Plagiarism-checker to prevent self-plagiarism

Summary:

Make sure you understand the standards of self-plagiarism relevant to your project.
Your institution's LMS likely provides access to an automated plagiarism checker you could use.
Automated plagiarism checkers are imperfect.
Some people think that commercial plagiarism checkers are unethical.

If you haven't already done so, talk to your dissertation committee about their understanding of self-plagiarism. What exactly are they concerned you might do? What are their standards, and are these standards reflective of common standards in your discipline?

Once you know how your committee understands self-plagiarism, talk to the people who administer the learning management system (LMS) at your campus. Many LMSs include access to commercial plagiarism checkers, and many of these services allow teachers or students to upload selected papers to the plagiarism checker's database. (The idea is that the plagiarism checkers allow teachers to check student work against unpublished papers that other students--like roommates or sorority sisters--have submitted in response to the same assignment in a different section of the course). If you put your publications into the plagiarism checker's database, you should be able to use the plagiarism checker to identify potential self-plagiarism.

HOWEVER, automated plagiarism checkers are imperfect. Whichever one you use, it will probably flag some stuff that isn't really plagiarism, and it might miss some stuff that is. The automated checker should supplement your own judgment, not replace it.

Finally, some people think that commercial plagiarism checkers are unethical because they collect papers and make money off of them without paying the authors. The courts have ruled that it's fair use, but you should at least know that the issue exists.


Is it appropriate to use others' images in publications?

You are writing a paper for publication: No

You are writing a paper for a class: Yes (If you cite appropriately)


Applying for MS, what role should a cover letter have?

A brife email with your attached CV is enough for information email communication with professors. unless you are applying formally to a MS program that define the length and the scope of the needed cover letter, you do not need to send one to your professors.


Assignments taken and re-used without consent

I am a professor in a UK university.  I would say that it is standard that if you teach a course and then hand it on to someone else then you should hand over all your teaching material, which your successor will typically modify to their taste.  Moreover, people do not usually keep track of authorship, except possibly in the case of a full set of notes that is similar to a book.  Of course it is polite for people to be open about what they are doing and to express appreciation for any material that they inherit.


Some departments need a lot of TAs. Math, for example, since there are a lot of people taking elementary courses. If there aren't enough graduate students in the department to cover the need they might need to look elsewhere, but probably within the same institution.

But this would vary a lot between institutions. I don't find it to be odd, but neither do I think it is common. If you are qualified to assist, or even teach, an elementary course then the position might be open to you. Note that it is probably also true that some departments have unmet financial needs for graduate students and this gives them a way to provide support.


Is it typical for a medical researcher to attend an industry conference?

I occasionally attend non-academic medical conferences, or attend the industry-focused sessions at mixed conferences. In my experience, these conferences are excellent for generating a couple things:

Contacts. Even if you want to stay in academia, knowing people in industry is occasionally useful - for example, if you want to be a PI, someday you will have students. Presumably those students willl need jobs.
Ideas. I actively refer to one conference I go to as a "hypothesis generating conference" - I leave it with a notebook full of ideas, and some followup emails to send.
Funding. Following from 1 and 2, industry contacts are a decent way to drum up industry funding.

That being said, they are more expensive to go to, and in my experience using travel funds for conferences where you're not presenting is a very hard sell.


Should the slides in a presentation be self-explanatory or be as minimal as possible?

I would say the two most important points are to make slides you are comfortable with and not to limit your oral presentation to reading your slides.

Furthermore, if you are presenting a research paper, i.e., where more written material is available to the audience, then the objective is usually to make people want to read your paper, instead of explaining the entire paper in 20 minutes.

Some people prefer to have full slides, arguing that when members of the audience are not understanding English very well, it can help them to have both the oral presentation and the slides, especially when the speaker does not speak a perfect English. It is also helpful for members of the audience who got distracted at some point, and who can quickly read where the speaker is. Other people prefer minimal slides, arguing that having both the full text and the oral presentation might confuse the audience. In particular, whenever a slide is displayed, the audience tends to read it immediately, and during the reading, to be less receptive of any spoken words.

In other words, the only "bad" presentation would be to have full slides, and to limit your presentation to reading them, because you become basically useless. However, you can have long slides, as long as you consider them as an aid for the audience who haven't followed what you said (for whatever reason), and not as your script to read. You can also minimal slides, containing only the key points. In the end, you need to be comfortable with your slides, and to give a presentation like one you would like to attend.


Can blogging about research results first affect your ability to publish them later?

I remember very clearly when an editor for Science was asked about whether or not they would publish work if it appeared in a blog post, the editor replied with "so long as it has no more than 70 likes, 20 share, or 30 re-tweets".
She was actually being satirical, and ended up having to restate that Science doesnt care so long as "the core scientific message" is novel in their publication.

Truth is, I hear a lot of stuff like this from journals claiming to be all about the dissemination of science. What i DONT hear is people who's work was rejected specifically because of a blog post. Probably because the rejection letter is the same old standard "Better luck next time." and the real reason is never known.

Long story short, if you want to keep publishers happy, do whatever you can to make the article valuable...


How to properly format and write a department/office/lab/subsection of a university?

In the context of describing affiliations of different authors on a paper "Department name, Faculty Name (optional), Institution name" is common. For example, see this paper:
https://arxiv.org/pdf/1609.06958.pdf


How to deal with people judging your 'overproductiveness'?

I'm not surprised that hard work isn't considered a convincing answer.  It's not plausible that you are putting in four times as many hours as your peers.  Hardly anyone actually works a hundred hours per week, and even that would achieve a fourfold increase only if your peers are putting in just twenty-five hours.  Instead, it's possible that you are working far more efficiently than your peers, but that's a tricky answer to give.  You'll offend people if it comes across as "I'm probably just smarter than you are" or "you sure must be wasting a lot of time", and you won't look good if it comes across as "I cut corners to try to rush my work into print as quickly as I can".

One common attitude in mathematics is that publishing a lot of papers is a waste of your potential: if you have the time and energy to do that, then you should be spending it trying to write better papers, not more papers.  How strongly this is felt depends on the subfield, so I don't know whether it applies to your area.  To the extent it does, there may be no compelling explanation you can give for publishing a lot of good papers but no fantastic papers.  (If you are publishing some fantastic papers, then you don't need to worry about this.)

  Is there any better ways to explain 'overproductivity' to peers, in a non-offending way, how I publish more (and good quality) papers than the average in my field?

Probably not. Your peers might simply be envious, in which case they already feel bad about the productivity difference and there's probably nothing you can say to make them feel better about it.  (They might need to vent to a friend about how frustrated they are or talk with a mentor about how to improve, but they probably aren't looking for an earnest conversation with you about how you manage to accomplish so much more than they do.)  Or your peers might have legitimate concerns about your approach, in which case no boilerplate explanation will address the concerns and you'd be better off discussing this issue with a trusted mentor instead.  Either way, I don't think you should interpret their questions as genuine requests for information, but rather as complaints.  There's probably no simple answer that will change their minds.


Am I responsible for that my PhD adviser does not have any fund or grant and as a result it really limited my research?

In general, this is bad form on the part of the advisor and your committee (shouldn't be approving thesis topics that are not viable if funding is not available). As a PhD student, you are in training and potential stumbling blocks should be made clear to you.

For example, for my PhD I worked in a lab where I wanted to do field work in another country, but my advisor didn't have funding for this. I decided to go ahead with this part of the project, partially using my own personal funds, as well as cobbling together several small research grants to cover these costs.

So I would recommend to you that you investigate research funds that might be available from your department, institution, scientific society, foundation, or other non-federal source. Funding begets funding and you absolutely have to be successful in getting grants to be a successful academic.

Additionally, it seems odd that an advisor could take on a student with no funding in the lab. That would not be allowed in my department (biology sub-field at a private, R1 university).

Finally, to your last question: I think you are correct and it is unreasonable to compare the contribution of a single graduate student with "famous" well-funded labs! The contribution to your field during your PhD can be modest- that's ok- but it has to be good science, so I would focus on how to make sure that you are doing the most rigorous and sound research with the resources you have available. And get to writing grant applications! Good luck.


If you had a bad mentor for an REU program, should put that on my resume to get into grad school?

Yes, I would include the experience on your resume. You gained research experience. Even a bad REU almost certainly taught you more than an unrelated experience or job. If the topic comes up about your REU experience during an interview, I would talk about what you learned in a positive way. For example, you appear to have learned about the importance of organization during research.
However, I would not list your mentor as a reference. Perhaps you could list on the graduate students you worked with during the REU. Also, do not worry about a lack of publication or presentations from your REU. In my experience as a REU participant and now an REU mentor, few projects result in publications even from well run programs and presentations are largely a function of your program and home university.


Inline referencing chapters, sections, subsections, etc

You can use command label, e.g.,

\section{My Section}\label{section:MySection}
\subsection{My Subsection}\label{section:MySubsection}

Then you can use:

...Sections~\ref{section:MySection} and \ref{section:MySubsection}...


Does a PhD thesis have to be theoretical?

While doctoral degrees in some specialized fields have a different designation, you can get a PhD in many non-scientific fields. English Literature or Philosophy to name just two.

