text:
Paper rejected. Should I appeal against biased reviews?
I received a rejection letter from a relatively high-impact journal based on the feedback from three reviewers. After I reviewed their comments, I feared that their comments were biased and am not sure if I should appeal. The comments from all three reviewers are all negative, but one is more bias than the other.
The first reviewer said that I need to carry out a lot more experiments that will involve a lot of cost, which is not practical. However, in the comment, they only suggested one additional experiment that needed to be done. The second reviewer complained about the quality of the figures, but I think they are fixable. The third reviewer complained about the novelty of the paper but I think they did not carefully read and understand the paper.
Is it still possible to write an appeal if all three reviewers were negative about the paper since their reason to support rejection wasn't strong?

I'm afraid appealing the decision will most likely be a waste of time. Some, most, or all of the feedback you obtained this time around is probably useful, so use your energy on strengthening the paper based on the feedback you obtained. Also, the editor and/or associate editor at the journal you submitted to may not truly appreciate your contributions, so do some soul searching about where a more appropriate venue will be for your paper.

What if I encounter the same sets of reviewers in the other journal? If the Reviewers don't like it for various reason, they can always find hole in the paper. How can I improve the chance of being accepted?

@user10694 Fixing the problems the reviewers pointed out will improve your chances of acceptance. That's the usual response to a negative review.

I find it interesting that people underplay the realities of bias and prejudice in paper reviews.  We all know it is unfortunately widespread in employment practices including hiring, firing and promotion. However we pretend it is unheard of in paper reviewing.  How many court cases are there for unfair employment practices based on racial,gender, sexual orientation bias every year?  Much of the advice here is really no better than "Take it on the chin. There is nothing you can do about it."

@felix ... based on racial, gender, sexual orientation bias. The problem with your logic, is that the reviewers do not know the OP personally. So, why prejudice against him? Isn't logical to assume that the paper was rejected because it was not good enough, instead of thinking that they rejected it because the OP was poor / ugly / unknown etc...

@Alexandros We have no idea if the reviewers know the race, gender or sexual orientation (or other relevant attributes) of the author do we?  I find it perfectly plausible that they would know or be able to guess at least some of these however. For a randomly chosen example it is a reasonable guess that the reason was innocent. However there will be many cases where it isn't and the system should be able to address those.

@felix I think what the answers and comments are responding to is that the OP says he/she got a biased review, then goes on to describe some very standard run-of-the-mill negative reviews. The community response would (I think) be very different if the user had given a reasonable explanation as to why he/she thinks these specific reviews indicate some kind of bias.

This may not be what you want to hear, but maybe you are biased and not the reviewers. The fact they all seem to agree on rejection can be an indication to that, though the fact that all reviewers seem to have issues with different aspects of the manuscript makes it less likely.

@ff524 That is a fair point. I think I was answering a more general question than the one the OP posed.  However the general concern still remains that there is no established way to challenge bias in reviews or reviewers for many conferences (and to a lesser extent journals too).

@felix: The best way to remove bias would be to double-blind reviews, where neither the referee nor the authors know "who's on the other side." It would make it hard to practice bias based on who the author is—you only have the material in the paper to work with. That makes outright bias easier to spot.

@aeismail  Yes. I believe experiments have been done to show the difference you get in results for accepted papers between blind and non-blind reviews although I don't have the reference to hand.

@user10694 Biased against what? (Your gender, ethnicity, country, academic position, topic of research, particular approach to topic, ...?) Otherwise word biased makes little sense. Bias (see Wikipedia) is not a synonym  of negative. So please, either expand or remove word bias from this question.

@Fomite's answer is spot on. I would like to expand further on the differences between a biased review, a lazy review, a significantly erroneous review, and a negative review, and which do/don't warrant an appeal.
The examples given in this post come from a contest held by the always-excellent FemaleScienceProfessor. Quite a few are real reviews, or based on real reviews.
Biased Review
Does warrant an appeal, if it's the reason your paper was rejected. Often editors are smart enough to identify a biased review on their own, and will simply discount its advice.
Example #1 (here, the reviewer clearly lets his personal goals get in the way of a fair review):

I am afraid I cannot support the publication of this paper. The authors present an idea that I myself have had for some time and just haven’t gotten around to writing it up yet. I think that when I write my paper, it will be better than this one. These authors would be well advised to wait until my paper is published, and then they can cite it.

Example #2:

Since the author is a woman, I had lowered my expectations accordingly, but the author did not even meet those. Even though I have never done experiments in my life and have never used any of these techniques, the experimental results presented were completely misinterpreted in my distinguished opinion.

Lazy Review
Does not warrant an appeal. If all of your reviewers give you a lazy review, you need to do a better job exciting the reader (thereby motivating the reviewer to carefully read the whole paper in detail because it's such compelling reading.) (Very rarely, this can be an indication of a bad journal/conference and you should find a better place to submit your work).
Example #1:

The topic of this paper is not of critical importance to furthering knowledge.
Sent from my iPhone

Example #2:

Paper Title: Linear and Nonlinear Methods to solve XXX
Review: "Why is the approach limited to linear methods, and the author does not propose nonlinear methods?"

Significantly Erroneous Review
(per JeffE's suggestion)
This is a distinct case from the Lazy Review. It does not include the case where the reviewer "erroneously" concludes that your work is not interesting or useful, just because you disagree with this conclusion.  It does not include the case where the reviewer says "I am concerned about X" and you believe you've adequately addressed X.
It does include cases where a review is affected by a significant factual, logical, or mathematical error.  This is grounds for appeal.
Example (the reviewer is mistaken as to the meaning of "graph" here):

Paper title: Graph analysis of System ABC shows differences in A-B connections during Condition X vs. Y
Review: This paper uses a novel method to study ABC system dynamics. However, I don't know anything about graph analysis so I'm going to interpret the paper through the lens of a different analysis method I do know something about. Thus the only constructive feedback I can give is that this paper is a poorly written explanation of a structural equation model of XYZ - the conclusions drawn make little sense given the data, i.e. they frequently refer to "graphs" but all I see are these pictures of circles and arrows.

(A minor error is highly unlikely to be the reason for a rejection. Therefore, for a minor error, an appeal is not likely to be successful - an appeal will be useful only if the point of appeal was the reason for the rejection. In the case of a minor error, I would advise to use the reviewer's mistake as an opportunity: to clarify in the text points that might lead people to mistakenly discount your results, or even to decide to ignore the criticism because it's not a common enough misconception to be worth addressing in the paper.)
Negative Review
A review that does not fit into the above categories, but still criticizes your paper, is just a negative review. It is not grounds for an appeal. It should be taken as constructive criticism, and you can use it to make your paper better.

@Cohen I can't take credit for the hilarity - the examples come from the FemaleScienceProfessor contest mentioned at the beginning. I will happily take credit for recognizing the hilarity and sharing it with you, though :)

Yeah, I realized that just a few seconds ago, but you do deserve credit for recognizing and sharing it. Thanks for making sure I knew the source!

There are also uninformed/incorrect reviews, where the reviewer is simply mistaken.

@JeffE Certainly. I would include those in negative reviews - no one said "take as constructive criticism" means "apply the changes the reviewers suggest." it can also mean "clarify in the text points that might lead people to mistakenly discount your results" or even "decide to ignore the criticism because it's not a common enough misconception to be worth addressing in the paper."

But uninformed reviews are reasonable grounds for appeal, unlike informed but negative reviews.

@JeffE Thanks, on further research I agree and have edited the post to include the "Significantly Erroneous Review" category

I had example #1 in your "Biased Review" section when submitting to a prestigious conference and the paper was rejected.  I then submitted the same paper elsewhere and the same reviewer reviewed it again.  There needs to be some sort of appeal system for conferences as well as journals.

@felix I've submitted to a conference with an author response phase, which can be a nice thing. Suggest it to your friendly local conference sponsor. Though I don't know how one might "respond" to Biased Reviewer #1  :)

@ff524 That does seem like a nice innovation. I hope it becomes more widespread!

First, I think the biased review can be easily discerned but not always explicit. The reviewers are smart to achieve their hidden motive by finding holes in your paper or purposely distort what you stated in the manuscript. For lazy review, why would the reviewers volunteer for the reviewing topics/abstract that they are not interested in the first place?

@user10694 The reviewers are smart to achieve their hidden motive by finding holes in your paper or purposely distort what you stated in the manuscript - do you have any reason to believe this is their motive? If it's so well-hidden, how do you know and how do you propose to convince the editor in an appeal?

@user10694 For lazy review, why would the reviewers volunteer for the reviewing topics/abstract that they are not interested in the first place  (1) they were interested on reading the title/abstract but then you failed to hold their interest with the actual paper (2) pressure from editor (3) it's a student and advisor said "review this paper for me" (4) etc. (many possible reasons)

Hilarious examples! Bet you have seen/written a couple of reviews.

You seem to be conflating "Bias" and "Negativity". Bias would imply that your paper was being reviewed unfairly, either because of its content, or its authors - if they were known or divined by the reviewer.
It's entirely possible, and fairly standard, to get negative reviews you disagree with. When it comes down to it, your paper was rejected, and the only time I've ever seen appeals to the editor work is for things that are flagrantly egregious and wrong, rather than just "This is weak and I disagree with it". And even then, it's usually a long shot "What's the worst that could happen, they say no again?" play.
I suspect your time would be much better spent addressing the comments of the reviewers within the paper and revising it, rather than appealing to the editors.

