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Overlapping sentences in methodology descriptions in separate journal articles - plagiarism?
Disclaimer - I'm neither in favor of, nor endorsing plagiarism with the following question. I'm only hitting on the fact that sometimes, the interpretation of self-plagiarism can be quite stupid.
Given the well-deserved emphasis on controlling the menace of plagiarism these days, various journals and even academic institutions have insisted on various cross-check measures. Mostly, this amounts to necessitating a clean chit from some anti-plagiarism software, which (I imagine) works by comparing string lengths of some x-words in the article, with its existing database. So, if some dumb guy didn't rephrase himself, there would be common sentences, which earns him disrepute and he gets tagged as a self-plagiarist.
Now, as a ''responsible'' author, I would try to minimize such overlaps, ideally to zero. But sometimes, you can't help it. Take this context for example. (Sidenote - I'm basically a Physics.SE user.) We have used one model in two different contexts, so there is no question of overlapping content between two articles. But, since it is the same model, when I describe it, in one place I write -

The free parameters of the wawa model, p1, p2 and p3 are fitted to baryon masses and vacuum characteristics in the wawa limit.

(''wawa'' = whatever)
Now, I don't see any self-plagiarism in repeating this one sentence in the second article, but if I don't, maybe I'm being the ''dumb guy'' in the previous paragraph. So, I'll try to work around this, finding synonyms, trying alternative descriptions, but even with all my maneuvering, that sentence was the best way to describe it.
My opinion is that, even though I'm not plagiarizing anywhere in the above context, this process is turning out to be a nuisance for me. Am I supposed to sit down and waste so much time rephrasing my sentences, when I have some meaningful information to communicate to the scientific world? (Worst still, I could've been investigating some hot problem in my discipline, where urgently communicating is invaluable.)
Also, as @mhwombat hit on in a comment, am I not compromising on the best way of putting it across, when I deliberately rephrase it, just because there is a ''plagiarism'' checker in place? That's surely not what the purpose of plagiarism check was?

I worry that even though I do rephrase every single sentence that I've written elsewhere, later on I might later edit the sentence back the way it was (unintentionally), because I decide it "flows better" that way.

@mhwombat - Right. When it flows better, we don't keep an encyclopedic retention of what we have written before. And that's not plagiarism. My question is - are we supposed to remember these trivialities, or focus on the bigger issue - what we are conveying through the sentence.

Also, note that you should define question 1 carefully to make sure it is not closed as a duplicate of this one

Thanks for the concern, but I think that one's in the context of copy-paste in introduction. Different works should be introduced differently IMO so I denounce it completely. What I'm addressing here is that whenever you use a model, you ought to describe it in short. And since it is the same model being described, you are naturally forced to rephrase the same description over and over again, which is stupid. I'll be very sad if it gets marked as a duplicate. Anyways, I'll take precaution. Thanks :)

Just like there are only so many ways to skin a cat, there's also usually only a limited number of ways you can logically and concisely write a scientific concept. It's a silly situation if you have to compromise the clarity of your explanation just so it's different to what was previously published.

@Moriarty - my point exactly!

I'm rolling this back to an earlier version, since the edits forced on to the post by a member of the site having >2k reputation points, were altering the intended meaning. "Dummy" isn't what I want to say. :)

I think the focus on self-plagiarism here is overwrought when it comes to describing a methodology that may be reused from paper to paper. You are going to cite the first place you wrote that sentence, and you shouldn't need to worry about changing the wording in the series of papers that use the same methodology.
Methodology descriptions should be clear and exactly the same when the underlying methodology is exactly the same from work to work. Any editor who used software to flag your words should see your self-reference/citation and give you a pass. "Self-plagiarism" of this sort is a bad label and no crime.
Edited to add: At most, you may need an prefatory clause to the effect "Following our prior methodology described in [1], the free parameters of the wawa model, p1, p2 and p3 are fitted to baryon masses and vacuum characteristics in the wawa limit." Or something similar. But that won't fool the detector software. You need to trust that an editor will understand this for what it is.

Or you could stick the quote in quotation marks and not have to worry about it.

Why? What purpose does quoting yourself serve that citing yourself doesn't. You could block quote several paragraphs, wasting column inches, or you could simply preface your remarks with something like: "We follow our previous analysis methodology from [1] and reproduce that discussion as follows." Self-plagiarism only seems to be problematic to me when you're trying to double dip for credit, but if the methodology isn't new, it's not the meat of the paper. Thus, it's totally fine to reuse text that you've already made as clear as possible.

So, this means the objective testing using a software is a first step, followed by a subjective decision making regarding issues of self-plagiarism. I like this perspective, and hope that my journal's think-tank has sensible people like you (though I'm a bit scared with what David wrote below)! And that clause is a very valuable suggestion. Thanks :)

I've been out of the journal reviewing loop for awhile. I would hope that if a journal was using software to spot plagiarism, then they would use common sense when evaluating its results. I don't know of any journal that is actually using such software, but it must be more common than I know.

@StrongBad, I have a similar problem as the poster, and while myself I wouldn't mind using quotation marks, I worry whether this would be accepted in a science journal. At least in my field (neuroscience) I have never seen quotations in quotaton marks or as a block, except maybe in review papers.

Just because two sentences are identical does not mean that the person who wrote the sentence second plagiarized the person who wrote it first. For your example sentence:

The free parameters of the wawa model, p1, p2 and p3 are fitted to baryon masses and vacuum characteristics in the wawa limit.

If you copy and paste that sentence from a previous publication (it doesn't matter who wrote it originally), that is a clear case of plagiarism. If you thought about the model and how the parameters were fitted and you happen to come up with the identical wording, it is not plagiarism. If you don't want to think about the best way of saying something and you want to use the words/ideas of someone else, then you need to provide proper credit (i.e., quote them).

But what is a journal editor likely to do if they find, say, one sentence in an article you've submitted to them is the same as in another article you've previously published? Will they automatically assume it's self-plagiarism, or will they use some common sense?

I don't disagree, but I think two issues are getting mixed up here. Irrespective of how many times I think about the model, the parameters are still fitted using the same procedure, which is a separate paper WHICH I CITE in the sentence. I haven't fitted these parameters, so that isn't the subject of the paper. Using the model (with those fitted parameters), I have investigated something which was hitherto unconsidered, so the originality is lying over there. The quoted sentence is used while I introduce the model, before describing what I've done.

(contd.) This is why I have used the ''rephrase''. When I use this model (with those parameters) five times, I guess I'm supposed to rephrase that sentence five times too, otherwise the software will say I've plagiarized. And if you consider that the subject of the paper isn't the fitting of these parameters, this rephrasing is not just unnecessary, but just plain stupid. That's the point I was trying to make. :)

@New_new_newbie it is not that the software will say you have plagiarized, it is that if you cut and paste, you have plagiarized.

@StrongBad - haha, I appreciate that point, but I guess with your ''happen to come up with the same wording'' thing, it becomes impossible to formulate an objective criterion for checks, which is what a software requires to work. If output looks the same, how do you prove that you have a clear conscience and didn't plagiarize? Software will label you a plagiarist either way.  . +1 nevertheless. :)

@New_new_newbie no, the software does not label people as plagiarists, it merely identifies things that are similar. I know of no system that doesn't require human interpretation to make a decision.

@StrongBad - That's what I'm hitting on, for these issues you would need human interpretation, since formulating any sensible objective criterion is impossible.

What StrongBad says about it not being plagiarism if you come up with the same wording independently is technically right, I suppose, but what you really have to worry about is whether certain other people (e.g. editors) think you've plagiarized, and those people are probably not going to be receptive to the argument that you came up with the same sentence twice. At least in theory, a sentence which is long enough to count as plagiarism is long enough that you can find a different way to phrase it. So I would say yes, you have to rephrase the sentence.
At least, this is standard practise in my field, theoretical particle physics, and I've been told that expectations are the same in other branches of physics and other hard sciences.

I think this is a crazy approach to the "problem". There is nothing gained by requiring authors to use circumlocutions to describe identical processes in order to hold to some over-strict notion of plagiarism. If you cite the original, there's no harm in using identical language to describe it.

@BillBarth it may be crazy, but as far as I know it actually happens

It happens that papers are rejected for reusing their own methodology descriptions, or that such descriptions are reused?

That papers are rejected for reusing methodology descriptions, and also that authors do try to do it, though rarely because most people know that it's unacceptable. At least in my field. And offhand I don't specifically know of any other field where it is acceptable.

Why the heck wouldn't it be acceptable if the methodology actually done is identical!?! Especially if it comes with a citation?

Also, I think it would be good if you named your field so that the OP can see if that relates to his.

@DavidZ - I appreciate your inputs, in spite of that -1, (which I've neutralized now). However, the reason why insist that these sanctions are stupid is because, I can't state it (radically) differently five times for example. The fact is, there is really no plagiarism here in the true sense and purpose, it is just a weird definition. Moriarty and mhwombat make good points above, in the question.

