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PhD thesis without acknowledgements
During the process of writing my PhD thesis, I was close to falling out with my adviser, the advice I received from other staff at the lab (including the director) was unhelpful at best.
I have since made up with my adviser and have successfully defended the thesis.
I now have to publish my thesis.
The department says that one can include acknowledgements. All of the theses I have seen in my lab and in my department feature acknowledgements.
Due to this special situation,  I don't quite feel that acknowledgements are called for. Yes, my adviser helped during the first half of the project but then almost completely reverted his stance. In terms of contribution, it is my opinion that he comes out at 0%.
I do not want to address any of the issues in the acknowledgements. I do not think that this is the right place. Likewise, I do not feel like thanking any of the involved people.
Therefore, I would just leave out the acknowledgements completely.
In academia, is this considered worse than lukewarm acknowledgements?
Should I actually care about the acknowledgement, because others do?

Don't you wish to thank your family for the support? Even if your advisor did not help enough, you had some funding right? And someone provided that. Should not be included in the acknowledgement section?

@Alexandros I figured it was rather an all-or-none situation. I'd feel awkward if I mentioned my family but not my adviser.

Short answer: yes, add lukewarm acknowledgements so that nothing is "strange". IMHO, the question is: what will be more useful for you in the future? I'd do is write in a positive way what I hated most, if you feel exploited then thank your adviser for pushing you to reach your limits, if you feel they did nothing then thank them for the freedom you had. Find euphemisms that work (and really look well) and everybody should be happy. IMHO.

You could use instead an anti-acknowledgement. You write: "This thesis was completed no thanks to: ..." then list the names.

In all seriousness, though, I find acknowledgements to be pretty smarmy, especially in a thesis. You should recognize your advisor, but not as an acknowledgement. It should be something like "This work was written under the guidance and direction of X."

@TylerDurden I think that would be the antithesis of a good idea.

This is one of the only times in your accadmic career you will have a chance to give a long grateful rant of thanking. Remember that it is a very finite resource you are giving up. The ability to be publicly and formally grateful only comes around so many times in your life.

Everyone should read the most (in)famous acknowledgment section in my field, Computer Science: http://scsh.net/docu/html/man.html

If he helped you in the first half of the project, how come it counts as 0? I know a guy whose advisor did 0 work (from beginning to end), but got his name on all his papers, and got sincerely thanked in the thesis! didn't he hate doing it? of course he did, but the guy got a decent job at the same department same year he graduated! would that happen if he went all "oh, no ack because it's sketchy"? probably no! maybe he would eventually get the job in a different year in a different place, but who knows? so it's your call, but my advice is to minimize the tension and move on!

A thesis is not a place to solve grudges. It is a professional document that is eternal. As such, it should be handled professionally and gracefully.
Still, I am having trouble why you do not want to have an acknowledgement section. Do you really believe you have done the entire PHD entirely yourself? Even if your advisor did not help enough, you had some funding right? And someone provided that. Should not he be included in the acknowledgement section? Someone also proofread your thesis. You probably also had co-authors in your papers. As you see, there are multiple people that contributed to your success.
But on a more informal tone. Don't you wish to thank your family or significant other for the support? Or your PHD co-students? The people that you share your office with? You have finished a PHD and especially since it probably was a rocky one this a very good reason to celebrate. Do not spoil the moment with petty grudges. Do what you are required to do, be professional and move-on to better things.

I agree - think about strategy for the future, not fairness for the past.

I'm in a similar situation because my "success" isn't any close and if I ever finish the thesis I will feel it completely as a Pyrrhic victory. To be honest, I feel I should apologize to my family for studying a PhD and not going to industry...

"Someone also proofread your thesis"? No one proofread mine, and I don't think any of the dissertations written by my fellow grad students were proofread either, even though most of us are non-native speakers. Who are these automatic proofreaders?

@Sverre Not having a thesis (or any document you want to publish) proofread strikes me as a bad idea. It's not only language; the amount of unclarities and small mistakes others can find is enormous. The author is always the worst at finding such issues. You can asks friends, family and colleagues, depending on their competence and what you want them to check.

@Raphael For sure, proofreading is always positive. I was just taken aback by the automatic assertion that someone proofread the OP's dissertation. It remains the fact that I have come across very few people who have had their dissertations proofread. I don't have any of my articles proofread either. It doesn't strike me as very common. At least not in my field.

In my MSc thesis that I am preparing, I have acknowledged everyone who has answered my questions, my family, computer laboratories, my professors and my classmates. It does not cost the author anything but is of value I think. I really like the acknowledgement part indeed.

@Sverre To be honest I find that quite shocking. All of the departments I have worked in have an explicit policy that anything that will be published with the department/institutes name on it must have been proofread by at least one person in addition to the authors. This is an absolute minimal level of quality control.

@ssmart My work is proofread by... me. And... me. Maybe it varies by subject, but I wouldn't know where to look for someone with time to proofread it for me. Certainly not in my department - I don't have any colleagues who know my subject area. The initial quality control comes from publicly putting my name to the work. The referee is the second level, if it gets published.

1 for this comment. This thread is kind of old but somehow it appeared on the front page, hence commenting here. I sort of understand OP's reason for not including an acknowledgement section (I guess for the sole purpose of NOT thanking their advisor/lab colleagues), but I don't think it will have the effect the OP intended, instead would reflect unfavourably on OP (if there's any effect). like Alexandros said, this is not a place to settle grudges. And certainly not a place to passive aggressively tell the advisor what you really think of him/her.

Not including acknowledgements when it is generally accepted to do so is likely to reflect badly only on you.

I feel the need to record a dissenting opinion on this.
It is my understanding that acknowledgments are not a required component of a PhD thesis.  They are a tradition and a custom, and like most traditions and customs, people participate in them because they find them valuable and enjoy doing them, not because they are obligated to do so.  One answer says that many grants "contractually require you to acknowledge the funding entity".  Yes, but that's a different kind of acknowledgment: for instance, in many published papers that goes on a footnote appearing on the first page, whereas there may (or may not) be a paragraph in the introduction or at the end of the paper thanking various people.  Moreover, a PhD advisor is not a "funding entity" in this sense, and I have never heard of anyone being contractually obligated to thank their advisor.  Let us assume that the OP is not.
After reading advice that amounts to "Yes, you should absolutely write acknowledgments in a way that conveys a positive impression of your advisor.  Since you in fact feel exactly the opposite way you will have to write them very carefully indeed" a few times, I got a bit worried.  I see a personal integrity issue here: really one should not record in a formal document sentiments which are diametrically opposed to those one actually holds.  Moreover, all the comments about the career risk one might incur for not including acknowledgments -- well, I must agree that omitting acknowledgments is a suboptimal career move, but such comments make me even more worried.  It seems to me that many people here are essentially viewing acknowledgments as a loyalty oath that one must make to one's thesis advisor.  That can't be good.  People stood on principle against loyalty oaths in the past, sometimes with cost to themselves.  They were right and courageous to do so.  I'm afraid I see a similar principle here.
My point is this: no, actually the OP certainly does have the right not to put acknowledgments in his thesis.  Is that the best career move?  No, probably not, but it is his choice and he may have good reasons for doing it.  Four final comments:

No acknowledgments at all seems much better to me than acknowledgments which are sarcastic or show bitterness, and probably even better than acknowledgments which are carefully written to extract exactly the level of thanks that a dissatisfied person can muster.  I do agree that it is less than plausible that the OP does not have warm feelings about anyone (e.g. his family and friends), but writing acknowledgments to your thesis and not mentioning your advisor is also worse than not writing them at all.  If you really want to thank your friends and family then you don't need a page in your thesis to do so.  (I looked back at my own thesis acknowledgments just now and was somewhat pleasantly surprised by the effusiveness with which I thanked my mother and a very supportive ex-girlfriend.  But now I have a sinking feeling in my stomach: I'm not sure either of them ever read my thesis!  A facebook message may be in order here...)
In case people are wondering whether I personally identify with the OP's ingratitude to his advisor: hell no.  My first reaction to the post was to roll my eyes at the sentiment that his advisor was helpful for half the time and then so unhelpful so as to make the total contribution 0%.  I am struggling to imagine what someone could do to make a contribution so negative as to cancel out years of support.  My first impression of the OP was that he is -- to put it mildly -- a peevish ingrate.  My second thought?  Gosh, this guy would make a much better impression simply by not talking about his advisor at all.  Not recording for posterity your own sentiments when you know that they contain inappropriate and unseemly negativity is a sign of great professionalism, more so than just lying through your teeth.
I recently read a PhD thesis from my own program without acknowledgments.  I must admit that I did notice this: when I saw the question I thought "Wait, didn't so-and-so not have acknowledgments in their thesis?" so I looked back and confirmed that it was true.  Without giving away personal details, let me say that I have every reason to believe that so-and-so had an unusually positive relationship with their thesis advisor, and that so-and-so has gone on to another academic job and, apparently, a promising career.  Why did so-and-so not include acknowledgments?  I simply don't know.  It's not my business.
In contrast to what some other people have said: other than in the context of my own graduate program, I rarely read people's PhD theses.  When I do it is usually to get some exposition or technical detail that I wish they had put into their published work.  In particular, I almost never read the theses of job candidates.  Does this sound weird?  I think it isn't: I read lots of other accounts of the material in candidates' theses: from their recommendation letters, from their cover letters and research statements and -- when I am really interested -- from the papers and preprints resulting from their thesis work.  If other people here specifically read PhD theses in the context of academic hiring, I would be very interested to know.  Also, as a hirer -- yes, times are tough and we can be very selective, but there are certain things that one does not want to take into account.  If I was at a hiring meeting and someone brought up a lack of acknowledgments in a PhD thesis as a point against a candidate, I would say something like "This person really must be great if you want to sink her and can't do any better than that."