+1, good response. Especially insightful: "You seem to be conflating "Bias" and "Negativity""

What constitutes bias? If the reviewer did not read the paper and gave negative comments, that is bias and that is exactly what is happening to me.

@user10694 That's not bias - again, that's negativity, and you don't know the reviewer didn't read the paper. Bias would be something like the reviewer knocking a paper because it didn't come from their lab, or a friends lab, or because "all theory papers are terrible". Not just "I didn't like it".

If the reviewer read the paper, why would one of the reviewer get confused while two others don't?

I'm sure I've read similar advice on this site, but what I've come to believe is that if someone didn't understand your writing, it's because you didn't make it clear enough. The onus is the writer, not the reader. If you can determine what it is the reviewer was confused about, write it more clearly and try again elsewhere.

What I'm saying is that the reviewer simply ignore the statement in the manuscript. For example, if I mentioned "something" in the manscript, in the feedback he said he did not see that "something" I have written.

Then maybe you need to make that "something" easier to find. A poorly organized paper is a valid reason for rejection. I concur with the others: forget about repealing, commence your revising.

A big +1 for the first paragraph.  I had the identical reaction.

@user10694 if a reviewer 'didn't understand' your paper then under most circumstances it is more productive to assume that the fault is with you: you wrote the paper poorly, so that an expert could not understand it, revise it and emphasize the parts they missed.

I generally agree, though (without changing the conclusion referring to what to do in the OP's situation) I'd like to remark that reviewers reading the paper sloppily/incompletely and then stating the lack of a definition for X (even though there is an explicit definition in the paper) as a negative point does happen. It is easy to claim the paper was not properly structured, but while in the age of full-text search that is already a poor excuse for not finding a literal definition, it usually shows throughout the whole review in such cases that the respective reviewer did a rather hasty job.

The second reviewer complains about the quality of the figures, but I think they are fixable.

You fix the figures and then re-submit. Not a problem.

The third reviewer complains about the novelty of the paper but I think s/he did not carefully read and understand the paper.

You write to explain why you think your paper is novel. You might still have a chance.
Now,

The first reviewer say that I need to carry out a lot more experiments that will involve a lot of cost, which is not practical. However, in the comment, s/he only suggests one additional experiment that need to be done.

In my opinion, this is a strong reason for rejection. I think the reviewer has doubts about the results you have in the paper. You truly need to do more experiments to convince the reviewer and other readers the results in your paper are correct.
My suggestion is to do more experiments before you consider the appeal. Not only you want to convince the reviewer but also yourself that your paper is good. You don't want to publish a bad paper, do you?

well, I think the first reviewer just blow the negativity out of proportion. If there were so many experiments that need to be done, why would he/she only suggested only one experiment. Also, why would he/she concern about the costs of the experiment?

Do this one suggested experiment as proposed, maybe this will be enough if you also fix all other issues.

@user10694: Also worth noting: you don't necessarily have to do even the one suggested experiment, if you can come up with a different experiment that better demonstrates the same point. (This happened to me with my first paper: a reviewer suspected that the stability of the steady state I claimed was merely due to insufficient simulation time, and asked me to run the simulations for a longer time. The editor, however, instead suggested simply showing that the steady state was attracting, which would imply stability; I did that, and the paper was accepted.)

About point 1: In my experience, there is usually an alternative to further experiments: give an honest discussion of the limitations of the study. As a reviewer I'm usually perfectly OK with a not-so-great study as long as the authors are clearly aware of the limitations in terms of conclusions that can be drawn - in my field, noone can afford all the experiments one would like to do and we're all aware of that. But papers that, say, claim to rescue the world after having compared a single patient with one healthy volountary member of the author list raise  very red flags.

In my field, you don't resubmit to the same journal after a rejection, even if you've fixed figures and such.

Short version. Do not do it.
Long version: You have to understand there is something wrong with the paper. One negative review might be unlucky / unjust. But three negative reviews?  That means that the paper needs some serious fixing before re-submitting again.
The other possible problem with your paper might be that you are aiming too high. Maybe your paper is actually good but not good enough for a high impact journal. That would also explain why the third reviewer just "brushed off"  your paper without really reading it. Your paper simply might not be interesting enough for such a journal. This is a phase that many researchers have in the beginning of their research. Living in our research "bubble", we believe our research and results are amazing, when simply they are not. It takes some research maturity to actually understand the real "size" of our results.
Also based on your previous questions on this forum and your problems with your advisor it is obvious that you lack guidance. You are simply not objective enough to judge the merits of your research and you need someone "wiser" to judge your work hard but in a fair way. But please humble down. Do not start a war with the world. Your advisor was "bad" and you had to fight back. Now the reviewers are bad? This is really not happening. Just improve your work, your presentation of the work and if your work is good enough it will be published accordingly. If it is not published, it is nobody's fault but yours. You should at least start considering the possibility that you might actually be wrong and the reviewers are right. After all, they are more experienced than you.

I suspect that the reviewers are responding to an unconvincing paper. A paper that does not convince them. While you have not reported evidence of their bias (or explained the reason that you suspect that they are biased), I find myself somewhat biased by the quality of the English used in your posts.
If the language in your paper, matches that in the posts, then it is unlikely to convey a convincing presentation of your research - however good the research might be. If you think this is a contributing factor to the rejection (or is responsible for the bias), then the best approach may be to enlist the assitance of a Technical Author or Technical Translator, to help you turn your paper into a convincing one for an English Language publication.
Alternatively you might find it easier to publish your research in a different langauge journal.
Please understand that I'm observing, not criticising. Your English is much better than my own efforts in any language other than English.

One thing I haven't seen commented on in the other answers or comments is that if you appeal claiming that their review was biased, you're poisoning the well -- you'll have accused three known and (presumably) respected reviewers of unprofessional conduct. If they didn't dislike you before this, they'll certainly have cause now.
From what you're saying, this seems to be your first submission and you yourself admit that at least some of the objections they have to your paper are fixable. Try fixing those and resubmitting. Don't start throwing around accusations of bias until you have a clear pattern, or you'll quickly develop an unwelcome reputation of your own.

You don't need to have a clear pattern of bias—you just need clear evidence. Moreover, an appeal on bias grounds would in principle be anonymous—the editor would ask for an additional review.


text:
Maintaining a Public Handbook: Collaborative editing, online viewing, plus good-quality PDF output?
This is a question for anyone who has had to maintain a set of guidelines or handbook which might be fairly long (book-length) with multiple sections. The ideal case would be a system where revisions can be suggested, but not immediately viewed by end-readers of the handbook. After approval, suggestions would be reflected in the handbook. Using this model, the handbook could be collaboratively improved over time. From what I can tell, systems like GitBooks and some other tools built for software documentation have these capabilities.
However, as a handbook rather than code documentation, it is also important that you can dump the whole thing into a reasonable, readable form such as a PDF that can be shared. Unfortunately, this second requirement seems harder to find in the collaborative space. While GitBooks meets some of the first criteria, I was not impressed with their PDF's (some failed to generate, other projects had images broken up across page breaks). One could theoretically do this with scripts and Google Docs or a Wiki (e.g., people edit willy-nilly on drafts of each section, where a script copies those into a single master document for new releases).
I am hoping that I am missing something though, and that other people have found good solutions to this problem. So then, what strategies have people tried for maintaining handbooks that should be updated through suggestions or community collaboration which have these characteristics:

Collaborative: People can suggest revisions that can be merged in (e.g., via track changes, change requests, etc.)
Reviewable: Changes are not immediately applied to the public handbook, but are stored separately for review and approval.
Single File Export: The whole handbook can be exported in a reasonable single file for reading, such as a PDF or similar document. This document should be reasonably formatted (such how LaTex works) rather than look like you took a single-page HTML file and pretended that is readable as a PDF export.

You can store raw latex files in a GitHub repository to allow collaborative editing, version control, track changes, etc. The drawback is that only people quite familiar with Git would be able to contribute.
Then, there are some online tools able to generate PDF from latex sources stored in the GitHub repository (e.g. LaTeX.Online). I haven't tested it myself, but it seems like it allows you to create single link which compiles the source every time you visit it and outputs PDF file.
Alternatively, you could set up a GitHub Actions to compile a source code to a PDF file (e.g. after every new commit in the main branch) and upload it somewhere for online viewing. In the link attached there is a suggestion to use additional branch and GitHub Pages to allow online viewing of the compiled document. While it may require quite a lot of work to set everything up and working, once done whole process of compiling and updating would be fully automated. This is the way I would personally recommend - compiling would take place on the GitHub servers and user would always have ready and compiled PDF file available for viewing.

I would only add that to those less tech savvy, git + some WYSIWYG editor for whatever files they have to work on is a workable solution, long as those files are "dumb" enough to not trigger a barrage of replacements each tiny diff. Markdown format looks fairly reasonable for this purpose but I haven't personally used this setup yet.