@BillBarth - I completely echo your sentiments regarding how silly these things are. But I should be worried with David's answer, since the above question concerns nuclear phenomenology, which happens to be a sister field of David's theoretical particle physics. :(  (Sometimes, I call myself a particle physicist too.)  Also, given David's credibility on the Physics site, if he's claiming this, he must be aware of instances where this stupidity might have actually transpired!!!

But @DavidZ, you mean, even with one sentence? Or is there any tolerence percentage, e.g. in APS Journals? It is never disclosed, I believe.

@New_new_newbie actually my field is nuclear phenomenology, specifically small-x physics of proton-nucleus collisions. (Unless you meant the other kind of nuclear physics?) And as far as I know, even one copied sentence can be considered plagiarism. Copying a small amount of content may reduce the likelihood of it getting caught, but doesn't make it any more acceptable when it is caught. Of course it depends on the editor in question (and the reviewer(s)); some are probably more tolerant than others. I don't know if it is standard practice at e.g. APS to check papers for plagiarism.

@DavidZ - Thanks for the inputs. Even the moderator had suggested that I post this last issue separately instead of including it here in the question. So, maybe I will go ahead.

According to Irving Hexham, "Like all plagiarism the essence of self-plagiarism is the author attempts to deceive the reader. This happens when no indication is given that the work is being recycled or when an effort is made to disguise the original text." This means rephrasing re-used text not just doesn't change the fact of self-plagiarism, it makes it even worse by trying to disguise it. (See what I did there? Proper attribution and quotation marks! ;)


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Publication dates: accepted date, version of record online, issue online – which one to use?
I have seen the other questions regarding which publication date to use, and it seems clear to use what the publisher uses.  But what if the publisher provides several dates such as the following?

Issue online: 25 January 2016
Version of record online: 25 October 2015
Accepted manuscript online: 7 October 2015

I find these definitions confusing. Which data should be used as the official publication year? What does version of record online even mean; is it important?

You have to define "use". Different purposes lead to different dates. For example, determining who published an idea first, you use the earliest date. For legal purposes, you may need to use the first version of record date.

I guess this depends on the journal. Most journals in math that I'm aware of tell you the year and month for the volume and issue number (or bi-month period, or season, or some other subcategory of the year, if such a subcategory exists for that journal), and that's what you use. See here for example, where any of the papers in this issue would be dated November 2013 (or maybe just 2013, as people often just give the year).

Incidentally, Version of record online is mostly meaningless for a lot of math papers, since in math one often cites papers from well before the 1990s. Knowing that a certain paper first appeared online on 12 May 2002 is pretty meaningless if the paper was received by the editors on 15 January 1963, revised on 28 June 1963, accepted for publication on 17 July 1963, published in an issue dated May 1964 (and of course the library's "received date" that is stamped on the front of that issue is probably something like 12 September 1963).

A journal citation looks like

Last, F. M., & Last, F. M. (Year Published). Article title. Journal Name, Volume(Issue), pp. Pages.

Since it refers to a specific volume and issue, you should use the date that issue was published. (For your example, that is 25 January 2016.)

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How to define “self-citation”?
What exactly is the definition of self-citation? I have looked around but I cannot seem to find a definition. There is even a publication, but I cannot access it at the moment. Also I would like to have a definition here on Academia SE.
For example, say I publish paper with a co-author. Then my co-author cites this paper in another publication in which I am not involved. This is clearly a self-citation for him, but is it also a self-citation for me? Does my indirect involvement suffice to make this a self-citation for me?
Maybe there are other ambiguous cases, feel free to edit the question.

Although it's another context, I'm wondering why the self-citation is not being considered in popular citation database like scopus, google scholar? Some authors are widely using this to increase their citations, I'm not against self citation, however this metric itself is useful to evaluate the impact of an article.

@Mithun Scopus does have an interface to display citation counts excluding self-citations.

There is no exact, official, legally binding definition of self-citation. The term occurs usually in the context of research metrics and scientific evaluations, and every developer of a system to measure such things is free to use his own definition of self-citation (or even, to ignore it).
That said, if I were to implement such a system, I would treat self-citation as a property of a paper, not as a property of an author. That means, I would consider a citation of paper A within paper B as a self-citation, if A and B have at least one author in common. The reason is
that some overlap between the author lists will already make it more
likely that paper A is referenced in paper B.
Note that "the citation of A within B is a self-citation" is not a moral statement. It does not mean that the authors of A, or the authors of B, or the joint authors of A and B did anything wrong. It just means that there is some aspect that makes this particular citation statistically more likely than a citation of A within another paper C, where A and C have no authors in common. Research metrics consider events that are more likely (say, a publication in arXiv) as less valuable than events that are less likely (say, a publication in Nature). They are based on statistical observations, not on a legal process that decides for each individual citation whether it is justified or not. Don't take it personally.

Your definition helps but it over-penalizes the authors of paper A that are not in paper B, as they are not citing themselves.

I've added a third paragraph; please have a look at it.

I think self-citation, as a verb, makes more sense for an author than a paper.  A paper self-citing should mean it cites itself (an internal reference).  An author self-citing would mean citing one of their own works.

@Kimball Yes, it's abuse of terminology, but it seems to be the established convention. The usual goal is to estimate the impact of an article (and indirectly, to estimate the reputation of researchers by looking at the impact of their articles). The impact of an article with authors X and Y, however, is independent of whether we consider it as an article of X or as an article of Y.

In my field (where citation metrics aren't such a big thing anyway), I haven't seen people look at "article self-citations."  Though I have seen people exclude author self-citations for things like the h-index (perhaps the g-index?).  Of course another meaning is in the context of journal self-citations.

@HermanToothrot you said "over-penalizes" and you seem to think self-citation is a bad thing. Improper or irrelevant self-citation would certainly be bad, but directly relevant self-citation is common and not problematic. In fact, in some circumstances, failing to do so could be improper.

Increasingly, an article should cite its own representation in a Research Data Repository as researchers are being encouraged to make their research data publicly available.
'Self citation' is not a property of the paper, and does not have binary status as the sets of citing authors may not include all the cited authors. What may be a self-cite for one co-author is not a self-cite for a non-author of the citing paper. Further, citing one's own papers may be necessary to avoid redundant duplication and repeating old history.

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What to do when you find out someone else presented your research without crediting you?
One of my collaborators recently sent me a link to a video of someone presenting at a professional conference.  In the presentation, they use some of my published research that I did as an intern, including figures from my paper, but they never credit me in the presentation.
I have several questions about this:

Is this normal or is this something that I should be credited for?
Is it typical for someone to contact you before using your research in a presentation?
Is it worth contacting the company about this?

On the one hand, I'm happy that more people are seeing my research.  On the other, it feels a little upsetting to see my research getting presented without getting the credit for it.

Were they presenting the work as their own, or as a presentation of your paper?

They were presenting it as "our work" at the company and they credit one of my co-authors.

Is this normal or is this something that I should be credited for?

No, it is not normal practice; yes, you should be credited whenever a result from a paper for which you are a co-author is mentioned. The only exception I can think of is if the paper has several authors and is cited in the style "[first author] et al. (2014) showed that ...". Even then, one would typically expect the presentation to include a full citation at the end that explicitly mentions your name as a coauthor.

Is it typical for someone to contact you before using your research in
  a presentation?

They do not need to contact you before mentioning your research in the presentation (and it is not typical for anyone to do such a thing), as long as two conditions hold: a. the research that they are going to mention has been published or is otherwise publicly available, and b. they credit you by name in their presentation as I stated above.

Is it worth contacting the company about this?

That depends. What are you hoping to achieve by contacting the company? It seems very difficult to judge from the details you provide whether this was some kind of egregious, intentional misrepresentation by the person in the video, or whether it was an accidental omission due to sloppiness or perhaps not copying correctly the list of authors. If it was the latter, although it is still a bit annoying I wouldn't bother complaining - at most I would send a friendly note to the presenter to politely call their attention to the fact that I am also a coauthor of the paper they cited, so that they can correct the error the next time they use this presentation. If it was the former and there is a clear intent to deceive or other unethical aspect, I may seriously consider contacting the company to complain.

You clearly said that your paper is published and has your name on it. No matter who presents this paper or this work, your name will be forever there. Everyone who will lookup this paper to find out more about this research will see that you are a co-author, regardless of who actually presented it.
TL, DR; I would not worry too much about it.

I think the concern in the question was that they were not cited in the presentation itself.  Though the wording is a bit ambiguous on the OP's part.

In theory, any errata should use the same medium and address the same audience. If an article is incorrect, the corrections should be published in the same journal.
In this case, it is unlikely that the same people will be called to another meeting, where they will be told that authorship was misrepresented last time. So there is no practical way to get redress. This situation is double-edged: on one hand, you have been slighted, but on the other, your slight has already been forgotten. Those people wouldn't remember your name even if it were said. So live and let live.
If we are talking about something more persistent - for example, a TED talk with millions of viewers on Youtube -, you could seek arbitration from the video host. Just like with journals, there will be some the initial hoops. But in the end, the video host will deal with it in a manner dictated really by what your lawyers could do to other guy's lawyers. I am not a lawyer, but I suspect it is cheaper than going to court, and gets the same results, burned bridges included.
There may be a way to kindly ask the other person so that this mistake will not be repeated. But its success depends on the personalities involved.