Like Pete, I'm a mathematician and have never read a PhD thesis in the context of hiring.  But a colleague of mine in the history department told me that in one recent job search he (and not only he) had read 13 PhD theses in their entirety --- those of all of the candidates on the "long short list".  I didn't specifically ask, but he made it sound like this was completely standard procedure.

@Mark: That's interesting.  I think it makes sense given the timelines of the two professions.  In math, you can't read PhD theses for postdoctoral applicants because they haven't been written yet.  For tenure-track applicants the PhD thesis is yesterday's news.  But in history they usually apply for tenure-track jobs straight away (right?).  In that case their PhD thesis is more like a draft of their first book, and I imagine that they spend a year or more literally writing it so can show it to prospective employers.  (Still, 13 complete PhD theses...in history?  They must be quick readers.)

My understanding is that, yes, in history people generally apply for tenure-track jobs straight out of grad school (and in this case, I know for a fact that the person who got the job did).  And the PhD thesis definitely is the basis for the all-important first book.  My colleague probably is a quick reader, but he also made it clear that reading those 13 theses, which were quite far from his own area (he works in German legal history; the job search was in Asian history), took up a lot of his time.  I'm not even sure if he was on the search committee!

I like your answer Pete, but I would say it's really a mathematician's point of view. In other disciplines, social interactions matter more. For example, a math student rarely publishes with their advisor, but this is not true in many other fields. No one tries to get you by saying you do not have an ack section. It will most likely be some sophisticated version of you do not get along with people! in either case, the question is does having an ack section help you in some way? I think the answer is yes. I see the dilemma in saying sth you don't believe in to get around, but that's just life!

Same in computer science: I've never read a PhD thesis in the context of hiring, even though most job applicants are applying directly from their PhD.  In CS, the thesis is viewed primarily as an administrative hurdle; it is assumed that any interesting results will be published separately, so we only look at the applicants' peer-reviewed publication record.

For tenure-track applicants the PhD thesis is yesterday's news. — [citation needed]

PHD Thesis are public, forever, and especially to people that might not read your thesis might seem like important ;) Thank your familly and friends there, then post a facebook message with a link to the thank you. They will feel much more grateful than a facebook message - and if they had to endure supported you during your thesis, they deserve the credit.

This is the best answer. Another reason why deleting the acknowledgement section entirely is better than other answers (suggesting the OP thanks their fellow students, family and friends) is that by thanking others and not your advisor it reads like a deliberate choice, and draws attention to the omission, whereas if you don't have the section many people probably won't even notice, and if they do it just looks like you didn't want to write that section and are bucking tradition, which will raise far less red flags.

As an addendum to the above, I have yet to meet any PhD student who defended without at some point coming "close to falling out" with their advisor. As PhD programs last longer than many marriages, this is perhaps unsurprising. Odds are, with the stress of the defense behind you, your relationship with your former advisor will dramatically improve. It never pays to permanently burn bridges, and striking your advisor from your thesis acknowledgements will certainly do just that.

You probably haven't met me but... I didn't come remotely close to falling out with my advisor. None of my friends when I was a PhD student came remotely close to falling out with their advisors.

@David Fair enough, perhaps my field is particularly vicious ;)

Perhaps the important takeaway is that fall-outs happen, are not that uncommon, and should be considered within the professional context. It's real easy to bear grudges, but rarely is it constructive.

You stated that you have "made up" with your adviser.  To be frank, it sounds like you are still harboring some negative thoughts and experiences.  You would be best served by putting these negative thoughts and experiences to the side and taking the high road.  Acknowledgments won't cost you any money, so give them generously in your career.  You have far more to risk by going against the culture of your department by not giving acknowledgments.  And, you did state that this adviser was helpful during the first part of your dissertation process.  Those efforts are worthy of acknowledgements, even if you had a bad experience later on.

There is a very interesting article, by Ken Hyland, titled "Dissertation Acknowledgements: The Anatomy of a Cinderella Genre" (2003), that sheds a lot of light on how dissertation acknowledgments operate. He analyzes 240 dissertations, from six different fields, to see what patterns emerge in their acknowledgments.
It's worth a read (even just a skim). Hyland does a lot to show how acknowledgments are much more than just a list of "thank yous" - that it's actually very important as a place for writers to promote themselves as initiate academics.
One of his concluding observations is that "acknowledgments can play an important rhetorical role in promoting a competent, even rhetorically skilled, scholarly identity while signaling important professional connections and relationships as well as the valued disciplinary ideals of modesty, gratitude, and appropriate self-effacement" (266).
Here's the Eric link to the article. If you're not able to access the PDF through your school, I'd be happy to post a link to the PDF (if that's allowed)!

Life Rule Number One: Never burn your bridges for any reason except ethics and integrity.  Your situation doesn't pass that test.
From a purely selfish standpoint, you don't want to seem petty or ungrateful even if you feel that way.  You can't know what the future will be like.  Someone who might want to offer you a position based on your thesis could get puzzled by no acks, ask around, and feel that someone who can't even "make nice" in such a trivial way would be a poor fit.

It seems to me that writing down a personal opinion in a formal document that is the opposite of the opinion one truly holds could be an instance of "ethics and integrity".

"Someone who might want to offer you a position based on your thesis could get puzzled by no acks, ask around...." I find this scenario most unlikely.  Not offering someone a position because of some rumors you heard about the imperfection of their relationship with their adviser is pretty shady.

By "ethics and integrity" I meant a substantive issue, not one of feeling ill-used by one's advisor.
Apropos not offering a position because the customary acks are missing, I can only note the surfeit of PhDs looking for jobs in their fields.

You should write the acknowledgements.
Many grants contractually require you to acknowledge the funding entity, you should check the specifics of your foundation.
And yes, thank your supervisor. Consider this: Someone interested in working with/hiring/inviting for a lecture/etc. your supervisor is very unlikelly to read your thesis, so omitting thanks to him will have no impact on his career. On the other hand, someone interested in you will certainly read your thesis and may read the acknowledgements to get a feeling of your personality. Since you are expected to thank your supervisor, the omitted thanks may strike as arrogant, specially because it won't be justified, so it may be harmful to you.
Of course, it shouldn't have a major impact, but still, it won't favour you.
This doesen't apply to omitting thanks to the staff, since an external reader will not know you worked with them, but may make it harder to work with them in the future. From my experience, many lab workers pay a lot of attention to this, and will feel offended by the omision.

regarding "won't be justified": good point, it would be unclear to a reader why the acknowledgement is left out.

If I were you, I would pay close attention to the implications in the citation above regarding a study of acknowledgements.
You mention "lab" so your field is clearly both "hard" and empirical.  If you think that nobody helped you at all in your thesis, your recollections are most likely deluded and selective at best, or your hubris is at a dangerously high level.
Moreover, acknowledgements in part have a character of dog whistles.  When you go to publish papers out of your thesis, do you think that an acknowledgement along the lines of, say, "thanks to the attendees at the Widgit Workshop at MIT for their insights and suggestions" carries any signal in the anonymous peer review process?
Summarily, I was young once, so I understand where you're coming from: it was a tough, crappy, job you got through with; it remains, in any field, a rite of passage with roots in the Medieval.
But if you don't get beyond it, you'll just be shooting yourself in the foot.

Like the other posters, I would agree that it is important to write acknowledgements although it isn't easy to get them right. I read them to get a feel for what a researcher might be like and am probably not alone in doing this, especially now more and more PhD theses are available online. I thought the following advice, from: http://people.kmi.open.ac.uk/stefan/thesis-writing.pdf was useful:
Once written, try to read the acknowledgement with the eyes of yourself ten years down the line, with the eyes of an employer five years later and with the eyes of the examiners and colleagues now. Always check the acknowledgements for unintended messages: for example, a four-page acknowledgement section thanking everyone in the address book including the cats and dogs of the neighbour's nephew, while barely spending half a line acknowledging the role of one's advisors, may give an unintended message of a broken supervision structure.
It isn't easy to write acknowledgements relating to somebody where there has been a conflict. Maybe mention your supervisor first, and then you can get away a little more with being less than effusive. And then keep your thanks to other people brief so it doesn't feel unbalanced.
Perhaps read some acknowledgements written by others in your lab or elsewhere, find a few in a style you like and ruthlessly steal/adapt their phrasing to your case "I am grateful to XX for their encouragement, wise commentaries...". There must have been something they got right, at some point, so state that. (Leave the rest for when you warn away potential PhD students who get in touch with you because they are considering joining your former group....)