I think that the barriers for having people need to understand Git would likely be too high. I could do some scripts that scrape something and put it into Git for the purposes of generating something else though via Github actions (and for versioning). For example, a CMS-driven site where people could edit freely (draft) like a Wiki, which then has some approval process to dump that to Git and publish to a non-collaborative release + PDF.  Though at that point, one wonders if there's just a CMS that can tackle the extra steps well.

source: Stack Exchange

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/

sort: votes


text:
How to cite my own report that hasn't been published?
I wrote a research paper in high school in the field of lasers and optics but did not get published. It is on the internet open for anyone to read. How should I go on citing this? I want to refer to it in an application where it asks me to cite all works I have been a part of.

I'd say, if it is on the Internet, it's published. It's not peer-reviewed, but that's another point.

Exactly the same way you'd cite something miscellaneous written by somebody else. If it is on the 'web, give the complete URL (and see if you can make sure it won't go away, stash away a personal copy for safekeeping).

If you create a profile on researchgate you can upload your work and it gives you a citation. It also gives you your own personal dio code so that you can cross reference your work with other sites. This is what I have used. Here is the web site: www.researchgate.net
Additionally you can also create a google scholar profile sync your work from researchgate and it automatically gives you a citation.

Sorry if this is a stupid question -- what's a dio code?

I think he ment DOI code. It's a special hyperlink used for scientific papers.
That being said, I would not recommend researchgate. Many people view it as the Linked-in of academia, and reserve a special kind of hate for it. The arXiv is a much more universally-liked platform.

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/


text:
Manuscript submitted to Crelle's journal without acknowledgement
I submitted a manuscript to Crelle's journal about a month ago but never received a confirmation email from the editor whom I emailed the manuscript. I sent him/her another email asking about the status of paper and never heard back. I was wondering if that is a common and that is how it works with them.

I don't have any direct experience with this particular journal but giving them a ring might help to clarify things. You may also want to e-mail other members of the editorial team.

I'm marked this as duplicate because I think the key elements of your question regarding communication and common practice, is answered in the linked canonical answer.  If there are more specific things that you want an answer for, please feel free to edit to focus on them and the question can be reopened.

I have dealt with Crelle's journal recently.  Some advice: I suggest submitting to the managing editor (he has a secretary).  If you've gotten no response at all after about a month, you should resubmit to the managing editor.  Whenever I have done this, I have always gotten a timely something in response....although strangely, almost every time the immediate response is that their office is unoccupied for a certain period, which can be about three weeks long!  But then they do always get back to me in a contentful way within a month.

@PeteL.Clark just emailed him and briefly went over my case. Received an email almost immediately saying  that he is "out" of office and he will be back on September 5th. I guess I am going to have to wait. Knowing the quality of my manuscript, submitting to Crelle's might be aiming too high and I am thinking the sooner I know about the fate of my paper, the better I can decide for my next move.

@BigM: You got the same message that I've gotten several times.  I would take it as a sign that things are back on track.  You have to be patient in dealing with journals....basically with all reputable math journals.  Notwithstanding the fact that seemingly no one is ever in the Crelle editorial office, I have found that they do their business rather well.

Finally the got back to me acknowledging the receipt of my manuscript. Now I will have to wait and see if the designated editor likes my paper.

@PeteL.Clark a side cliché question. Do they have a very long review process? My manuscript is very short.

@BigM: I have only submitted two papers to Crelle in my life, so the sample size is much too small for me to meaningfully address your question.  Moreover, almost any mathematics journal could have a long review process depending on the referee you get.  Most of the exceptions are actually very poor journals.

@PeteL.Clark after a few weeks I received a rejection letter from Crelle stating that the result wasn't strong enough. I managed to improve the results and rewrote the manuscript which of much higher quality now.I dared to submit it to Acta Math.if it will take them several months to referee the manuscript so be it. At this point I don't mind gambling.

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/


text:
How to acknowledge a colleague's authorship of text in a syllabus
Here is a situation that I have been in several times, but have only recently begun to give careful thought to.  Suppose you are asked to teach a course that you have not taught before.  A fairly common practice (at least where I teach) is to approach the colleague(s) who taught the course most recently and ask if you can adapt their syllabus (on the grounds that reinventing the wheel is in nobody's interest).  In every case in my experience, the colleagues have freely given me not only their syllabi, but also their assignments, exam questions, and any other instructional materials that they used, and have given me permission to make use of them however I wish.
Of course being something of a control freak, I never use those materials without re-engineering them somewhat; like many (most?) academics, I feel the need to take ownership of the course by putting my own stamp on it.  But I do usually take large chunks of those older course materials and incorporate them into my own.  I suspect this is not uncommon (although maybe I am just wrong on this point).
It has only recently occurred to me that if one of my students did something comparable to what I do -- copy large blocks of text from somebody else's work and insert it into their own without attribution -- it would be a clear case of academic misconduct.  And I would never dream of doing something like this in a work that was intended for publication.  But somehow until now, doing this in a purely instructional context has always seemed innocuous.
So my questions:

How common is this practice?
Is it generally viewed as a form of plagiarism (and have I just been oblivious to something that should have been obvious to me all along)?
If one does make use (with permission) of a colleague's course materials, is there an appropriate way to acknowledge that?  For example, by putting an "Acknowledgement" note at the bottom of the first page of the syllabus?  At the very least, doing something like that would model good behavior for one's students.

What is a syllabus for you?  For me it's usually just a vague list topics I plan to cover in each week.  Also, how much originality is the course design?  I could imagine this being more appropriate for interdisicplinary courses or courses covering state of the art research than a run-of-the-mill calculus course, say.

It depends a lot on the course. The one I am thinking about right now is a Masters-level math education course; the syllabus is 10 pages long, and includes a 600-word section on "Course Purpose and Goals", plus detailed descriptions of the assignments to be completed in each of the four major units of the semester. Those are the sections where I have made the most liberal use of my colleagues' text.

On the other hand when I teach a Math content course, the Syllabus is usually only about 2 pages long, and more closely matches your description. I suspect that there may be a disciplinary distinction here; Education courses (in my experience) tend to have long syllabi that resemble white papers.

I tend to take the point of view that a syllabus is a sort of "corporate work" whose "author" is the department as a whole, and as such it's not necessary to credit the contributions of specific people. Should you want to take individual credit for it (e.g. when applying for promotion or a new job) then the onus is on you to show which parts are your original work. I don't know whether everyone feels this way, though.

This sort of practice is quite common, and documents of this type are often treated as the "community property" of a department.  This is a lot like authorship on a community wiki, where there is no expectation that the document is the original work of any author and there is the expectation that further authors may freely modify and contribute more text.  It is therefore not plagiarism to use your colleagues notes as a base, any more than it is plagiarism to contribute to a Wikipedia article.
Often, these documents have no copyright or authorship markings, and are simply handled by custom and tradition.  If you want to make the collective agreement more explicit and remove any doubt for those that come after you, then you should probably select a creative commons license (like CC0 or CC-BY) and put a small marking to that effect in the header or footer of the document.  If you choose to formalize it in this way, however, you should explicitly get your colleague's consent as well, because you are moving the document beyond the informal method of relationship-based exchange in which it was given to you.

This answer (and that of @user1258240) essentially confirms that my long-standing attitude to this was correct and I shouldn't be worried about it. But I still wonder: Do you think students view these documents as having "departmental authorship"? Or do they think the person whose name is on the syllabus is its author? If the latter, I worry that we may be unintentionally modeling very bad academic behavior.

@mweiss That's a very good question... and might be a good new question to ask to specifically get the student perspective.  I know that as a student I never even thought of the question, but that doesn't mean others don't...

I disagree. In my experience syllabi were never seen as handed down to the professor by the department. No two syllabi were the same. If students saw the same syllabus across a department with only the topics changed for the specific course, then I'd agree that it's the property of the department, but they don't. Because each syllabus is unique, it's disingenuous to present "your" syllabus to the students for "your" course without a citation. This seems to me like we're making excuses to feel better for following tradition instead of ethics.

My point is that many professors do not present a syllabus as "their" course, but rather as "the department's" course, which they happen to be in charge of teaching for a particular semester / section. There are other instances where this is definitely not true, but it's entirely within the realm of reasonability for a group of colleagues to choose an informal "community property" approach to the authorship of course materials, especially for long-running core courses of a curriculum where year-to-year consistency is desirable.

It is an extremely common and very accepted practice to copy other people's courses in their entirety or partially, with or even without asking for permission. At least in my field (computer science) people often put course material online with the intention of letting others use them freely. Unless explicitly written otherwise on a course website, I usually assume that it is ok to use any freely available material from there. Of course if someone actually gives you the material then there's no problem at all.
There is a big difference between journal papers, the sole purpose of which is to present new knowledge, and courses, where the goal is to teach known material to students. In the first case there is always a claim of originality, and if you are copying other work you are therefore commiting plagiarism. In the latter case, as long as there is no implicit claim of originality there is no problem.
People still like to be credited for their work, though. So for the sake of honesty and also giving credit, I usually tell my students where I got any significant part of the course material. If my course has a Web page, I state my sources there as well, and provide links to relevant notes or course Web pages when it's possible.

I think that even when one has permission to use the results of someone else's efforts, a word of thanks is always appropriate, and perhaps a reference to a URL or such. This also does set a good example for students.
For that matter, even if "the facts" are 100+ years old, as often happens in mathematics, insightful presentations are not automatic... and deserve acknowledgement.
Analogously, even though some disparage Wikipedia, if one has literally used Wikipedia to obtain useful links, keywords, bibliographic pointers, I strongly believe one should acknowledge this. Be honest! Not only to give credit where credit is due, but to avoid false pretenses (to students, et al) about how the enterprise actually works.