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How to cite a chapter from a report with different authors?
I have to cite a multi-chapter report. Every chapter has different authors. Should I cite with the name of the main author and then the specific chapter? Or should I use the first author of the chapter I am citing?
If the main author is Smith but Jeff is the author of a chapter where Smith is not in the authors’ list, should I cite with “(Smith et. al 2000, Ch 6)” or “(Jeff et. al 2000)” and then add a citation for each chapter in the cited literature section?

Zimmerman's answer is correct. I would also add that many style guides or journal publishing instructions will even have a specific example showing this. This is a common question, not like citing a gravestone or something else bizarre. (If not, do something similar to what Zimmerman gave you. Typesetter may fix exact details.)

This does not provide an answer to the question. Once you have sufficient reputation you will be able to comment on any post; instead, provide answers that don't require clarification from the asker. - From Review

In your example, you are citing the chapter author's work, not the work of the compiler/editor of the book as a whole. According to the APA Publication Manual, use the following reference format for this situation.

Author, A.A. (1967) Title of chapter or entry. In A. Editor & B. Editor (Eds.), Title of book (pp. xxx-xxx). Location: Publisher

Of course, your intext citation would reference the chapter author too, not the book author/editor. The same general format holds for other reference styles as well.

If authors are identified for the chapters, then this document is best treated as an edited collection. In this case, the chapter authors are the author and the chapter title the title. The overall report title is then the collection title (filling a similar role to journal title) and the "main" authors the editors.
The exact details of how this is formatted depend on the style where you are submitting, but if any names are appearing in the main text, they are of the chapter authors.

This is not a book but a multi-chapter report, and it is unclear who are the editors. It is a IUCN report for the record.

Please note that nothing in my answer assumes a book. It should apply to any multicomponent document, including the report you described.

should I cite with (Smith et. al 2000, ch 6) or (Jeff et. al 2000) and then add a citation for each chapter in the cited literature section?

I've checked The Chicago Manual of Style and the New Oxford Style Manual and it seems that the second style is preferable. I don't know if there is a standard way to abbreviate if one has to cite many different chapters.
However, if you're writing for a journal, there might be a preferred style, which can be described in the journal style guide or applied directly by the typesetter.

Remember that the reference in the text is "only" a flag to enable the reader to find the important information, the reference, in your reference list. With the "author-year" form the in text information provides a knowledgeable reader with a flag that can make the reference known without looking into the reference list but in a system where references are provided with only numbers (Vancouver style). So the important information is in the reference list.
With that background, it is clear that referencing the authors of the chapters is the way to go. If no clear author exists for chapter the compilation or book editor can be referenced but adding the specific chapter number in the reference (assuming the chapter IS numbered). There is no major point in adding the chapter number to a reference pointing to a chapter given by its author. All such information will be given in the references. Even if more than one chapter has been written by a specific author (team) you can still provide only the usual "author-year" but label the references, for example, (Smith et. al 2000a), (Smith et. al 2000b) etc. All will be explained in the reference list.
So as a conclusion, use references as if the chapters where articles in a journal but be careful by providing all necessary information about full publication information of the chapter (number and name of chapter) as well as book editor, title, publisher etc. in the reference list. Please refer to journal instructions (equiv.) for details.

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How to cite indirect sources in CSE/CBE (name–year) system?
I’m writing my first review paper and I don’t know much about the CSE system. I couldn’t find the indirect citation rule for CSE (but for others). So how do I cite indirectly in this style?

If you mean by "indirect citation" citing a source cited in another document (which you, most likely, cannot access for some reason) then your citation would be for example:

(Rawls 1971, cited in Brown 2008)

See the CSE style guide for more information.
Anyway, I would strongly encourage you to find the original source and to avoid indirect, secondary citations as you do not know whether the citation is correct.

If you find a useful reference in a review paper, get thee to a library (or a web browser), track down the original paper, and read it yourself.  At that point, it becomes a primary reference.

@R Blazer @Redwana Blazer If this is the answer you were looking, you can mark it as "accepted answer". Do you need to know more?


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Is it OK to select an editor if I solved his conjecture?
I am about to submit a paper to a respected math journal. In this paper I solved a conjecture that was raised by a member of the editorial board (and this is one of the main reasons I chose this journal).
When submitting, I need to choose a member of the editorial board to handle my submission. Given his relation to this paper, is it OK if I list this person as the requested handling editor? Or does this cause some problem?

In fact, I think that is the best choice!  That guy is likely to know more about the subject, and be aware of previous attempted solutions.

Definitely. Plus if it is a true proof to the conjecture, I would think the editor would be extremely delighted. Mathematicians aren't often incredibly egotistical so it shouldn't be an affront to him/her.

@Cameron: "aren't often incredibly egotistical" -- or at any rate, they don't publicly conjecture until they're ready to accept they might need someone else to prove it ;-)

@Steve most definitely!

Yes, it is OK. There's certainly no conflict from my external perspective, and if they decide that there is a conflict, the person in question can either decline the assignment or otherwise pass it off to a different editor at the journal. No one is going to get you in trouble for requesting this editor.

Other then OK, do you think it is a good idea?

From an economical point of view, chosing this editor seems pretty reasonable. He is probably experienced with the field and thus probably best suited for selecting referees or may even decide to review the paper himself (and then probably hand the paper over to another editor). In both cases and on average, this speeds up the review process and raises the quality of the reviews.
However, the editor may be biased regarding the importance of your work, which however is no real issue if the work is clearly over the journal’s relevance threshold. Moreover, the editor may overprioritise it and be more lenient towards it. All of this is in your favour and I would argue that dealing with this is the editor’s or some supervising editor’s job and not yours. One could however also argue that you should select another editor for this reason.
Just selecting another editor may however also have negative repercussions, as editor that raised your conjecture may feel omitted or you may be regarded as having been sloppy when choosing the editor and thus wasting the editors’ time.
Thus I would suggest to elaborate either decision of the editor in one brief sentence in the letter to the editor (or the journal’s equivalent), for example:

Note that we did not choose X as a handling editor because we already suggested him as a referee.
Note that we did not choose X as a handling editor to avoid conflicts of interest.
Should our choice of X as a handling editor be regarded to cause conflicts of interest, we kindly ask the journal to choose another editor.


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Why would an academic write a textbook for free?
Recently, I became aware of a Java programming textbook
Introduction to Programming Using Java, Seventh Edition
which is to my surprise, free as in:

The most recent version of this book is always available, at no charge, for downloading and for on-line use.

Question: Why would the author (David J. Eck) make this textbook free?
I have found that almost always,
authors of academic textbooks prefer to make money
from sales of their textbooks,
rather than writing a textbook which is available freely without cost.
(I don't have any statistics to back up this assertion.
However, throughout my undergrad and my PhD studies,
in about 95% of the courses which I took,
the prescribed textbook was published by an academic publisher such as
McGraw-Hill, Pearson or Springer.)
Closely related question:
Massimo Ortolano
claims in this comment that most authors would not be able to make much money
from sales of academic textbooks they have written.
Can someone give me an estimated amount of earnings per textbook sold?

Comments are not for extended discussion; this conversation has been moved to chat.

Your "closely related question" should belong in its own question. But it is a hard number to assess.

Three other closely related questions: why would people write open source software for free? Why would people give tutorials in conferences for free? Heck, why would people write journal articles for free and they will be sold by the publisher for high amounts of money the author will never see? I'm sure if you figure out the answer to these three closely related questions, you will realize what the answer to your original question was.

@juhist Why would people give advice to strangers about working in academia for free?

As a general rule of thumb, common in anthropology (even if you can get untrue responses) you can always ask the person himself. In this case you got lucky. All the better.

This is actually reasonably common with more advanced mathematics texts. Plenty of authors (Allen Hatcher, Anders Kock, Ravi Vakil etc.) put their textbooks online for free, and even those who don't put up a final version, still often put a close-to-final draft online for free.

A similar question I have wondered for a long time is that how does the author obtain copyright if he or she does not publish in traditional press! In addition, some books are published in a traditional press (having an ISBN), but are freely available (legally), which is also strange!

