polymath 7 on the Hot Spots Conjecture (here is a link to the most recent progress page). It's slowed down, but they've done some interesting things and the polymaths are generally good about leaving a clean trail of breadcrumbs.
Ask about showing research potential and getting letters of reference. Instead of worrying about what's the absolute best thing, I think you should worry about doing the best that you can do. You've tried to set up some research with professors and that fell through. You haven't done math research before, and you're probably not going to get far in the next 4 months. In particular, it's unlikely that you're going to come up with a result great enough to inspire someone you haven't worked with to write you a letter of reference. This is all to say that you should get your letters of reference from those best able to recommend you. If these are lecturers, then so be it. But I hope that you've been attentive, proactive, and inspired in those classes. For that matter, if you're inspired, you might be able to ask your dynamical systems professor for an interesting project - approachable projects exist. It might not be new research, but at least it would be something you, and others, could talk about. As a final note, you should talk to your math professors and ask them for advice - I suspect that at least one of them will be able to say something, and they're more familiar with your situation.
Have you done any research in your 'some engineering?' Conceivably, a great letter of reference could come from your advisor/a great teacher/I don't know these details. You should talk to them about this, and get their advice.
Determine what schools you're interested in applying to (apply to many), and their requirements. Brown's Applied Math department does not require algebra. But they do (essentially if not officially) require the math GRE, which does require algebra (though for less than 1/4 of the test). On the other hand, Brown's Pure Math department (the one I'm in) has a severe algebra requirement. Interestingly, PDE is done in both, though in different directions. Many schools require algebra, or require it in the sense that they will have qualifying exams and one of those is in algebra. My undergrad, which I'd say has an applied bent, had quals in algebra and both real and complex analysis. So you could consider taking algebra if you needed to or wanted to, based on looking into what universities you want to apply.

However, algebra II without algebra I sounds incredibly perilous, especially as the fall semester is upon us already, or is about to be. Perhaps possible with a lot of pre-work. If you are going to attempt to hop into algebra II, I recommend getting a copy of Dummit and Foote's algebra book (clear exposition at a low level).

Finally, plan on taking the math subject GRE. It's only offered 3 times each year, and you've missed the summer one. You should take it both times this fall, and those signups might already be occurring.


Computer science central source for CFPs

Here are some other sites for multi-disciplinary CfP's

PaperCrowd*
Research Bible
H-Net
Conferize
Conference Submit
OurGlocal
BrownWalker
All Conference Alert
List of conference.org
All Conference Alerts
Conferensum

*Disclosure: I'm a co-founder at Ex Ordo and we built PaperCrowd as our contribution to the research community. It's restriced to academic research conferences and is free.


How do I make sure I get strong recommendation letters for faculty positions?

One way to solve this problem would be for me to ask Prof. X if he is sufficiently familiar with my work to write me a strong letter.

No.  Do not play mind games.  The best approach is to be completely straightforward.

If you already know that he is familiar with your work, suggesting otherwise is dishonest and potentially insulting.  What you really want to know is whether he's impressed by your work.  The only way to find out is to ask directly.  If possible, ask in person, preferably over coffee/beer or in some other informal neutral setting; conferences are really good for this.  Be straightforward about your desire for a strong letter, but use the opportunity to develop a stronger collaborative relationship.  Ask for honest feedback on your work.  Ask about future opportunities to work together.  Ask where he thinks you should apply.  Be sincere in asking whether he can write you a strong recommendation letter; he knows what that means.  Be sincerely ready to be turned down.  Listen.

If you're not comfortable asking him directly, or you think that he might not be comfortable answering you, ask your advisor to informally sound out Prof X's opinion of you first.  (Ideally, your advisor already has some idea what Prof X will say.)  But the actual letter request must come directly from you.

  If he only responds neutrally, e.g., "Sure, I can write you a letter" then simply neglect to follow up with him and ask someone else for the letter.

No.  Do not play mind games.

First, unless you already know Prof X extremely well, you should not attempt to read his mind through email.  "Sure, I can write you a letter" says nothing about his level of enthusiasm.  If his response to your request makes you hesitant to use his letter, ask him again.  Second, if you decide, for whatever reason, that you don't need his letter after you've asked for it, you must tell him directly, so that he doesn't waste his time.


Should I use an out-of-order version of my name for academic publications?