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/


text:
Re-using text from a grant proposal in a paper (or vice versa)
I have a grant proposal that I'm ready to submit, and I would like to re-use a significant amount of the text (on the order of 5-8 pages) in a paper that I intend to submit to a journal for publication.  Is this considered self-plagiarism?
As I suggested in the title, I am also interested in the reverse direction of this.  Is it okay to take significant amounts of text from (e.g.) my own unpublished doctoral dissertation and use it in a grant proposal?
If this were an issue of paper-to-paper copying I know both of these would be clearly off-limits.  The key issue that I am wrestling with is whether the rules are different for unpublished works like dissertations and grant proposals.

Just to be clear, I'm not talking about just a couple of paragraphs here, but something like the entire lit review section or the lion's share of the theory section.

Copying proposals to papers: I am sure many have not thought about this but many have copied material to and from proposals. Copying from a proposal to a paper should not be a problem since a proposal is normally not a publication and I have never come across a funding agency that claims copyright on proposal texts sent to them. If anyone knows of exceptions, it would be very interesting to know how they handle proposals. Taking the idea to the (silly) extreme one could argue that copying what you write in a notebook to a computer-written manuscript is self-plagiarism. The key lies in what sources are considered published and which are not.
Copying papers to proposals: Copying from a journal paper to a proposal should normally not be a problem either since the proposal is not a publication and not something that should be distributed. But, the journal text may be subject to copyright so it makes sense to see to what extent one might infringe on those rights by copying text to  a proposal. I doubt any journal would care much (or indeed find out) as long as the proposals are not made public. Since most application processes are very strict and reviewers are not allowed to disclose materials (some actually ask you to physically destroy any printouts) I doubt there is a problem but strictly speaking this may indeed be a grey zone.
EDIT: I will add a definition for self-plagiarism: Copying material you have previously produced and passing it off as a new production from the site plagiarism.org. From this perspective the question becomes, is one trying to pass of the copied material as a new product?

I was thinking of this less from a copyright point of view than from an ethics perspective, but I appreciate the input.

If you own the copyright on the journal article, the details in the second paragraph shouldn't be an issue, either.

I can't really get behind this answer, since (as I wrote in mine) I've been shown examples of grant proposals which were rejected due to plagiarism.

one could argue that copying what you write in a notebook to a computer-written manuscript is self-plagiarism – that's why I prefer the term "duplicate publication" over "self-plagiarism".

As in your comment on PeterJansson's answer: there are two different issues, namely, the literal copyright business, and then also "ethics". The copyright aspect is quasi-objectively decideable.
So, suppose there's no copyright conflict. The "ethics" issue still needs clarification. First, there's the idea of accidentally or intentionally double-dipping in terms of getting two status-credit-points for just one thing. That's the main external objection to "self-plagiarism", as opposed to plagiarizing from others. A grant proposal scores no status points in my world, so that element of ethical problems seems not present.
It's true that an over-the-top notion of self-plagiarism would seem to dictate that one is never allowed to re-use anything one has written, no matter what. I can't agree with this, even at the level of work done for courses, where I have very mixed feelings about declaring students cheaters because they re-use their own work to varying degrees. One objection I have is that this only really makes sense if either the university or instructor declares that it "owns" all the work done by students, or, worse, that the only point of the enterprise is in-the-moment... no accumulated expertise is re-usable? Odd.
Similarly, it seems to me that too often our thinking about self-plagiarism in professional settings is exaggerated, due to thinking of things as mostly pointless except for status/money-scoring aspects.
Srsly, we're not allowed to ever re-use bits of things "of our own" that have been polished a bit, etc? Start over every time? A very artificial constraint. For that matter, isn't most progress fairly incremental? Obviously... so it is perverse to require that everything be retyped every time, etc. And be sure to use different words... even if one took considerable pains with the earlier wording? Old effort must be discarded? :)

Summary:  Yes, you can reuse text from your own grant proposals because you
did not assign the copyright to the NSF.  The NSF states that proposals are the
property of the proposers.  A publisher could, in theory prohibit this, but that is unimaginable.
Going the other way—using material from a paper in a proposal—is less clear, but should also be fine.  See below.

The issue is not what constitutes a "publication".  That matters only for conferences and journals that refer to it in their policies.  For anything else—such as grant proposals—the important issues are (a) "copyright infringement" and (b) "self-plagiarism".  (I'll throw in regular plagiarism below, for context.)

Copyright infringement.  If you assigned copyright to your
(or someone else's) published paper to the publisher,
then you no longer own the copyright.  Therefore, if you use it in
your proposal, you may be guilty of copyright infringement.  However,
such use would probably qualify as "fair use" since it is
non-commercial and does not diminish the financial value to the copyright
owner (publisher to whom you assigned your copyright).
Yes, you could be guilty of copyright infringment, for using something that
you created yourself.  For example, imagine if a programmer at Microsoft (or
wherever) was paid $200K to write some code, and then took it and sold it on
the side.  Since they were paid to do it, it would be copyright
infringement.  If you have assigned your copyright to a publisher, the
situation is actually similar.
Takeaway:  It is best not to use work that was published as "archival" with
the copyright owned by a publisher, but even that would probably be excused
as "fair use".  This only deals with copyright (lawsuits), not allegations of
plagiarism (below).
Plagiarism.  The National Science Foundation (NSF) defines “plagiarism”
as “the appropriateion of another person's ideas, processes, results or words
without giving appropriate credit.” (45 CFR § 689)
This is separate from the issue of copyright.  Even if someone gives you
written permission, it is still plagiarism if you don't give them credit.
Self-plagiarism. If you submit your previously used text in a setting
that requires only original (i.e., first-time use) text, and you have not
attributed the original source clearly and dilineated the quoted text,
then you are guilty of self-plagiarism.  This depends entirely on the policy
of wherever you are submitting to.  For example, many conferences state that
previously used text can be used, if it was from a "non-archival"
publication.  Then, they (hopefully) define what "non-archival" means to
them.
The laws that govern the NSF's rules on research misconduct do not mention
self-plagiarism. (45 CFR § 689)

More information on the NSF's position and enforcement actions regarding plagiarism
is contained in this detailed report by the NSF to Congress (pp. 40-42).  Also, searching for
searching for unattributed text within the NSF site
reveals many examples of prior investigations by the NSF Inspector General.
For example, a professor was accused of copy-pasting text from a former student's dissertation.

This clearly addresses the "reuse of material from a a paper in a grant proposal" part of the question.  Does it also apply to the "reuse of material from a grant proposal in a paper" part of the question?

Yes, you can.  Clarified.

The 'right' answer seems to be field-dependent. In my field, mathematics, it is customary for phd students to convert any unpublished parts of their thesis into papers after graduation. This is not only  accepted, it is even expected.
I myself would have no difficulty reusing any amount of a submitted grant in a paper; I don't believe this constitutes any form of Questionable Research Practice, and I believe that that would be the opinion of my peers too. (The Dutch Royal Academy recently wrote a letter on reuse, which doesn't explicitly mention grant proposals, but gives guidelines for published sources that support this point if view; it takes 'false impressions' and 'harm to others' as central criteria, which exonerates reuse of material from your own grant proposal).
The best advice I can give you is: talk to the people around you, find out what they think.

Well, the operative question is not really whether this is called "plagiarism" - it definitely is - but whether that's a bad thing. After all, the intended audience of any given document you prepare might be okay with copying large sections of another work; if that's the case, go ahead and plagiarize all you want, nobody will care. But if the people who will be reading a document do not want to see plagiarized material, you'd better not do it, regardless of whether the document will count as a "publication."
From what I've heard, grant review boards generally fall in the latter category. There are probably some exceptions out there, but I've been told in no uncertain terms that plagiarism in a grant application will result in instant rejection, and perhaps even punitive measures such as a temporary or permanent ban on submitting any further grant applications to that funding agency. I've seen examples of proposals which were rejected because they copied as little as one paragraph, or one figure, from decade-old papers, despite the proposals having excellent scientific merit. The copying need not even be exact, so tweaking a few words per sentence from your existing writing doesn't make it okay (as is the case for plagiarism in general).
Bottom line: everything in your grant application should be written exclusively for that application, not repurposed from elsewhere, just as you would do with a published paper. Grant reviewers treat plagiarism much the same as journal editors do.
(And also: though this answer treats plagiarism in general, as far as I'm aware the same rules apply to self-plagiarism.)

But the question was not about using text from an extant paper in a proposal; it was about using text from an extant proposal in a new paper, or using text from an unpublished dissertation in a proposal.

@mweiss That directly contradicts the second paragraph of your question... but regardless, my point is that no wholesale copying is acceptable in a paper or a grant proposal. Even though your dissertation is not published (in the sense of being in a journal), it is a public document. It's available through your university's website, or on request from their library, right? So it is a source that you should not plagiarize from. Someone may catch it if you do. I guess if your dissertation is actually not publicly available at all, you might get away with it, but it still seems sketchy.

I'm curious about how the downvoters would explain away the examples I mentioned...

