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Is copyediting good for an academic career?
I have recently been involved in managing a special issue in a scientific journal. The chief-editor was somehow appreciative of my work and now wants me to join the journal's board as a copyeditor. I am puzzled by this request since I have no example of an academic being involved in such a task. Usually, being an editor (see Why become a journal editor?) involves more content evaluation.
Would my academic career take advantage of such a duty?

The only benefit you'll get as a copyeditor is clear: money (assuming he offered to pay you).
The downsides are numerous: it takes a lot of time, it will not be considered a plus to your CV (it's a technical job, not a scientific one)… none of the benefits from being a journal editor apply to a copyeditor.
Also, I don't know exactly what you did when you say “I have recently been involved in managing a special issue”, but if you were guest editor, offering you a copyeditor job is clearly not showing appreciation for your job as a scientist.

While I generally agree with your answer, isn't this a bit too harsh "...it will not be considered a plus to your CV (it's a technical job, not a scientific one)"? Writing skills are an important part of being a scientist, and being a (good) copy-editor shows that you have strong writing skills and can evaluate texts critically (logical consistency etc).

"Technical or scientific job" is a nice way of summarizing the question. The specificity of this journal is that it is both in French and English (usually, an English article with an additional French summary). A copy editor would therefore be involved in the consistency of wording (technical) and concepts/notions (scientific).

@fileunderwater I stand by my wording: a great way to show good writing skills is by writing good papers, good research projects and a good application/letters. Being copyeditor is negligible in applications…

@F'x Yes, but due to funding, job opportunities and interests people choose different paths, and I do not think that copyediting work for a scientific journal should be seen as completely irrelevant (if coupled to actual scientific work). But I agree that in a direct comparison of CVs more science > copyediting experience.


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Does significant editing of a paper with the possibility of minor contributions to its scientific content warrant co-authorship?
The question of whether writing/editing alone merits authorship is already addressed here. This question is about writing and editing with the possibility of minor scientific contributions.
I have been asked to review a draft paper written by a colleague (a more senior PhD student in the same research group), whose native language is not English. The main purpose is to improve the style and grammar of the paper, rather than make substantial comments to the scientific content.
It is possible that I will be able to contribute some science to the paper, however not likely of the "pedagogical oversight" variety that is normally the domain of the last several authors on a ten-author paper.
Should I approach my colleague with the request that I be placed on the author list, only if I can make a reasonable contribution to the science (by way of some substantial comments or extra data analysis)?

(closely related: Is it common to claim co-authorship by helping writing a paper without doing any research)

You may want to consider why you are being asked to edit a multi author paper. It sounds like the co-authors value their time more than yours, which seems rude unless they are going to offer you something in return (e.g., help with stats, data collection, etc.).

Can you explain why it the current question is not a duplicate of the question you say it is closely related to?

@StrongBad I am the only native English speaker besides the last author (who is, I think, a Master's or undergrad student). My colleague's office is just down the corridor, so perhaps I will ask a favour in return ("write me a bash script that argles my bargles automatically"). I think it's not a duplicate because I could offer and try to contribute some science to the paper, but my knowledge about its contents is well below the first author's.

I've edited the question to focus on the part that's different (per your comment), and remove the part that's already covered in the linked question.

@Moriarty: So one of the current coauthors is the only native English speaker and also scientifically junior to the other authors?  I would think that would make that coauthor precisely the right person to do what you are being asked to do.  If someone's scientific understanding of a paper is so minimal that they cannot be trusted to edit it for style and grammar, how can they be a coauthor?  (What did they do?)

@PeteL.Clark  I bit the bullet and wrote to my colleague, who has agreed to ask the last author (who did "similar work") to read the paper. By journal policy, every author must read the manuscript. As long as the paper is understandable and unambiguous, it's the policy of the journal to help with further language edits. Since it might feel a bit awkward to shoehorn in some substantial contribution of my own, unless I later get approached with a feasible opportunity I will refuse to edit the rest of the paper.

The short answer is: it should not. But the reality is some think it should. Since there is no law that dictates authorship the closest to an answer is to look at the Vancouver Protocol and derivatives here exemplified by the ICMJE (Internationa l Committee of Medical Journal Editors) which defines an author as follows:

Substantial contributions to the conception or design of the work; or the acquisition, analysis, or interpretation of data for the work; AND
Drafting the work or revising it critically for important intellectual content; AND
Final approval of the version to be published; AND
Agreement to be accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved.

With these guidelines in mind many co-authorships would disappear but it becomes quite clear that help with language simply is not enough for co-authorship.

I would view a significant revision of the work as a substantial contribution the interpretation of the data. If I write the interpretation of the data, I certainly contributed to it.

@OswaldVeblen Note the emphasis: all 4 criteria should apply.

Yes, I am saying that significant editing would satisfy the first two. The third and fourth are trivial. @Lilienthal

I have the feeling this may be field dependent. In my field/experience (biological science/bioinformatics) people that are asked to help with English do not get co-authorship. Indeed, in many journals where the contribution to the manuscript has to be stated, editing of manuscripts is not considered as enough contribution to warrant co-authorship. Most of the time the person that edited the manuscript ends up in the acknowledgements. That being said, I know also of cases in this field where the person editing the English would get systematically a place in the list of authors.
Personally, if I ask someone to check the English, I would not feel comfortable if the changes are substantial. The manuscript writing is critical for the work to stand a chance of being published and in such case I would most likely offer co-authorship. If the changes are minor then I will just include him/her in the acknowledgements section. At any rate, it is an important thing to discuss with your colleague before accepting the task of editing the manuscript.

@shane it's a fool who offers to do such a task, but  a known grammarian and pedant who gets asked ;). Perhaps I need to learn to say "no", but he is a close colleague so helping each other out is just what we do. We also share the same primary adviser.

@shane, not being native speaker myself, I saw colleagues being exploited with constant requests to the point that I was (almost) happy of not being native speaker myself. Only "almost" though.

@shane great advice! Indeed, is like asking for professional copyediting. With the advantage of direct interaction and possibly lower rates.