But even in those other fields, a dissertation is normally theoretical in some sense appropriate to that field. Many are more like mathematics, actually, extending a thread of thought, rather than gathering data and applying statistical methods or other tools.

I question the premise that most CS dissertations are "product development" actually. None of them in my particular purview have been. All have contributed to knowledge, though that knowledge can often be commercialized in some way.

Some CS research in the language area results in the development of a new language, of course, but that doesn't mean a commercially viable language. They are normally written to test out some ideas of semantics or implementation and so really do extend the range of human knowledge.

But CS, in general, has been concerned for a long time with building things, so research that is closer to the "real world" is natural. But companies find it difficult to justify doing "pure research" that can't be turned into a revenue stream in a predictable way. That sort of thing is left to universities and to doctoral students.

And, of course, there are many CS topics if that is your chosen field. You can be as theoretical as you want to be. Some subfields are nearly indistinguishable from mathematics.


Why would a "poorly written" paper get a reject and resubmit decision rather than major revision?

A "major revision" decision generally implies that, if the reviewers' concerns are addressed, the paper will probably be published. (See this related question, What does a "major revision" mean?)

Sometimes when a paper is poorly written, it's hard for reviewers to judge its technical merits. (Because the presentation is so poor as to make it difficult to understand.) In these cases, a "revise and resubmit" decision often makes a lot of sense. It wasn't possible for the reviewers to properly evaluate the paper, so it's hard to say with any confidence one way or the other whether the paper will be publishable if the presentation is improved. The obvious course of action is for the authors to improve the presentation and resubmit the paper for a proper review.

Based on your description, it sounds like that may be what happened in your case, as one reviewer wasn't able to comment on anything besides presentation.


"Catching up" after two years in the wrong school

First of all, nothing is off the table. You are still in the very beginning of your academic path and nothing is closed off irrevocably. You are correct in thinking that a CS degree will require you to catch up on fundamentals. The question is how much time and effort would you like to invest in this endeavor. I don't think that dropping out of the engineering program is necessary. A lot of people transition from engineering to CS, you are by no means the first to want to make the switch.

So what are the options of a master of engineering holder to get into a CS PhD?

Doing nothing: You can probably get into some CS PhD program right now if your research statement/references are good, though you are not likely to get into one of the top international programs. School rank does not matter in PhD as much as your ability to find a good advisor with whom you are able to publish! This is a function of your mutual fit and joint capability, not the school's ranking.
Getting a master in CS: if you want to get some foundational knowledge and have time to familiarize yourself with the field, you can just take 2 years to complete another master's degree. The downside here is that it takes time and money, the upside is that you get another degree to your name and time to gain the necessary experience.
Getting a CS undergraduate degree: this is really resetting your academic clock to some degree. It will take you a while (though you may have the option of getting credits for your existing classes, depending on where you take your undergraduate degree). There's nothing wrong with going back to basics, but it is a bit extreme.

To conclude, what you want to do is not easy, but certainly within the realm of plausibility. I would say that the current hype around AI/ML is not playing in your favor. The competition for these programs can be quite fierce, especially in top schools, so if your life dream is joining them it may require you getting some professional training via a masters at least.


Academic freedom and unpopular or offensive views

First, academic freedom as it is commonly understood does not refer to one's views and publicly stated opinions, but to the freedom in which they conduct teaching in the classroom. The reference in US is the 1940 Statement of Principles on Academic Freedom and Tenure stating that

  Teachers are entitled to freedom in the classroom in discussing their subject

But as a rule, academics do not get special treatment outside of the classroom with regards to freedom of speech. It's certainly not the case in the US, and I am not aware of any other country where it might be the case.

Now, regarding the impact of unpopular or offensive views on reputation, it will heavily depend on your colleagues! I personally find that, while freedom of speech is highly valued in academic circles in general, Academia as a system is a rather conservative institution and I suspect you would not find much more sympathy for extreme views than in any other workplace.

NB: Academic freedom is also used to refer to a US jurisprudence applying to universities and colleges; in that sense, it is unrelated to rights and duties of an individual teacher.


How to acknowledge unhelpful conversations

I agree with Anonymous Mathematician: There are lots of non-obvious ways to contribute to a paper, and it never hurts to be generous.  But if they really did not contribute to the paper, then there is nothing to acknowledge in the paper.

If you really feel you owe them thanks for something that isn't a contribution to the paper, just call and thank them.


How to find out someone really holds a Doctorate in Electrical Engineering from Hungary?

You could try writing to someone who teaches mathematics there --- see the course coordinators listed here. Pick someone who is likely to have heard of you (or your Ph.D. advisor, or any of your co-authors, or someone who might be marginally interested in anything you've worked on) and make sure the email subject line reflects this connection. I've done this sort of thing MANY times, even a few times in the early 1990s by postal mail. Also, try writing to a reference librarian, something I've also done successfully several times.

To hopefully not overstate the obvious, if you write to someone in mathematics (a field I chose because you said you are in mathematics), this person is almost certainly not going to know the answer to your question, but he/she should be able to assist you in locating someone who can investigate your question, and you should be clear about this in your email to any such person in mathematics.


How important is the exact name of an undergraduate degree?

The students would be perceived the same. When applying for a graduate program, you submit your transcripts. The classes you took, your letters of recommendation, and your grades would be more important than the name of your degree.


Why scientific articles do not include year/date?

For most purposes, the publication date is more important than the date the work was done. There are some exceptions, but they are few. The author doesn't know the publication date when the work is done.

The publication date is a kind of meta-data about the publication, not precisely relevant to the work itself (most cases). That meta-data is maintained by the publisher, of course.

Some work, of course, is time dependent and so the authors will, then, likely say  when data was gathered, and so on.


Are non-mandatory sensitivity trainings mandatory?

I just read a couple of your posts about how you interact with your students. Sensitivity training isn't optional. The people who will be voting on your tenure think you have a problem. Frankly, I agree with them.


How do I find call for papers for special issues?

Subscribe to different publishers' mailing list specifying you'd like to receive call for papers in your field, and chances are the publishers will be more than happy to send them to you when they come. That's likely to be more efficient than trawling the target journals' website every day looking for call for papers.


Is there hard evidence that the grant peer review system performs significantly better than random?

No such study exists.

You have to realize that the current model of funding research through grants is rather recent. Fifty years ago, research was funded with recurring credits: a lab/researcher got a fixed amount of money each year to do research as they saw fit. Only applied researchers got industrial grants to develop precise new applications, but this wasn't the core of their funding.

The current system arose due to the combination of two factors:

The growing hegemony of the neo-liberal ideology in the 80s-90s and the commodification of society as a whole. According to this ideology, research as a whole is supposedly more efficient (for an ill-defined notion of "efficient") if researchers compete with one another on the global market of research funding. They will "naturally" tend to research what works in order to keep their funding.
Politicians' will to govern research. Research, and especially fundamental research, is a notoriously difficult thing to govern: you never know where an idea might lead, or what new ideas will come up along the way. You don't know what will work and what won't. You don't know what will be applicable and what will remain a nice theoretical idea. Otherwise it wouldn't be research.
But rulers want their word in this: they want to tell their voters that their policies improved lives in a very direct way as a result of such and such decision they took. This is why words like "governance" and "steering" are becoming more and more prevalent in modern academia: administrators are not in the business of just helping researchers carry out their research, they are in the business of ensuring that researchers are researching what they are supposed to. And how do you force someone to do what you want, short of physical violence? Through economical violence.

Of course, this yields absurd situations, such as the fabled year when the French National Research Agency spent more on administration than on research. And such thinking paves the way for short-term research with zero long term goals, and especially not goals reachable in more than five years (the usual length of "long-term" grants). But these decisions are not driven by rational thought; they are driven by ideology.


What should I do if I find a mistake in my submitted master's thesis?

Everyone makes small mistakes from time to time and it is expected that there should be some mistakes in a master's thesis. What you should perhaps do depends on the nature of the mistake. If you are talking about a small or even a big typo, I would suggest just leaving it be and not alerting your professor. Typos are expected and a few won't impact your grade very much, if at all. However, if you have made a major scientific, analytic, or other substantive mistake, acknowledging it and offering a correction is the right thing to do. Depending on the rules of your institution, the professor may not be able to accept a modification to the document you turned in, but if they can, you are sorted. If they can't, them knowing that YOU know that this was a mistake is likely better than them finding the mistake and thinking that you don't know, from a grade point of view.


Is worth accepting to review manuscripts in low quality journals

I think a lot depends on what you define as "low-quality journals". If you mean lower-tier but legitimate journals (typically subscription-based, or free OA) with high acceptance rate and low impact, listing these will have neutral to slightly positive effect. Indeed, someone has to start curating the quality in order for some of these to raise in quality and impact.

If you mean fake, pay-to-publish "predatory" journals then the effect will be strongly negative. By accepting to review for these journals you are encouraging a business that hurts science and scientific publishing. Also, you're wasting your time since these journals will accept papers on the basis of whether the authors paid, not on the reviewers' recommendation.


whether to make a tenure track faculty job talk interactive

In the right circumstances you can. For example, if you are studying color vision and have worked on the dress it might make sense to poll what color people see as a way to highlight the ambiguity. I job talk I saw on the psychology of magic, involved magic tricks and breaking them down. It was useful. If you are going to interact, it really needs to be critical to the talk.