I did not downvote, because I appreciate the response, but my guess is that some people think the jump from "plagiarism in general" to "self-plagiarism" is too facile. I mean it seems obvious to me that using somebody else's words (even if from an unpublished dissertation) in a grant proposal without attribution is totally out of bounds. But using one's own words, from an unpublished source, seems (to me) entirely different. Do you know any examples where a proposal was rejected on those grounds?

@mweiss No, I don't. I think one of the examples I saw may have been self-plagiarism, but still it was from a journal article. (For what it's worth, I do not consider the distinction between a dissertation and a journal article significant when determining if inappropriate plagiarism has occurred, but I guess others think differently.)

As Mark Peletier wrote in his answer, in many fields it is expected that one will take chunks (whole chapters) of one's dissertation and publish them as separate papers. Nobody considers that 'plagiarism'.  Is it different in your field?

@mweiss Yes, that would be wholly unacceptable in my field, and would lead to rejection of the paper if caught during the review process, or severe disciplinary measures if caught after publication. The reverse sometimes does happen; people submit "staple dissertations" which consist of previously published papers with a custom-written introduction and conclusion, but in those cases the PhD committee has to approve it in advance. It fits with the point I made about the intended audience (here the committee) making the choice to be okay with "plagiarism" or not.


text:
How to manage theorist's "labbook"?
Question:
Are there any guidelines, sources, or examples of good practices for maintaining theorist's research notebook?
Motivation and context:
Maintaining a lab notebook is a much advised (if not a vital) tool for doing research. Many do that nowadays also in electronic form. While the methods for writing and maintaining a labbook might differ in details, in "dirty-hands" (no offense!) experimental, or field disciplines, the basics are relatively straightforward and clear. The advice tends to boil down to keep a labbook per single topic one works on and then record all the experiments and thoughts related to those experiments into the notebook. Simplifying a lot, in the end, the researcher (team) would compile a paper from the notes in the notebook.
Now situation of a researcher in a more theoretical discipline is strikingly different. Usually one engages in research on several topics at the same time. The problems a researcher works on are often intertwined and one's view on them changes over time, often merging originally separate streams of thought into a single one, or vice-versa. The work revolves not around experiments which would have a clear objective, but rather around currently prepared papers and then "a cloud of ideas". In summary, theorist's workstyle tends to be very non-linear. Maintaining some kind of a notebook is still a good thing, if for nothing else, then for not forgetting about stuff. My question is about how to go about doing it.
I am after a practical tool helping me to archive my thought process for long-term, as well as efficiently manage and keep an overview of the evolution of the several interacting topics I engage in.

You may be interested in answers to this question:  http://academia.stackexchange.com/questions/1085/software-app-for-electronic-research-notebooks/1089#1089

...and Non-linear note-taking software.

(Supplementing F'x's answer.)
Physical notebook
I use it all the time, as it is the quickest way to write mathematics and jot diagrams. It's low tech, so it's "always on" (e.g. I cannot run out of batteries).
I have one A4 notebook (so I take it anywhere), with removable pages.
I try to devote a single page only to a single project. On each page I note 3 things:

date,
title (or, actually, a pictogram) of the project,
"page number" for pages on the same project in a given day.

After some time (could be the same day, could be never) I take off pages, to fit them into thematic folders (and usually throwing away most of things, because they are "non-recyclable" rubbish; if it is "recyclable" then I scrap the important things, writing them on a new page).
However, such operation has trade-offs:

(+) sorted by topic,
(+) higher valuable content density,
(+) can be viewed "all at once" by putting pages on a desktop,
(-) I cannot take all of them anymore,
(-) it's somehow easier to loose it, unsort, or torn/coffee split/... it.

Electronic notes
Electronic content is much more linkable, searchable, easier to share, more polished etc. However, it takes much more time to write formulas or draw diagrams.
Different things work for different people, but some kind of personal wiki (or a well-organized text file system) seems to work the best.
I'm not settled down, but I'm switching from TiddlyWiki (very neat but requires a browser to run) to Gitit (so I can write in Markdown, with LaTeX inclusions, in any text editor).
I tried Evernote as well (and I'm using it for other content) but for highly-linked content it does not work for me.
See also:

How do you keep your research notes organized? - MathOverflow
Is there any efficient non-linear note-taking software?
Software/App for electronic research notebooks

I accept this answer and award the bounty because, even tough not as detailed as I hoped for, the material covered and the link to the MathOverflow advances my own current practice most (w.r.t. the other answers). Thanks.

Your notion about mathematics and diagrams, it reads like it is way easier with hand which is true in the sense it works faster, but LibreOffice's/OpenOffice's math support is really great. But then I thought you probably mean calculations and sketching things but the wording alludes the former aspect, imho.

@henry MathType is also a great option if you can afford it, and you can set up all sorts of shortcuts as well.

I cannot say that this is the perfect way to do it, but I'll cover how I do it.
Background on my perspective: I'm a mathematical/theoretical epidemiologist who came up not through applied math or one of the related fields, but through a circuitous route from laboratory biology. So, as far as I can remember, Science Is Done In Lab Notebooks.
A couple work patterns I've developed:

My lab notebooks are actually notebooks. I experimented with a Wiki for awhile, and just using something like EverNote, but I found they didn't work for me. They didn't capture the same feeling of permanent documentation, and freedom of notation. So now I use notebooks from Black and Red. Mainly because the generic black-and-white composition books remind me too much of undergrad.
Like wet-lab science, I keep one notebook per topic - but to address your problems, I tend to broaden the topics. A particular focused project (like something I'm being hired to consult for, or a one-year RA, etc.) gets its own notebook. Projects involving the modeling of a particular type of disease all get a notebook. Side projects involving a different aspect of theory...you guessed it, get a notebook. I've also got a small notebook that is literally "random musings and paper ideas". So rather than one lab notebook, I have several. These are identified in ways that are sometimes logical (a GitHub sticker on the very code-heavy project book) and governed by whimsey.
Always have the book out. Just like a wet-lab notebook, if you're working on a project, you should have the book out. Don't be afraid to write random musings. If you've done some math in your head, write it down. See also diagrams and sketches. Print stuff out and tape it in the notebook, just like one might do pictures of a gel or western blot. In the notebook currently on my desk, I've got several graphs, and even a printout of a question over at CrossValidated that makes up some portion of my thoughts at that point.
Reference yourself. Occasionally, as you've noted, ideas cross-polinate. I page number all my lab notebooks, so occasionally I will end up referencing myself. "See Lab Notebook X, Page 47."

Thanks for linking to the Black n' Red notebooks. I love that they state on their home page that their notebooks have "endless battery life".

First, the fact that you're asking the question is already a good step forward. Being a researcher is about managing ideas and data, and some researchers don't fully recognize it!

After a few years as a researcher in theoretical chemistry (all computer, no wet lab), I have seen pretty much every kind of notebook possible:

Single notebook documenting your progression linearly. I started with that, it hurt a lot.
No notebook, everything in files: put a 00README file in each topic/subtopic directory, then simply write in there to document your progress. In meetings, either type directly (if you have a mobile device) or write meeting notes then scan them.
Thematic notebooks (well described in other answers).

What you need is something that works for you. Draw inspiration from the examples above, the other answers, and try it! If at first you don't succeed, change the way you do, identify things that prevent you from fully using the workflow you set out to.
In particular, important factors to be considered are: how much do you travel? where do you work from? For me, thematic notebooks are a no-go because I work from the office, work from home, work from conferences, work from hotels and planes, work from vacation (I know, I know…). Thus, I can't carry around 5 or 10 notebooks.
To be honest, the combination I have seen used very efficiently (by me or people around me) is:

One single “take everywhere” notebook (I make it a Moleskine: because it feels special, it makes me want to write in it). Each lasts about a year. They are organized as follow:

at the back, few pages reserved for key information (important dates we set, strategic research decision, contact numbers for project leads, that very funny quote that had me laughing throughout an entire hour)

at the back, just before that: a few pages per project, with very high-level tracking of the progress (I write about one line or two per week, when the project is running). This allows me to remember

from the front: everything else, chronologically but clearly dated and labeled. Notes during meetings, notes about important stuff running and its analysis when it has finished running, etc.

everything else (long math derivations, paragraphs of text I started to write, full meeting minutes, detailed graphs): electronically

You can further refine: a colleague of mine uses small colored sticky index-tabs on the top of the notebook to index the content that turns out to be the most important (important results on each project, color-coded). I cannot force myself to do that, but I must admit that it really helps her access older information quickly.