Related: https://gamedev.stackexchange.com/questions/166313/why-are-people-developing-and-publishing-games-online-without-charging-money

As the author of this particular free textbook, I can say that the previous answers have covered things pretty well.  "Introduction to programming using Java" started in 1996 as a set of class notes written in HTML with embedded Java applets -- which all seemed pretty exciting in the heady early days of the Internet.  I had published an earlier textbook in the usual way, and made not much money from it, which is true of the large majority of published textbooks.  I had recently been promoted to full professor, possibly the most secure job in the world where the only further promotion available to me would move me into (shudder) administration, so it would make little difference to my career if I self-published a book instead of submitting it to a regular publisher.
I lost creative control over my regularly published textbook.  The copyright was assigned to the publisher until it goes out of print, which it will probably never do in these days of print-on-demand.  There has never been a second edition.  My Java textbook, on the other hand, has gone through seven versions and has been updated fairly regularly.  I get the ego boost of hearing from people all over the world who have read it (something I can never seem to get most of my own students to do).  The web site still gets hundreds of visits every day.  It has certainly had more impact on the world than if I were selling it.  And if someone doesn't like it, I can politely point out that they can write their own textbook, or even make a modified version of mine.
So, my main motivation was to write a textbook that I could use in my own courses.  Selling it would make me very little profit.  And since I use free software all the time, it's also a way that I could give back something to the open source / creative commons community.

I never expected to get an answer directly from you, the author himself! Thank you for sharing your knowledge with us.

+1 for copyright issues. With traditional publishing, you lose control over your book for pennies. It's almost worth just giving the book away to help people

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For the regularly-published textbook, does the publisher have an economic motive to perpetually retain copyright ('evergreen') the book by printing-on-demand and never revising it? Kind of like Disney?

If I may ask: given the poor revenue of published books, may the revenue you get from your website traffic be higher in the long run? years of advertisement and being linked from all over the internet must bring back some money, and maybe more than the published alternative...

@ΈρικΚωνσταντόπουλος: Rep isn't everything. Upvotes can still help towards badges (tag badge, great answer, ...) : David J. Eck got 6 badges from this question alone. Anyway, he's a full professor and a known author. He probably doesn't need much more recognition. He could play guitar in a famous rock band, though :D

@Shautieh He hosts the book on his universities .edu server.  It doesn't appear to have any direct monetization on the pages (my blockers give it a clean bill of health).  I can't rule out indirect income (eg speakers fees related to the book) but the page doesn't appear to be generating any income itself.

Just having read the question, I would not have expected this to be under an open license. This is of course an important distinction.

Cory Doctorow has expressed similar sentiments.

I don't know why Eck made his book freely available, but I can tell you why I make my course materials freely available, and will continue to do so even if I ever take the final step of turning them into a book.
Because I want as many people as possible to use what I've written.
As others have pointed out, the expected profit from publishing a textbook is minuscule, especially a textbook in a well-worn topic like Java programming or algorithms.  By making my notes freely available instead of selling them, I potentially lose a small amount of money, but I gain a significantly wider audience. And that wider audience justifies, in my mind, the thousands of hours that I have put into writing, polishing, illustrating, rewriting, and maintaniing them, far more than any monetary compensation would.

And even from a totally economic/selfish standpoint, you can probably obtain much more benefit from the prestige given by your book being widely used (and it's possible effects on your career) than you would earn from publishing it.

@Ben Crowell Images in Wikipedia have a different license than Wikipedia text. You can use them even if your license is not open, as long as you properly attribute the image and publish it under the right license (details may vary according to each image license).

(Thanks for the link to your materials, and making them available! It looks like great stuff and appreciate it very much!)

As soon as I saw the name Jeff I immediately knew the link is linking to algorithms.wtf :) Although I didn't take CS374 with you, your name still appeared everything in the lecture notes.

Other answers are right but I would add about the selfish economic point. Authors get about 10% of cover price, and most academic books aren't likely to sell more than a few hundreds of issues. Therefore, a single author can't expect to get more than a few hundreds of euros or dollars in the whole lifetime of a book.
In the other hand, academics need citations, since most promotions and grants are directly or indirectly linked to citations. In fact, a large part of academic work is writing papers that aren't paid, mainly to get more citations. Publishing a book and making it widely used by distributing it for free can attract more citations than journals. Furthermore, the prestige boost that a widely known textbook produces may lead to collaborations and citations that promote the author's career, which can lead to larger income than the one lost by giving away the book for free.
Furthermore, self publishing a book in Internet is easy compared to trying to find an editorial wanting to risk their money publishing the same academic book.

10% of net, not gross, and for a paper book, net is half of gross or even less. Also, it is literally easier to write a textbook to use in your course than to choose someone else's and plan the course around it. So why not give it away, you never wrote it for money anway.

@KateGregory: Don't know if there's a typo, but the assertion "it is literally easier to write a textbook to use in your course than to choose someone else's and plan the course around it" is very false IME.

I've done it. I did it because I was fed up of trying to find a book and the students always hating it. I've written over a dozen books. The effort of working around a flawed textbook is huge. Writing one came very easily to me.

Authors need citations -- Yeah, but citations to (computer science) textbooks don't really count.

@JeffE Citations, unlike dollars, have no particular universal value.  That is you can find promotion committees or even people in charge of hiring that will literally look up your citation count or h-index without considering it any further. A book cited 1000 times will then be worth a lot to you at that particular institution. As a side but related note, many academics fear the day that Google implements a "remove self citations" feature from Google scholar.

@Lembik: Google Scholar should have done that by default!

My professors always made us use their own written books and make us pay a lot of money for it. That always felt wrong: take the course of a professor, pay a lot of money for the mandatory book the professor wrote himself. I like this way a lot better.

Also for the same reason that underlies much of the work of initiatives like open-source software, Wikipedia, Doctors Without Borders, OpenStreetMap, Open Science... and even StackExchange: to give something back/advance the field/help others...

Someone who is entering a situation where money is no longer a significant priority... perhaps an aging professor who is monetarily comfortable but wants to leave a larger mark on his field as sort of a final legacy... or someone facing new health issues who is suddenly very aware of having limited time.
A professor who is frustrated that many people (either those in or coming into their field, or even those in the general public) don't have a better understanding of some important principles in their discipline, and who hopes to change that.
Someone who believes that furthering the field by simplifying information will eventually result in growth or advancements in the field that results in greater opportunity for them (probably most pertinent in relatively small/nascent fields).
Those passionate about seeing information and opportunities better available to those with less resources, such as inner-city kids or developing nations.
Those doing so out of some sort of religious conviction to give to/serve others.
Someone moved by a sense of gratitude from all the benefits they've reaped from their years in the field.  You see this a lot in sports... people talking about "giving back to the game".  No reason you wouldn't see the same in computing subjects or sciences.
Someone frustrated by some other reality... perhaps an overall lack of intellectualism in society... or political policies that they see as against their field or education in general... or being pigeonholed into work or research that they don't feel is very useful... or a company/university that blocks wider endeavors (and so they put out such a textbook with their free time).

In the end, many of these alternative motivations seem to boil down to one principle: be the change you want to see in the world.  And hooray for that!

I upvoted your answer because it so exactly describes why my forthcoming book will be free.

Or with a lot of the Free software - I need this tool/program/whatever. It really has no commercial value, or would need too much work to give it commercial value, so here it is.  Only hard part is picking an appropriate license

Just another echo of other answers and comments: I write to communicate. For the moment, at least, there is an amazing low-cost internet, which allows me to offer up whatever I write. Really, in the context of academe from 30-40 years ago, this is unimaginably wonderful. Not so many of us wanted to make money, but we did want to be able to tell other people what we'd thought-of.
Yes, to be able to think in terms of communicating ideas, rather than in terms of some variant of profit, is a luxury.
(There is too much to be said here... It disturbs me that more senior academics so fail to communicate... or that young people so disregard... or... Dangit.)

Why would an author distribute his textbook for free?
  Almost always, authors of academic textbooks prefer to make money from sales of their textbooks.

Multiple kinds of "non-economic" incentives would make an author still write and publish for free: enjoying the experience of writing and publishing, generating discussion, leaving a legacy, altruism, etc.
If we restrict ourselves to economic incentives though, it has long been the tradition that a reader would pay for a book and that a part of the money would trickle down to the author. This changed with the internet. It is now really easy and convenient to find any popular data for free, whether it be books, music, movies, or anything of the kind.
Cory Doctorow wrote a great book about the subject "Information Doesn't Want to Be Free: Laws for the Internet Age". Long story short, in the current environment, creating new information is similar to being a street performer: anyone can enjoy the show, anyone can choose not to pay. While authors used to enjoy more direct economic rewards, nowadays the rewards are pushed more towards donations and gaining social capital and recognition.
It's no surprise that you mention a programming textbook. Computer people are at the forefront and are more aware of this reality, as exemplified by free softwares and websites such as StackExchange.

"enjoying the experience of writing"... you misspelt "the experience of having written".

"enjoying the experience of writing"...tenured professors are already being paid to do the research and write the books. Unless they write those books in their free time.........