Is there any risk of having my research scooped after posting my manuscript onto bioRxiv?

In fields that use arXiv, publication in arXiv does establish a definitive date-stamp on the work (and an accompanying archival DOI) that is generally understood and respected by practitioners in the field. Nobody could reasonable "scoop" a work published there without being called on it by their peers.

bioRxiv is intended to provide the same for biology-related fields and technically does so. The culture of those fields, however, is often not yet as accepting of the idea of pre-publication and incrementally evolving works. Hence, for example, the much greater concern with the ideas of "priority" and "scoop" to begin with.  A few journals still even consider sharing a pre-print in bioRxiv to be a sort of "self-scoop" that prevents you from submitting for peer review in that journal!

Still, the only way to change this culture is to embrace more open and sharing practices. I would advise checking whether others in your sub-field use bioRxiv, checking the publication policy of your target journal in SHERPA/RoMEO, and checking if your co-authors are amenable to pre-print sharing. If you see others in your subfield sharing, and if there is no veto from the journal or co-authors, then go ahead!


Can we just send the same two recommendation letters to every colleges? And will I be able to look at what was written in each recommendation letter?

In the U.S. you do have a legal right, if not supposedly waived, do see the letters written on your behalf. However, within the U.S., there currently seems to be the general expectation in faculty's minds that students will "waive" this right, the idea being that the letter writers will be more candid without the risk of upsetting the student. In particular, the set-up is such that letter-writers will see whether or not a student has "waived" that right, and, note, possibly write a considerably different letter if there is no waiver.

At the same time, I have read that the "waiver" is not legally binding...

At the same time, I have the strong impression that people in academic depts in the U.S. (certainly in math depts, for example) would think it quite "tacky" (=gauche) to ask/demand to see the letters, whether or not one had signed the waiver. It's simply not the style.

I'm not arguing that this is a good situation, since it amounts to students not quite knowing what people really think of them... for better or for worse. Somehow there is an inflation of unusable/cheap praise, and a drought of substantive praise here, as a cultural style.


How to deal with your research results becoming obsolete?

While I sympathize with you, I find it hard to answer your question.

On the one hand, as phrased you are asking whether an emotional response is valid.  Well, it is not really for anyone other than you to determine the validity of your emotional responses, and in all of my experience, "That is not a valid emotional response" is rarely a useful piece of advice.  On the other hand, your question is pitched in a certain level of generality, but understanding why you feel the way you do seems to require knowing more particulars of your situation than you have disclosed.

But let me say what I can and what might be helpful:

  The way I see it, a paper has a certain lifespan in terms of being read and cited. Once it has been generalized, that lifespan is in most cases over. If someone wanted to understand a theorem, they would probably look for the most general version. Of course, this does not always apply, for example if the work represents a milestone of some kind. One consequence of obsolescence is the stream of citations to my paper is short circuited. This will, in a sense, benefit them at my expense. Of course, I realize that my paper will eventually (hopefully) be generalized and become obsolete (i.e. no longer state-of-the-art).

Since you speak of "theorems," I gather you are working in mathematics.  (This is corroborated by one of your other questions, where you identify yourself as working in applied mathematics.)  I am also a (pure) mathematician, and the way you describe "obsolescence" is neither the way I think about mathematical results nor how I have heard other mathematicians talking about them.  Maybe it is quite different in applied mathematics, but in pure mathematics there is not any prescribed lifespan on papers being read and cited.  To try to quantify this, I just looked back over my last 10 accepted papers, and for each one identified the earliest cited paper.  Of these ten papers, the latest one was published in 1976.  (Moreover the 1976 paper came from a five page note with only a few citations.)  In other words, in all of my recent papers I have cited papers that are more than 40 years old, and in fact usually older than that.  In my department I have many colleagues who are 10-20 years older than I but who have a similar number of publications to me (publication pressures have risen in recent years).  Most of these colleagues have higher total citation numbers than I do -- I think because their papers from 10, 20, 30...years ago continue to be cited.  My most highly cited works were published in 2013, 2005, 2006, 2010 and 2003, respectively.

[Moreover, in mathematics, citation numbers are not (yet!) the ultimate metric of academic worth.  Papers written on finite graphs tend to get more citations than papers written on admissible representations of p-adic groups because there are more people working on the former and many more people who know what the former are.  I think most mathematicians realize this.]

So I have to wonder about the specific situation you are describing.  In a different question, you mention a colleague of yours who worked on the same problem as you and came up with a result that was in some but not all ways more general, and then you published at least two papers together.  I don't understand why this would "short circuit" your citations.  Now you describe a situation in which your colleagues are working on generalizing one of your results, apparently without any new ideas.  In this latter situation especially, I would expect that if they publish an improvement of your results using ideas essentially due to you, then that should augment your results in every way (including citations), not detract from it.  (You are aware that senior mathematicians do this all the time, and the work of their students is usually viewed as an extension of their own work, I trust?)

Then you say:

  I just rather prefer that it wasn't my coworkers who are working towards that goal (they even started while I was still drafting my paper).

If it gets to the point of an independently published generalization of your work, then I don't see how it makes any difference whatsoever if your coworkers were involved.  However, before that happens the fact that it is your coworkers puts you in a much better situation: namely, in the worst case you have much more advance knowledge of what they are working on and can plan accordingly.  In the best case you can pursue a collaboration with them in whatever way seems best to you.

If I may take a guess -- are you perhaps most upset by the fact that your coworkers have chosen to pursue these generalizations of your work without your involvement, so that they seem to be competing with you right under your nose?  I could understand why that would be upsetting.  If you feel that way, I think you should be much more proactive about collaborating with them.


Email to a potential master’s supervisor, initially responded but no reply after I sent my transcript

Any answer to this question would at best be a guess.

It doesn't necessarily mean that he's not interested in it anymore. Perhaps the professor is just busy. Maybe he read your email, thought he'd get back to it later and then forgot about it as more emails piled on top of it.

It's been a week since your last email. If I were you, I'd email him about this. That's the only way to know. Bite the bullet and send that e-mail now or a couple of days later asking if he is okay with your transcripts and if you could meet him as discussed. The worst that could happen is that he'll reject you. He won't be angered if you send him an email asking for clarification.


Why don't most law schools show, let alone teach how to draft and interpret, complete contracts?

I went to law school in Australia, not the US, but I also had this experience --- that courses on contract law never involved reading any actual legal contracts, and that this latter exercise was almost completely absent from the whole program.  Across my LLB and LLM, the only time we ever did anything like this was in a legal skills workshop in LLM (required for registration as a solicitor) where the teacher went through an actual legal contract and the class discussed the drafting of each of the sections, and their good and bad points.  This exercise was probably about one hour over the course of about five years in law school.
As to why this is done, I can only assume that legal academics believe that it is more valuable to focus time on discrete legal issues, and the theory pertaining to them, rather than spending substantial amounts of time holistically analysing an actual legal contract.  Furthermore, I think the law schools regard this kind of exercise as something you learn on-the-job in a legal firm, rather than in university programs.  There is some degree of demarcation between legal theory and ideas taught in university (which is more abstract), and the on-the-job knowledge you get from supervising solicitors when starting in a legal firm (which is more concrete).
To give some historical background to this, it used to be the case that law schools did not exist at all.  You became a lawyer by doing an apprenticeship under an existing solicitor, just as you would have to become a blacksmith, etc.  Throughout the middle ages the legal profession was conducted on an apprenticeship model, so students learned skills by performing or observing tasks from an instructing solicitor.  The size of the profession was small, and limited to upper-class males, so you might have had a solicitor who agrees to take on one or two apprentices who do clerical work for him while observing his practice.  In the 1200s an institution called the "Inns of Court" was established in London to teach young upper-class men legal skills and the broader social graces and skills of becoming a "gentleman".  Even then, formal legal training was light, and most of the learning was done on-the-job by apprenticeship under a practicing lawyer.  (Incidentally, this institution is still around, and is now a professional association for barristers.)  Students were also encouraged to learn by directly attending and observing court proceedings.  In more recent times, when the universities began teaching law, they had to demonstrate some value-added in conducting courses through their own institutions; they did this by taking the view that they would teach the kinds of higher-level abstract principles of law, while leaving other skills to remain within the apprenticeship.  Gradually the apprenticeship model has waned and disappeared, but there is still some degree to which the universities consider early career at a law firm to be a supplement for this.
I partly agree with the Sedburry quote --- it is descriptively accurate about what happens at law school.  I disagree with his assumption that academics assume that concrete knowledge of how to draft good contracts follows automatically.  To the contrary, I don't think that legal academics think that the ability to draft contracts automatically follows from conceptual understanding, but they do seem to regard this as a skill to be learned during one's early career in a law firm, rather than something to devote time to at university.  Personally, I think that is a mistake, and that it would be beneficial for the degree to include many more exercises involving full reading/critique of a whole legal contract, even if this crowds out some of the theory knowledge in the curriculum.
Finally, I will just note that you are probably not alone in viewing this as a deficiency in the law school curriculum.  This is a situation where you could take the initiative and start your own study group, with the goal of reading and analysing actual commercial contracts.  You could treat this like a book-club --- each week you all get a legal contract to read and discuss/critique for the next week.  If you can find ten or more other students who are keen on this, you could probably go to some of your lecturers and see if any of them are interested in helping you (e.g., attending a one-hour study session each week to help with discussion).  Some academics won't have the time for this, but if you've already done the leg-work of organising the group yourself (and if you meet in a room very near to their office!), you will probably be able to find a willing academic.