This is a problem I struggled with for three years. My background is computational physics, and like you I have many active projects at any one time. My work involves three main activities: scientific research, software development and paper writing.
During my first post-doc position of three years duration, I managed to come up with many different ideas for research and features for the software package I was developing, but simply lacked the time to progress with them all. I flitted from one to another, trying to devote a little bit of time to each idea, but never making real progress on most. I also never kept a proper lab book, just having a directory on my computer for each project. This meant that I often left work untouched for weeks, and couldn't remember what I did last, often having to rely on time stamps to see which data was newest - very unsatisfactory indeed.
However, I recently made two changes which have made a massive difference to my ability to effectively deal with many projects. The first is dedicating large blocks of time (3 hours generally) to a single project and focussing on that one task exclusively - no email, no meetings, no Internet if I can avoid it. The other change is setting out a master plan for each month. I prioritise the best quality ideas and time critical work such as project reports, conference abstracts and talks. Other projects are put off until I have free time or they develop into something better, at which point it becomes a priority anyway.
My tool of choice from a practical perspective is Evernote. The ability to group collections of notes and restructure/combine them as needed is crucial to dealing with many related ideas which may converge or diverge at different points in time. Also when I finish a block of work on a project I religiously add my thoughts and results to the lab book, so that next time I come back to it (which potentially could be weeks or months hence), I know exactly where I got to. I also refer to specific directories on my computer so that I can always recreate the data/figures at a later date, without having to hunt for the right directory.
When I have a new idea I start a new notebook under Research, which contains a few bullet points about the idea - enough that I can recreate the thought should I completely forget about it (it happens!). Later I will usually come back and add a project plan, from which point things are usually pretty linear. Given each idea/project has its own directory of notes, I always have an overview of what is going on, while the linear series of notes catalogues the thought processes and data. Using this approach I find it much easier to keep control of my research and its direction, and I am much happier and productive for it.
For me an electronic lab book is essential. As others have mentioned if you travel a lot then physical notebooks are suboptimal. I still have a book for quick notes and equations, but they get typed into the lab book/LateX as soon as I get to the computer. Although my lab book is currently quite small, as it grows I want to be able to search for data and text. There is of course a potential downside with my current solution - it relies exclusively on the existence of Evernote. If the company fails for some reason then I potentially lose all my notes (since they are hosted on their servers). I am always on the lookout for new software which does the same thing, and preferably open source which takes away the heavy reliance on a single commercial entity.

I few years ago I moved to MacOS and discovered a journaling program called Day One. My journal is automatically backed up to a server. You can have one journal per topic, or use tags to identify research projects within a single "research" journal. Many of my thoughts apply to more than one project, so I use tags and one journal.
Perhaps the most important feature is that there are apps for iPhone and iPad, and you can add pictures to the journal. So, when I am talking to someone and she writes something on the board, I can take a picture and add it to a journal entry. I can also take a picture of a calculation I do on paper, or export a mind map (I love Inspiration mind-mapping software) to an image and import that into the journal entry.
I also have great ideas while jogging in the park, at the gym, driving to work, and I can add them to my journal from my phone. I can add longer notes using my iPad when at a conference.
Since it is journaling software, everything is organized in date order, but you can click on a tag to see just the entries with that tag. I don't know how I lived without it.
You can export your journal to pdf for extra backup or sharing.
There might be something for Windows too (not OneNote, which is more like a Wiki). I had problems with EverNote losing my notes, never to be found again.

If you lab notebook could be used to document a patent-able device or process then you must use a stitched notebook with numbered pages, and do not remove the pages.
Even under the first-to-file rules, some cases can draw on the history of notes and creative documentation.  (e.g. same claims on the same day)
As annoying as this is for modern methods (hyperlinked docs, etc), there is no alternative yet.
(Source, a 20yr patent attorney's career)

I suspect that this is advice relevant to, in particular, patent law in the US. Other jurisdictions may enforce the first-to-file novelty requirement strictly.

@Nicholas I addressed that implicitly in my answer.  E.G. if two parties file the same claim on the same date, then first-to-invent becomes part of the litigation.  The downvoter was inappropriate.

My original comment was to highlight that there were other jurisdictions other than the US, in which a reader of your response might reside. In those jurisdictions their patent laws encode absolute novelty - there is no appeal to "first to invent" as there is in the US.
In the time I spent practicisng patent law in the UK and EU, I often had to disabuse clients of the notion that a set of notes pre-dating the filing date of an application can overturn novelty.
I did not down-vote your answer. I just wanted to make sure that your contribution is useful also for non-US readers.

I hear that we are in agreement, and I hope readers will disambiguate a filing date takes precedent, except where competing applications have filing dates that are identical.

I did not claim to be a "20yr patent attorney's career" — I said that is my source.  That guy's advice has saved me repeatedly, and so I trust his exposure to case-law that backs the recommendation to use stitched lab books, which will leave evidence of tampering (restitching) when someone would try to add or remove a page.  Having pre-numbered pages (from the manufacturer) is another important facet.

I'm a PhD student in mathematics, and I am finding a physical research notebook to be very helpful as a "clearinghouse" between (1) my research scratch notes, which are very messy and usually on the back of paper that has been used for something else, and (2) my typeset notes or code. I first work out a proof/calculation/algorithm on scratch paper, probably scattered all over my desk. Then, once I feel that a given proof is ready to write up, I write it out carefully in my notebook. In the process, I often discover gaps or inefficiencies in my scratch work.
I do something similar if I'm reading a paper and writing my own interpretation of what I find there (e.g. if someone gives a constructive proof and I want to turn it into pseudocode, or if they prove something in a general form and I only need a special case). The notes I make while reading will be on scratch paper, often on the printout of whatever I'm reading, and then what goes in the notebook is my takeaway, ready to consult later.
I don't try to keep different notebooks for different projects -- my two or three projects bleed into each other enough that trying to separate them wouldn't be worth it.


text:
Which free online academic plagiarism checker is closest to Turnitin?
Which free online academic plagiarism checker is closest to Turnitin by quality  standard of rigour?
Turnitin features that even somebody plagiarize the context of a passage by use synonyms or simply rephrase the sentence, it is still able to catch the student cheating...
Please notice that Turnitin is not free and some of free software are not rigorous enough or even people called it a joke!

There are none, otherwise it wouldn't sell.

This question doesn't seem answerable in its current form.  What do you mean by "closest"?  Are there specific features you are looking for that Turnitin has but some free programs do not?  Is it a judgment of overall quality (with Turnitin setting the standard)?  Are you trying to run your work through another program to discover whether you have anything to fear from Turnitin?

@AnonymousMathematician - Is it better now?

In this analysis you must not forget that anti-plagiarism softwares DO NOT DETECT PLAGIARISM but only SIMILIARITIES. It's up to the teacher to evaluate, case by case, whether the similarity constitutes a plagiarism case, or not.

may be helpfull http://en.wikipedia.org/wiki/Plagiarism_detection

I have recently (2 year ago) done a fairly thorough search for good, free alternatives to TurnItIn. My motivation was that my school did not use TurnItIn but that does not stop me from caring about my students' work. In the end, I found all of them (and there are many) are simply terrible in comparison to TurnItIn.
I've been using TurnItIn for 2 years now and I find it quite solid (of course there are things I would change but the basic functionality works well). The system has flaws but as I see, they maintain it and when a vulnerability is found (allowing a student to game the system), they generally fix it.
Add to this the fact that most often (my) students copy from previous students, searching freely available online sources will not do a proper job.
TurnItIn has a bit of a natural monopoly so it seems unlikely that any free alternative will ever gain much market share, meaning they will not have the papers to check leading to a vicious circle.
I see you are a high school student which makes me wonder why you want to know. Without knowing your true intention, I'm afraid my answer will be less useful to you.
If your purpose is to recommend a system for your school, they need TurnItIn. If your purpose is to check your own papers, you should use TurnItIn's student version (I know, it's not free).

I never tried any software thoroughly enough. If you google your question, you can find a lot of solutions, and it's just a matter of contacting the vendors and benchmark the different options.
The question you must ask is: what are the sources against which the system makes a comparison? If you only look for free sources, your possibility of finding similarities are limited. If your system matches also the high amount of academic literature hosted by publishers, the odds to find a match are higher. But since the highest amount of academic literature is accessible only via paid subscription, your anti-plagiarism system has to make some sort of agreement with the publishers.
So bottom line is: the best software is the one which searches through the highest number of resources. If a product is only limited to what is freely available on the web, it is very short-breathed.

I suspect that given the breadth of material that can be plagiarized (not all of which material is available for free), a free option of the same calibre as paid options will never exist.
I have not got the personal expertise required to give you a product comparison. If you're looking for a free product, I'd suggest making your own sample text and using it to test all the free ones. For a list of what's available, I like to use Google's Similar feature, which is hidden behind that little green down-arrow next to the green URL in search results, and which gives something like this: http://www.google.ca/search?q=related:turnitin.com


text:
Should I always keep my professor in cc
I have recently joined as a research staff (after finishing my PhD) under a professor, and my primary duty is to interact and provide day-to-day support (mostly academically) to all of his PhD students. Should I always keep my professor in cc when interacting with the students via Email?

Ask your professor what they prefer? (though in general I would assume "no")

@xLeitix, that seems to be the only reasonable answer. Why not make it so? Only the professor has an answer for this.

Related from a more general workplace perspective: https://workplace.stackexchange.com/q/14510/63134

You have to ask your professor. Some of them always want to be kept in the loop while others prefer a cleaner email inbox. There is no way around asking him directly (which shouldn't be a problem anyway?).

It really depends on the professor, some of them like to be in every correspondence, while others like to have a general overview of how the student are.
In general, as suggested by other users, I would suggest that you talk to the professor, since he is the one who offered you the "research staff" position in the first place and see his preference. And maybe explore the difference avenues with him, maybe

Daily update
Weekly summary

Or you could keep CCing him on Email tell he starts to complain about it (though I would not recommend this)


text:
Giving a third party credits for contribution in publishing journal paper
I have done a masters program and three research papers have been composed as the result.
During my research, I was a part of two collaborative parties, my university and a private research center managed by a private company. Both parties need to have credit from publishing these papers.