I recently started reading a great freely available textbook named "Operating Systems: Three Easy Pieces".
Remzi H. Arpaci-Dusseau, who wrote the book together with his wife Andrea C. Arpaci-Dusseau following a shared experience teaching the Operating Systems course at the University of Wisconsin-Madison, offers a well-written explanation about what led them to create the book in the article The Case for Free Online Books (FOBs): Experiences with "Operating Systems: Three Easy Pieces". This article concludes with the following bullet points:

Linkability. Classic textbooks trap their material inside of expensive volumes, making it difficult to link to or learn from unless you are dedicated enough to buy the entire (expensive) thing. FOBs make their content available to all, enabling linking to chapters from other sites; Google searches will find your materials.
Broader Readership. As related to the previous point, classic    textbooks are (usually) bought for class. FOBs can be perused by anybody interested in a topic that the book covers, and thus more likely to be read by more people. This type of casual usage broadens the audience. If your goal is to deliver information to as many people as possible, free and online works better.
Partial Usage. Classic textbooks almost mandate usage of the entire book; it would be cost prohibitive to require students to buy three different books, much less one. FOBs enable usage of subsets of many books, perhaps pulling together a whole that is better than the sum of the parts. While there are reasons to use just one book (style and tone, for example), there could also be reasons to pull together materials from various different sources.
Frequent Micro-Revisions. Classic textbooks are revised with great effort, and often for the wrong reasons (e.g., to force students to buy new books instead of used    ones). FOBs evolve as they need to, and when they need to. Indeed, we update chapters regularly thanks to feedback and comments from random people on the Internet.
Just Feeling Good. Making a free book simply makes you feel good, like you are doing the world a (small) service. Every email you get saying "good job!" or "thanks!" makes you smile. We've received hundreds of said emails, and appreciate each and every one.

Arguably, writing books for profit/ promotion/ prestige is a violation and corruption of the scientific method. Descartes, Discourse on the Method, Part 6:

And so I have had to give up the idea of completing physical science
  all by myself; how far I get in the knowledge of nature will from now
  on depend on how many of these crucial experiments I am able to
  conduct. I was going to make this known in the book I had written, and
  to show there how generally beneficial such experiments could be,
  presenting this so openly and plainly that virtuous people would be
  obliged both to report to me the experimental results they had already
  achieved and to help me to work on the experiments that remained to be
  made. I mean really virtuous people — ones who desire the general
  good of mankind — not ones who merely claim to be virtuous or are
  merely thought to be so.

The quotation doesn't support your claim.

I disagree. Or I wouldn't have quoted it.

"… so ... that virtuous people would be obliged both to report to me the experimental results they had already achieved and to help me to work on the experiments that remained to be made." There is as much a promotion/prestige aspect here as there is a "furthering the general good" aspect. Why report to him? He's clearly positioned himself as an authority in the field. Of course, that's not surprising for Descartes, a man who refused to accept the authority or relevance of any philosopher who had ever come before him!

@CodyGray: That is addressed later in Part 6.

The answer is good and could be better if it had an additional argumentation of why such quote is relevant and what other section supports the main idea. Also it resembles a famous short text by Richard Stallman. Science must push copyright aside.

@CodyGray my reading is that the truly virtuous would be obliged to report to him, not because he is an authority, but because he had "[presented his results] so openly and plainly".  He is stating there is a cycle of virtue in which people are morally obligated to donate the results of their scientific endeavours to each other for the "general good of mankind".

@Chan-HoSuh, it seems to me that what he has presented "so openly and plainly" is the argument that the knowledge of nature depends on conducting experiments, but that's not really the key issue. The key issue is that this is an argument for journals to be free, not textbooks.


text:
How to support a student whose aspirations I don't support?
I am advising an outstanding graduate student who is currently doing a summer internship with a government agency. He is also applying for a permanent job with the same agency, for which I was quite proud to recommend him strongly. That said, his prospective employer has been the subject of recent news reports which have led me to oppose its work.
I will certainly not renege on my duties as an advisor. But I don't have a good poker face, and I'm afraid that my changed attitude will be all too clear. What would be the kindest course of action? To share my thoughts once and once only, or to keep my mouth shut?

When in doubt, be honest.

You advise, he decides.

An advisor should never ever force his or her political opinions on students, for whatever reasons.

@user774025 There's a big difference between forcing one's views on someone else and giving one's opinion/advice.  I would be very upset if my advisor didn't advise me.

@SteveP.And I would be extremely upset if my advisor hinders with my future aspirations because of some political or non-academic reasons.  And there is nothing to really to "advise" here.And whether an agency is "good" or "bad" is just a matter opinion.

@user774025 - I don't think that's actually a supportable claim, that an agency's value is always "just opinion"--unless you also mean that it is "just opinion" that people should not be imprisoned, killed, etc. on a whim or out of bigotry or whatever.  Agencies tend to have good and bad aspects, and there's usually some room for disagreement about which is which.  But there have been some, in some countries, where the positives are very hard to find indeed, and many more where the negatives outweigh the positives.  Maybe "opinion" is true in this case, but not in general.

So, he asked you to recommend him for the permanent position? Please clarify.

I don’t really understand what part of your “support” your question is about. In short: is the problem how to support him personally (in your discussions with him, in your work relations in general), or how to support his PhD work, or how to support his job application?
For his PhD work, I hope you are able to prevent outside circumstances from impacting negatively your work. As an advisor, this probably happens at some point with any student… and  any coworker, really.
For his job application, you don't need to state to support his future job, just to say he would be excellent at it. Just to give an example, stating that “Dr. Martin has all the skills necessary to excel in numerical simulations of deep offshore oil drilling” doesn't require you have to state “I strongly support offshore drilling”, nor does it imply it. Moreover, most recommendations are done in written.
Finally, regarding overall personal support throughout his graduate studies: that's a bit harder, but you truly have to put it past you, and it may not be easy. The best approach is clearly to be upfront with him: discuss it, preferably in an informal manner (i.e. don't make it a big deal). Points that seem important to mention:

I have strong feelings about your future employer, and I think it is best that I am frank with you about it.
It shouldn't change our work relationship, and I don't expect it to. I continue to support you wholeheartedly.
If you think you notice a negative impact in the future, please come and discuss it with me, we'll work it out.

But honestly, it's not a nice situation to be in. I'm a bit surprised as to how what could gather so much distrust from you that you cannot simply separate it from your work.

About the last paragraph, I'm gonna venture  a wild guess: NSA ;).  If that is the case, I think the supervisors opinion on a basically political matter should not influence the student future... It only matters what the student believe in...

@NickS It only matters what the student believes in - keep in mind that one's beliefs change as one gains new information. It is our job as educators to give new information.

@NickS I second to earthling. I am over 60 years old. My belief in that matter (as most people here, I think I know what OP is talking about) changed three times since my college days.

While I understand the distrust in that particular matter, the point I am trying to make is that opinion on that matter change and are probably split. Do you want to force on the student an opinion which changed few times, and which (improbable but not impossible) could change again?

@NickS - I completely disagree.  This will degenerate into an example of Godwin's Law pretty quickly without care, but many of the worst abuses in history arise out of a culture of not calling people on less-than-admirable behavior.  McCarthyism was at the time a "basically political matter", as was the internment of Japanese Americans (both in the U.S.).  The NSA (or other agencies) have a much better shot at being and staying positive and non-abusive if the people going in have felt the concerns and pressure of those outside.  Concerned advisors should influence (but not determine).

@RexKerr The issue is a little more complicated, while those are some very good examples, how many times different agencies/people get called out and were painted as the ultimate evil because of the wrong reasons? Also, keep in mind that there are always at least three sides to every story, and in press we only find one, most of the times exaggerated... Anyhow, the main issue in my opinion is that there is a very thin line between the advisor advising, influencing and deciding,this line is completely different from student to student.I completely agree that people going in should be aware.

@NickS - Sure, agencies can be unfairly blamed and advisors can be wrong.  Using that as an excuse to engage less is foolish, though, as history shows.  You want a more robust dialog, more sharing of opinions, not less.

If your student is very talented perhaps you could help him to find a better position than the one with the government. If you know what your student cares about then find a better use for his skills and propose it to him.
If that doesn't work you could always have a heart-to-heart talk with him to help him to see your concerns.
I believe it is our job to educate our students on more than simply module content (should teach critical thinking, proper citation formats, etc.). I would not recommend cramming your value structure down his throat but I think giving him your ethical perspective to think about is quite reasonable.

In my opinion it is a tough situation, and no answer cannot be complete without knowing more details about the situation.
Before deciding there are few things for you to consider. As earthling said, we should typically educate our students on more than just academical things, but you should also keep in mind that when it comes to many government agencies, opinions vary a lot. Is not necessarily that our opinion about one agency is the right one.
What matters most is your student's goals. If he really likes the position, and it fits his goals for the future, that should matter more than your personal views [there are few exceptions to this rule, if the agency contradicts the basic morale codes of everyone and everything, again it really depends on particulars of the situation].
Last but not least, I should point to you that your student worked there for few months, his inside knowledge about the agency is most probably much more accurate than what you found out in the news. Since he applies for a permanent job there, I would guess that he enjoyed the experience, and he didn't find anything wrong with its work.
As you are the only one to know the specific details of the situation, you should try to find the answers alone, we can try to guide you towards it but don't value too much the very general answers we can give, they might not apply to this situation.
In my opinion there are few things you should ask yourself, answering those will tell you what to do:

What does the student really wants?
Is this a good opportunity for the student or not?
Do you think the student can get a better position? Note that better should be "better" in his opinion, not yours?
Is this agency really bad, or just your opinion? How much can you trust the news you heard about this agency?
What does your student thinks about these news?