I do know someone who signs their email as "John Aardvark S.," and authors their papers as "John Aardvark." In their case, the "S." is a married name, so I would guess they added it after their first publication (but don't know for sure).
Putting them out of order makes me think that your name would constantly be getting rearranged (people thinking you filled out your name wrong, especially if your middle name is typically a first name, and your last name is typically a last name). And think of nametag confusion! In other words, being known as "Dr. John Smith" but publishing as "Dr. John Aardvark" isn't a common fix, so people won't know how to interpret it.
Another option would be to make "Aardvark Smith" your last name (hyphenated or not), I definitely know people who go by only one name of a double-barreled name. Or to just accept that sometimes your name will be abbreviated to "JA Smith." I suppose it depends on the usual citation format in your field. Most of time time, my field uses initials only when the author uses them, so that wouldn't be a big deal to me.


An undergraduate said they may hire a freelancer to do their work for them. What should I do?

[The student] remarked (in writing) that they might as well just buy solutions to their projects on a particular freelancing website for that price, as their friends do.

That does not sound to me like "admitting" that they "would" cheat. If I said to a prospective financial advisor, "your rates are so high I may as well just declare bankruptcy now", that does not mean that I am going to declare bankruptcy, it is merely a way to express that the advisor's services do not seem cost-effective.

Given this, I would do nothing -- you offered legitimate tutoring services and the student declined your offer. You have no compelling reason to suspect that the student will actually cheat.


Is use of the word "via" appropriate in an academic essay?

There is nothing wrong with the word "via," and in fact I personally have a weakness for it: sometimes it just feels more elegant and specific than alternatives like "through" or "by means of."  I also, however, have a weakness for a lot of somewhat archaic phrases, due to spending a lot of my childhood reading old books.

The general principle which I think academic writing should subscribe to is Orwell's notion of "transparent prose," in which the words are as clear as a window, letting one through to the ideas with minimal obstruction.  Using too many unusual words, such as a lot of "via" and "thus" can be distracting, particularly for an international audience.  Sometimes, though, a word is simply fit and elegant in its context, and there is no reason to avoid using it.


Is it professional for a professor to ask "surprise" questions on a test?

I don't see a reasonable answer beyond "it depends."  It depends on the question: some surprise questions are not actually so difficult and could reasonably be asked on a test with no special preparation, while others are very difficult indeed.  It also depends on the students: you can demand more of experienced and talented students than you can of typical beginners.

There's certainly no rule that says you can only ask test questions that are similar to previous questions the students have seen.  Sometimes asking unusual questions can be an excellent way to judge how well students have mastered the material.  At the same time, test questions that are too unfamiliar or difficult can be unproductive.  This is a balancing act that can be solved in many different ways, depending on the style of the person writing the test.


Is it common for an undergraduate thesis in pure mathematics to prove something new?

I'm going to disagree with Oswald. In my experience, undergraduate students do not often prove new things in pure math. I wouldn't even say master's theses often contain new results. There are a few main reasons for this.

Firstly, pure mathematics operates at a level that is not very accessible for most undergraduates, even those doing research. Undergraduates doing research are often well out of their depth and holding on for dear life. This can mostly be attributed to just not having enough time to get up to speed with what is considered modern mathematics. Most courses in mathematics at the undergraduate level are about math from 50-100 years ago (if not older).

Secondly, undergraduates do not often have the mathematical experience to know what the right plan of attack is when faced with an abstract and new problem and they may not know how to check their work thoroughly to make sure there are no major oversights or blunders. A lot of mathematics involves lateral thinking and it takes a lot of time to build those connections. The hardest part of a pure math PhD (in my opinion) is learning how to attack a problem no one has considered before. Standard techniques that others used may not be useful at all to you for one reason or another. An undergraduate won't have the creativity to navigate this kind of issue because the kind of creativity that is needed comes with a lot of experience. Even when an undergraduate student thinks they've proved something, the nuances of their argument likely will not be apparent to them. (This is especially true when it comes to functional analytic/measure theoretic arguments - the devil is in the details.) Thus a proposed proof may not even be close to being right.

Lastly, not many undergraduates in pure math do research because the gap they have to overcome between coursework and modern mathematics is pretty substantial. Those that make contributions in pure math are those that are very, very talented and have very thorough backgrounds (backgrounds that rival master's/PhD students).