How can I give them the credit if I publish my paper in a journal?
Can this credit be indexed in ranking systems, so they get a real benefit from it?
How can I consider more priority for one party over the other, according to their contribution on my research?

Thanks @Matinking for the edit, when a university student or member  publish a paper they can get benefits by increase their rank, also research center can got indexed in international list.

How to give them credit?
You indicate your affiliation (i. e., the fact that you was a part of a research center / a university and used their resources) while publishing. You may indicate as many affiliations as you wish; I have definitely seen authors with three affiliations.
Do they get benefit from you indicating them as affiliations?
In most cases, they do. A university in my country (Russia) will be ranked higher if its students publish more papers. Both universities and research centers need to show that their students publish papers to justify the use of money they receive through grants. For these purposes, indicating affiliation on a journal paper is usually sufficient. You might want to check with your department to find out if your publication (and you crediting your university in your publication) will benefit them.
How to assign them priority?
This is not something I have seen in affiliations. However, you might wish to expand the Acknowledgments section in your article. Indicate which kind of support you received from each party. Acknowledgments section is also a place to indicate if your work was supported through any grants.

@Matinking, I will be very pleased if you provide a better answer of yours.


text:
Writing On the Board vs. Showing Slides
There is a new trend on some Universities (in engineering and science majors), that professors show lecture slides over a video projector on the screen instead of writing on the chalkboard. They enter the hall, stay two hours totally passive before the students and read the slides aloud without explaining it. I even have had a mathematics course, in which the professor read the slides like a textbook without explaining them on the board or working examples.
Are you also affected? Which method do you think is more effective? What are the advantages and disadvantages of each? (I myself believe the chalkboard is much more effective.)

Closely related question: In teaching, what are the advantages of using slides over doing board work?

To me, this question sounds like "What is better? Your crop fields getting flooded completely or a little drought on your field?" - that's a no-brainer, and also not a good question to ask, as the answer doesn't tell you anything about what is best.

As currently written your question is a very bad fit for this site. "Are you also affected" is a poll. "What do you think is more effective" is opinion-based, though it could maybe be made more objective with a request for references. Also, you seem to have formed a strong opinion anyway, and as such I am not sure what you are trying to achieve here.

Also, I like that you think this to be a "new trend". I entered university in 2002, and I can count on one hand the lecturers that used chalkboard rather than pre-prepared slides (powerpoint or handwritten prepared).

@xLeitix I do have an opinion on it, but it does not mean that I am totally right. Everybody sees that from his point of view and having different views helps to see those angles that you might have missed and eventually build up a better big picture of the subject. That is one of the goals of such Forums. People do not ask questions because they do not have an opinion on the subject but because they want to to know other people's views on that matter.

Voting to close this question because if stripped from the polls it would be a duplicate.

@Infinity Unfortunately gathering a lot of opinions is not how Stack Exchange works. Specifically, this is not "one of the goals of" this specific forum, even though your statement is certainly true for forums in general.

@Infinity: Stack Exchange is not a forum. And while Stack Exchange may be helpful for forming educated opinions, it is not for just asking for opinions.

What you describe is not teaching with slides, it is teaching very badly with slides.  A teacher can teach very badly with the board too: as an undergraduate, I had one mathematics professor who only mumbled inaudibly while either facing at an oblique angle to the class or else while writing small unintelligible letters on the chalkboard in a descending arc.
Slides can be an excellent teaching tool, in that they allow a professor to show images, data, illustrations, and other things that cannot be readily drawn by hand.  I find that their main disadvantage is that they are fixed before the class, and thus cannot be readily adjusted or corrected to track the interaction with students on the fly.  Conversely, working on the board can be more interactive, but must remain much simpler, which can be either a good or a bad thing, depending on content.


text:
Changing fields after PhD?
I have two fields that I am interested in. Field A is historical and requires me to learn two new languages and I would love to focus on this first. Field B is more accessible, that is, there are no extra languages to learn or mathematical methods to comprehend. But it is a more contemporary discipline. I would like to move into this field afterwards.
How does one do this? The fields do not overlap much.
People are often saying 'the value of a PhD is to show that you can do research, so once you have shown this, there is no need for a second PhD. You can move into a new area on your own now.'
However, I feel like it is incredibly important who one's supervisor was, and I am not sure how seriously people would take me in Field B. I would be 'not really one of theirs', as it were. I am also not sure how to get a job in Field B, after having done a PhD in Field A. I could apply for jobs in Field A and try to somehow move into Field B. But then, if a university hires me, to do research & teach in Field A, which I studied for my PhD, how do I explain to them that I happen to have a paper ready in a completely different field? And how would I even find the time to write such a paper, considering that it will be expected of me to do research & publish in Field A - because, this is after all what they hired me for.
Questions, Questions, Questions. :)

Is there any way to construct an interdisciplinary project involving Fields A and B?

Are Fields A and B so different that a job's scope might include one but not the other?  For instance, in my own area of mathematics, suppose your fields were PDEs and group theory.  There isn't a lot of overlap between them, but many departments wouldn't really care which of them you worked on, as long as you were successful.  They wouldn't be hiring you to do PDEs - they would hire you to do math.

The most typical path for shifting your field after a Ph.D. is by means of one or more postdocs.  A postdoc is an opportunity for more training and is often used by people to move between fields.
The challenge is finding the right postdoc (or chain of postdocs) to make the shift, which may be easy or difficult depending on the particulars of your fields. For example, shifting from computer science to systems biology is generally pretty easy; moving from Sanskrit literature to aerospace engineering would probably be quite difficult.
Once you have a more more permanent position, on the other hand, you are likely to find much of your time is consumed by the other responsibilities of that position.  For example,  if hired as faculty you will find much of your time is spent not as a researcher but as a teacher, advisor, department committee member, fundraiser, and administrator.  Combine that with something like a ticking tenure clock, and it can be quite difficult to change fields once you have passed the postdoc phase.


text:
What makes good research questions good?
I am in Computer Science and currently in my proposal phase. For my problem statement, I want to come up with good research questions. However, at the moment I am struggling with the definition of "good" research questions. My professor usually comments that my current questions are not "why" questions, but instead are "yes/no" questions.
Any recommendations what make good research questions good?

Related: How to come up with research questions that are well-defined and suitable in scope and relatedness for a thesis?

Read chapters 3 and 4 of Booth's The Craft of Research.

Do you want to know the answer?  Really?
Do you realistically have a good shot at finding the answer, in a reasonable amount of time?  Really?
Will lots of other people be happy to learn the answer (even if the question had never occurred to them before)?  Really?
Are you sure nobody already knows the answer?  Really?

If you can answer yes to all eight questions, it's a good research question.
(Unfortunately, some of these points may depend on what the actual answer is, which of course you don't know.)

Thx for your answer! You wrote, "If you can answer yes to all eight questions, it's a good research question.", however I only see four. Do you mean by eight question to question your question, by "really"?

Yes, I counted "Really?"

In my opinion, a good research problem has at least the following properties:

It is a small piece of a big problem.  In other words, it needs to be both small enough so that you can reasonably make progress on it, yet connect to a larger problem.
It is possible to do a small "pilot" to sanity-check your approach and whether results are promising.  Most research problems can take a lot of work to really tackle.  It's good to have milestones along the way that can let you figure out if you are on the right track and whether the project is likely to be worth the full investment.
Something can be learned from the work, whether or not it comes out the way that you hope.  A large fraction of interesting research projects don't work out the way it was hoped: either the driving hypothesis was wrong, or turns out to be too hard, or something else shifts and things end up obsolete.  A well formulated project will still contribute knowledge, whether or not it actually ends up advancing you toward the original goal.

Let me illustrate further with nice example that I saw recently: a group of undergrads at NCTU Formosa put together a project to modify E.coli to manufacture PBAN neuropeptides to stimulate pheromone production in the Heliothis virescens moth.   This is a really specialized and esoteric-sounding goal, but relates to a much bigger idea: doing this could lead to a general approach to radically improved insect traps that could greatly reduce the need for industrial pesticide use.  The narrowly scoped project they set for themselves thus connects to a much larger goal, but has a set of clearly delineated milestones along the way (e.g., create PBAN-expressing sequences, verify they work in E.coli, test the extract on female Heliothis virescens moths, verify the increase in trap efficacy, pilot tests with local organic farmers, etc.).  Furthermore, even if it turns out the bigger vision can't be achieved, there still can be a lot of things learned about neuropeptide engineering, which may turn out to be relevant to a great many other questions, both foundational and applied.


text:
How to deal with errors in well established papers
I am currently supervising a Bachelors student for his thesis. I gave him a well-established paper to read of which I only knew the results but never checked the calculations in it. It was first published in 2006, is currently in its 6th version on arXiv and has about 330 citations, so I expected it to be mostly without mistakes...
Well it turns out I was wrong. My student stumbled over several mistakes and I found some more while trying to explain some calculations to him. In total we have found about 10 errors - some minor like a wrong index in a formula, some major like claiming that a function is convex while it is in fact concave and an inverted inequality sign in the final result...
Under different circumstances I would write the author, but I feel somewhat silly writing an email that basically says "Hey, this paper you wrote 9 years ago contains some errors." I really cannot imagine that we are the first to find these mistakes...
I also thought about commenting on the paper on https://scirate.com/ - this way the author needs not bother with it, but following generations could still see the corrections. On the other hand this could be a big insult to the author...
Is there any other way to make sure following generations don't stumble over the same mistakes? (The results are basically so well established, that active researchers take them for granted and don't try to verify the calculations - but following students will surely stumble over the wrong equations)
Should I just drop it? Should I still write to the author?
What is the "proper (scientific) way" to handle this situation?