Why shouldn't it be field-dependent? To take extremes: in experimental medical research, one already has research products (e.g. research protocols, data, and numerical results of statistical analysis) independent of the final paper. In philosophy research, the only product is the paper itself, and it's not really possible to separate the idea of the research paper from the actual words of the research paper. In the first case, significant editing might not warrant authorship; in the second, it might indeed. I don't see any way to find a one-size-fits-all solution. @shane

You don't say (here) what field you're in.  I suppose that by doing this you intend to invite answers from different fields.
In my own field of mathematics, it would be quite strange for someone to be added as a coauthor primarily for their editing work.
Nevertheless I had a situation recently where I did substantially edit and rewrite a paper in which I was not an author.  (I think this is already a bit unusual, but it's hard to know for sure.)  In addition to the writing I included a small amount of content: "minor scientific contributions" covers it rather well, actually.  Towards the end of the process I was offered coauthorship on the paper.  I appreciated the offer but turned it down immediately: though I had contributed to the writing of the paper and contributed some mathematical content, the amount of mathematical content I had contributed was much less than that of the named authors.  My perspective was, honestly, that they had already done the work but were having trouble writing it up in a way that would make it publishable in a good journal in a reasonable amount of time.  To me, a good rule of thumb is that if subtracting your contribution would result in a paper which (i) still exists and (ii) could -- with additional routine work -- be submitted to the same journal, then your contribution was not sufficiently substantial to warrant coauthorship.  In the case at hand, a description my contributions to the paper appears in the acknowledgments...written by me!
There is another way to look at it that in my case made me even more convinced that I did the right thing.  When contemplating adding an author, ask yourself what that person would gain by being added versus what the other authors would lose.  In my case I would gain at most one more publication -- in fact, the third of a series in which I was a coauthor (the most senior one) on the first two.  The two student coauthors would lose the prestige of having written a nice paper which does not have a faculty coauthor....as they deserve, because they did more than 95% of the mathematics of the paper on their own, without any guidance or direction from me.  Adding myself as a coauthor would be undermining my own future plans, as I have and will again in the future talk about this work when recommending these students.  But even if I was just a postdoc or a more senior grad student, fundamentally speaking how much credit can I get by being an author of a paper when as soon as anyone asks me about it I will feel honorbound to describe the minimal nature of my contributions?
I hope that by the end I have waded back into a point which is relevant to your question.  Academics should not be in the business of maximizing the number of papers which appear with our name on them.  I don't know of any academic field where this is really the route to substantial academic success: you get hired for the actual strength of your work, not the number of your papers.  Adding yourself as an author to a paper that you mostly just copyedited and then made some minor comments from a position of lesser insight/expertise than some of the named authors: in so doing you're not actually adding strength to you research program, are you?  Anyone who might have been impressed with the paper is going to be distinctly disappointed when they learn what you actually did, right?  I know that in some fields (much more than mine...) the quantitative standards for publication are very high: in some branches of engineering and the sciences you most certainly want to ensure that you are writing a lot of papers rapidly.  But then you want to really be involved in the work of those papers, right?  We've seen on this site how easy it is to publish papers in the absence of actual academic content.  It's too easy to be a plausible route to legitimate academic success in most parts of the world.
As I mentioned in a comment, you said that the one coauthor who is a native English speaker is the most junior author on the paper (a master's student).  Well, that confluence of lightness of intellectual contribution and superior skill in this other domain makes that student the perfect person to do the copyediting, it seems to me.  If their understanding is so limited that they can't even be trusted to edit the paper for non-content related issues, then I am worried about their being listed as an author at all: what could they have done?

Note that in some fields, "having written a nice paper which does not have a faculty coauthor" does not carry more prestige for students than co-authoring with faculty. And in some fields, depending on your reputation (current or future) in a particular area, adding your name to a paper can increase its reputation and reach, in which case the other authors would benefit from it. So  weighing the relative gain to you/loss to other authors is not always a good way to make this kind of decision. (I agree with the rest of this answer, though.)

It seems the posture/attitude of mathematics with regards to authorship is admirably sane (I assume here you are to some extent speaking for prevailing practice in the mathematical community). This is also corroborated by discussions I've seen in places like Math Overflow. However, this is most definitely not the case in most academic areas. In most cases I'm aware of outside maths, the idea is indeed to get your name on as many publications as possible, by hook or by crook.

"Senior" academics consider they are entitled to co-authorship on papers authored by "subordinates" under any circumstances, and are outraged if anyone suggests otherwise.

Although discipline is relevant to the question, it (ideally!) shouldn't be. For that reason, the omission that I'm in astronomy is deliberate.

I think your "subtracting" guideline is too severe. If three authors each, independently, write one-third of a joint paper, but it would still be publishable with only two of the three parts, your idea might suggest that none of them should be an author! Of course, if two of them write 95%, and one only 5%, then the situation is more tricky.  Students in particular should pay attention to the possibility of "impostor syndrome" (cf. Wikipedia) in which they downplay their achievements and feel they couldn't really have contributed to a paper in a significant way.

I do think the scenario here is an example of what I think is the best practice in math: based on your contributions, although they were somewhat minor, you were offered authorship. This allowed you to make the personal decision about whether to be an author, rather than having that decision made for you.

@Oswald: I agree: it is best for the contributor to decide whether the contributions were sufficient to merit coauthorship.  About the rest: well yes, my rule of thumb is not perfect.  But I did say submit to the same journal: if it is possible to remove 1/3 of a paper and not substantially decrease the overall quality, that's at least something to think about.  But I think I should have included the proviso that if your contribution is not significantly less than any other author's, coauthorship is probably okay.  Is it really a tricky situation if I contribute 5% of the content of a paper?

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Can a peer review be too positive?
I have recently been invited to peer review an article for the first time. I must admit I went into the process expecting to find at least a number of faults with the manuscript and the idea that I could rely at least somewhat on the number of reviews I have received on my own work to structure my own review.
However, it turns out that while this is in my field, this is a vastly different paper from the ones I ve been publishing. I tend to submit manuscripts that present some new kind of design or method, when the one I have been asked to review is an extraction and analysis of data, and it seems to me well done.
The target and the reason it was chosen is clear, they clearly present their methods and the reason they chose certain tools, the vast majority of references are recent and relevant, the topic current, and the results very clearly presented and formatted, accompanied by a great amount of figures and tables that either make it more comprehensive or condense data that would be tiring in-text. Even the level of english is good.
I find that I have no negative comments to make, but I am afraid I'll come off as unhelpful and too naive. However it seems to tick all the common boxes and even the fact that I have to search for something negative to write seems like it should be testimony enough that this is good work. The only thing that makes me less confident is that this is my first review. Is there such a thing as too positive? And what kind of impact would there be if, say, the view of the other reviewer was vastly different from mine?
Note: I am still a student but with significant research experience.

Related: I peer reviewed a paper and found it to be sound - technically and language-wise. How should I write the review report?

@Wrzlprmft thanks for the link, however most answers seem to say something along the lines of: its not just about the level of English which is neither the OPs or my point...

If there are N human beings who review papers, and each one reviews an average of n papers, and N is much bigger than n (which seems plausible), then for about N/n people (a lot of people) the first paper they review will be the best one they review!

It seems that the paper should be published as it is.

Maybe there are some other things you can comment on? Did the paper inspire you in any way, e.g., is there any additional analysis that would be nice (you don't need to suggest that the authors need to do it in this paper, just think about and discuss it)? Are there any additional connections to other work that you know that you could point out (maybe in your personal niche of expertise)? Those would be useful for the authors even if you start the review "I'm happy to recommend acceptance as is".