Can a cat be a co-author in academic paper?

Regarding whether or not all authors must be human, the answer seems to be no.

Combinatorist Doron Zeilberger, for example, has published many papers jointly with Salosh B. Ekhad (his name for his computer).


PhD supervisor is taking really long to read my thesis

A good starting assumption is that your supervisor has good intentions, but like many of us, has trouble getting things done because of workload and/or procrastination.

Artificial deadlines may help.  Perhaps your supervisor is too busy right now but would be able to agree on a date several weeks in the future by which he can read the chapter.  Or even better, perhaps you could agree an overall schedule for completing your thesis, including deadlines by which you will send each chapter, he will review it, and so on.  This could help prevent the problem from recurring in the future.

If this doesn't work, I would have a chat and share your concerns with him about how you feel this is needed for your own successful completion of your thesis.

If all of this still doesn't have any impact, you are in a tough position.  You are dependent on your supervisor, but outside of extreme situations, there is no real formal mechanism requiring his action.  You could try getting your second supervisor involved.  Even if you have had no contact so far, you do have a formal relationship with this person, and that is a good enough basis to do so.

Talking to the director of studies would be a last resort.  It probably isn't worthwhile until the continued inaction is clearly going to delay your PhD completion.  If you want to maintain a good relationship, I would discuss this with your supervisor first, making it clear that the delays are about to have a big impact on your life, and you feel you have no other choice.


Depends what university you will apply for. However, because the Msc is expensive in the UK, even for the British students, the students tend to look for jobs after Bsc; and therefore some universities accept students with lower grades.

Little bit of advice: Look for the courses in details to cover your interests; For example an Msc in Computer Science at one university might involve more than theory; than the same Msc at another university.


Graduate school that does not require a statement of purpose

Two groups of departments often do not request SoP:

The departments, within which the diversity of the research among the corresponding faculty members are such noticeable that the applicants would be admitted to the program based on the merit, firstly. Then, they would have sufficient time to communicate with the faculty members and choose their desired research track.
The departments, within which the interview with applicants is routine before any offer of admission. So, one might conclude that the coherency in view of the research interests with the faculty members will be investigated within the interview.


How necessary is research for a collegiate teaching job?

Yes, it is possible.  Of course, you will probably teach more than you would if you were in a "traditional" professhorship (with teaching and research), but if you love teaching, maybe that is great.

This article from the Chronicle of Higher Education has some useful statements, to wit:

  research and writing are not part of a faculty member's typical workday at a two-year college.

Also:

  The good news is that the vast majority of two-year colleges do not require faculty members to publish a single word in order to earn tenure.  [...] most community colleges do still offer tenure. In many state systems, earning tenure is simply a matter of doing your job in a satisfactory manner for a set period of time—generally, three to five years.

There are also positions at four-year liberal-arts colleges that are primarily teaching-oriented.


Is it okay to do a PhD in the domain you barely know?

It's totally OK!

When it comes to PhD, enthusiasm, dedication and perseverance worth far more than prior knowledge and intelligence.

In fact, many of the people I know started their PhD without even knowing the slightest basics of their topic, but they excelled nonetheless.

This includes me. Since were in similar fields I suppose I could share my experience. I chose machine learning (ML) out of impulse because I was passionate about AI. I didn't even know the definition of ML when I started my PhD. Now, I'm recoding ML algorithms twisting them to my research needs. Moreover, I'm even teaching my students and colleagues to do the same. It's truly a magnificent experience.


Letter of recommendation from Post-Doc or Professor

You should ask the professor for the letter.  It is likely the professor will get help from the postdoc in writing the letter.  There is a traditional belief that the professor's opinion is worth more, so whoever is reading the letter will expect to get a letter signed by the professor.


Apply for two different Ph.D. positions at same group?

Personally, I would prefer to get one application in which you clearly indicate that you are interested in both of these and also showing your qualifications for them both.
But I don't know what rules there might be at the institution you are applying to or what constraints the PI might be under. So, it would be best to ask first and see what advice you get. It isn't outside the realm of possibility that the PI is delegating the examination of the applications to others for initial assessment.
Alternatively, prepare applications for each separately and when you submit them, do so with a note that you are interested and qualified for both and that the two applications have overlap in some ways.


How can I remain motivated while studying for comprehensive exams?

The strategy that I used was to divide the work into chunks and assign them to finite periods of time.  Let's say your exam is in three months and you have two books to read and two course notes to review.  That means that you'll have 12 weeks to study.  The 12th week should be reserved for "hitting the hotspots" before your exam and general review of all the materials covered in weeks 1-11.  Then divide up material to be covered from the two books and two courses across the remaining 11 weeks.  I would suggest that you divide it into 11 weekly topics.  Assign reading to yourself.  The goal of each week worth of studying is to create your own "cliff notes" for that week's chunk of material that can be studied during week 12.

A good strategy to avoid burnout is to schedule time for no studying.  This especially important since you have family.  Make sure that you schedule your no study time during a time that they also want to interact with you.  For example, no more studying after noon on Sundays would be a good amount of time.

Since you do have family, also consider scheduling alone time for yourself where you get to do only what you want.  Doing nothing, watching tv, or checking on your stackexchange questions are okay during that time.  But make sure to limit those activities to only that time.

Good luck!


How to cite a phd thesis that was published as a book?

Provide the citation form that you think will be most useful to readers in the middle or long term, or provide both.

If it's self-published, then cite it as you would cite a thesis. On the other hand, if it was published in book form by a respectable publisher (i.e. it will be easy to find 10 years from now), then cite the book. This is commonly done in some fields of humanities.

Citing both is also an option, and it does not have a downside, except it's a bit longer.


Dropping UK PhD - is it worth switching to MPhil?

This might not be the most popular of answers and it might not be the answer you're looking for, but it's what I would sincerely advise a friend facing similar problems.

You say you have limited work experience, so I'm guessing that you are pretty young. In that case, look at what you've put into the PhD:

You spent two of the best years of your life on this (around ages 20-30 is one's intellectual and physical peak).
You also spent tens of thousands of GBP on this. Maybe it didn't come out of your pocket, but there was certainly an opportunity cost from not taking a better-paying job using your MS degree. Quantified, this difference is likely in the tens of thousands (especially if accounting for loans / investments).

If you leave with nothing now, both the time and money you've invested go to waste. You will forever be someone who dropped out of a PhD program, presumably because you weren't good enough (these first impressions apply even if you can justifiably claim to have learned a lot from the PhD). However if you leave with an MPhil, you have something tangible to point to. You have your university's brand name behind the skills you claim to have, and you get to avoid questions such as "Is it possible to make leaving a PhD look good on a CV / Resume?".

It's true that MPhil from my cursory searching is not the most empowering of degrees - for example reed.co.uk lists 200,000 jobs, but only returns 4 results for "MPhil" - but it is better than nothing.

I would strongly incline towards getting the MPhil. DPhil would be even better. "I need a PhD because it helps me find a better job afterwards" may never impress a graduate admissions committee, but if it motivates you to finish the DPhil, it's good enough.


What's the most efficient way to schedule a joint meeting with multiple faculties?

Use a polling tool, like Doodle. You create it, they fill in which times they are (not) available, and based on the results you choose a meeting time.


PhD in theoretical physics after dropping out of PhD program in Engineering?

The only problem I can see with cases like yours is that some people may look at the file and think "This is someone who can't finish what they start."  It is essential for you to communicate in the statement of purpose why you left the old program and why you believe you will complete a new one.


Are Graduate Schools Less Likely to Fund and/or Accept Nontraditional Students?

this is because 40+ year old students rarely get tenure track positions.

False.  PhD students of any age rarely get tenure track positions.

Even at the master's level, however, would I have difficulty getting funding at my age?

Not because of your age; however, PhD funding is more common than master's funding.

Also, are nontraditional students more likely to be rejected?

In most cases, no.  You may experience confusion if the program has never had a nontraditional applicant.


You're probably thinking of PlanetLab.

  PlanetLab is a global research network that supports the development of new network services. Since the beginning of 2003, more than 1,000 researchers at top academic institutions and industrial research labs have used PlanetLab to develop new technologies for distributed storage, network mapping, peer-to-peer systems, distributed hash tables, and query processing.

  PlanetLab currently consists of 1335 nodes at 645 sites.

More generally, there are lots of "testbeds" (as these networks of distributed resources are called), including Emulab, PlanetLab, ORBIT, DETER, Seattle, and many others. Each has various advantages and disadvantages, depending on what you're trying to do. These are often federated so that users can access resources from multiple testbeds; projects like GENI and FIRE are federations of testbeds.