Does this paper only appear in arXiv or it also appears in some other journal?

I have had a lot of experience both with mailing authors and with posting errata on my website. The first approach works the better the more recent the paper is; I agree with you that a 9 year old paper will probably not elicit much of a response beyond a "thank you" (or even less), but it might still be worth the try. As for the second approach, I tend to use it in situations where there is really a lot of errors (enough that I suspect a reader will gain more time than they lose from reading my errata) or where I have more to say than just corrections of errors (e.g., when I am ...

Closely related question: What should you do if you spotted a non-trivial error in a highly cited paper?.

... able to simplify a proof or generalize a result "for free"). I cannot say I have obtained much feedback on those errata I have posted, though. I have almost no experience with scirate and the likes (I have tried to use SelectedPapers.net once, but the bugs inherent in their very fragile Google+ API have scared me out). I fear the visibility of corrections posted on any of these social-network-like platforms will be even less than that of corrections posted on your website.

What I don't fully understand from your question is whether the errors you and your student found are serious or easily correctable. In the former case, that might be material for a bachelor thesis. For example, here is a bachelor thesis around an error in a paper: http://www.math.wm.edu/~vinroot/Undergrad_Research/MattHall_Thesis.pdf

@darijgrinberg all errors are easily corrected and the result as it is written in the paper still stands. The derivation to obtain that result is faulty and incomplete though. When it says "as f is convex this minimum is a global minimum" you have to read "as f is concave we have to perform a lengthy calculation to show that this is the global minimum". When they say "assume a>b" you have to read "assume a<b" to follow the calculations. Where they write a sum from i=1 to N there should be a sum from i=0 to N+1 and so on...

I usually expect one or two such mistakes in any paper - but there  is almost one typo of the kind of wrong indices per formula...

@scaaahu it was published in Phys. Rev. B and contains the same mistakes in the version published there...

@example: Isn't it even easier to minimize a concave function than a convex function?  The minimum of a concave function on an interval must occur at an endpoint of an interval, cf. https://www.quora.com/Why-is-a-maximum-of-a-convex-function-over-a-convex-set-always-found-at-one-of-the-extreme-points-of-the-set.

What's your impression about the source of the mistakes? Is it a fabrication, misconduct, sloppiness, or simply a typo?

Why doesn't arXiv have a comment section?

Hi Professor OP, what finally happened?

The most important thing, I think, is that the core results stand.  This means that correcting the errors is not about substance (which might require a new corrective paper or a retraction, depending on the nature of the errors), but is instead about making the road to understanding easier for others who also read the paper.
Since you say the paper has been revised multiple times on arXiv, it seems there is a decent chance that the author may still be tracking on it and be willing to update and correct it.  I would thus start by writing to the author---it's entirely possible you're the first to notice the mistakes, simply because everybody else thought they saw the things that were supposed to be there (copyediting equations is hard).  If that doesn't produce a result within a few months, write to the journal and see if you can get the errata corrected in their version of the paper.
Beyond that, I think there is not currently a high incentive to put in further effort or to put material up on a third-party website, simply because I suspect that most people who look for the paper are unlikely to readily encounter such annotations.  Search engines are pretty useful, though (as this site readily attests), so there's no reason not to put the corrections online somewhere as an FYI to help others who might happen to search for "errors in Paper X."

Since you say the paper has been revised multiple times on arXiv, it seems there is a decent chance that the author may still be tracking on it and be willing to update and correct it – Note that if the LaTeX source of the paper is also on ArXiv (in which case they are downloadable for everybody, so you can check whether this is the case), correcting a minor mistake is very easy: Log-in; download the source file; fix the mistake; upload again. No need to search your old files or possible hassle with your LaTeX installation.

I think I will write the author - and if he does not react on it post the errata on my homepage. Maybe with some additionally expanded calculations and arguments so that it is not just a "everything wrong with X" document.

I start my answer by emphasizing on the last sentence of your question:

What is the "proper (scientific) way" to handle this situation?

One possible course of action can be this (I emphasize in the words "proper" and "scientific"):

Step 1 - Maybe not yourself, but get your student to write an email to the authors, stating that he/she was trying to work out the paper from scratch, but came across a few issues which appear to be some minor mistakes, and that his/her adviser (i.e. you, with your name and affiliation fully disclosed) agrees on their implausibility. Attach with this a detailed write-up of your calculations, and the error-diagnosis, and why all this is plausible.
Step 2 - Wait for some amount of time, for them to respond. (They would have schedules too.)

Thereafter, depending on the type of response, Step 3 possibilities branch out:

Step 3(a) (If they respond and reason you out regarding the correctness of what they have done, and/or point out the mistake(s) in your calculations (which is definitely not impossible)) - Thank them for their time, and be magnanimous in accepting that you made a mistake, and you were making a fuss out of it.
Step 3(b) (If they respond, but it is more of a brush-aside-the-criticism type of a response, i.e. they don't reason you out, don't point out any flaw in your reasoning, or point out some incorrect mistake, or it is just some high-brow hand-waving) - Think about whether this responsible can be plausible at all, does it make any kind of sense whatsoever. Collect arguments in favor of why it doesn't if it doesn't, and prepare another detailed email. Repeat steps 1-2-3 again.
Step 3(c) (If they say they went through your write-up, you've made a valid point, and they will much over it and publish an erratum, thank you) - Say thank you, and move on. Wait for the erratum to emerge.
Step 3(d) (Either no response to your email for a very long amount of time, or some nonsense/personal attacks (that's theoretically possible, but practically a bit unlikely. Normally, they'll just go quiet.)) - Forget about them completely. Recheck your calculations once more, and post the write-up on arXiv as "Comments on 06NN.NNNN [cond-mat]" (or whatever it is). Be scientific in your approach. Start by praising the authors for their good work, make this explicit. Then say, "However, the following points are worthy of a careful consideration", and give a detailed exposition of what the mistake is, and why it doesn't make sense. With arXiv, this shall get linked to the original arXiv work, and your purpose is served perfectly well. Also, as pointed out by  Wrzlprmft in a comment, in this case, Physical Review B also publishes comments on articles, so that could be a further option (if you are willing to avail it).

The last one isn't an extreme response. There is a huge credibility that goes with a Physical Review B publication, and that's something even the APS people would want respected. Making a mistake is human, but when that human being is a scientist, one expects enough scientific magnanimity for the person to own up his/her mistake. You win respect when you do that, i.e. behave honestly, since the same is a virtue in science. If you know you made a mistake but are still misleading people/ brushing aside criticism, that's plain dishonesty, and that has no room in science. The truth always comes out in the end.

In this case, we are basically talking about a list of typos. I am not sure whether that would be accepted as an arXiv submission.

@NateEldredge - Sure, for typos, arXiv isn't the way around, but I don't think OP's talking about typos. For instance, some phrases, like "My student stumbled over several mistakes and I found some more while trying to explain some calculations to him", and "some major like claiming that a function is convex while it is in fact concave", seem to suggest otherwise!

I would also classify those as "typos"; at least in math, the term is used broadly for any minor error where what is written is clearly not what the author intended, and a little thought suffices to see what was meant.  I would disagree with the OP that swapping "concave" and "convex" constitutes a "major" error.  To be worthy of an arXiv response, I'd think you'd want to expose a serious conceptual error that invalidates the results.

@NateEldredge It's a typo if he wrote "convex" when he meant "concave". It's not a typo if he meant "convex" when the function is in fact concave.

I think that the concave vs. convex issue is an actual error in their argument - one that can be remedied though. In the solution described in this answer I don't really feel comfortable with 'hiding behind' my student part, but I think I will write the author in the end. Thank you for your elaboration on the topic (hopefully it won't have to come to 3(d)) - though I am going to accept jakebeals answer for the 'own homepage' bit.

It occurs to me that you might write to the journal's editor and ask what their policy is. I'm not privy to what happens behind the scenes but I imagine that they might  contact the author themselves.  Alternatively they will surely have experience about the best course for you to take - this won't be the first time it has happened..
I don't think you need give the actual errors immediately - simply say what you said to us and ask for the editor's advice.
I hope this helps.


text:
How are academic relations between mainland China and Taiwan?
Both mainland China and Taiwan have internationally notable universities. How are the relations between their academic research communities?
Does getting involved (as a Westerner) with either of these research communities lead to political obstacles regarding the other?

The relationship between the Chinese and Taiwanese academic research communities are generally friendly from my personal experience (a family member of mine is a professor at a Taiwanese university, and has collaborations with Chinese universities).
As far as I know, getting involved in the research community does not get you into political obstacles as long as you are not doing research in politics (which the Chinese government might be more sensitive to).