You add an acknowledgement not only for your adviser but also for your family, friends, institution etc.
As you yourself said he helped during first half – so do remember the starting is always the most difficult one. Moreover you should be thankful because I think you do not know how difficult it is to even get a PhD adviser in some places.
Just sit back and think – didn’t his “0% contribution” ultimately help you to learn so many things on your own, which you would not have learnt otherwise?
And the most important – your not adding the acknowledgement may show your un-thankful nature and in future (in your interviews etc) you may not always be able to defend against: “why you didn't added acknowledgement?”

+1 for Didn't 'his 0% contribution' ultimately helped you to learn so many things on your own [...]

I am in a similar situation, yet not writing the thesis but I am so tired of my advisor (or well... lack of it) that if I ever reach that day I will not write any acknowledgements at all and by reading the answers here I am even more convinced of doing so.
The thing is that if you write them, they have to be somewhat positive because they may affect your career in a way. So if the consensus is to write something positive just for the sake of doing it, then we can assume that there are plenty of thesis out there with fake acknowledgements (I omit the ironic or sarcastic or double meanings in them anyways). And I think that even worst than no acknowledgements at all or even the real truth.
But on the other side, academia is as fake as any other industry; and so you cannot fight the system, so you must go with it. Which means you have to write nice acknowledgements just because everyone else is doing it and you are expected to do it.
So I think it is better to have no acknowledgements because that does not give any information extra. If acknowledgements are there, they can be positive or nice, but you will never know if they are true unless of course sarcasm, irony and other language tools are identified in them. For negative acknowledgements I think that those are not really needed to be written on your thesis because in the end time will show the truth and you don't want to be the one to point things out about someone (or some people) even if you are right.

Not so. It's not about lying. It is about being aware of contributions of others. Everyone has run-ins with various people. But it is absolutely essential that one keeps in mind what these people brought to the table (yes, even people one detests may have, at some point, brought something to the table). Keeping this in perspective is not about sucking up to them, but making yourself understand where you sit in the whole context and how much you got from these people, as much as you may detest them. And acknowledgments are the perfect place to do so, even grudgingly.

Whilst I can sort of understand why you don't want to offer gushing tributes to your supervisor, why not include a brief statement such as 'I would like to thank the following people for their support in completing this piece of work'.
Then simply list everyone appropriate including your supervisor in alphabetical order.

Short answer: You don't need acknowledgements at all if you don't want to. I have seen many theses without but this might also be a culture thing of the country you work in (my case is Central Europe).

I stumbled on this thread as I am helping a friend edit his acknowledgments and trying to word something he feels represents how he feels without offending anyone. He is in a similar quandary about the acknowledgement section but instead of hating his advisor is so burnt out by the process and feels the thesis he is writing is so worthless he doesn't want to associate anyone with what he is committing to his thesis. I feel the same way about my dissertation and have planned on not writing an acknowledgements section myself. Only when we were trying to craft his to mask his disgust at his creation did I think about the social obligation of this practice and that it must contain some value for the people who it is written for...
But even as I recognize the social obligation of this practice I am really surprised at all the answers here, and large amount of value that is placed by the respondents to this question on the importance of an acknowledgments section. I feel like everyone has given this issue too much thought and given it way too much value.
Why does an acknowledgements section matter?
If the OP is conflicted they should leave it out and shouldn't mention it, I would be really surprised if anyone (even the advisor notices), unless I am wrong and advisors are starved of praise and desperate for a note in paper that few if anyone will ever read? Many of the posts say it would a bad career move to not include the acknowledgments... are search committee noticing you left one out? That is a stretch... Academic hiring committees have better things to do, and thousands of other pages to read.
I think it is better to leave it out and ignore the situation than it is to write a dishonest one. In the end, two months from now, no one is going to care that you didn't have an acknowledgment section. But if you write one that is really a backhanded compliment your advisor is going to notice and that will further test a weak relationship....

This seems like a different question from the OP's. Or a restatement of his/her question. Consider posting it as a new thread.


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Options to publish a paper "as is" without being able to produce "more results"
I had worked on a computer vision problem three years ago, drafted a journal paper and submitted it to a top-tier journal. My rebuttal to the reviewers answered most of their concerns except "more results required" comment, so got rejected. By then I had changed jobs, but wanted to get this paper published, so quickly made some changes and submitted to another journal, after two rounds of to-fro with the reviewers, the editor rejected it saying, "come back with more results". I don't have access to data as I have changed jobs, so "more results" is out of question.
I am now toying with the idea of getting this paper published in an open-access journal (where I believe, my chances of getting it published is high) or Arvix.org.
Should I go for a low-quality open-access journal or arXiv.org? I want my work to be out there. It may not be award-winning work but it's research and I want it out there.
How does publishing in a low-quality open-access journal (or arXiv) affect a candidate's chances when applying for a job? I know some people who hire use a point system i.e. A-grade journal = 5 points, etc. Do they have a "negative point system" for low-quality open-access journals?

"Open access" and "low quality" are orthogonal.

@JeffE Sure? I observe at least some correlation: http://www.ijorcs.org

@Dirk "orthogonal" might be a too strong hyporbola by Jeff. Still, it's true that most of the open-access journals show good quality of papers. On one hand they might not do so well in the quantitative criteria such as IF or similar, because if you're open-access, you don't have the money to push yourself up in the rankings. On the other hand, many open-access journals are recognized as high-quality simply because high-level researchers publish in them.

Out of curiosity, not knowing CV, but instead doing systems work: Would it be possible to trim it down and turn it into a conference submission? At least in systems, there are conferences that are almost as prestigious as journals, and smaller page limits make the insufficient results qualm less forceful.

might be a too strong hyperbole — Well...maybe.  Open-access papers do tend to be cited more often, so perhaps there is some slight positive correlation between open-access and quality.

@MatthewG. Conference registration costs around $1000. With low-quality open-access journal, I could probably get away with $200-300. I have to pay this out of my pocket as my previous affiliation will not bear the cost!

@ALL  Hypothetically, a candidate with 3 top-tier publications and 1-very low quality open-access, do you consider this person as having 3 publications or 4 publications?

@JeffE 'Open-access papers do tend to be cited more often' That doesn't sound like a convincing sufficient evidence of quality to me, it's far more likely that they get cited more because they are easier to access. I'm all for the idea of OA, but you have to admit that there are a lot of bad OA journals.

There is also the option of submitting to a less prestigious subscription-based journal. It will be seen as more reputable than a pay-to-publish journal and you won't need to pay anything. Putting a pre-print online will insure anyone can access your work.

That doesn't sound like ... sufficient evidence — I agree!  Hence "perhaps" and "slight".  Sure, I'll freely admit that there are a lot of bad open access journals, but you must also admit that there are a lot of bad closed access journals.

First: Put your paper on the arxiv. It's a preprint server. Then the work is "out there" and you are still free to submit it to any reasonable journal (as noted in the comments, not every journal takes papers that are already on a preprint server, so check that in advance). So my short answer is: do both.

This is not necessarily true. Some journals do NOT allow publication on a preprint server. Check before you submit!

Maybe true - (however, any journal I know do accept papers from the arxiv, sometimes you only need to send the arxiv number to do the submission).

"Any journal I know" does not equal "any journal." Some of my papers (which are computational physics, and therefore discipline-relevant to arXiV) cannot be uploaded if I want to submit to some journals. Again, that's why it's important to check explicitly if this is OK.

As far as I know, all computer science journals accept submissions that have been previously posted to ArXiv.

@Dirk I would rather publish the paper either in an open-access journal OR in ArVix not on both!

@user2979010 why wouldn't you want to do both? The more people read your paper the better.

Are your results only reproducible on one specific data set (the one you no longer have access to)?
If "more results required" is the comment you got from two different journals, I suggest you try to provide exactly that. Of course it's understood that having access to a suitable data is not always easy, yet  often a requirement. Hence I think it would be worthwhile if you could try to get your hands on a different data collection on which you can perform further experiments. Also, if you repeat the ones you already did on the first data set, this can only strengthen your results.
This may be a lot of work, but remember, if your findings cannot be applied to anything but a data set that almost nobody has access to (including you), then there's little value to your results.

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How to effectively explain why my research is important?
I gave a presentation on my PhD research at university last week, and it was criticised for lacking practical significance. A different comment suggested the presentation was not placed in context. Could somebody provide some advice on how to place research in context and convey its practical significance? How can I effectively assess who/what/where/when will see the benefits of my research?

It is annoying that (in general in academia) you are forced to say that your research is significant. So it is... (which is hard to tell before) or you make it up.