Can a postdoc conduct collaborative research with people that are not their PI?

It is likely not legally binding that postdoctoral activity must go through the supervisor, especially not if the additional work was beyond "normal working hours" and uncompensated. For example, if the postdoc had wished to donate time to a charity, no permission from the supervisor would be necessary. However,
Yes, you and Postdoc A had a professional obligation to inform Dr. B about your collaboration, especially if it was intended to result in publication and was not just for Postdoc A to learn something new. Dr. B has committed to training and advising Postdoc A, and Dr. B's financial and intellectual commitment to Postdoc A makes your unpaid collaboration possible. Also, you might be hard-pressed now (after the fact) to demonstrate convincingly that none of the work ever took time from the projects with Dr. B. Therefore,
You should take the fall for this one. Apologize to Dr. B, say that you should have known better and that you wrongly advised Postdoc A. Offer review and editing of the manuscript and possibly minor authorship to Dr. B. Or, collaboration on a follow-up project. Give a gift of coffee, tea, or a favorite food (I have found this to be a surprisingly effective apology strategy with academics -- citing my personal experience here).

Citation for all advice -- personal experience in the lab of another Dr. B, watching another Postdoc A.


Does posting paper online anonymously prevent me from publishing it in journal?

There are two complicating factors involved here. It may or may not be possible, but it depends on these issues at least. Even if it is possible, there may be some "risk".

When the "organization" published your paper, did you assign your copyrights to them? It is possible that you did, and also possible that you retained all rights and just gave them a limited license to publish. The outcome is very different for these two situations. What did you sign or implicitly transmit to them to make it possible for them to publish. If they hold copyright or an exclusive license then there are things you cannot do yourself. Copyright law varies widely from place to place but is generally becoming more restrictive.

The second issue is that many places won't publish anything that has already been published. Many of them actually want you to sign over the copyrights and don't want to be limited by some prior license that you gave to another organization. This is very strict with some of them. But it is a limitation imposed only by their now policies and these vary. It would be a mistake to try to publish with such a journal without informing them of the situation.

But even if neither of the above considerations apply, you might have difficult claiming that a work is yours. If the original publisher makes the claim then it will be believed (most likely), but if only you make the claim it might be open to dispute unless you are backed up. In an ideal world (not this world, unfortunately) this would be a simple matter.

Therefore, the place to start is with the original publishing organization. You don't describe its nature. I worry about reputable organizations publishing the work of students anonymously as you have stated unless the is very controversial and you need some form of anonymity for personal protection. But you don't describe the circumstances.

But is that organization that holds the key. If you ask and they say no, without a legal reason, then you proceed with some repetitional risk.

An additional complication is that if you simply reuse what you previously published, without citing it properly, you can still be accused of self plagiarism. Normally one cites and quotes ones earlier work, rather than just reusing it.

By the way, turnitin isn't a sufficient check to prove the absence of plagiarism. Plagiarism is much more complex and subtle than what can be judged by an algorithm.


PhD Perfect fit topic + insecure funds vs. non-optimal topic + secure funds

If you are anything like the numerous phd students before you, myself included, your interests are very likely to change as you are exposed to different ideas from new colleagues.

The Helmholtz position sounds like a great place to do a PhD. Firstly, you get funding. That is important. Secondly, you get a large group of colleagues where you will be exposed to new ideas and ways of doing things. You might find that your knowledge of things like gradient descent and differential equations fits perfectly with machine learning. You might discover you have a love for programming when scripting simulations.
You might even be like a friend who decided to leave theoretical physics and pursue finance in New York.

And there is nothing to stop you from pursuing your interests during your phd career or even in a postdoc.

As for your post-doc position, it depends on the position. Sometimes a PI wants a post doc with a very specific set of skills and knowledge. Sometimes a PI wants a post doc with a lot of potential who is also hungry and hard working. Sometimes a PI wants a post doc with a proven research production stream.


As an undergraduate student, should I put my temporary address and manuscript on my CV?

For an undergrad, it is fine to list papers that are not yet submitted.  List them as "in preparation".  Also, if the REU requires letters of recommendation, ask your letter writers to comment on the status and quality of the project.

Yes, the address is just in case someone needs to send you physical mail.  Any place where mail will reach you is fine.  These days I'd say you could just leave it off, since it's unlikely anyone would actually need to do that.  If the program is limited based on place of residency, there would be a specific question on the application for that.


Prioritizing subject matter of future PhD versus university and professor

Some people are fairly agnostic about their choice of dissertation topic and are happy learning to become interested in whatever interests their advisor. The fact that you are posting this question suggests that you are not one of those people.

You'll be happier, do better work, and set your career in the right direction if you pick an area that genuinely interests you. It's true that an advisor's prestige has a lot of currency, but it's not worth so much that it makes sense to sacrifice what you feel is best for you in the long run. Grad school is tough enough without the stress of added friction.


Invalidating a method because its "Dated"

Older methods can be tied into older biases, mistakes, and bad assumptions.  In mathematics this is very rarely a problem, but in social psychology it can be a massive one. There may be bad mathematics involved, poor controls, cultural biases, confounding variables that weren't known of then, etc. I don't know where economics and rational expectations falls, but I'd hazard a guess that it's closer to the social psychology end of the spectrum than it is the mathematics end. There's a huge number of factors that impact economic behaviors, and any model is going to have to make simplifying assumptions to try to single out what the model's creators have deemed the most important and interesting things.

While research trends are not an objective evaluation of merit, it does tend to suggest that if something is no longer receiving attention then it is not suitable for addressing modern problems and concerns.  The exact reasons may be hard to pinpoint, but in this case may boil down to "today we're really interested in modeling how widgets and wodgets interact" versus "this older theory is meant to model how gadgets and gidgets interact".  It's not necessarily that the older theory fails to achieve meaningful insights on gadgets and gidgets (though it might, because some of its assumptions may no longer be considered good ones), but that nobody cares about that any more, and it is intrinsically unable to address what people do care about.


Colleague claiming first co-autorhip of my work

First, I know the struggle is real. One of my three wishes would certainly be for us to somehow separate career and prestige from the collective pursuit of knowledge.

There's an expression I recall from redneck NASCAR culture that seems relevant here: "Rubbing is racing." There will always be some pushing and shoving concerning who did what, particularly as scholars are trying to jump from fledgling academics to something tenured. If it's a little irritating, I'd just keep pursuing knowledge.

If it's more than a little and you feel as though you are not being treated fairly, then I encourage you to not care about how others perceive your bringing it up. The higher we climb, the less accurately we seem to predict how supervisors will respond. So why worry about that? If he's getting undue credit, speak up; if he kind of deserves some credit, why split hairs?


Are there any downsides to sharing a successful proposal with others?

Funded NSF proposals are requestable directly from NSF through the Freedom of Information Act. Proposal authors are given the opportunity to suggest redactions to NSF of proprietary or other information that should not be disclosed generally, but their FOIA office has final say on what gets sent. This kind of information might include not yet released product specs that would be bought with the grant funding or salaries of non-public employees. I suspect that all non-classified US federal agency grants are FOIAable through a similar process, but I only have FOIA experience with NSF.

Some people put their successful grants online, some people keep them secret. Your special sauce, in the end, is probably not that special, but good writing and good organization may be informative to weaker writers in the world. We don't publish our grant application texts online, but they're definitely out there due to FOIA.


Is there a single term to define all sources (e.g., academic papers, grey literature, books, blogs, etc.)?


How to manage your advisor's jealousy over your work?

I'd distinguish between three scenarios:

If you have accomplished something genuinely magnificent (e.g., you just proved the Riemann hypothesis), then it may be natural for your advisor to feel a little envious, particularly if it was something your advisor had hoped to do someday.  Hopefully they'll soon switch to feeling proud of their amazing student, and in any case your career success is assured by your great accomplishment.
In less extreme circumstances, this could be a real problem.  If your advisor feels threatened by your success, then you may need a new advisor, since you certainly don't want an advisor who goes around explaining how you aren't as great as you seem.  Before you reach that point, it's worth discussing these issues.  For example, you could say "I've felt some tension recently, and you seemed upset with me at the X Symposium.  Am I doing something that's making you unhappy?"  This may be an awkward conversation, but it's worth a try.  It's possible that you are somehow making the problem worse (for example, by publicly saying things about your advisor that could be interpreted as disparaging, even if you didn't mean them that way), or that your advisor will feel a little sheepish that you noticed this behavior and will try to change.  If talking about it doesn't work, then I don't know what to suggest.  You either find a new advisor or put up with it as best you can.
It's also possible that it's all in your head.  I become suspicious whenever I hear someone attribute other people's behavior to jealousy, since it's an awfully convenient excuse.  Until you have really clear evidence, you should keep an open mind regarding other explanations.


How much to say about a conditionally accepted paper on a resume?