“Is this agency really bad, or just your opinion?” — duh? How can an agency being “good” or “bad” not be a matter of opinion?

@NickS - Agencies essentially never contradict the "basic morale codes of everyone and everything" (moral?) because the people there would refuse to do the work.  But it's not hard to develop an internal set of morals that isn't consistent with those on the outside.  This sort of groupthink is an extremely strong trait of humans (see, for instance, our susceptibility to cults).  To keep a subgroup grounded, you need to set your threshold to be much lower than "everyone and everything".


text:
Do editors ever "overbook" referees?
Is the following common? An editor for a journal sends a paper out to, say, three or four referees. After getting the first two referee reports, the editor makes a decision and tells the third and fourth referees not to bother (so that they have potentially been wasting their time).
I can see this happening in some circumstances, e.g. if one referee finds a substantial error. However, I was asked to referee for one journal, and I get the impression (which I have not yet confirmed) that they typically send the paper out to lots of referees and take only the first couple of referee reports.
This practice, if it is indeed what they are doing, seems likely to produce quick turnaround times, but also seems disrespectful to referees who might be half-finished when they are told their reports are no longer needed.
Is this common? (In particular, in mathematics?)

There was a discussion of this practice in Sociology journals recently on the scatterplot blog.

I've heard this is common practice at MPDI publications. More generally, I think the former circumstance is more likely.

I think this one will be very hard to answer with hard data. So, I'll just throw in some anecdotal evidence, along with a few things learnt from some editors that I know.
From a reviewer point of view, it has happened to me exactly twice in a decade (i.e. very rarely) to receive an editor's review saying “I've reached a decision based on input from other reviewers, and you do not need to review the manuscript”.

The first time, the email came as my review was already overdue (a week or ten days), so I suppose the editor asked another reviewer when I didn't reply on time, and the new reviewer was fast to reply.
The second time, it was sort of the other way around: I was asked to review a paper, then 5 days later the editor wrote, saying the reviewer who was uncommunicative had finally replied, and my review was no longer needed. He apologized profusely, and offered to actually wait for my review if I had started doing it and wanted to finish. (I was happy to let it go.)

I think for an editor, growing a list of trustworthy and willing reviewers is crucial. So, they simply cannot make them work for nothing! (pun intended)

Let me point out that, as a referee, you could have been "overbooked" many times and never know it: if the editor does not write "I've already reached a decision" to you, there is no way for you to know that you have worked for nothing.

@FedericoPoloni I agree there is no way to know systematically, but in most cases articles for which modifications are advised/requested will come back for a second review, in which case you know whether you voice was heard

I'd guess that the first time, there was more than one reviewer invited, so the editor made a decision based on the reviews which had already been submitted.

An editor that cancels the review for a referee within the "normal" referee period will end up angering the referee and likely losing her as a reviewer for future papers. So this is a very unlikely practice.
Many journals will request multiple reviews (three is not uncommon for many of the journals I submit to), and will wait until the end of the standard review period to return any comments. If two of the three (or four) reviewers have returned reviews, and the others haven't, then the process can reasonably truncated at that point. (If you're behind schedule, you don't really have a right to complain in this case!)

To add support to your last point, I recently had an editor base their decision on only 2 of 3 reviews because the 3rd reviewer was quite late.

I know this question was asked and answered long ago, but I thought it might be useful to contribute some real data from an editor / program chair point of view.
Because reviewers are volunteer labor, they are unreliable.  I personally find that I get about a 75% rate of return on useful reviews.  For journals, pretty much every review that is actually returned is useful, but many do not return.  For conferences, where the PC members have signed up in advance, the rate of return is much higher, but there are a significant number of essentially useless 1-sentence reviews that give a score but no justification.
At the same time, an important dirty secret of the reviewing process is that there is rarely a fixed number of reviews that are actually necessary.  In the venues in which I am involved, typically 4 reviews is best practice, 3 is acceptable, and 2 is only supportable if there is very strong agreement on a clear accept or reject.
Moreover, when you are recruiting reviewers for a journal submission, the reviewers don't necessarily respond to the request to review immediately.  Thus, I will typically significantly overbook the initial set of requests, asking 6-8 reviewers.  Generally somewhere between 2 and 6 of those will accept, from which typically 3-4 will actually return reviews, giving me enough for a well-justified decision. If things go unusually well and end up with five reviews, that's just fine and will make the author feel we've taken them very seriously, but I'm not sure such an overabundance has ever actually happened to me.
If not enough reviewers accept, I have to send out additional batches of requests, all of which can lead to a significant skew in the times at which reviews arrive.
Moreover, it is an extremely rare reviewer who will return a review significantly in advance of the due date.  So for me at least, overbooking isn't to get quick turnaround time, but to prevent excessively slow turnaround time that can happen when you need one more review and a reviewer drops out at the last minute, forcing you to start the clock all over again on a new reviewer.
Because it is all volunteer labor, however (and because I do my own turns as a reviewer in other venues as well), I am very mindful of the importance of not taking a reviewer for granted.  If somebody has promised me a review, I want that review.  It is only when they have become significantly late that I will send a question along the lines of: "I am currently only waiting on your review before I can send a decision to these authors; are you still able to provide a review?"  The only time when I simply cancel a review request is when the reviewer has become repeatedly unresponsive, and then they get a black mark for unreliability in the appropriate set of organizational records.

Inviting more reviewers than is necessary is very common. In fact I'd be surprised if most editors didn't do this. The reason that you can't expect invited reviewers to always agree to review your article. Some of them will decline, some will wait a long time and then decline, and some will never respond.
Let's say your journal needs 2 reviews to make a decision, and you wait a week to hear back from your reviewer, and you start by inviting two reviewers. Suppose this happens:

You invite 2 reviewers (days past = 0)
After two days, one reviewer declines to say they have no time; the other doesn't respond. You invite one more reviewer. (days past = 2)
One week later, you invite one more reviewer, who also declines after a day saying they have no time. (days past = 8)
You invite two more reviewers, who don't respond. (days past = 15)

So it's two weeks after manuscript submission and the manuscript hasn't budged.  You could argue that you have been respectful to your reviewers, but someone else could argue that you have been disrespectful to your authors.
What is not common is for journals to make a decision with reviews outstanding. Typically in this situation the journal will wait for the reviews, especially if it's only a short while till the outstanding reviews are due. Exceptions apply. For example, if after 30 days you have received two reviews, and then a reviewer who didn't respond suddenly accepts the invitation, with a review date 30 days into the future. In this scenario the journal could reasonably ask the reviewer to cancel.
Concerning this:

referees who might be half-finished

This is much less common than one might think. See source. The median amount of time spent per review is 5 hours. Unless the journal cancels exactly during these five hours, the reviews won't be half-finished; furthermore, if they do cancel exactly during these five hours and the referee says they are half-finished, the journal can probably wait an extra five hours before making a decision.
Granted, this might not apply to mathematics, where as far as I'm aware the time taken for review is measured in months, not hours.

My experience in reviewing for math is that the actual in-depth reviewing takes at least a couple of days (say 15 hrs total time). These hours are spent over the course of say a week, so most of the time is taken up by waiting for a suitable week (or to get to the front of the queue). However, if I have a 3-month deadline and an editor cancels after 2 months, it is pretty likely I have started to review.


text:
Probation in the UK
In the next two months, I am supposed to devise a Probation Professional Development Plan for a lectureship in the UK. People often declare probation to be a "paperwork exercise" but looking at the documents, I am to set my own goals for what I want to accomplish and I am supposed to make it challenging yet realistic.  There are many questions I have for this exercise.

What happens if I am unable to deliver on my research goals? I am ambitious on what I plan to accomplish (hopefully many papers and grants), but it seems like not the best location to demonstrate this ambition? The documents seem to support you being very ambitious, but if I make bigger goals will I be penalized if I don't achieve them? This whole part of designing my own goals and then being graded on it is very counterintuitive for me.
In what ways should I expect clearing of probation to be decided?
How do probation reviews actually work in practice?

Edit: changed tags due to comment's suggestion.

I gather (based on a quick nose around your SE profile) that you're in pure maths: you might want to make this extra detail clear in the question. I haven't got a quick and useful answer off the top of my head but the first thing to do is to is to talk to whoever has been assigned as your "mentor" as a new member of staff, and to get as much advice from others in your department who have been through the same process. (Unlike e.g. tenure track, there is no sense that you are competing against other newly hired staff, except in the very vaguest "not wanting to look too much like a rube" sense)

BTW, I think "tenure-track" is a potentially misleading label. Having been on a tenure-track in Canada before taking up my present post in the UK, and having talked to friends about the tenure-track (in maths), passing probation in a UK pure maths department is nowhere near as formalized and demanding a process as going up for tenure. If you were thinking of the two as equivalent, then perhaps you might be putting yourself through unnecessary stress

@YemonChoi That very much depends on where you are and what you do - in my department probation review is very much seen like tenure review. You get 3 years. You have challenging criteria (mine were publish 3x3* or 1x4* paper first or last author, obtain a qualification in teaching and get at least £400k in research funding) and people who don't make the criteria are sacked.