@Piotr Migdal: I disagree with you. What I find annoying is two things: that there seems to be little place for fondamental research, and that in response fondamental researchers lie about their motivations to make it look more applied than it is. But one should be able to explain at least why she is interested in the question she worked out for years, and this has to be related to some sort of significance.

@BenoîtKloeckner Actually, I agree with you. The question "Why do you consider this topic worth investigating?" is crucial (and when it is a PhD student is is usually not yet possible to judge significance, without story-telling). But when it comes to "practical significance"... well, for fundamental research (as opposed to applied, or - engineering) it almost certainly not cure cancer, solve environmental problems and create a quantum computer (and again, Roentgen didn't work on "saving millions of lives with better diagnostics" - he was just working on a potentially fruitful thing).

I have similar issue but with my advisor. He always asks me for applications (applied scenarios) for my research ideas. I believe its out there but I do not know what's the name of it. I either come up with application from my little head or the whole paper will be screwed.

Ask yourself a number of questions:

Why am I doing the research?
What problem am I solving?
Why should anyone else by interested in this research?
How can my results help solve someone else's problem?

The first two questions will help you understand what you are doing from your own personal perspective, as well as establishing the context of the work. The latter two will help you establish why someone else would be interested in your work.
In short, ask What? and So what? about your work.

I think that for many PhD students the answer to the first question is "because my supervisor picked this project for me"... Of course, the real reason is never stated publicly...

Definitely, your advisor is the person who should help you most with this question, so make sure you talk to her.
With this disclaimer, I would like to distinguish two things: the good and the bad way to justify the significance of your research. To be clear, good and bad are personal (but motivated) judgments and are not related with what will please people asking you that question, but with what is sane argument.
Let's start with the bad way:

this is the most important thing and most others are specialization of it: giving false but vaguely plausible reasons to study what you studied, hopping to reach other's expectations,
claiming applications that are often claimed in the area, or vaguely related but at best very long term applications (e.g. "my study of cell migration is crucial for understanding metastases, so it will help cure Cancer"; this works with any fondamental research in cell biology),
name-dropping (e.g. "Nobel Prize Trucmuche has studied this 20 years ago, so surely that must be interesting"),
generalization for the sake of generalization -applies maybe mostly to maths, but applies a lot there- (e.g. "Finsler geometry is a generalization of Riemannian geometry, so surely it is interesting").
lacking any clue (e.g. "My advisor told me to do it, so I did"). If you don't know why you are doing what you do, at some point you should find out or change subject.

Note that 1. is very, very often seen in grant application, and it might be impossible in some cases to apply successfully without resorting to this kind of argument. This does not make it a good argument; we should be as thorough in assessing the relevance of our research than we are in assessing our research result.
Now the good way:

this is the most important thing and all others are specialization of it: explaining the reasons why you where interested in the project, why you find it fascinating or interesting,
giving perspective applications that sincerely did motivate your work, either from start or that you realized during the research process. This may not exist, which is not (rather, should not be) an issue, at least in fondamental research,
placing your research in context: how it relates to what has been done before, to which previously raised question it answers, which previously held beliefs it contradicts,
explaining how it generalizes previous work to meaningful, existing examples (e.g. "My theorem on Finsler geometry explains such and such features of Hilbert geometry"),
explain the perspectives opened by your work (e.g. "if we believe this principle applies even more generally, then we can hope to use my methods to understand such and such important phenomenons"),
explain why it is fun (e.g. "look at this dancing corn starch: weird, huh?")

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Citing references consistently
Many of the journal references in the bibliography of my thesis contain bird names. Journals use birds names in the titles of papers in at least four different ways:

Titlecase, eg Teal
Titlecase plus scientific name, eg Teal Anas crecca
Lowercase, eg teal
Lowercase plus scientific name, eg teal Anas crecca

These different ways of using bird names makes my bibliography look untidy and inconsistent.
Should I adjust the titles of the papers in my bibliography so all bird names are used in a consistent way? Or should I use paper titles exactly as how they are given?

As a general academic principle you should not adjust the titles -- or other essential bibliographic data*, e.g. the form and ordering of the authors' names -- of papers that you reference in any way, with the possible exception of necessary typographical concessions for "exotic" characters.
(For instance, in my branch of mathematics is it common to use the cyrillic letter Sha for something named after a Russian mathematician whose name begins with this character.  If you simply don't have cyrllic characters available, you have to do something else.  But even in this case it would be better to try to take a little trouble to "get cyrillic characters".)
So my answer to your question is no: it is obviously not your fault that different papers you cite refer to teals in different ways.  So if there is any untidiness and/or inconsistency, you are simply faithfully replicating it, as you are obliged to do.
This answer comes from someone with precisely zero avian-specific academic knowledge.  So it couldn't hurt to get a second opinion from someone in your field.
*: I confess that I sometimes mess with "inessential" bibliographic data.  For instance, most journals come with a volume number followed by a number of the issue within that volume, and I usually omit the second number: you simply don't need it to access the paper.  I don't specifically endorse this practice and mention it only for "professional honesty", but in my defense I just checked around and I am far from the only one who does this.
Moreover in some fields there are different formats for referencing.  In my field (mathematics), on the one hand we are not too picky about the format, and on the other hand we have standard repositories of all papers: MathReviews/MathSciNet and Zentralblatt, from which I assume that most contemporary authors simply copy the bibliographic data (and then the philistines among us delete the number of the journal within the volume).  It is a good idea to choose a consistent format throughout all your bibliographic references: e.g. put last names first always or never, and so forth.  But still: the title is not yours to monkey with, as far as I know.

Regarding omitting issue numbers, I always thought they were completely unnecessary, but then I learned that a few journals are paginated by issue rather than volume.  If you're looking through hard copies or navigating the journal web site, then knowing the issue number becomes genuinely helpful.  (But it's still irrelevant if you are doing a web search.)

You should never add or remove words from the title of papers you cite. The reason you add citations is so that your readers can find these papers, and the title is one of the most important pieces of information. While it might be obvious to you that "Teal" and "Teal Anas crecca" mean the same thing, this might not be the case for others, e.g. scientists outside your field.
The issue of capitalization is a little less cut and dry. Different citation styles treat titles in different ways (title case, sentence case, or even all-caps), so you have more freedom here to be internally consistent. In addition, some automated reference systems mess up capitalization, so in my experience this is frequently something you have to fix by hand. If there is no semantic difference between "Teal" and "teal", I would pick one and apply it consistently.


text:
How to add scientific names of birds to manuscript?
A common task in scientific writing is adding scientific names after the English name. This is a highly laborious task with a lot of room for error. It seems remarkable that nobody has come up with software to do the task. Or am I missing something? What methods do people use to efficiently and accurately add scientific names to manuscripts?
Here are some that I need to follow, although these vary among journals:

add the scientific name after the first mention of each English name in the main text
scientific names need to be in italics
once a genus (the first of the two scientific names) has been mentioned in the main text, the genus needs use the first initial
any mention of the English name in the bodies of tables always needs full scientific name adding
in figure captions, each English name needs scientific adding, but as with the main text, once a scientific has been used it does not need repeating and once a genus has been mentioned then only the first initial should be be used

Perhaps related: Automatic species names in latex

I’m curious, is this really considered ‘a highly laborious task’ for a researcher?

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How to 'stay up to date' in your field?
In academia, it's important to stay up to date with the latest 'hot' hypotheses in the your field. By 'hot', I mean the hypothesis that are most important/topical/relevant/popular. Perhaps the best way of staying up to date in a given field is by reading the literature. But  I'm wondering if there are any shortcuts? Are there any websites or papers that list the current most 'hot' hypotheses in each field? Google Scholar lists the most cited papers but I'm wondering if any resource goes one step further by listing topics?

To my perception, there are so many implicit hypotheses in this question that it's hardly sensibly answerable. To begin, "hot hypotheses"? I don't object to the language, but... is this really the/a primary issue? And trusting Google Scholar's most-cited index as guide to reading? Surely the questioner is thinking of a far more specific field of inquiry... in which, conceivably, the premises make more sense?

@paulgarrett If we replace "hypotheses" with a near synonym like "conjectures" or "open problems," and also "hot" with "most important/topical/relevant/popular" (which OP says are his or her definition of "hot"), it may not be too absurd to find it important to stay up to date with the current statuses of "hot hypotheses" in mathematics. Maybe the problem is that mentioning most cited papers on Google Scholar suggests that by "hot," maybe OP  means "trendy," "fashionable," or something along those lines, which I think can contradict OP's claimed definition.

@YuichiroFujiwara, yes, tweaking the language can make the question semantically more sensible or definite, but/and then my reaction is something like "You don't want what you think you want..." :)

@paulgarrett Please have my upvote, sir.