I usually have three categories for papers on my CV:

Peer-reviewed accepted papers (if published they have the bibliographic info, otherwise they just say "Accepted by journal name")
Submitted preprints (with the month and journal of submission and a link to the readable preprint)
In preparation (means there's a file started but not finished)

You shouldn't move things from 2 to 1 until they're really officially accepted though.  Be honest and accurate, but list it.


Sharing preliminary draft versions of papers with people in the field

Per Pete L Clark's comment:

When you feel like you've developed the idea enough to present it to anyone else, show it to your advisor and see what they say. One of the main things that advisors can help you with is to tell you which other people to contact to get help and information.


What do you do when you are asked to perform an official review for a journal of a manuscript written by your supervisor?

If this is an informal request for internal review -- definitely go ahead. It is common practice to have close associates review work, and your thoughtful comments will gain you respect.

If this is a formal invitation from a journal -- it is a clear conflict of interest.  It probably should never have been sent to you, quite honestly.  This is not to say you couldn't provide an unbiased, thoughtful review, but to an outsider this would really be questionable. I suggest you take the high road, decline the invitation, and send a letter to the action editor reminding him of your close association.


Effect of passing management courses on research career

It clearly depends on what kind of future research you want to do but a lot of MBA content will not be relevant to anyone who will manage a non-profit lab, although it might help with the business of running a lab (e.g., a for-profit lab).

Here are just some examples:

business environment: Here you are going to learn about international trade, competition, etc. and how those impact competitiveness of a company. I don't see how this will help you run a lab unless your lab is operating in competition with other labs for customers (or other constrained resources).
accounting: Here you will learn about creative ways to maximize your organization's profit leveraging tax law. I believe most labs are non-profit and, thus, I do not think creative accounting is an important skill (but I might be wrong here).
business law: Here you will learn national and international laws which can impact trade. You would naturally learn about contracts, negligence, and other related topics. This might help you understand what makes a valid contract or what the impact is of leaking private data but I am not sure it will help you much other than avoiding being tricked when someone says 'I will fund you if you just sign here.'
human resource management: Here you will learn about how human resources add to a company's profitability and how to plan for them. The focus will generally be more strategic in nature and could help you do some strategic planning. One such issue is 'employer branding' and clearly you do want people to want to come to work for you. This might help you but as you are smaller, the benefit will be smaller.
finance: Like other modules, the focus here will be on strategy. How do different funding sources, and different balances between sources, impact profitability by minimizing your cost of capital. Non-profits have a much more limited choice in their sources of capital so this will be of very limited use for you.

Normally, MBA programs do include a thesis which includes research. This clearly can tell someone if they want to do more research and it will give them some research skills.

Now, there is (hopefully) going to be a change in the way the student thinks. That is, students should think more strategically. This skill (strategic thinking) should give you a benefit in most things you do in life by encouraging you to think more long-term.

All this said, if you want to start a for-profit venture which focuses on research (selling your output) then, yes, an MBA would be quite helpful. However, you should not think an MBA is about managing people better. It is about that but it is much more about how to maximize your profits through maximizing your revenue, minimizing your expenses.

If someone is going to run an academic lab, I would encourage them not to take an entire MBA (unless they really want to think like business people) but rather take a class on a subject where they want to be stronger (e.g., human resource management).

EDIT: I think Edward's answer is good but to go a bit further about project management courses, this might actually help a researcher, especially if that research is managing a team.

In project management courses, you would learn about different topics than an MBA. For example:

Feasibility studies
Planning, organizing, controlling (general management issues)
Reporting progress on your project
Risk management
Change management
Leadership, motivation, human resource management
Several others

Because most research is a project (has a start date and an end date, has resources including people and money, etc.) this could be much more suitable (than an MBA) to someone leading a lab. I would recommend starting with a single project management class (which will generally give you an overview of each topic) then, if you want to really dig into more detail, consider getting a master in project management or perhaps an industry certification like PMP.


Can I publish an article as a sole author if my supervisor agrees?

Everyone can submit articles to journals, there is no degree requirement.
There is nothing negative about single author manuscripts.

Manuscripts should (ideally) be evaluated by its content not by its author list.


Can grant money be spent on travel to program committee meetings?

For each grant, or type of grant, there are rules specifying what it can be used for. You should follow these rules and, unless you ask us about a specific funding program or agency, it's impossible to give more specific advice.


Saying "After doing this work we learned..." in a paper

In part, I agree with you: if one finds out the result one has proven is in fact "trivial" (for various definitions of trivial), the "right" thing to do is to not bother submitting it for publication. (Though leaving it up on arXiv, for example, may be useful.)

But, here are some possible defenses:

In mathematics it is not always the result that matters: the journey getting you there is a big part of it. This sentiment is very well-expressed by Thurston in his essay "On Proof and Progress". Just because one has re-proven a well-known result doesn't necessarily mean that the paper is trivial! If the approach is new this can lead to better understanding. But in this case I, at least, would advertise this fact in the introduction beyond a single sentence.
As indicated in the comments, most of the time when I saw such a sentence it refers to fairly recent (perhaps even simultaneous) publications. Given that sometimes mathematics research takes time to complete, it is not entirely impossible that the authors genuinely started working on an open problem only to have the result solved in the mean time. And if the problem is somewhat obscure, I think the authors can be forgiven for only doing a detailed literature search before they start their research and not repeatedly doing it once every few months. In this case the language you quoted seems rather appropriate.
It could honestly be a case of ignorance! Suppose the same essential problem manifests in two distinct field of mathematics which have their own lingo. Then it is quite possible that even most experts in either field would not have recognized easily that the two results are the same. (The "two-way" relation above can also be a "one-way" relation, where researchers in field A generally don't know about result B in field C, while for researchers in field C the applicability of result B to problem D seems obvious.) In this case having the duplicate paper published will (a) help raise awareness that the problem has been solved and (b) perhaps even help the two fields become aware of each others' results.
Similarly, one may have discovered a simplified proof for a special case of a very powerful general result. While the result may be well-known, having this simplified proof in the special case maybe worthwhile, if only for pedagogy.
In the modern day of electronic communications this should happen less, but one should remember that in the history of mathematics there are many results which have been discovered, forgotten, and then rediscovered. And even with the advent of MathSciNet, sometimes very technical results are hard to search for: you have to know exactly the right string of keywords to discover it in the literature.


Why do US universities have strict formatting requirements for dissertations?

I think this is a historical issue more than anything else. Until quite recently, dissertations were usually sent for microfilming, microfiching, or both, for later reproduction and distribution. As a result of this, they needed to be carefully formatted so that they would reproduce correctly when photographed. Thus the requirements for font size, margins, line thickness in graphics, positioning of page numbers, and so on.

In recent years, this has not been so important, but that doesn't mean universities have completely relaxed the rules regarding formatting. There is definitely an interest in having a consistent "look and feel" for theses from the same institution.


In which sections of a paper can I find literature reviews?

The portion of a paper where previous literature is summarized and elucidated upon is also known as (but not restricted to)

Literature Review
Background
Related Work
Previous Work etc.

In my brief life as a graduate student, I have heard of multiple strategies to write a literature review. I will describe one such path which I personally utilize (in part, because this is what my previous adviser always trained me to do)

  The Annotated Bibliography Approach

What is an annotated bibliography?

This is perhaps the best advice to start writing one. Note that I am also affiliated to Cornell University but this has nothing to do with my affiliation.

Example:

Assume that I am writing a paper for CHI 2014. My area is in privacy and surveillance. I want to look at the relationship between manual location sharing and privacy concerns.

I look at all the related papers I have read in the area and realize that their are four major categories that could evolve from this reading and still be relevant to the writing of this paper.

So, in a draft, I write down:

Literature Review

  Privacy Frameworks

  Location Based System Research

  Privacy Measurement Scales

  Privacy Aware Design

Then, under each category I start writing the references (in the style of your area ; in my area its in the ACM style) of the relevant papers and a couple of lines about each paper which explains the main contributino of the paper. For instance:

  Location Based Systems Usage

  Janne Lindqvist, Justin Cranshaw, Jason Wiese, Jason Hong, and John
  Zimmerman. 2011. I'm the mayor of my house: examining why people use
  foursquare - a social-driven location sharing application. In
  Proceedings of the SIGCHI Conference on Human Factors in Computing
  Systems (CHI '11). ACM, New York, NY, USA, 2409-2418.
  DOI=10.1145/1978942.1979295 http://doi.acm.org/10.1145/1978942.1979295

This exploratory paper examines why people use foursquare, a manual location sharing application. It determines three major reasons why people do so - to gain points and compete with friends, to track their location as a form of a diary and to earn discounts and special offers from business venues that they visit. Emerging social norms and online identity management are also briefly alluded to in the discussion section of this paper.

Now, once you have all your relevant papers written up in this format, your annotated bibliography and by extension, your literature review is almost done. You copy the references to their rightful place at the end of the paper (References or Bibliography section)

Then, the final step is to simply integrate the few lines that you have written about each paper in to coherent paragraphs and voila, you have a very passable first draft of your literature review.

I hope this made a little sense of how you go about writing one. I can understand that writing a literature review for the first time can feel like a very daunting task.