The purpose of a review isn't to praise or condemn a work, but to help the authors improve it as needed and to help the editor make a decision about publishing.
Your review should say what you think and if you don't find things to improve, you can say that. But for the editor's benefit, say what it is that makes you recommend publishing: correctness, utility, innovation,...
The only way you sound naive is if other reviewers disagree with you, which could happen, of course, if you are new to a field. You suggest that isn't the case, so you should be fine.
I know people who write things that are very difficult to improve. It is a combination of skill, insight, and experience that puts them in that position.

It is not that it is some kind of revolutionary work. But it was a simple, straightforward concept and the execution very good. There is not anything for me to judge but the methods and presentation. Should I only include such comments when addressing the editor and be more brief when addressing the authors?

That can work, but you have to judge it.

You can recommend accept from the first review. Something like:

The target and the reason it was chosen is clear, they clearly present their methods and the reason they chose certain tools, the vast majority of references are recent and relevant, the topic current, and the results very clearly presented and formatted, accompanied by a great amount of figures and tables that either make it more comprehensive or condense data that would be tiring in-text. Even the level of english is good. I am happy to recommend acceptance as-is.

is good. It wouldn't be too positive either, since accept recommendations (either at once or later in the review process) generally read like this.
What if the other reviewer thinks very differently from you? Then there'll be a problem for the editor to solve. Chances are they'll make a revise decision and the authors will concentrate on the other reviewers' comments. There's a chance you'll be invited to review the revision in this case, although the editor can also decide not to invite you since you've already recommended acceptance.
It's unlikely the editor thinks less of you even in this situation. After all, you clearly read the paper. Divergent reviews are also not that rare - as a very rough estimate there are a few per 100 manuscripts handled. The editor might get suspicious if the other review goes "this paper is so bad I'm outraged the other reviewer recommends acceptance", but given your assessment that seems very improbable.

Do you feel qualified to judge this paper? The journal believes you're qualified, since they asked you to review it. If you feel qualified, then don't hesitate to express your enthusiasm for the paper and don't worry about how you will appear to others. I think you could only appear naive if you don't really understand the paper and you think it's wonderful when it's not. Only you can be the judge that.
It's quite common for reviewers to disagree about a paper, sometimes rather strongly. That can be confusing for an author, so be thorough and clear in your feedback so the author understands your reasoning, especially if you request changes (which isn't the case here).
The purpose of your review is to help the author, the journal, the field, and readers by offering commentary that ensures that only high-quality papers get published and that the author has made the paper as good as it can be. If you can't think of even one way to improve the paper then say that. That would be unusual, but it's certainly possible.
Thank you for being conscientious. That will be appreciated by all concerned.

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History MA Thesis: Advisor wants my research sent to her
So, in my planning phase of my MA thesis in history, my advisor says I should have my research to her by X date. What does this mean? What does this look like? I asked her and she answered me with three more questions. That is what she does, she expects you to find the answer to most any question you pose.
So, I guess I am asking, what do I give her? Primary and secondary? Everything I have looked at or just the important things? I have like 10 or so pages of primary research that is mostly quotes or paraphrases for reference when I begin writing. Do I give her that?

Please explain what are Primary and secondary. You call "quotes or paraphrases for reference" primary, then what are the secondary stuff?

Have you tried talking to other current or past students of your advisor? I've been a student in 4 different graduate programs, and in each one of them there was quite a bit of department gossip by students pertaining to all kinds of things about the faculty members. However, the culture and climate where you are might be very different from my experiences (U.S. math graduate programs, but graduate students I've known in other fields say the same, especially in the humanities fields), and thus perhaps more context about your situation would probably be helpful.

Unless you have some evidence that the professor engages in improper conduct (stealing the student's work), I suggest that you give her everything she asks for. There is no downside to this if the advisor is honest and helpful. The most likely explanation would be that she is trying hard to keep you on track and wants early warning if you seem to be wandering.
You may not think this is necessary, and it may not be, but some students do wander and lose focus.
So, assuming a good and fair advisor, sharing can shorten your path to success.
But, if you have evidence that she is not a good actor, you should find a way to work with someone who is. Bad actors are rare (I hope) but they do exist.

Upvoted, but I think the question isn't about whether to trust the adviser. It's "given that I"m not finished, just have some progress, what to send her?"

@gnometorule. Yes, I think you are correct, but wanted to cover the bases. Too many horror stories on this site.

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Does some degree of stubbornness help for a researcher?
Doing research requires exploring a tree of different ideas and then, upon failures, tracking back to some extent, up to giving up on the whole project and changing topics (or even quitting your PhD). You might err on both sides: change approach too much, give up too early, or too late. (See for instance this answer or Half good and some not good results in a research paper?). Most importantly, though, often you won't know that you'll actually succeed until you did, and things might look bleak until then.
Does some degree of stubbornness help being a researcher (I couldn't extract an answer so easily from 2)? Lacking that, do you know any metaheuristics to approach this decision?
EDIT: I read this idea off the mention of "stubbornness and self-delusion" in this rant - and I've observed this trait in at least some researchers.
EDIT 2: an answer suggested that I talk about persistence instead. And probably that's the right compromise and what you actually should have. But I prefer the more provocative phrasing, also because I've anecdotical experiences of stubbornness as a "professional risk" of the profession.

It certainly helps me.

Although I understand what you are getting at, I would like to say that stubbornness is perhaps not a good trait for a scientist. My dictionary provides the following: Stubborn: Having or showing dogged determination not to change one's attitude or position on something, esp. in spite of good arguments or reasons.
Clearly a scientist needs doggedness and stamina to endure long and hard experiments, field work, often monotonous work on data and theory, as well as other issues met in the workplace. To be able to change footing in light of new evidence is, however, an important trait. So being stubborn, in the sense of the definition, would be very counter productive in our effort to have science progress. Persistence and perseverance are perhaps synonyms that better reflect the traits you aim for.
So, yes it is important to be able to endure. Being a scientist is usually based on a deep appreciation for the subject and the research, which is why it is possible to endure the pressures that exist. It is a bit like being a top athlete, very few will excel without a deep love for what they do. As soon as you lose the drive it is difficult to continue because of the demands. Maintaining the drive is therefore a very important aspect of academia and the workplace in which you act.

You're right, "stubbornness" might be too provocative. That's why I emphasized that you can change tactics too early or too late.

I've revised a bit the question, though not exactly in the way you suggest (although I agree with your conclusion). Overall, stubbornness helps to avoid changing (too much) your position because of seemingly good arguments. But probably, it's enough to not lose confidence (whichever way you manage) and simply analyze the arguments.

✓ determination. ✓ skepticism. ✗ stubbornness.

Yes, you've got to be stubborn in order to get results, because everyone encounters failures and roadblocks. Giving up too early can withhold good results, but aimlessly slogging towards a dead end can be a waste of time.
I only give up on something when I can justify why I should give up.

Identify the cause of the difficulty.
Find out what you need to do to solve the roadblock.
Assess whether it is feasible to solve the problem with the available time and resources.

Most failures are still useful to you, because you can usually find out why those ideas did not work. Learn from your mistakes, and (if appropriate) publish why a method did not work as expected (as a prelude to a subsequent method that did) so that others can learn as well.