I suggest some ways of becoming up to date:

Following the related top scientists and authors on that field on Google Scholar
Following the related top researchers and professors web sites and their research lab and groups publications.
Ask to contribute to work for or work with them.
Check related Linked-In groups to know more about academia and industry.
Visit their labs and talk with them.
Take part in the related conferences.
Check the related conference proceedings. For example, the IEEE web site has lots options to help you.


text:
How to ethically approach publishing research with conflict of interest?
I have an opportunity to participate in a contest with a nontrivial monetary prize, which can be summarized as "Describe in details a secure way to do X using technology Y and provide an explanation of why you think it is secure." The contest does not require a grant of any exclusive rights for the work, hence I am free to use my work elsewhere too, e.g. to publish it. Clearly earning money from the contest and getting a publication sounds nice, but can it be done in an ethically sound way?
The tricky thing is that it is debated in the literature whether doing X using technology Y is a good or a terrible idea from the security point of view. While I intend to do my best to present a balanced point of view including the advantages and disadvantages of the proposed solution, I recognize the obvious conflict of interest, and, hence, that despite my attempts to be unbiased when I rewrite the paper for a journal, it is unlikely that it will become completely unbiased. In general I want to avoid doing anything that might be considered unethical with respect to reviewers or readers of the paper.
What is the best ethical way to handle the situation?

FYI: this is not duplicate to:

Can I Publish Research if I work for the company?, which addresses issues specific to the interaction with the employer on the right to publish (not an issue here), and issues specific to ethical control required for studies on human subjects (not an issue here since this is IT).
Clear explanation of Conflict of Interest with examples in journal articles asks for the explanation of what CoI means and examples of it in papers, and receives "Potential conflicts of interest" paragraphs in the acknowledgments section of the papers in response. While I recognize the need to include such paragraph in case of the publication, it seems to me that such paragraph may not be the only thing I would need to consider.

Book authors get money. Invited speakers might get money. Even teachers get money (not much, admittedly). Conflicts?

@Buffy In this case the compensation is granted only for developing a secure way to do X using Y, not for arguments that doing X using Y is a bad idea from security PoV. If such research is published, it is in a potential conflict of interest with the desire of potential readers to know an unbiased answer to the question "Is it a good idea to do X using Y?": they would prefer to read the paper resulting from a research sponsored regardless of the outcome.

What is the relationship between the contest and the publication?  Is this contest run by a journal?

@Anonymous Physicist: There is no known relationship between the contest organizers and any journal.

Unless I'm missing something, I don't really see the conflict. Write the paper when the time comes and submit it. If an editor or reviewer thinks you have a biased viewpoint that incorrectly impacts on what you have to say, they will probably catch it and reject the paper. But, I think a biased outcome is different from a conflict of interest.
And your comment suggests that if you don't develop the methodology you won't be in the running for the prize in any case.
For full disclosure you can include a statement in the paper (or to the editor) that "This paper was (awarded top prize)/(a finalist)/(submitted)/(soundly rejected)/(disparaged from the podium) at the 87th annual underwater basket weaving festival of doing Y to achieve X securely". Whatever best describes the history of the work.

Good answer.  The conflict is that the company is providing an incentive to show that Y is better than Z, when it might be that Z is better than Y.  Asker didn't say what Z is.

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text:
If I receive written permission to use content from a paper without citing, is it plagiarism?
Let's say I find an article online. I contact the writer of this article and, without expecting anything in return, they agree to give me full, unrestricted rights to use any portion of their article, including directly using quotes from the article, without citing it. The agreement even allows me to claim the work as my own, even though it isn't.
Because I have all the rights to do this, would this be considered plagiarism?

I can't imagine this scenario ever happening.

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

It doesn't really matter that the author gave you "unrestricted rights to use any portion of their article" without the need of citing it. We, the readers, want to know that you're using it.

Because I have all the rights to do this, would this be considered plagiarism?

Yes.

Might be important to note that plagiarism does not necessarily have to violate a law (which could be avoided by such a 'contract') but in science is mostly seen as a violation of science ethics which on its own might have repercussions, e.g. rectraction of an article / revocation of an academic degree.

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Yes, it is plagiarism. The permission is irrelevant.
Consider this simplified but actually equivalent example: if your neighbor allows you to copy her answers in a written exam, is that not cheating just because she allowed you to use her answers? Of course not, that is ridiculous! It is cheating simply because you didn't come up with the answers yourself; whether or not you had your neighbor's permission is completely irrelevant.
You are confusing two orthogonal things: plagiarism and copyright violation.
Plagiarism is an ethical concept; it refers to passing off other's work as your own. Copyright violation is a legal concept; it means using a creative work in a way that is reserved for the copyright holder without acquiring a license from the copyright holder.
Those concepts are orthogonal: if you copy large portions from a book and you properly cite and attribute them, it's still a copyright violation even though it's not plagiarism. And in your example, it's still plagiarism even though it's not a copyright violation.
Note: plagiarism may come up in a legal context as well. For example, in most institutions of higher education, there are rules forbidding plagiarism, if you are a student, you often have to sign or acknowledge an honor code forbidding plagiarism, if you are faculty, a tutor, a TA, an employee, there might be a statute about plagiarism in your employment contract, making it a finable or fireable offense. Also, your thesis will have a signed statement that you did not plagiarize, and if you did, signing that statement may be considered fraudulent. In that case, plagiarism may not only have ethical/moral dimensions but a legal one as well (you get expelled / fired / fined / your degree revoked). In the case that the degree is a prerequisite for practicing in a legally protected profession (e.g. lawyer, doctor), falsely signing that document may even be considered a criminal offense or even a felony.

Even without contract, plagiarism is a (also) legal problem in many countries.

It might be useful to mention the concept of self-plagiarism for illustration.

It's an overstatement to say plagiarism and copyright violation are unrelated.  You summarize the distinction well, but they are clearly related since both involve using the work of another, hence the confusion.

This is... not really an answer to the question. It clarifies important misconceptions, separating the question into its relevant parts, but why not go ahead and actually answer those relevant parts?

@E.P: the direct answer to the question is, "in your example, it's still plagiarism". The rest explains the reasoning for why the information the questioner provides about written permissions, is not relevant to this conclusion.

@MarkMeckes: I replaced it with "orthogonal" which I had already used in the third paragraph.

@E.P.: I highlighted the sentence. Should I add an explicit tl;dr section or restructure the answer to distinguish between making the distinction between copyright and plagiarism and answering the direct question?

@Murphy: Unfortunately, I am having a bit of trouble with clearly understanding that concept, so I chose to ignore it. Feel free to edit! The article linked to in another comment, unfortunately doesn't clarify things at all, it actually confuses me more. They offer two examples, but one example mixes self-plagiarism with plagiarism (because the original paper was co-authored, the second wasn't) and then they dive into copyright, which as I tried to make clear in my answer above is an orthogonal concept to plagiarism.

@Murphy: I also don't understand that concept. Plagiarism is passing someone else's work off as your own, so it makes zero sense to say that passing your own work off as your own work is plagiarism. There is no notion of time anywhere in the definition. (If you disagree, show me the corresponding definition of "plagiarism" in a dictionary.) It might fall under "lying" if you somehow claimed it was done at the wrong time, but it logically cannot be plagiarism because it was your own work to begin with...

@Murphy: The misunderstanding probably comes from assuming that self-plagiarism is a subset of plagiarism, but this is not the case. "Self-plagiarism" is passing your own previously published work as new, "plagiarism" is passing someone else's (published or unpublished) work as your own. The latter could be called "other-plagiarism", but that'd be... unwieldy, hence just "plagiarism". You could also subsume both under a definition of "plagiarism" as "misrepresenting the novelty or authorship of a  work, which -- together with correctness -- are the sine qua non of an academic publication.

A different term for the former would have been less misleading, but that's the one that stuck. Best to treat it as a terminus technicus.

@JörgWMittag I think the wiki explains it well: https://en.wikipedia.org/wiki/Plagiarism#Self-plagiarism
personally I'm of the belief that getting too upset about mild cases of self-plagarism is silly but it is a thing and it sort of makes sense. It's simply based on dishonesty. For example someone publishing the same paper twice with only the title changed in order to boost their publication count. Even if the journal doesn't take the copyright it's still an ethical issue.

I quite like this answer as a complement to the accepted answer - that one provides the TL;DR and this one provides the essential details.

When you said "self-plagiarism", I was reminded of a news story years ago about a scientist who had written an article on a controversial subject under a pseudonym. Later he used material from that article without attribution and was accused of plagiarism. Then he had to prove that he was really the same person. :-)

RE "plagiarism may be a legal concept" Sort of. To the best of my knowledge, there are no laws in the US against plagiarism: it's an academic violation, not a crime. Yes, if you put a no-plagiarism clause in a contract, I guess that would turn it into a legal issue, but only in the same sense that you could turn anything into a legal issue by putting it into a contract. If your boss puts in your contract that you must wear a pirate costume while working as a server at his restaurant, then if you don't, he could get you in legal trouble for breach of contract. But it wouldn't be fair to ...

... say that therefore in the U.S. people are required by law to wear pirate costumes.