@IanSudbery Thanks for the warning and extra data. However, I did say "passing probation in a UK pure maths department" and I stand by this. The OP is going to be working in a maths department (admittedly with some math phys leanings) where I know one or two of the people already there. In particular I think the OP is almost certain to be asked to apply for a EPSRC-ish grant but probably won't be required to succeed as a condition to pass probation. Finally I reiterate that probation in a UK pure maths dept is far less rigid and demanding than the average corresponding tenure application in NA

Obviously if you know the department in question, then i'm sure your advice is the most relevant. My experience so far of the UK system has been that it is almost impossible to talk about the "average" department, even within a discipline. I do however think that it is become more common for probation to be less of a "paperwork only" exercise, and probation committees, requiring evidence packets etc, more common.

@IanSudbery This last point is true, I may have chosen my words poorly and implied it was all still waved through by some kind of "gentleman's agreement" -- as you say, this is no longer the case, and suitable evidence/portfolio stuff has to be assembled. (Your area is going to be a lot tougher than mine, for instance!) But tenure applications feel to me about half an order of magnitude worse, at least

I'm going to describe how they work in principle, and at my institution. As the comments from @Yemon Choi note, you'll really want to talk to your mentor to get a better understanding of how things happen in your institution.
First, the idea of designing your own goals and then being graded on it is central to performance reviews at all levels in my institution. After the initial document, these would usually be discussed and revised in each (yearly) meeting, but it's still up to you to put your goals down in your own words. This is, after all, part of what you do in writing a grant proposal: set your own goals for where you're going to get to.
Second, as far as possible, you should focus the goals you, personally can achieve. For example, you can apply for 2 external grants in a year1: you can't control if they're accepted or not. By making sure you list as goals what's under your control, you minimize the chance of not achieving them.
Third, as noted in the comments, this is not (meant to be) a competitive process. This should be about helping you develop and fit in as a member of staff. It should be about identifying which of your goals you have the skills and knowledge to complete, and which you need more training for. Have you been on the required training courses to administer a research grant, or to supervise a graduate student? Have you got the experience and skills to manage a research group of the size you want (more training to find and take there)? By saying where you want to be in terms of your career, your mentor and your reviewer should be able to suggest what you (and the department, and university in your support) need to do to get there. There's clearly a distinction to be made here between short term plans (do before the next review), medium term (before the end of probation), and long term (before you apply for promotion).
Fourth, make sure that you have plans and goals for all aspects of your job. If you're on a balanced role (as I would expect as you've termed it a lectureship), I would expect a 40-40-20 split across research, teaching, and administration (or service). Whilst the latter two are predominantly duties that are given to you, you should still have medium and long term goals as to how you want to develop your skills and what direction(s) you'd like to go in2. If nothing else, I'd expect "completing the required teacher training course" to be one of these.
On how completing probation is decided, and on probation reviews. Typically there will be a one-to-one meeting with your line manager on a regular (6-12 month) basis. You discuss your progress, saying how it aligns with your goals, and how your goals have adjusted. If, by the end of your probation you're working at a level of a lecturer in your institution, the line manager will recommend you progress. They may consult with other colleagues, particularly your mentor, but I believe the decision is usually down to them alone.
So, you should know what the role descriptors are for the lecturer role at your institution: I would expect that to be on your HR department's website or similar. You should also ensure at each one-to-one meeting that you have an explicit idea of how you're matching up to your line manager's expectations.
I'm not going to cover how the probation process can go badly, or go wrong, as I've very little experience in that, and it seems to be very case dependant. I would just note: this department has already put a lot of time, effort and money into hiring you so they want you to succeed. If you keep communicating well with your mentor and line manager, then you'll usually find it straightforward to fit in and meet expectations: that's exactly the point where probation becomes a paper exercise.
1: You won't have full control over submitting a grant, as your finance department, and line manager, and... will have a say: but you get what I mean, I hope.
2: Even if you want to focus 100% on your research, you can use these goals to attempt to control what tasks and duties you're given in order to get the "least bad" solution for you. Being, or at least appearing, willing to take on your full share of these duties is an important part of fitting in within the department.

Thanks. I was wondering what it all meant. This actually sounds a lot like what we did (retired now) for post tenure annual review. Faculty makes a plan, revises it with advice from the dean and is then at least partially evaluated the next year on how well you fulfill it. The dean can suggest you do more when you work it out, of course, and can detail consequences if you don't. The results were mostly for salary increases since this was post-tenure. I found it to be very useful. It wasn't very time consuming after the first year since you develop your own boiler-plate for next year(s).

+1 for ask your mentor! Actually, ask several people in case your mentor has a skewed or outdated perception.

I think it is important to note that the process @Ian above outlines is not how it works everywhere.
Where I am you do set probation goals in discussion with your head of department, but there are some base line goals you have no choice over. For us these notably included securing (not just applying for) a full RCUK project grant sufficient to employ research assistance for 3 years. Success or failure at probation is decided by a panel of all HoDs in the faculty, along with the head of faculty. People can and have failed probation, sometimes against the wishes of the head of department.
All this is to say that it very much varies from place to place, and even time to time (strict criteria for probation is a new thing here) and you very much need advice from someone local.
You might be interested to know that a group of new PIs in the UK is currently processing data from a survey of how new hires at UK universities are treated, and one area of focus was probationary requirements. Look out for the results soon!

Did you mean @Yemon ?

BTW I completely agree that advice from someone in the dept (and if possible the faculty) is crucial, and completely trumps anything I might have said above!

No, I did mean the other answer to the question by @Ian.

+1 for pointing out this Varies Substantially. So you should definitely discuss with multiple people in your own department. By asking, you look wise for understanding how much the process varies, not foolish for being ignorant of a standard practice.


text:
Postdoc at a research hospital for a physicist (non radiation)
I am a physicist with a background in computational physics and imaging, and I received an offer for a NIH postdoctoral fellowship at a very good research hospital on the East Coast. I would join a group of medical doctors working on a particular protein, and I am trying to decide if it would be a good choice career wise. The lab has good instruments, but I am a bit worried of being the only one with a quantitative background in the research group.
Is there anyone who successfully did the physics-medicine transition? And is it possible to go back to more basic science after a biochem-med postdoc? Other things I should consider?

As always it is good to know what do you want after. Being a physicist who is very well trained in medical imaging and has good connections to doctors seems to be a good niche for me, that can lead to jobs and foundings,  but if you want to be a particle physicist after, it has less appeal, i understand.

I'll answer the second two questions.

Is there anyone who successfully did the physics-medicine transition?

Yes, medical physicists exist.  Some are specially trained in that field, others made the transition.  A few years back they were in high demand.

And is it possible to go back to more basic science after a
  biochem-med postdoc?

Possible, yes.  Probably few people want to because it's likely to lead to a pay cut, as last I heard there was high demand for medical physicists.

Medical physics is a strange field.  IMO, mandating that physicists come from CAMPEP accredited programs and that you must complete a CAMPEP accredited residency is not helping the field.  While there is a demand for radiation oncology physicists, there is a bottleneck to get the residencies.  It's a great field to be in for research, but I would recommend someone give it serious thought before going down the road of ABR certification to be a clinical physicist.


text:
Is Academia.edu useful?
I received a mail today from Academia.edu (a site I wasn't previously aware of), asking me to confirm that I co-authored a paper with a colleague.
Having looked into it a little it sounds like it might be a useful site - the idea of a "social network for scientists" is one I've seen the need for in the past. However, partly due to bad experiences with the seemingly similar ResearchGate, I'm also skeptical.* Without signing up for an academia.edu account the site doesn't offer much information, so I would like the following information:

What specific features does academia.edu offer to its users?
Is it genuinely useful for any of the following purposes (each of which seems genuinely needed)

as a platform for networking with academics
for discovering relevant research
as an effective system for post-publication peer review
for organising references among a small team of people working on a project

Will it send out mails to my colleagues without my express and explicit permission? (I.e. are the mails I received today the result of a deliberate action by my colleague, who is aware that I will be emailed and wishes me to join the site; or are they essentially spam from a social networking site aggressively trying to expand its user base?)
It's clear from its Wikipedia page that it's a private, venture-capital funded company. What is its business model?

In short, is this a site that has some genuine utility for academics, or should I just ignore it?
*I've never signed up for ResearchGate but I regularly receive spam from it purporting to be from my colleagues, who aren't aware that it's being sent on their behalf. I would be mortified if my senior colleagues received such mails claiming to be from me, so I won't touch it with a barge pole.

Academia.edu doesn't email spam to your colleagues in your name, so it's got that over ResearchGate. Other than that, I've yet to see much indication that it has sufficient buy-in to be of particular use.