As @Peter Jansson makes clear in his answer, stubbornness may not be a good quality to have, but tenacity and perseverance certainly are. See this post by Matt Might  for an insightful look at why PhD students need persistence and tenacity in order to survive and thrive in what can be an exercise in long-term frustration and failure before reaching success.

Thanks for the great link, I'm perusing Matt Might's blog now.

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What is purpose and meaning of "Propositions" in PhD thesis?
I found a weird and intuitively strange document that is submitted with the thesis. It is called

Propositions To accompanying a dissertation on the.....

and it is such a strange thing included, that maybe it is a cultural thing specific to Dutch academia? Its content is as follows:

To cycle up a steep hillside one needs to accumulate strength beforehand. This is a similar process to planning one’s work. Democracy is forbidden in science. Doing science is similar to the Chinese martial arts (Kungfu). Alongside learning and practice, both are capable of creating physiological or psychological disorder.

In the end, this proposition finishes with

The contention is that these propositions lend themselves to opposition and are defendable, and have been approved as such by promoter [promoter’s name] and co-promoter [co-promoter’s name].

for me, this is so strange and not understandable. Why would this be submitted with the thesis? Please, can someone explain me the meaning?

The formatting that you originally used is intended for reproducing exact formatting, such as if you want to discuss code or the layout of a document. Please use > this is how to format a quote  to format quotes.

@StellaBiderman a wanted those quote in the way they wont be indexed in google

Apparently, your attempt to block the quote being indexed by Google failed since it's already indexed and placed near the mentioned paper.

This is indeed related to customs in Dutch academia. Precise practice and regulations vary between universities, but usually there is the opportunity (or even duty) to provide this list of propositions, usually distributed as an inserted leaflet with the thesis. The propositions themselves vary from serious scientific statements (typically related to the content of the thesis), to more "humorous" statements like the example you posted. These statements can be part of the defense, i.e. the committee can ask questions about them and the candidate has to defend this thesis. In practice (insofar they do not relate to the thesis itself), this only happens when the committee runs out of "real" questions. This can happen because for the defense in the Netherlands a fixed amount of time is prescribed, which cannot be shortened.

In my experience, some 25 years ago, the committee usually did not have enough time for each member to ask one question each, much less getting to the propositions. This was in physics/materials science, where a good technical answer might take a while.

@JonCuster: yes, I think I have only seen it happen once out of 10 or so defences I visited. Certainly not very common.

@JonCuster weird, this was part  physics/materials science thesis

Hmmm. Actually, I think it is very cool.


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Definitions in Glossary?
While writing my thesis, I was putting down some definitions of terms as they are used in the scope of the work.
Does it make sense to move them to the glossary and write their definition as well?
Looks like the Glossary is used mostly for acronyms in the thesis/diss I have seen.

Yes, it makes sense.
Doing so will add value to your thesis, if you do it well, and help the readers. Most people don't do this because they think of it too late or do not have the energy. Start doing it early and do it well, or don't do it at all.


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Optimizing a thesis writing workflow for Bachelor and Master theses
We are at the moment designing a document which we can hand out to Bachelor and Master students to give them a general idea on how to efficiently write a thesis. We also do this to make correcting easier for us. We are working in the field of cell biology. A thesis in our field is usually structured like this:

Abstract
Introduction
Materals and Methods
Results
Discussion
Acknowledgements

What we've come up so far is the following list of best practices. This is based on our experiences with previous students and our own theses.

You can already start writing your materials and methods (M&M) section during your regular lab schedule. This will save you time later on.
You will have discussions with your supervisors on your results, in which you will decide on what to include in your thesis.
Start by making the figures for your results and a corresponding caption.
Lay out bullet points of your results. Afterwards, start writing the text around these bullet points. After finishing, send this part to your supervisor for proofreading.
Proceed with the discussion. Again, lay out bullet points, but this time, before writing, clarify each point with your supervisor. This will prevent you from having to rewrite large parts.
Continue with the introduction and, if you haven’t written it yet, M&M.
The introduction should contain everything the reader has to know in order to understand why you did what you did and what the results mean. Be brief and clear.
Finalize by writing an abstract (“Zusammenfassung”). This has to be written and edited very carefully because it will be the part most people read. Your thesis also needs to include an english abstract which is an exact translation of the german one.
Don’t forget the acknowledgements (“Danksagung”). This is the second part everyone will read, and it’s extremely unpolite if you don’t have one. It doesn’t have to be formal and can be personal.

My question: Is there something important missing and would you recommend things differently? Maybe you could elaborate how you handle this in your lab.

It is a very good set of advice. There are two very practical areas that seem unaddressed and that are, in my experience, somewhat… problematic with some students:

Proof-reading. Find someone, other than yourself, who will do a final proofreading of the thesis for language and clarity. Not necessarily someone from your field, but checking typos, missing figures, acronyms that are never defined, that sort of stuff… That person should not be you, because when you've spent so much time writing the thesis, you won't even see these details any more when you read it.
Also, check with your supervisor what are his expectations regarding proofreading/corrections. It depends on your university and the supervisor himself, but in many cases they will want to read it themselves, and possibly offer some remarks and corrections.

Scheduling. You are aware of the submission deadline, but mind that the final stuff takes time. In particular, if your supervisor has to read it, make sure to give him enough time to do so. So, start with a clear set of intermediate deadlines, and if you start to miss them, take action! Nothing's as bad as procrastinating ’til the last day thinking “I can still write that in 24 hours if I get to it”.

I think your list looks great, but I would suggest adding a couple of "soft" recommendations; e.g.,

If you are struggling with a certain topic, idea, or way forward, ask for assistance as early as possible after you have exhausted your ideas.  Do try to solve problems on your own, but don't let that take too much time that you fall behind.

I don't know much about the cell biology field, but do your papers normally have "Related Work" sections?  I assume they must also have a References (or Bibliography) section?

For me, the difficulty was that the research part was too interesting, so I ended up writing papers, trying new techniques etc., but neglected the thesis writing. If you have students like me, make them to write some parts of their theses before they are allowed to do more research in the lab.

Of course there are departments where a thesis basically consists of those papers stacked together plus some minimal elaboration. And hey, why not, DRY after all


text:
How to check citations and references match in a manually prepared document with APA author (year) citations?
I like to use bibliographic software (e.g., Endnote, BibTex, etc.) to manage my references. However, sometimes I am working on an existing article that has been written with APA citations and references written manually. For example, I might be working with a collaborator who has written the first draft or I'm adapting a student thesis for journal publication. As a result, citations get added and deleted, and there are reference errors: (1) citations present with no reference;  reference needs to be added (2) references present with not citation;  reference needs to be deleted.
So, a common task when such documents are being finalised is to go through the document and pull out all the citations and check them against the reference list and fix any errors. This is generally a frustrating task, because (1) unless you are careful errors can be made, and (2) if the document is edited further, the document may need to be rechecked.
Question

What is an efficient strategy for identifying citations without references and references without citations in a  document with author (year) style citations (e.g., APA, Harvard)?
Are there any automated tools that perform this checking?