Plagiarism is passing of the work of someone else as your own. So regardless of the authors permission, this is absolutely plagiarism.
This is quite similar an increasingly common form of plagiarism where students purchase an essay or pay someone to complete their assignment for them. At the universities I've been involved in this is treated very seriously and students fail entire units when they are caught. As serious academic misconduct they can in fact be removed from a course entirely.

Offenders  like is are often removed from the school on a second offense.

that is only part of it and not the important part. The important part that makes it plagiarism is "taking and claiming" as your own. if as Frank's scenario states the work is "given to you as your own and claimed" as your own it is no longer plagiarism. This is regardless if it is frowned upon for not citing things in academia but it still does not make his scenario plagiarism.

@CcDd Plagiarism is about who completed the work (or produced the ideas), not intellectual property ownership. You can actually be removed from an institution for submitting an essay that you purchased, and therefore "own" in a legal sense.
To quote my employer:
"Plagiarism is the presentation, without any form of acknowledgment, the ideas or words of another writer as if they were your own. This is more than just another form of cheating. It is literary theft. It is stealing someone else's work."
http://learnline.cdu.edu.au/studyskills/studyskills/avoidingplagiarism.html

@elvey regardless of the venue and what happens when using already produced or produced for you works, the definition of plagiarism still stands as requiring to take something and then claim it as our own. There is no way being given something to claim as your own fits the word plagiarism. and your definition is correct you cannot steal your own work and if you hire someone to make it it's yours and you can claim it's yours without acknowledgement. This might be frowned upon, might even get you kicked out of an institution, but it is not a definition of plagiarism.

@elvey I disagree with that definition of "plagiarism is theft". Plagiarism is a breach of a contract clause that requires one to present only novel work made by oneself. Infringement of copyright may also be done on the course of plagiarism, but it is not a necessary act.

Even if you yourself are that other author, you still need to cite your old work in your new.
Citation has nothing to do with copyright. You cite your sources to give attribution to the ones before you, to let your readers know which giants' shoulders you stand upon and to differentiate the parts you wrote from the previous works of others, avoiding passing their work off as your own. It's perfectly fine to cite something that nobody in the world is allowed to read due to copyright reasons or what have you (allthough a bit mean to your readers).

@scaaahu I disagree: self-plagiarism is a typical situation where all premises of the question apply (and maybe it is the only realistic such situation),  so it is a proof that these premises don't dismiss the citation duty. Maybe the answer should be lengthened with some justifications.

too many people who don't know the meaning of plagiarism and using it incorrectly. you cannot plagiarise your own writing unless you specifically gave it in full to someone else at this point if you copied it without permission and claimed it as yours then it would be plagiarism.

@CcDd Yes you can, that's called "self plagiarism", "duplicate publication" and many other names. Copyright concerns aside, it has several unethical implications in academia, such as artificially pumping one's paper count up, wasting reviewer time on already-reviewed material, and making the literature, as a whole, more confusing than it needs to be. See https://en.wikipedia.org/wiki/Duplicate_publication

I am not talking about copyright concerns I am talking about the definition of plagiarism and how it is not being used correctly and self plagiarism is an opposite of itself. It simply has been used enough people seem to think it means something it does not. you cannot steal a document from yourself and so you cannot plagiarise that document. You can fail to cite it however.

@CcDd Too often people are too lazy to make the case for or consider better alternatives and follow the first one to propose a direction, regardless of the shortcomings. I appreciate your effort to correct the flow.

@PrinceYann I agree. I also wish people would do their homework and look up definitions before blurting out "yes" to the original questions. They could have said "this is not plagiarism, but you should still cite it to avoid any possible repercussions". The reason for this distinction is the specificity of Frank's question, which is important. If you have someone translate or type for you (disabled, don't speak fluent local language, proofreader) it's no longer your words, and therefore would be considered plagiarism.

Plagiarism is committed when you don't cite the article regardless of any written consents.
Copyright is violated when you reproduce portions of a published article in the sense described by a copyright law.
Stealing intellectual property may be committed when you reuse ideas from the article without the consent of the owner of the intellectual contents of the article.

The writer cannot protect you from 1. In usual cases, from 2 neither. In certain cases, his/her consent might be your protection from 3.
Said that, don't copy-and-paste. Rewrite, quote, and cite properly.

[Other answers have pointed it out - this answer attempts instead to put it in terms that someone who simply doesn't understand the difference between copyright violation and plagiarism could understand]
This happens every single time a work is placed in the public domain.
Every work by or for the US government; every work produced before some dates and some works thereafter; every work explicitly licensed CC0.
All of these works grant complete ability to reproduce, remix, and reuse the entire work without credit. Doing so is perfectly acceptable.
Whether it is OK to do this, however...
Consider that any one of us may reprint the entire works of Shakespeare and put our own name to them, without crediting Shakespeare. Or Nabokov. Or translate the Illiad or Odyssey to English without crediting Homer. Or...
And then consider the fact that despite it being perfectly 100% legal, nobody ever does this.
In the field of academia, plagiarism is seen as a far greater sin than elsewhere, so the backlash would be far worse.
[Edit: You could argue that you were using only some small, fair-use portion of a document in a copyright sense. But that could still get you an accusation of plagiarism in adademia.]

"nobody ever does this" Are you 100% certain that whenever a character in a TV show quotes a few lines of Shakespeare, this is properly attributed somewhere? Of course, this example only further illustrates your last sentence: it is acceptable in the entertainment business because nobody really cares, it is not acceptable in academia.

@T.Verron: and here I thought the trope of person A quoting Shakespeare (or the Bible) and person B identifying the exact line quoted, was a one-upmanship game. Really it's just the screenwriter clumsily working in the proper citation ;-)

@T.Verron: I meant "this" in "nobody does this" to be a back-reference to my "reprint the entire works", not to merely quoting a few lines. But you highlight an interesting point: quoting a few lines would be fair-use in terms of copyright, but would still be seen as plagiarism in academia.

I wonder if this question was inspired by answers / comments on another question.  This answer makes exactly the same point I did in a comment there.  (So luckily I don't have to repeat myself here :)

@PeterCordes Dagnabbitt! I coulda plagiarized your comment, and it would've been a beautifully ironic way to illustrate the points. What a missed opportunity :( [Edit: I do remember seeing that question, so may have subconsciously plagiarized? Yay!]

exactly what I was thinking :)

@DewiMorgan "quoting a few lines would be fair-use in terms of copyright" this depends on a lot of factors: context, reason for quoting, amount the owner of the copyright is willing to invest in a lawsuit... And it is also true in academia: quoting Harry Potter in a dissertation on modern english literature is certainly fair use, for example. Copyright and plagiarism are orthogonal concepts, as other answers pointed out.

Others have pointed out that something can be plagiarism without violating copyright.
In addition, even if an author gave you permission to use something from an article it may well still be a copyright violation because in many cases when you publish in a journal you also sign over the copyright. As such even if the author gives you permission, they may not be the copyright holders so legally it's not theirs to give.

One general comment about plagiarism:
If an African-American says, "I have a dream," any allegation of having plagiarized MLK is ludicrous. Such allusions are shorthand quotations.
Plagiarism is presenting someone else's work as your own, according to the combination of stated and implied claim to originality, without explicitly marking the quote. An allusion is not intended to be perceived as original; it is intended to be a shorthand quote, and it just does so without quotation marks as a metaphor drops the word "like" from a simile so that "time is like a river" becomes "time is a river".
I found it rather ludicrous when Orson Scott Card was accused of plagiarism in incorporating bits of story that are apparently well-known to people who know Mormon Scripture. I am not a Mormon and personally have no interest in reading Mormon Scripture, but there seemed something extraordinarily confused about what, to Mormons or non-Mormons who understand that tradition, is a common theme. Neither my own The Sign of the Grail nor any other work since the twelfth century Historia Regum Britanniae or the Brut pseudo-history is simply guilty of plagiarism by vice of using the character of Merlin without explaining that Merlin was taken from earlier works (and the Brut is probably not original; Merlin's name was altered from an earlier Celtic character name apparently to avoid collision with a French swear word).
(And as those of us in the U.S. are nearing an election, I might point out that it is a thoroughly established practice for anyone remotely near POTUS candidacy to use speechwriters, and needless to say I have not heard anyone indict anyone else for giving a speech written by a speechwriter without an academic style of attribution. On a much less influential scale, authorship is a bit fuzzy in the business world; there is such a thing as unacceptably stealing credit, but most of a company's messages to its audience do not include attribution of who made the copy, who made the graphics, who did XYZ in the background.)
The standards for plagiarism are different in academia from other places; for me it has been only in academic settings that people have been concerned about what constitutes plagiarism. I've run into people who care about honesty and I've run into people who thoroughly believe in giving credit where credit is due (one CEO asked me to co-sign a letter to customers about a new offering, although that is a novelty). And this question isn't really in a grey area; it arises from failing to distinguish plagiarism from copyright issues. But I have only seen fine-grained discussions of shades of grey about plagiarism in academic circles, where a good probable rule of thumb is probably, "If you can express quotation or debt to a source you have used, however unimportant, footnote it."