Undergraduates in pure math are not expected to make contributions. That is not what research is about for them. Introducing an undergraduate to research serves a couple of different purposes: it introduces them to more advanced topics and it gives them a taste of what research is like so that they can make an informed decision about whether or not graduate school is right for them. As such, the theses are more like surveys of a specialized topic in mathematics. There is a lot of independent learning involved and there may be some unique examples, insights, and connections contained therein. They may not be presenting "original" work, but poster sessions are there to present what they've learned regardless of whether or not it was original. So yes, it is kind of like a lecture. They are undergraduates and far from being experts in their field.

Note that I am not saying that no undergraduate ever produces new results in pure math (there are some high school students that are better than most PhDs), but it is not a common occurrence and is not expected or considered the norm.


As I was observing this in Academia it works like "get as much clear funding as you can work out"? With a decent funding, you can diminish all stated problems; inversed move is much harder. That concerns from a side looked like you're already at a peak with a solid financial foundation and choosing from a huge amount of options. Maybe, the situation differs, but recheck the reality, just for sure.


Does an unpublished document you upload to ResearchGate count as prior publication when submitting to a journal?

The problem is less ResearchGate and more your field. As far as I know, ResearchGate, unlike Academia.edu, does not claim copyright or commercial license for your uploads; and they refer to their upload service as more self-archiving than anything else. That said, different fields and different publishers have different attitudes toward what it means to be prior publications.

In Mathematics (my field), for example, almost certainly no journal will count uploads to pre-print repositories or online social media or your own webpage as prior publication.

In fields like Medicine and some subfield of Biology, the rules are much stricter, where sometimes too-detailed conference posters can count as prior publication when it comes to journal submissions. Wikipedia has a listing which shows, e.g., journals of the American Society for Microbiology having this type of strict pre-publication rule.

So the only general advice for your question is: consult the website of the journal to which you intend to submit your articles.


How to return to academia after "don't walk, run"?

“Don’t walk, run” is a shorthand for taking immediate action to extricate oneself from a rapidly deteriorating situation.

Note that this may not require leaving academia altogether, or even one’s current institution. You may be able to find a workable solution where you are by switching projects, advisors, or departments, as appropriate.

But sometimes it is necessary to leave, for economic, personal, or medical reasons. You may want to return. In that case, it’s not really all that different from other cases. The critical step is explaining to whom ever you’d like to hire or admit you that whatever situation caused your previous departure will not affect the present situation. You’ll need to make that case clearly and convincingly so as to reduce the “risk level” of your potential boss. If you can’t make that case, then you may want to reevaluate if returning is the right move at the present time.


Where to find journals or other publications for my work?

When you want to figure out where to publish something do the following:

Figure out what journals the articles you cite are published in. Try there.
If that doesn't work, look at the other outlets that the authors of those papers also publish in. Then try there.


How to present preprints that are not publicly accessible on a CV for math academic job search?

If the paper has been submitted, then of course you can list it as "submitted", whether it's public or not.

Otherwise, I think that about all you can do is to say "in preparation", but this won't really have much impact.  My impression is that "in preparation" means about as much to a search committee as "I had this idea for a paper", i.e. practically nothing.  They aren't really likely to believe a candidate's estimate that the paper is "99% done", since it's obviously self-serving.  And anyway, the last 1% is often where you discover a critical gap that takes months to fix, or can't be fixed at all.

If the paper really is done or nearly done, your best bet is to work hard and try to get it submitted or posted publicly (preferably both) before you send in your job applications.

If you can't get to that point, then the next best thing is to make sure that at least one of your recommendation writers is familiar with the project.  (If you have co-authors, ask one of them to write you a letter.)  They can write about how awesome it is and assure the committee that it really is practically done.  In this case you still say "in preparation" on the CV, but you have some third-party backup.


Most of the "legal requirements" associated with MD-PhD programs are financing related. In general, such programs are usually sponsored and funded by national health ministries (or their equivalents). Therefore, it is preferred (or required) only to have legally qualified citizens participate in such programs.

As for the choice of major, in general, computer science is not one of the usual entry points for MD-PhD programs, which tend to be more closely related to experimental programs and majors (e.g., chemistry, biochemistry, biology, bioengineering). That said, there is more of an emphasis nowadays on computational science in medicine, and more and more MD-PhD programs are expanding their scope to include bioinformatics and computational biology. But it is still definitely not a universal, and CS majors will be at something of a disadvantage.