I would rewrite the document in LaTeX, using BiBTeX and apacite.

In the "old days" this was what had to be done manually. I simply printed the reference list (one-sided print) and went through the text and checked the references I passed in the text and checked the corresponding one in the reference list. This would take maybe 20-30 minutes(?). It is clear that this is easier to do on paper than on screen but it is a very safe way to do the checking. In the end you will (hopefully not) end up with references missing ticks in either the text or the list.
So considering, the time it takes, doing the manual check on paper copies, is perhaps boring but not a terrible loss. Sometimes you pick up on other errors as well. Although one should not rely on external help to solve ones own problems, many journals use copy-editors that check for inconsistencies so there may be a back-up for the stray miss.
As for software, I cannot point at one directly. It would have to be able to match first author name and the year between text and the reference list. I does not sound like an impossible task but I would probably just do the job the manual way in the few cases where this is necessary. You can also ask your collaborator to do a separate initial check (as "punishment" for not using bibliographic software). In addition, if you author in LaTeX then writing the bibliography directly with \bibitem and using \cite (or natbib cite commands) commands will at least do half the job.

Take a look at
www.keytectype.co.uk/keypreps.htm
KeyPreps contains tools for matching citation to references and vice versa for any Word doument.
It gives you a report such
"The citation Smith 2009 has no corresponding entry in the refernence list"
"The reference Bloggs and Layabout (2009) is not cited"
etc
30 day free trial available of the complete KeyPreps package

The following online solution is (currently) free: https://reciteworks.com/check
From the website:

Recite checks that your in text citations match the reference list at the end of your work.
Recite is optimised for those who use APA or Harvard referencing styles.
Recite may be of most use to those who don't use reference management software like Endnote or RefWorks.

Whilst this may theoretically answer the question, it would be preferable to include the essential parts of the answer here, and provide the link for reference.


text:
What is the backup strategy of online-only journals/repositories on the very long term?
Disseminating printed documents in many places on the planet is a very robust "backup" strategy for scientific literature. Printed documents (and other forms of ink-on-paper documents), or fragments of them, are known to last for millennia and with a high redundancy (many copies spread in many geographic locations), the chances of being able to reconstruct the original content is high.
All current electronic data storage require continuous catering (electrical power and servers maintenance) or frequent re-copying (i.e. of laser discs, magnetic hard drives, etc.) to last more than a few decades.
How do online-only journals and articles repositories intend to ensure very long-term archival of their content?

For interest see also: http://worldbuilding.stackexchange.com/questions/28505/computer-that-lasts-for-centuries (Speculative)

@Oxinabox looks interesting, to clarify I'm interested in the actual policy that journals have nowadays. I understand that "They have none" is a possible answer.

I asked specifically about the arXiv policy here: http://academia.stackexchange.com/questions/47416/what-are-the-archiving-policies-of-arxiv

I'm seriously tempted to ask the symmetric question: "Disseminating online documents in many places on the planet is a very robust strategy for scientific literature... How do paper-only journals intend to ensure very long-term archival of their content?"

@JeffE wouldn't the answer to that be the same way they have been for decades?

@JeffE ... For paper archives: One change has been to used acid-free paper, so that it takes much longer to become brittle and disintegrate.

@JeffE the answer to that question is stated in my post.

Many modern libraries have developed a habit of discarding paper versions of documents because they have electronic versions that take much less storage space. Books go out of print and are damaged, destroyed, lost, or discarded, and publishers go out of business, sometimes before their content can be digitally preserved. My question stands.

@GEdgar: acid free paper is good, but what do we know about long-term preservation of laser printing? Most Springer or Elsevier journals are now printed with on-demand laser printing, and given their look (at least in math) I would bet it's not the top quality in that technology.

@JeffE it's true that if libraries start to burn their books, that will weaken the strategy. Although I'm sure not everyone everywhere is actively destroying printed content. But so the assumption is that there will be infinite monetary support to maintain the online repositories?

No, of course not. But neither do I assume that there will be infinite monetary support to maintain repositories containing megatons of cellulose.

@CapeCode: I haven't heard of any libraries burning their books, but many of them sell books that haven't been checked out for a certain number of years.  Of course in that case the books still exist, somewhere, but the content is less effectively preserved for posterity if it's scattered all over the world.

@CapeCode Hosting physical books costs money https://leverpress.org/wp-content/uploads/2015/08/CourantandNielsen.pdf suggests 0.86$ per year for the cheapest way to store books and 4.26$ for storage at a place where it's easily accessible by library users. The amount of money you need to maintain online repositories is orders of magnitude less.

Most publishers use a preservation network such as Portico or LOCKSS. The principle is that numerous electronic copies are saved, and released in case of certain events (e.g. the publisher stops permanently giving access to the works).

Open access journals and article repositories have a good option of ensuring very-long term access that is similar to how printed documents were handled in the past: Wide dissemination over several repositories.
In the life sciences, open access articles are often deposited in additional repositories by publishers themselves, for example at Pubmed Central or it's European equivalent Europe PMC. I think also additional repositories actively mirror some open access journals - at least I frequently seem to get results of such additional repositories through internet searches. That means even if the publisher goes bankrupt and shuts down its servers, the papers should still be easily accessible through these mirror repositories. See for example Biomed Central's statement on permanency of articles.
This strategy is only possible for open access journals, since only those typically allow redistribution of their articles and thus permit the mirror repositories to act as they do. I have no idea how commercial, non-open access publishers handle this problem.

This strategy is only possible for open access journals not really, subscription journals also post pre- or postprints on external repositories.

@CapeCode The key word in your sentence is allow.  If they wanted to ensure long-term availability, journals would require wide dissemination over several repositories.

Besides, how is dissemination over several repositories better than having multiple replicates of a database on several commercial servers?

@CapeCode Because it's several institutions as well. If a publisher goes bankrupt, I'd expect all replicates to become inaccessible simultaneously, if no specific counter-measures are in place.

Currently lib.gen/sci-hub build an archive of all papers and textbooks. Publishers fight the legal battle to stop the project but it's highly unlikely that they will stop lib.gen/sci-hub and it's various mirrors in every country of the world. Elsevier might win the suit in the US but they probably know why they don't pick the fight in Russia where the lib.gen/sci-hub servers reside.
There are applications like IBM's Watson that work better if they have access to more data. That means that companies like IBM, Google, Baidu and Facebook have an interest to have all the data of all scientific papers.
Isn't it expensive to store all that data? No, it isn't. In 2014 Facebook added 4 petabyte of data per day to it's database. That's likely more data than all scientific papers together. All the arxiv PDF's together are 270 GB.

This doesn't seem to answer the question, either at a literal level (sci-hub is certainly not how most journals intend to do long-term archiving) or in spirit (sci-hub faces exactly the same long-term archiving challenges as publishers do, plus the added difficulty of not having all the content in the first place).