Regrading the authorship:
If you buy Pablo Piccasso's paintings and copyrights to them, you own the paintings, you can earn money for displaying them etc., but they must be creditted as Pablo's paintings, not yours. Period.
Regarding the copyrights:
When a paper is published the copyright to the paper usually belongs to the publisher. Copyright to property, that the article is based on, belongs to the writers.
In your case you are entitled to use, edit and make profit based on their work freely. Still, they shall be creditted for their work.
Approaching from different point of view:
Scientists are said to be people with higer knowledge, wisdom and morality than the average folks. At least, not citing actual authors is immoral.

The last part doesn't make any sense at all. So it would be OK not to credit Bertrand Russell or Anthony Trollope because they weren't scientists? Would it be OK to not credit somebody with less (lower?) knowledge who was both more foolish and less upbeat than average? (I guess you probably meant 'morality' rather than 'morale'. So I don't need to credit people who are less moral than average?)

@cfr Point taken. Your guess was right.

@cfr: I don't think the last sentence is intended to say that average folk deserve to be plagiarised. It's saying that scientists hold themselves to a higher standard than average folk, and so shouldn't plagiarise anyone. Of course not all academics are scientists. Personally I don't see it that way: the need to cite correctly in academia isn't a matter of academics being finer people than the average folk. Rather, in academia, attribution and the ability to look up sources is a practical necessity for the reader.

So if I read Umberto Eco's work in linguistics and semiotics then I expect to be able to look up all his references, whereas if I read his novels then I do not expect, or even want, a footnote for every literary allusion he makes saying what book and chapter he's alluding to. That's for me to puzzle out. Same person, same knowledge, wisdom and morality, different purpose of the work.

While I generally agree this would be plagiarism, in some circumstances it would not - and not only in the allusion case (see @JonathanHayward 's answer).
Specifically, if you believe and have the author's concurrence that part of the article is folklore, or should not be considered an integral part of the article somehow and not really attributed to the author, then it's possible you're not committing plagiarism.
But you really should:

Apply common sense, but
Always err on the side of caution = the side of citation

Note also that you can make a qualified citation, e.g.
\footnote{This is discussed in Prof's John Smith's monograph on
the Frobincation of Bars \cite{JSFrob}, but blah blah blah}.

If I say it's folklore on the basis of hearsay, but I don't really know myself, then I should cite a source.

If the "author wants or needs to not be named," I would cite this way (Anon. 2016).  The format is my school's style guide; the content is my application.  In USA, "fair use" limits copyright slightly, but I ould still consider an author's wishes if I thought there were a chance he/she might be in a situation where they must protect their identity or their location.
I would never pretend someone else's words were my own.  Although, I must admit there were times I have read something after saying it myself and wondered whether I had come up with it independently or whether I had read the work earlier and forgotten.
Anonymous (Anon.)  2016.  Private communication (author wishes to remain anonymous).

My two cents:  If you have to ask if something is plagiarism, consider it plagiarism.
Always err on the side of caution.  An ethics/honor code violation is not something you want.

Although you have rights, It comes under "Plagiarism"
When you use it without citing it (although you have full rights) which gives readers the impression that you have written this (which is not), it comes under "Academic misconduct"
You're confused all of those things with copyright law.
You can say that the writing is owned by you (copyright holder), but you cannot claim that it was written by you, if you say that you've written this by your self (which is not) it comes under "criminal law"

!-3 are correct (says me, a NON-lawyer).  But having permission to use the material is not the same as owning the copyright.  And I doubt that copyright violation is criminal rather than civil.


text:
When exactly are you “promoviert” in Germany?
In Germany, acquiring your doctoral degree usually involves the following steps (in that order):

You hand in your thesis.
The examiners review your thesis.
You defend your thesis and possibly take an oral exam (usually on the same day).
You publish your thesis (or provide proof that you already did so).
The diploma, certificate is prepared, signed, and given to you.

Step 3 usually is the big thing after which you are congratulated, celebrated, and get to wear the mortarboard, as there is hardly anything that can go wrong afterwards. Nonetheless, it is usually prominently made clear that only after step 5 you may call yourself Doktor (doctor) and you can get into big trouble otherwise. I am not asking about this.
However, in German, there is another prominent term for acquiring a doctoral degree or the process of doing so, namely promovieren or Promotion, respectively. I have some reason to believe that these terms refer to a slightly different thing, namely completing everything up to step 3:

Some people say this is the case.
When publishing your thesis (step 4) at my university, it is common or even required to write Tag der Promotion (day of “Promotion”) in the thesis with the day being the date of the defense (step 3).

However, apart from the above, I failed to find any evidence for this: Internet searches yield all sorts of unrelated stuff and dictionaries do not make such a fine distinction. Hence I am asking: When exactly can you call yourself promoviert in Germany? Be aware that I am looking for some information that goes beyond hearsay (I already have such).
For the search engines: Wann genau ist man promoviert?

I suppose asking the university administration could clarify this

I'm not exactly sure what kind of answer you are asking for. From the disagreement between different relevant sources, in particular, dictionaries on the one side and your university on the other side, I think it's clear that no universally accepted definition of the word "promoviert" exists.

@BioGeo: For whatever it’s worth, I am quite familiar with my faculty’s examination guidelines and it doesn’t say anything about it. I am also rather confident that the administration will not easily produce an answer.

@lighthousekeeper: I would not say that the dictionaries do not disagree. Rather, it’s a detail that rarely ever matters in common usage and that is not reflected in the dictionary definition.

@Wrzlprmft In Duden, the leading German-language dictionary,  "promovieren" is defined as "to acquire the doctoral degree". Strictly speaking, this definition actually contradicts any definition that does not require acquisition of the doctoral degree (such as that of your university) - it's not "less detailed", it's a logical contradiction.

"Man habilitiert sich, aber man wird promoviert," i.e., strictly speaking. promovieren is something, that somebody else does with you. However, this is drastically different from how the word is used currently where people say "Ich promoviere über…"

Please keep the comments on-topic to the original question. Other discussion should move to [chat].

While your question on this site will be read by many academics, few of whom will have direct exprience of  the answer, http://german.stackexchange.com/ has many, many Germans, some of whom, no doubt, have been promoviert.  Since the full title is German language and usage, this would be an appropriate question there.

@Mawg: I am aware of that site (see my profile) and I decided against asking there since this is more about detailed academic procedure and I thus considered it a better fit here. I do consider the question on-topic on both sites though.

If you want to be pedantic (and which mathematician doesn't?), the Duden (the traditional German dictionary) defines the base verb promovieren as

a. die Doktorwürde erlangen,
  b. (über ein bestimmtes Thema) eine Dissertation schreiben
jemandem die Doktorwürde verleihen
(bildungssprachlich veraltend) fördern, unterstützen

Here, Doktorwürde is a slightly more pompous synonym of Doktorgrad (the PhD degree).
Point 1 covers the intransitive usage: a. to acquire the doctoral degree and b. to be in the process of (working towards) acquiring the doctoral degree. Point 2 covers the transitive usage: to confer the doctoral degree (on someone). (Point 3 is going out of fashion and coincides with the English cognate to promote in the sense of to support or encourage.)
Note that 1a. and 1b. are different meanings, but only one of these -- namely 1a. (or 2.) make sense as a past participle; 1a. and 2. are also the only meanings concerned with a formal status of any kind.
Hence, you are promoviert as soon as the university confers the degree, which is done (retroactively, which often leads to confusion as you point out in your question) by handing you the official diploma (or the preliminary diploma, if such a thing exists).

The Duden has lost any official status twenty years ago, and even before its official status was only with respect to orthography, not regarding the meaning of words. As for the latter, it only documents the meaning of words, which it can only do up to a certain precision. It will usually not cover such fine distinctions as I mentioned in the question and if it does, it usually explicitly mentions this.

@Wrzlprmft Fair enough, I changed to "traditional" which I hope is noncontroversial. And of course you are free to use the word promoviert in any sense you wish, but the common use (and hence the way it would be understood in general) is the one I gave. Whether calling yourself promoviert before the degree is conferred is a civil offence on the same level as calling yourself Doktor is a different question. (If I had to guess -- because I'm a pedant but not a lawyer -- I would say yes; any way of falsely pretending to have a doctoral degree would open yourself up to litigation.)

The faculty of natural sciences of the Leibniz-University Hannover has a slightly more elaborate page on the Promotionsverfahren on their webpages. I will be quoting from the original plus their official English translation.

Die Promotion in acht Schritten
Das Promotionsverfahren umfasst acht Schritte, die als Überblick im Folgenden skizziert werden:
[…]
Schritt 6: Mündliche Prüfung oder Disputation und Gesamtbeurteilung der Promotion
[…]
Schritt 8: Promotion
Die Promotion wird durch Aushändigung oder Zustellung der Promotionsurkunde vollzogen, nachdem Sie die Veröffentlichung der Dissertation nachgewiesen haben und nachdem Sie nachgewiesenermaßen alle Ressourcen zurückgegeben haben, die Ihnen für Ihr Promotionsprojekt vorübergehend zur Verfügung gestellt worden sind.