Your CV should explain well what you have done in the past. Your SOP should be more future directed while also attempting to bridge the past and future. But don't think you just need to explain what is in your CV and neglect what you see as your future. Think about what you want to do and what you have already done that puts you on the path to achieving your future plans. So, yes, say something about your quantitative abilities and such.

People will understand that others may want to change fields for a variety of reasons. You aren't unique in that so don't dwell too much on it. Say where you want to go, what you've done to get there already, and how this program will help you even more. But put the focus on the future, and not just the program you are applying for, but beyond that.


Endnote: inserting page number at the end of the citation

You asked a slightly different question earlier (here) but this one differentiates your goal to separate the citation and page number.

I prefer to do as @Mark mentions in the comments, I add an endnote formatted citation for the author and year, then manually type in the page number. You can type field codes for the citation to list the author in-text by putting {jackson, 2017@@author-year}. Depending on the reference style you are using it might be appropriate to put the author, year, and page number before the quote, which you can do with the field code {jackson, 2017 @1@author-year}. Lastly, you can put a citation with just a page number by excluding the author and year from the reference (right-click or go to the "Edit & Manage Citation(s)" menu) yet entering the page number in the citation. If you know the record number the field code will simply be {#616@3}.

Here's a summary:

{Jackson, 2017 #615@1} turns to

  (Jackson, 2017, p. 1)

{Jackson, 2017 #615@1@author-year} turns to

  Jackson (2017, p. 1)

{Jackson, 2017 #615} said “quotations are important” {,  #615@1} turns to

  Jackson (2017) said “quotations are important” (p. 1).

Whether you insert the citation multiple times from Endnote, as long as you are referencing the same record you'll only see 1 reference in the document or in the manage citations menu. For example, I have a document with the all three combinations and it has 4 citations but only 1 reference.

The main reason why I manually enter the page numbers is the difference in citation formatting for page numbers. If I end up submitting to a different venue, thus changing the citation style in Endnote, I've had page numbers disappear. So I prefer to have a little more manual control over that aspect.


Acknowledgement of Submission of a Paper

Let me first state my strong opinion, and ask everyone to agree, that for an editor to not answer a request for acknowledgement of a submission in a reasonable amount of time, assuming they actually received your email, is inappropriate and unprofessional. Yes, we have probably all seen such behavior. I don't care that it happens, maybe even not infrequently; I don't care that editors are overworked, busy, tired, absent-minded, or that they are volunteers who are not paid for their services (note: unpaid, but not uncompensated, since they very much enjoy the prestige that comes with being a journal editor, and in many cases receive benefits such as a teaching reduction at their institution). A journal is a professional entity and needs to conduct itself professionally. If you are an editor, you signed up, voluntarily I assume, to perform a job, so there is simply no justification for not doing that job. So, repeat after me: not acknowledging a submission, especially when requested, is wrong. Feels good, doesn't it? ;-)

The point is that if nagging the editor makes them angry or annoyed, I don't see that as a problem. It is 100% the editor's fault that they are being nagged, not the OP's fault for nagging. And if their anger leads them to treat the OP's submission vindictively in some way (as the OP seems to worry it might), then that editor is an unprofessional loser, and their behavior reflects very poorly on the journal. In that case I would seriously advise the OP to consider not publishing in such a journal and seeking a fairer treatment elsewhere. (Also, as @user24094 commented, an angry response is at least a response!)

It's also important to note that mistakes do happen, so there is a non-negligible possibility that if you are not getting an acknowledgement then your submission was actually not received. That is why acknowledgements are needed in the first place! Here are two related stories that happened to me:

Many years ago I submitted a short paper to a good journal. I don't remember if I received an acknowledgement, but I definitely did not receive a referee report... until two years later, when an apologetic email from the editor came. He confessed with embarrassment that my submission had been on his desk that was stacked with lots of other papers so that he lost track of my submission, and that at one point my paper fell into the crack between the desk and the wall, where he now found it while cleaning up his office. (I guess in those days some submissions were not handled electronically.) To my surprise (since I myself had some misgivings about the paper and had given it up as being possibly unpublishable) he then added he liked the paper very much and would be happy to accept it, assuming I was still interested, which of course I was.
A couple of years ago I saw in my files a note about an old gmail account I had set up to receive email forwarded from an institution I had left several years before. I had completely forgotten about the existence of that account, so I logged in to see if there was anything important there. I assumed there wouldn't be, since anyone who is trying to reach me can just google my name to get to my current home page on which I list my current email address - right? Well, to my surprise, I found on the old gmail account a series of increasingly desperate emails from the editor of a certain combinatorics journal, asking me to referee a paper, then some months later asking if I had received the earlier email, then asking for an acknowledgement, etc.... What seems to have happened is that the journal had some kind of automatic system for tracking the email addresses of authors who published there (obviously a bad idea), and the editor was sending me those emails through the automated system instead of doing the sensible thing of just looking for my email address and sending me an ordinary email.

To summarize, my advice to the OP is to consistently nag the editor, including indirectly through any intermediaries you can think of (editorial assistant, managing editor, colleague at the editor's department etc.), every week for a few weeks. If you do not hear back after 2-3 weeks I would assume that the submission had not been received, write one final email in which you politely inform the editor that you are withdrawing the submission due to the lack of response, and submit the paper elsewhere.


What should one do if they've discovered a "breakthrough" but lack academia credentials?

I see a few approaches you could take (or some combination):

Write up the idea as a white paper and submit to http://arxiv.org (or something similar). This gets the idea documented, public, timestamped, and allows people to easily cite it.
Reach out to researchers in the field to see if they would be willing to help you form a scientific paper based on your idea. Not all professors are scary!
Submit to the industry track of a research conference if you have an industry background (if not, then maybe a workshop). Some conferences elicit papers from industry that can get your idea out there, generate discussion, and allows you to get feedback. These tracks are often less competitive and very open to non-researchers. For example, Software Engineering In Practice at the International Conference on Software Engineering


Open Access for journals : extent of the content remix (CC-BY) license?

Short answer - CC-BY is most common in OA generally but it's not
  ubiquitous, and you'd not be alone if you didn't use it.

It's certainly a topic of some debate. Generally speaking, humanities academics/journals are more concerned about it than the sciences (see eg the Royal Historical Society position. Concerns about commercial reuse (NC) are usually more common than about derivatives (ND).

CC-BY is by now more or less the standard in the sciences. Almost all all-OA titles that I've dealt with in the earth sciences & biological sciences use this as the default, though there are a small handful that use CC-BY-NC or CC-BY-NC-ND as their standard license (CC-BY-ND is rare), and a few that run on a more traditional "no license but we're always free to read" basis. I have seen CC-0 and CC-BY-SA papers but this is very unusual.

Hybrid titles (subscription journals with a per-article OA option) tend to have more mixed arrangements, with some offering only CC-BY, some a choice of CC licenses, some a generic "free to read" option, etc. Hybrid titles published by the major commercial publishers tend to have a one-size-fits-all license policy regardless of their subject matter.

Some numbers to illustrate this: in 2014 my institution published 93 CC-BY papers, six CC-BY-NC, and four CC-BY-NC-ND. Four of the NC(-ND) papers were in hybrid titles with a choice of license, the others were required by journal policy. As noted, this is a mix of publishing in the earth & biological sciences.

Meanwhile, much of the drive for licensing comes from funding agencies. These tend to either (a) require the CC-BY license (Bill and Melinda Gates Foundation, Wellcome Trust, Research Councils UK), or (b) not specify a license as such (NSF, HEFCE). UK funders have been more aggressive about specifying a fixed license than US ones.


Equal contribution noted in paper draft without prior discussion

How to handle an equal authorship appearing in the final paper draft which was not agreed upon in advance?

This can be tricky. I strongly suggest that you bring up your concerns with your advisor and figure this out together. The key point here is that you should be collegial, but if you believe the attribution is undeserving you should definitely be assertive and explain why. Your advisor should have consulted with you before making any changes to author contribution (this is something they should know how to handle), but given that they didn't, it's reasonable to bring up the topic.

I would not change things myself, I would not confront anyone aggressively. If you have other strong publications that showcase your independence then it may be better to let this go as the marginal effect on you is minimal. My experience is that these things rarely get turned back, but I may be mistaken.

  What are the conditions to equal contribution of authors?

Well, if the two authors have made roughly equal contributions. This is often hard to quantify. Here’s another perspective: the other person in your example, call her Alice, could say: “I implemented a complex algorithm that took effort and skill to do. All that ResearchNewbie did was run a few experiments using this algorithm. I could’ve gotten an undergraduate programmer to run them! Why should they be first authors?”

  What are the implications for the first author, if any?

It’s very important. You should show some degree of independence before you graduate. Graduates who have no lead authorships can be perceived as unready to be an independent scholar.


Can I negotiate a research assistant position if my PI moves to a new univerisity?

I think it is more than reasonable to ask for a "bump", but you may want to reconsider moving. The way I see it is you are currently in your 2nd year as a post doc and the move isn't for 9 months so at the time of the move you would be approaching 3 years as a post doc in the same lab. This is getting to be a long time and you do not want to lose the time associated with the lab move to move to a new lab for a year. You need to make the move to the new lab desirable enough that you want to stay for 2+ years. The reason you may want to reconsider the move is that you would be effectively doing 2 post docs in the same lab instead of 2 labs. This means less of a chance to learn new things (both technical and interpersonal skills) and meet new colleagues (specifically ones who can write letters of reference for you and help you get the next job).