Note that the 270 GB figure is apparently as of February 2012, and likely is quite a bit larger by now.


text:
How can we fight junk science?
Fake science is hurting academia and society at large in many ways. Legitimate scientific literature is being drowned in an ocean of junk journals and articles. Almost everywhere in the world, there seems to be simulacrums of science where people wear pompous titles, pay to publish seemingly scholarly literature, go to conferences, etc. but produce 0 contribution to human knowledge. This might be still manageable now because legitimate scientists can easily weed out the junk, but if the amount continues to increase it could go out of control.
At stake are the trust from the general public, the appropriate use of public and private research funds and the advancement of science in general.
Who knows, we might be going towards a new Dark Age but where science is not hindered by powerful religious and aristocratic organizations but rather by an overdose of junk.
What can be done at the individual or institutional level to fight junk science?

Edit: by junk science I mean pseudo-science (i.e. work done with flawed or frivolous methodology), deliberately faked results, and generally very low quality research. I'm not interested in a debate about what is junk and what's not, I'm looking for tangible actions that an individual can take or advocate as an academic, member of a professional/scientific society, employee of a university, etc. very much like what Murphy or Thomas wrote in their comments.

Produce more good science.

First and foremost, you should clearly define the term "junk science".

I think it is important to distinguish between pseudo-science which is based on flawed methodology and deliberately faked scientific results which are produced/bought to support certain political/lobbyist agendas (cf. https://en.wikipedia.org/wiki/Merchants_of_Doubt).

While this is an important question, I am not sure that this site is a good place for it: it's a topic for discussion and debate rather than clear answers.

"Produce more good science" is the one right answer. Don't bother with the other stuff pulling things down. Good science work as exemplar; it's the same with leading by example. It's slow, but it works best on the long run.

Ultimately the junk is like pop music; it's popular for the time, but in the long run no one will remember it. Be a Mozart, not a Justin Bieber; that's all one can really hope for.

I don't think this question is too unclear. It lays out the problem and asks for what measures individuals can take to improve things.
Simple ones would include pre-registering your experiments, call out bad science when you see it, publicly call out bad methods and bad data, encourage your colleges to follow best practices. Attempt to replicate what you can and always publish your results, positive or negative.

The edit doesn't match the question, in my opinion.  Much of the work referred to in the question is likely correct; it's just trivial or irrelevant.

Teach critical thinking and the scientific method.  Skip the junk science.  That really is the only answer.

Also, never forget who the true enemy is.

@Wildcard I don't understand what this comic is trying to convey.

@CapeCode the mad scientis' true enemy is ignorance. The alt text says: "In order to destroy one's enemy, one must destroy its place to exist". If the robot educates the young, ignorance won't find a place in their heads.

@Devin unfortunately, homeopathy is as popular as Mendelssohn.


text:
Someone cited my paper in an irrelevant manner
I checking my google scholar page, when I noticed that one of my papers, of which I am a co-author, had been cited by an unknown academic. I read the article, which was on gene regulatory networks, and my paper is in computational neuroscience. The reference wording doesn't make any sense though. The only connection is the concept of an attractor network.
If I met this person at a conference, and he went about relating my paper to his work, I would call nonsense. This must happen to more well known academics all the time, so is it best just to let these things slide? I suppose if I was really famous and getting 200 citations a week it would be too hard to track every bad reference down, but I only have a few.

Don't take this the wrong way, but in the cut-throat world of academic papers, having only a few might make you want to leave it. If someone digs, they'll see "Wow, this person cited him/her for no reason; awkward" with the chance of negative impact on you being minimal. If you did have the citation removed for whatever reason, then that's one less citation you have. Like you said, you're not exactly getting 200 a week - a single citation might be important for crossing some threshold. Not that people should be putting such emphasis on a single number, but they seem to be more and more.

I would be glad someone in another field had read my paper and was citing it. It wouldn't bother me whether the reference was relevant or not. Maybe reading your paper inspired them in some unrelated way. Then again, I've just finished my PhD and every citation counts. But I don't see much point in being antagonistic.

@Phil, citations may be better overall, but this will confuse readers. If your thesis was 'Evidence shows that roses are red, violets are blue', and I wrote: "Flowers, see Phil(2013), are by pollinated by bees". You might say my citation totally missed the specific impact of your work. If I wanted a reference to flowers, I should be citing an authoritative field guide. My paper was on a special class of attractor networks, which have been around for decades. The author should have cited a seminal paper in the field instead of mine. Any reader would likely get confused about my work was about.

@Ksiresh Nice example. I once had someone cite one of my papers in support of the statement that plants need light :) Had I been asked to review the paper, I would have pointed out how silly that was (and I have done this when reviewing papers with similarly egregious citations to my own work), but since I wasn't asked to review it, I'm happy to have the citation. A couple more like that, and my h-index will increment.

Well, what can you do? Not much. I can confirm that it does indeed happen… sometime people even cite a paper of yours to justify a conclusion that you have not reached in the paper, and even one that you strongly disagree with.
One option is to let it slide. You are not responsible for the content of papers that refer to yours, or the accuracy of their citations for that matter. The paper author is responsible, and to some extent, the journal’s referees. (I tend to spend quite some time checking citations  when I review papers, but that might just be me being overly sensitive to this particular issue.)
Another option is to contact the paper’s corresponding author, and ask him point blank. You have read his paper, and you are unclear as to the extent of the connection between his writing and yours. See what it gives.
Finally, in the current way academic research works, you do not really have any mean to call out their behaviour publicly. I do not believe you should, either.

Thanks for your pragmatic response. I do agree with your opinion that is not my business to call them out on it.

There is a huge gulf between what would happen in an ideal world and what the norms are in this case.
"Ideally", you'd get in touch with the author(s), explain that you don't see what their paper has to do with yours; they'd explain why they think it is relevant or agree that it's not, and modify the paper accordingly.  (Almost everything is online, so modification after publication is a possibility.)
In the actual world, citations are of benefit to you, even if they are stupid.  Journals are mostly not set up to remove citations easily.  No one will check, and if they do check, the detriment will be to the citer, not the cited.  So you "shouldn't" do anything about it, and the author would probably be quite surprised if you did (especially if you weren't discreet about it).  If you really feel like re-calculating your h-index with that paper removed, go for it.  But this sort of thing happens all the time (I think all of my papers with over about 50 citations have been cited stupidly at least once), so you're free to just consider it part of the measurement error inherent in looking at citations.
Incidentally, the ideal isn't necessarily the pragmatic ideal.  Doing anything important on the basis of small differences in numbers of citations is fraught with error even if all citations are sensible ones.  There's a reasonable argument to be made that you shouldn't bother unless the paper is in your field and is citing you in support of something that your paper showed the converse of.  Getting your work exactly backwards to advance their own idea isn't doing you or them any favors, so you should try to work that out.