Somehow, I thought it was Academia.SE in the title, and folks here were having an existential crisis!

There is no duplicate to this particular question, but browsing through our previous questions on academia.edu may be helpful.

@StephanKolassa I did that before posting of course, and indeed it was useful - but after doing so I still felt the need for this question.

...a few days later, a new mail: "___'s co-author tags are waiting for your confirmation." Marked as spam, will never touch again.

This kind of question "Is X useful?" is opinion-based, in my opinion. It may or may not be useful at this moment. It may or may not be useful 3 years from  now. It may not even exist a year later.

According to the Academia.edu Wiki page, as of December 2017, 58 million users from around the world. I guess I have to disagree with myself (the above comment I made two and half years ago) that it may not exist a year later.

@Wrzlprmft: I don't have much invested in this question remaining open (rather than closed), but I would note that the accepted answer at the meta post you link to says that "Questions about whether to trust a possibly sketchy organization" should be on topic. While that's not the whole of my question, it certainly is part of it, particularly regarding my point 3 in the question. (In my mind this is now pretty much resolved: Academia.edu definitely is a sketchy organisation and I was right not to trust it.)

@Nathaniel: the accepted answer at the meta post you link to says that "Questions about whether to trust a possibly sketchy organization" should be on topic – Yes, but only if the question is generalised to an entire class of organisations. Your edit does more or less the opposite than the linked meta post.

@Wrzlprmft Sorry, but I think that the notice you added and the pinging of the OP and the answerers,  after more than two years,  are more confusing then helpful and probably not warranted, regardless of the meta question which, in this case, is of difficult interpretation. I really suggest you to remove the notice.

@Wrzlprmft I disagree. It does comment that "these are often something that can be generalized to a class of organizations, like how to assess whether a conference or journal is predatory," (emphasis mine) but it doesn't say they must be generalised in that way in order to be on topic. If that was the intention then the meta post should be fixed, because otherwise the instructions are just confusing.

@Wrzlprmft  but ultimately I agree with M. Ortolando here. I've made a good-faith effort to fix this three year old question in the way you seemed to want. I did this because its answers are doing the community a service in warning of the practices that academia.edu follows. If your intention is for me to turn it into a different question, such that those answers would not be valid (and thus would be deleted), then I would request instead that you revert all recent changes and apply the historical lock, keeping the answers intact. The other option would destroy the value of this question.

I distrust it for an entirely different reason. I once wanted to download a paper, and could only do it if I signed up. I signed up by logging on with my facebook account... Well, academia.edu took my profile information, and, without me knowing it, created an academia profile. With my picture, publications it could find via search engines, and a list of interests that were half right and half ridiculous. I'm a neuroscientist; it listed me as being interested in marketing, among other things. I only discovered this profile about a month later.
Apart from it being entirely unprofessional, I simply do not trust information that is on there, as I have first-hand experience that information on me was wrong.

This is a very good reason to steer clear- thank you for this information.

Same here. I never remembered signing up for an account but yet it has all my interests as listed on ResearchGate along with a paper. I wonder if I could even reset the password.

Having an Academia.edu account (which I'm pretty sure I've had for around 2+ years), I can say that I am not real satisfied with the service. My particular field in social science has a relatively small online footprint, and I thought Academia.edu may be starting to have a big growth when I signed up, but it still has never really caught on with any more than a small minority of my field. This point will come up again in my responses, in that if Academia.edu has more infiltration into your field it could work slightly better.
So for 1, you can peruse the site and see for yourself. Basically a profile page where you can post your CV and other links if you wish, and then upload pre-prints. You can then assign tags of interest to follow for yourself, and follow specific colleagues. Using these links, it has a front page feature, similar to Twitter/Facebook/LinkedIn, but the page is filled with pre-prints of people in your network and of the tags you follow.
The upload of papers is pretty wide open (there is no quality checking), and I've seen people starting to upload syllabi as well. I've stopped uploading pre-prints because of the crazy terms of service. Unfortunately, some anecdotal evidence of my papers suggests that their promotion of papers across the network (and with search indexing) is less rigorous when you don't upload an actual pre-print. Also I've always been a bit annoyed I can't just upload a bibtext snippet to fill in the meta-data.
For 2.1 and 2.2 it would work better if there were more uptake in the field. IMO conferences work pretty well for 2.1, and Google scholar works pretty well for 2.2.
2.3, post publication peer-review is no, it does not offer comments on particular papers. 2.4, managing a bibliography among a research group is no as well (see these responses to that question). It does offer a bare-bones email type system, but that is obviously no better than email to begin with.
3, I don't know specifically. When you have co-authors you do need to verify them.
4, I don't know - it is similar in functionality to LinkedIn and Facebook, so I presume the same type of business model just a different user base.
In retrospect I would not have signed up for an account. I'm happy with posting pre-prints to SSRN, and there are similar sites for a variety of different disciplines. If you want a barebones free personal online website it kind of works for that, but I enjoy having a free wordpress blog that does the job and I have much more control over the content and format of the site. Google scholar works quite well for finding content. Strong networking ties in my experience happen more in conferences and just naturally being in the field over a time period. "Friending" someone on Academia.edu is a bit superficial.

No. Academia.edu is academic spam.
The unsolicited emails I received from academia.edu had absolutely nothing to do with my research. They sent me a weekly digest of utterly random papers that I did not recognize, but they seemed to think might interest me. They also sometimes asked me to confirm a coauthor. This was either someone I didn't know, or someone I did know who made the mistake of using their "service" and thereby unwittingly spammed their coauthors. They do host content, which I guess is a legitimate service, but they generally insist that people sign in to view it, which makes it more annoying than useful.
I clicked the unsubscribe link in their emails and it asked me to create an account in order to unsubscribe! (Is that even legal?) To me, this is a clear sign that they are not operating in good faith. I think they are spammers, plain and simple.
By the way, if you want to unsubscribe from their communications, email the CEO at richard@academia.edu as well as copyright@academia.edu. That worked for me.

I also had an email from academia.edu asking me to confirm that I am a co-author of a paper ("XY tagged you as a co-author on a paper"). I was not 'brave' enough to open the email but could see that the topic was poles apart from any research I might ever have done, so will just delete the email.

I had an email from academia.edu asking me to confirm that I am a co-author of a paper ("XY tagged you as a co-author on a paper"). So I asked the other "author" what it was about since I did not recall writing such a paper with him. He had no idea either, Conclusion: something fishy....

In my experience, Academia.edu is useful mostly for [2] - discovering relevant research. [1] happens mostly through participating in feedback sessions for unpublished manuscripts. Definitely not for [3] and [4], as they are not supported.
Usefulness for discovery comes in 3 ways:
a) The home News feed: you will find out about:

publications of people you follow;
papers read by several of the "people connected to you" (those you follow and also their followees), or papers recommended by one person connected to you;
activity in manuscript feedback sessions. Of course, the quality of the feed will depend directly on how many people you follow and how relevant they are for you. If you follow people whom you know but about whose research you don't care much then your feed will be boring, especially because the 'people connected to you' that they will introduce will be even less relevant to you. Just follow people you really want to know about.

b) Navigating through topics of interest: each topic allows one to see a list of researchers who follow that topic and, more interestingly for me at least, to see a list of papers recently posted under that topic. Keep in mind that topics are user-defined, thus there may be several similar formulations for each subject that you would consider following (such as "humor", "humour", "humor studies", "humour research", etc); it is best to follow them all, as they have partially overlapping communities.
c) Mixed text-author search: jumping from texts to their author's profile, then to other texts by the same author or her co-authors, and so on.
Unlike Google Scholar, where one searches and navigates in a universe of ranked text lists and interlinked texts, Academia.edu introduces the researcher profile as a "bridge" that connects different publications. It is up to you how much you will enjoy this new mode of transport, so to say.
I find it useful to check publications from authors I like, publications I would most likely not have found through a keyword-directed search on Google Scholar. While you could also use Google Scholar profiles to this effect, I find that Academia.edu is more pleasant to look at and also has more opportunities to connect texts with author profiles as you scroll in the news feed or in various lists. For me this text-author jump is the most useful feature of Academia.edu.
d) Last but not least, I find it energizing to look at texts which have been recently written or read by a living person. It gives a human touch to the entire enterprise. Of course, it also anchors literature searchers firmly in the here-and-now at the expense of past decades and centuries, so this is something I have to compensate for.
This sort of discovery works best, I think, for publications which are not in a very specific niche of keywords which you already master and you can search for in Google Scholar. For me, it works for publications that depart somehow from my pattern - eiter by nuancing the topic, or going meta to reflect on methods and the philosophy of the enterprise, or taking a diverging theoretical stance which I do not usually tap into, and so on. This gives me some space for serendipity in extending my scope of thinking.

The next issue of the Chronicle of Higher Education has a piece on academia.edu ... the blurb for it:

The academy has always been a hothouse of invidious comparison. This website makes it worse.