If you chose to stay, the argument for a bump is that (1) this would effectively be your second post doc, and (2) you would be taking a hit in your research associated with the move and need additional support to over come that. The reason keeping you is advantageous to your PI is continuity and the ability to get started quicker. Finally there is the issue that the PI probably has a start up package so can actually afford a bump (both salary and resources).


Publishing on Scholarpedia: Experiences & feasibility (early career)

Also, what do you think about the feasibility and career value of publishing on Scholarpedia for a beginner researcher and scholar?

It sounds feasible enough, but the career value depends on your job and goals.  If you are aiming for a job in a research university, then research publications are far more important than survey/review/expository articles, and Scholarpedia would fall into the latter category.  Occasional high-value survey articles could help your career, and a Scholarpedia article might fall into that category if it got a lot of citations (but it wouldn't have the benefit of appearing in a prestigious venue, so you'd need some argument like citations to get hiring or tenure committees to take it seriously).  Writing lots of Scholarpedia articles would actually look bad, by giving the impression that you are taking time away from research to do that.

On the other hand, if the job you have/want is more concerned with active scholarly engagement than original research, then Scholarpedia might be just fine.

If you devote a lot of time to Scholarpedia, then you'll probably have to deal with questions like "What is Scholarpedia, and is it any good?" in your job applications or tenure case.  It's worth trying out this discussion with colleagues or mentors, as a test case for gauging how hard it might be to convince other people later.


How do I handle a mistake in a mathematical proof that does not invalidate the main conclusion of our paper?

The most important step to take is to contact the journal and tell them that you wish to publish a corrigendum to your article.
Journals have systems in place for making the existence of a corrigendum clear to readers who search for the original journal article. (So does MathSciNet, by the way—which reviews journal articles, not arXiv articles.)

When people cite articles, they cite the journal versions (when they exist, such as in this case). Therefore people who are reading a future article that cites your journal article will believe, quite reasonably, that they will be accessing the best version of the scientific record if they go to the journal article. A correction on a personal web page or the arXiv does not accomplish this important contribution to the scientific record, causing all kinds of problems (as user124672 mentioned in their answer).

user124672 also makes the valid point that publishing in a venue where somebody disinterested in the article has version-control power over the article (that is, editors of journals) is very important for establishing what is and isn't the definitive version of the article—which is again crucial for the scientific record. A corrigendum is the process by which an author can convince an editor to use their version-control power to update the definitive version in rare circumstances (and the rarity, and necessity for a disinterested party to agree, are features and not bugs of this system). Precisely because authors can update their arXiv and personal web page articles any time they want, such updates cannot ultimately be considered trustworthy in the careful, scientific sense.

By all means, also correct the arXiv version (with a clear explanation of what has changed), as well as the version on your personal web page—but only as supporting actions to the crucial one, which is to correct the scientific record by updating the journal article itself.

(One could imagine a world where later articles cite arXiv papers even when journal articles exist, and where arXiv has some structure in place to prevent frivolous author updates; in that hypothetical world, one could reevaluate the relative importance of the above steps. However, in our actual world, where citations are invariably to stable journal articles, I stand by the above statement.) (One can also reasonably criticize the limited-access and even financially predatory nature of many mathematical journals—I have done so myself—but that discussion about the optimal relationship between academia and capitalism does not alter the facts above.)


Error discovered in an accepted conference paper but not yet presented

Talk to your co-authors of course. But also talk to the conference committee and provide, or offer to provide, corrected copy. They may be able to help or not. But for the presentation, give the latest, most correct, version and note, if necessary, that the printed version has small errors not affecting the conclusions.

Some CS conferences will print proceedings and some of them will have a version ready before the conference. It may be possible that a second version, for general distribution, can differ a bit in details, but that is up to the conference and to the publication board of the organization sponsoring the conference.

But letting everyone know immediately is the best overall strategy.


Is the title Ph.D. or Dr. meaningless in the sense that anyone can use it?

I know a businessman who has received a LOT of mileage off of using "Dr" and "PhD" with his name

I don't know which country we are talking about, but at least in Austria, Germany, and Switzerland "Dr." is a protected title, and pretending you have one when you don't is a criminal offence. In Austria, for instance, this is part of federal law (see also the Bundesgesetzbuch). I would assume that PhD is also a protected title in the US and Great Britain.

However, note that this law explicitly only covers "pretending to have a doctoral degree", which leaves some wiggle room. For instance, there is an notorious Austrian bus company called "Dr. Richard", where the "Dr." are officially just the initials of the name of the owner (Dragan Richard).


How bad would it be to graduate with a thesis not able to show positive results?

While your advisor can probably help, don't misunderstand the purpose and process of research. It isn't making some unsupported claim at the beginning and then "proving" (dammit) that your claim was accurate. Research is a reach into the unknown. The answers you get depend on what is, not on what you want them to be.

You are actually seeking knowledge (truth), not verification. If the results of your research disprove your original hypothesis that is still a valid result.

If your "new" technique isn't actually better than the old, then it is useful (maybe vital) to know that.

In an ideal world you should be able to write that up. We hypothesized X. We used process Y to explore it. We found no evidence that X is true. That is still knowledge.

Hopefully, however, your advisor has such a view. And hopefully your process Y was sufficiently sophisticated that you haven't fallen in to easy errors.

If every hypothesis came up with positive (supporting) results, we wouldn't be working very hard and only making trivial initial hypotheses.

But, start out with "what is true here" rather than "this is true and I'll beat it until it yields". That leads to propaganda and isn't research. It is often the basis of misconduct. Tobacco and pesticide "research" too often fall into such errors.

So, it isn't "bad" at all if you reach truth.


Is it okay to publish my thesis when it was done 2 yrs ago?

Is the information offered in your thesis interesting?
Useful?
Original?
Previously unpublished and not known?
Pertinent to the subscribers of the journal to which it is to be submitted?
Would the visibility of the published work be useful to you, professionally?

Now none of those questions have anything to do with how long this work has been sitting around (like for 2 years).  If all of the answers to those six questions was "yes", what reason in the world would there be to not publish?

Even if it was, say, 4 outa 6 "yeses", why wouldn't you publish?

There was some things I did in grad school that I thought was crap, yet I was encouraged to submit to publication (and I didn't).  So, Sofia, you need to look at the content of your thesis and ask yourself if the work has value, if someone else reading it will find authentic value in it.  And you need to make some attempt to evaluate its novelty (but don't worry, the reviewers/referees will let you know if there is uncited previous published work).

I can't think of a reason in the world where, if the content would otherwise be worthy of publication, that the two years would make any difference at all.


Rules for affiliation for student doing unpaid research in his/her free time?

I don't think there are any "official rules".  (I can't even find a clause in my employment contract that officially requires me to list my university on my papers.)

But as long as you are a student, it's a good idea to list your university as an affiliation.  Even if the university isn't paying you, you do benefit indirectly from the intellectual environment and resources that the university provides: professors, fellow students, library, internet, health insurance, nearby coffee shops, and so on.  It costs you nothing to be generous.  Also, for better or worse, readers will take your paper more seriously.


Big caveat up front: many people struggle A LOT in their early graduate school career, and this doesn't mean that you can't be successful. A better guide to whether you should switch to theory might be whether or not you find the day-to-day process of debugging your experiments satisfying - even when it fails a lot of the time. (Also, if you like programming much more than being at the bench, that's another good sign for switching.)

If you are early in your career (first couple of years of graduate school), switching may be relatively easy, especially if you want to stay in the same university and department/program. I certainly knew many students who changed advisors early, though relatively few switching theory/experiment.

In general, I would suggest looking at prospective advisors, and talking with their current students to see what you'd need to know, and finding out if they would take students. Classes are useful, but most advisors will have their own recommendations for which are most important. Even beyond your own skills, other factors like research funding, will be critical in which advisors can accept you. Also, personal fit with an advisor is just as important as research area. Because of these points, it is probably better to figure out what group you want to join first, and then see what courses you should take.

I would also recommend that, if you have strong computational skills (programming) and a good physics/analytical methods background (i.e. good grades in core courses or other evidence of this), and are interested in biophysics, there is no need to limit yourself to systems biology / biological networks. There are a lot of computational biophysics topics out there, ranging from bioinformatics, protein interaction networks, computational neuroscience, biomechanics, molecular dynamics, etc., and if you have evidence of flexibility and learning a lot of different skills, you could be considered by groups focusing on topics further away from your past experience than you think.

All that out of the way: for a biophysicist with an interest in theory, other courses that are worth it are things like statistical mechanics, especially something focusing on non-equilibrium statistical mechanics. That could be in chemistry/chemE departments. Within network fields (which I know less well), you might want to infer network structure from data, which means there may be some statistics or machine learning courses that are worthwhile. For biomechanics-related theory, a continuum mechanics class (elasticity theory/hydrodynamics/etc) might be worthwhile.