"Almost everything is online, so modification after publication is a possibility." - no, please don't introduce that aspect into the system. If I reference a paper now, I need to be sure that in a few years, readers will still find the same paper that I reference, not something modified. Almost everything is online, but that does by no means imply it could or should be modified. (Adding new revisions is another topic, but the unchanged original version would still be around then.)

@O.R.Mapper - I was assuming robust version control in our ideal world.  Also, if you care that your reference actually mean anything, people who follow it should get any erratum up front, so they can immediately tell if your reference still supports whatever you wanted it to.

@O.R.Mapper I guess in the ideal world, papers would be published with version control and your reference would point to a particular version.

Let it go.  There are probably many times you are inappropriately left out.  A few times when you are improperly cited.  And some times where they didn't understand what you were doing.  As long as there is not some clear pattern--for example your former advisor pushing people to cite you (really him)--it's not worth dealing with it.  There is just so, so, sooo much imprecision in the arena of citations.  You will drive yourself crazy if you obsess on individual instances of citation. (Note, I'm not saying not to worry about general trends...they have validity...but don't obsess on individual data points.)

is it best just to let these things slide?

Possibly. It's certainly a reasonable thing to do. Also, if you have many citations of that paper, I'd definitely say let this slide.

The reference wording doesn't make any sense though. The only connection is the concept of an attractor network.

So, the references makes a bit of sense, but the wording doesn't. Unless that paper makes an invalid claim regarding the contents of your paper, that's not so bad. Certainly it doesn't reflect poorly on you.

I would call nonsense.

You're being much too harsh. Maybe the author typed in the wrong citation? Maybe they meant to reword the text near the citation and forgot to do it when submitting the final version? etc. Give people the benefit of the doubt.
If this really bugs you, email the authors of the citing paper, tell them you noticed the citation, and ask them if they could explain briefly in what context they used your results (i.e. not giving them your impression beforehand). If they don't respond - let it go. If they do explain, and get it wrong, then you can write back saying "Oh, but you wrote that XYZ while in fact my paper is ABC"; note you are not judging their abilities/skills/intelligence, just politely pointing out a discrepancy. If they at all care, this is the point they might consider a revision and/or an erratum, and/or a change in future uses of the same text/ideas (e.g. journal version of conference paper, placement in thesis or book chapter).
It's still quite likely that they'll tell you "Oh, well, maybe you're right, but what's done is done". You'll have to live with that, I'm afraid.

Additionally to what F'x suggested, I would suggest you to discuss the details of this situation in a personal website or blog.

I strongly advise against that. Don’t get drawn into a flamewar when the benefits are unclear (what would you gain that you cannot from sending an email to the citing author?) while the risk is very real (at the very least, being perceived as overly critical or rude).

I think it is useful to give other alternatives to the person asking the question. I just proposed one. For instance, you may approach the author of the paper citing your work, and then you can publish the dicussion on a personal website. You might tell to the other author what your intention is.

you most definitely need the other author’s permission to post an email exchange online


text:
Why do some reviewers mention their decision explicitly?
Recently, some of the reviews I received mentioned their decision at the end of the review (i.e. 'I recommend acceptance of the paper'), while others do not have such statements.
What is the point of adding the decision statement while the overall evaluation (i.e. on EasyChair system) explicitly says it? Is it just the reviewer's habit?

Why not include the recommendation in the report?

@JeffE I will preface this by saying that I am not an editor but through conversations I have had with editors in my field (biology - ecology), they seem to prefer that the specific recommendation (accept/reject) go only to the editor and not the authors.  This is because the decision comes from the editor based on the recommendation of the reviewers.  If the reviewers reveal their recommendation to the authors, then it potentially makes it harder for the editor (e.g, both reviewers say accept but after considering both reviews as a whole, the editor decides reject).

@KennyPeanuts: This is an argument for including the recommendation in the report, not against.  If both reviewers recommend acceptance, the editor had better have a damn good reason to reject.  Of course there are circumstances where rejection is the appropriate decision, but then the editor needs to own that decision.

@JeffE I agree that the editor should always own the decision.  The editor should always reference evidence from the reviews that they used to make their decision regardless of whether the reviewers revealed their specific recommendation.  In the end it is the content of the review that is most valuable to the author.  The recommendation by the reviewer is made with incomplete information and should be taken as just a recommendation.

Typically I include an explicit recommendation in the report to be shared with the authors when I have a strong opinion, but not necessarily otherwise.  In the former case, the editor can still decide either way (referees make recommendations, not decisions), but if they disagree with me at least the authors will know for sure what the referee thought.

what is the point of adding the decision statement while the overall evaluation (i.e. on EasyChair system) explicitly says it? is it just the reviewer habit?

It may be habit, and it may reflect uncertainty about what information from the web form will be available to the authors.

The only reason I can think of to include a outright recommendation the authors can see is if the "feel" of my comments and the decision don't necessarily align naturally. For example, if I've issued a lot of criticisms, but most of those are "With fine tuning, this would be an outstanding paper", or hoping to see what is an adequate treatment of really spectacular data turn into a great treatment, I might not that despite the page of suggestions, it could probably fly as is.
At the same time, I've reviewed a paper with a very small number of comments, but in those comments have been tempted to use words like 'fatally flawed'. So including a 'I would reject this paper' comment might help with "There are only three things you need to change, but you need to take them seriously."

As far as I can see there are two main reasons:

The editor usually isn't an expert in every area. Adding an explicit recommendation (accept, reject, ...) may help the editor.
An explicit recommendation (accept, reject, ...) is the reviewer's ultimate summary. The reviewer should only provide it if they can defend it and feel it's fair. In that sense adding the recommendation strengthens the review.

I am down-voting this because the question is asking about a recommendation that the authors can see.  One always has to provide an explicit recommendation for the editor.  But more importantly most of the editors that I know frown on writing the recommendation in the review for the authors because the editor should be the one communicating the decision to the authors not the reviewers.

@KennyPeanuts So you don't think that adding the recommendation of the reviewer adds more significance to the review? In my experience the reviewers' opinions are usually included.

This may be a difference in our disciplines but as I say in my comment above to JeffE, essentially all of the editors that I have talked to in my field (biology - ecology) have preferred that the reviewer only indicate the specific recommendation to the editor and not the authors.  This is because the editor makes a decision based on a consideration of the content of all the reviews.  It is not simply a vote by the reviewers.  If the recommendation is included in the review it makes it harder for the editor to go against that recommendation if the other reviews warrant it.

@KennyPeanuts, I share JeffE's reaction.  If that is the rationale for your field's practices, frankly, I find them bordering on dysfunctional.  If the editor wants to go against the recommendation of the reviewers, maybe he/she should feel a little pressure to justify the decision; that seems only appropriate and reasonable to me.  I find it hard to be sympathetic to the idea of "hiding the ball" from the author, to preserve the editor's power to hide the reasons for the decision.  Perhaps I just care more about authors than about editors, and view editors as public servants.