Eight steps to obtaining a doctorate
The procedure for obtaining a doctorate has eight steps, which are outlined below.
[…]
Step 6: Oral examination or thesis defence and overall assessment of the doctoral research
[…]
Step 8: Conferral of doctorate
The doctorate shall be conferred by handing over or delivering the doctoral diploma after you have proved that the doctoral thesis has been published and provided proof that you have returned all the resources which were temporarily made available to you for your doctoral project.

This webpage makes it pretty clear that the faculty of natural sciences of the Leibniz-University Hannover considers Promotion (and thus, although it is not explicitly mentioned, likely also promovieren) to cover the entirety of your steps 1 to 5.
Furthermore, the requirements for the reverse of the title page additionally state that the Tag der Promotion is considered to be the day of step 6 according to the website or step 3 in your overview.
I assume this is because the Promotion is considered to be the entirety of the process, while anything that happens after the defence is considered automatically happening.

There is even a title for this strange time between the oral exam and obtaining the certificate that (retroactively) awards you the doctorate. You must have published the thesis (or handed in enough copies) before you can use the final degree. This goes back to Theodor Mommsen ("Die Promotionsreform", In Preußische Jahrbücher, 1876, Vol. 37, April, pp. 335–352.) who was angry at the universities for selling doctorates (and theses) to anyone who shoved enough money over the table (see Ulrich Rasche, "Mommsen, Marx und May: Der Doktorhandel der deutschen Universitäten im 19. Jahrhundert und was wir daraus lernen sollten" in Forschung & Lehre, 03/2013).
The title is "Dr. des.", Doktor designatus or designated Doctor. Of course, other people are allowed to call you "doctor" and you are no longer obligated to say "no, no, I am still working on my doctorate." I really enjoy calling those who have survived the oral exams (Rigorosum) "Dr.".

It's important to point out, though, that only some faculties allow their doctoral graduates to use this title. In other cases, the relevant regulation (Promotionsordnung, PO) actually forbids people to use this title. There is also a grey area of cases where the PO does not mention the title all. In theses cases, it might not be a bad idea to apply a conservative interpretation, that is, not use the title when it has not been awarded.

The general answer is (as @Rolands example of TU Munich shows):
Whatever your university faculty's regulation tells.
They grant you the title, so they also are legally enabled to decide from what point in time on you can "wear" your title. The right to grant doctoral degrees lays in the hands of university faculties or institutes*. For example in the education law of federal state Saxony (Sächsisches Hochschulfreiheitsgesetz) you find the legal notice in Paragraph  §40 "Promotion" that says that the details have to be declared by the regulations of the universities.

§ 40 Promotion [...] (5) Das Nähere [...] regelt eine Promotionsordnung. [...]

Universities are free in the handling of their process of proving the necessary qualification, as they are in their self organization. This freedom is legally granted by the freedom of teaching and research (Grundgesetz [Germany's "constitution"] article 5 paragraph (3))
(!experience based statement:) Usually any final university degree is granted from the day passing the last exam (a defense / Disputation / Rigorosum etc. or even without writing a thesis e.g. in some xyz "of arts" degrees). One should find the legal rules about the exmatriculation / certification date in either the study regulation of the program, or a general regulation for the whole institution (like at TU Munich)
Anyway the earliest time you can give proof about your title, is after receiving the final certificate (or a temporary one like in @Roland's example) of your granting institution. I'd suggest waiting these couple of days or weeks (if your staff members in the examination office are on vacation, or the dean who's signature is needed)
The publishing of the dissertation is usually an obligatorily step, that can be fulfilled after the title was granted. It depends on whatever is written in the study regulation (Prüfungsordnung / Promotionsordnung) of the institute or faculty that can decorate people with a title.
Keep in mind that there can exist great differences between faculties (e.g. doctoral degrees in arts could not require a dissertation if the federal laws allow that, another possibility is a cumulative doctorate due a number of published articles in A+ journals)
In doubt wait with the use of the degree until you have the written evidence (certificate)

*federal exceptions exist: e.g. Hessen, Baden-Württemberg in planning. These federal states have conducted laws - or plan to - that enable universities of applied sciences (earlier called "Fachhochschulen") to grant doctoral degrees.

That's exactly the kind of answer that the OP is not looking for.

Wrzlprmft asked when a person can call himself promoviert. Above I mentioned that the only legal and official way to receive such a degree in Germany leads over faculties that hold a right to grant such degrees.
Or does he look for suggestions how to get some of those honorary doctors one could buy from theological church universities in the usa for a donation? (They are not eligible to use the name prefix Dr. in Germany)

Sorry, but I concur with @Dirk. This is not about the degree itself.

If it is about the word promoviert itself. Shouldn't the question then be moved to German:SE?


text:
Where to draw the line for authorship for a software-announcement paper?
I am currently working on a scientific software, for which I want to publish a software-announcement paper in a pertaining journal. While I am doing and probably will continue to do the vast majority of the work, it may be that others will contribute in a manner that brings up the question on their authorship on the paper. To avoid disagreements and subsequent issues, I would discuss authorship as early as possible if such a contribution seems plausible.
In a regular paper, the central criterion for authorship is intellectual contributions, while technical contributions such as a straightforward software implementation of some existing algorithm do not qualify. Moreover (at least in my field), it is rather untypical that somebody contributes only a small piece to a paper such the grey zone of authorship is rarely an issue.
In a software-announcement paper, however, I can think of several aspects that could be considered essential and contributors to which could be considered eligible for authorship:

Developing new algorithms and approaches. While this is clearly an intellectual contribution and could even justify a paper on its own, not all new scientific software features such a thing. Therefore it cannot be the only aspect qualifying for authorship.
Choosing the algorithms and methods to implement.
Devising the interface, usually targetting some particular scientific application.
Actually writing the software.
Testing the software. Given the application, finding proper test cases with a known behaviour can be a challenge on its own.
Writing the actual paper.

Moreover, it is much more likely that somebody makes a small, grey-zone contribution such as a bug fix, providing an example for the documentation or testing, suggesting a feature, or similar. This applies in particular if development versions of the software are published.
My target journal does not provide any guidance on this matter and neither could I find any general rules on the Internet. Hence I am asking whether there are any good (preferably established) guidelines on deciding authorship of such a paper, in particular as to which type of contributions can qualify for authorship at all and where to draw the line.

I don't have time for a full answer but these links might be helpful for consideration in the research software engineering world: https://www.software.ac.uk/tags/software-research-object and http://www.rse.ac.uk/index.html

"Testing the software. Given the application, finding proper test cases with a known behaviour can be a challenge on its own." Doesn't it include all your users at some level?

@T.Verron: … which just illustrates how difficult drawing the line is.

See http://ivory.idyll.org/blog/2015-authorship-on-software-papers.html for a discussion of this: there are a lot of comments.

Another more recent post that's a bit broader than "one paper" but does address the issue is https://medium.com/@matthewturk/citations-credit-and-the-yt-method-paper-1034e4080eb .

I have published an open source software for academia. What I did to make sure everyone could get credit for random/future contribution is create a function called "citeme(methodname)". This will print the paper of  the person who contributed their method to my software, thus making sure that anyone that uses the software gives them creddit

As the discussion underneath this post shows, there is no set of established guidelines within a single subfield, let alone across all academia, as to where to draw the line.
A different, not unrelated question: what are you trying to achieve with this paper?
If it's about trying to properly apportion credit for the work done in producing the software, then this is a hard problem: there's the work of the FORCE11 Software Citation Group and their paper. But as the software grows and changes, you're going to have to keep making these decisions.
If it's about growing a community around the software, to improve it, get more people to use it and contribute, then there's a thoughtful post here. That's about much more than just a paper, but notes many problems with giving the proper credit when a software project is updated and the members of the community change.
My opinion, for what it's worth: the more broadly you extend authorship invitations, and the more broadly you're seen to do so, the more likely you are to get community buy-in and future support. By making clear expectations about concrete contributions to the paper-writing process itself, you may reduce conflicts around the free-rider problem.

+1 I like the approach of the development group getting the citation as an abstract group since this is an announcement it makes more sense to me to see Development Team. (2017). "Super Useful Scientific Software", Journal of Scientific Software than some laundry list of names that are debated. Plus, speaking as someone that used to do this type of work, it saves on internal politics about who's included versus not and allow people that want to go on to pursue academic roles some (extremely minor) CV fodder.

I am still working through your references. Could you state or summarise the policies suggested or employed by them (e.g., the authors of this post have the policy to offer authorship to everybody contributing to the GitHub repository).

That post is the only one that (in my recollection) specifies a policy that isn't deeply person or field specific.