@D.W. I guess I don't place as much value on the actual recommendation as I do on the content of the review.  No one is advocating hiding the ball. A proper review should be comprehensive in its evaluation and provide an unambiguous picture of the paper's strengths and weaknesses.  Nor should the editor hide his or her reasons for a decision.  The editor should always include the evidence that was used to arrive at the decision.  The rec. made by the reviewer is not made with all of the info available so it's not really that valuable to the author, regardless of who cares more about whom.


text:
Do we know what proportion of scientific reproducibility issues are fraud-related?
A few days ago there was an article on the LSE blog about scientific reproducibility which made little sense to me until I realised they were equating 'low reproducibility' with 'scientific fraud':
http://blogs.lse.ac.uk/impactofsocialsciences/2016/07/21/could-blockchain-provide-the-technical-fix-to-solve-sciences-reproducibility-crisis/
I've tended to assume that most reproducibility issues are poor reporting of experiments, poor recording of external factors, poor statistical analysis inflating p-values etc but I realise that I don't have much evidence to back that up apart from personal experience. Are there any studies that report the relative proportion of irreproducible experimental results resulting from fraud versus poor experimental/statistical/reporting standards?

Could be very difficult to distinguish. For example, with statistical analysis, poor understanding, lazy implementation or genuine intent to deceive could all lead to exactly the same result.

Philosophically, the kind of study you have in mind seems nearly impossible to execute properly, since fraud is inherently hard to distinguish from mere lack of reproducibility. On top of poor experimenting/reporting, one aspect is that an irreproducible result can be always be an outcome of chance/randomness (p=0.05 means that it's randomness in 1 case out of 20).

"Are there any studies that report the relative proportion of irreproducible experimental results resulting from fraud versus poor experimental/statistical/reporting standards?" How would you establish the ground truth for such a study? The only people that know whether a certain result was fraud or just sloppy are the authors, and they won't tell.

Sometimes, mistakes can be told from deliberate fraud, as the Poincaré and the fraudulent baker anecdote illustrates.

In principle, one could compare (1) the rate of papers in field X where replication was attempted but failed to (2) the rate of papers in field X that were retracted due to discovered fraud.  That would be a poor proxy for a comparison between unreproducible papers (most of which are untested) and fraudulent papers (most of which are undetected), but it might be interesting in its own right.

To go further than @lighthousekeeper's comment, you actually expect many unreproducible results to be published without any fraud---see publication bias.

While not an answer, this question is essentially about how one could carry out such a study.

@Kimball Even without publication bias, some studies conducted on null effects will show positive or negative effects because of randomness.

@lighthousekeeper I would assume that many fraudsters are trying to publish "valid results" but are simply too lazy to do the necessary work.  If their intuitions happen to correct, then their fraudulent results would actually be reproducible.

Statically speaking, once you get a big enough sample, you will have false positives.  How do you then deal with that?  Obligatory XKCD comic

I very much doubt we "know' this in the empirical sense, as:

As a scientific problem, the "reproducibility crisis" is fairly new, and we're still developing the methods to really understand it.
It's very hard to distinguish fraud from error except in the most egregious cases. You can say, for example, that there's clearly some bias in a body of work in a field, but it's hard to say that any particular paper is clearly biased.

For example, is a convergence error that you chose to ignore because it was "pretty close" to the convergence criteria you set for a statistical model an error, or fraud? How about using Bayesian priors that turn out to be stronger than was probably justified? How do you distinguish fraud in the form of "nudging" a result over the line into significance from a largely insignificant effect being estimated with error that sometimes crosses the null.
Frankly, there's not even, IMO, a solid definition of "irreproducible". Is that "Finds a statistically significant result"? "Effect estimates are on the same side of the null"? "Our clinical/policy conclusions would be the same"?
Lacking even that, I'd assert it would be particularly difficult to attempt to assess fraud vs. error in any systematic fashion.
It would also be an exceedingly difficult study to run, as you'd need the cooperation of a bunch of people who comitted fraud.

If you are asking what percent of experiments are reported as reproducible, when in fact they are not, I would think it is very, very low.  The scientific method defines reproducible as an experiment that can be recreated, or performed by others, using the exact method. If these scientists have any conflicts of interests, they must be reported. After any trials of an experiment/study it is reviewed by another group of scientist. If a experiment isn't peer reviewed, it isn't a legitimate study to begin with. It is unlikely that you would be able to find a few, let alone a large portion of the scientific community to be in coercion and conspire to fake a theory.

That's clearly not what OP is asking, for two reasons: firstly, because the question talks about irreproducible results rather than irreproducible experiments, and secondly because the contrast is not reproducible vs irreproducible but "fraud versus poor experimental/statistical/reporting standards". Also, FWIW, in fields where the standard is a p-value of 0.05 and negative results aren't published (which is a whole separate issue) we would expect 5% of published results to be irreproducible in the best case, assuming no statistical errors.

I consider advanced science as it's done today (a few separate teams tackling a particular issue with often very expensive equipment and/or materials) having great prospect for fraud by its very Nature. Consider, for example, science at the times of Copernicus and Galileo and science today. One can tell you it wasn't much of a cost to build a primitive telescope or laboratory then and anyone with more means could be scientist with a relatively low cost. Can you say the same for science today? How many people can spend the cash to build and equip (the costly part here) modern laboratory in anything compared to the same costs a century or two ago (or even a few decades ago)? (Exclude the millionaires-also consider some legal issues coming with modern and advanced laboratories.)
The more expensive and more profiled research gets the less people are actually available there to tell you the intentional fraud from the real sloppiness. As the research gets ever more profiled and more expensive to reproduce even the people who can argue the validness of a certain result are getting fewer and fewer, so how can anybody judge was it intentional or not? It's next to impossible. And it will probably get worse with time.
So, the study you suggest amounts to more than impossible. High research costs, lack of enough specialized personnel, greater abundance of claims to be falsified and not the least-doubtful interest in verifying them all amount to its impossibility with the advance of research efforts and costs. The more science is moving into an ever more profiled and costly activity, the more the very idea of falsifying every single claim someone makes into a paper is becoming implausible. And if you can't even spare the resources to clarify all mistakes how can you determine are they intentional or not? There may be some cases here and there where enough resources may be spent to clarify certain issues but you can't make a serious study out of those, right? Consider the amount of cases you are actually studying to the amount of possible cases of fraud. How can you get any statistically meaningful results if you are just picking up cases where you can determine the fraud was a real issue versus cases there may have been fraud? What standards will you use to discern this group from the group where you put errors made by sloppy research methods? What about a control of "impeccable research" (Is there even such a thing in any modern science?)? How can anybody devise "firm" criteria for putting anything in any of these categories when the effort to discern a false claim versus the number of possible claims is overwhelming. Just like nobody can pursue the validity of any claim due to the high costs and the lack of experienced enough personnel, so one can't make any "statistic" (except highly cease-sensitive and "narrow" field one) of the number of claims versus the number of fraud cases which could has any chances of being reliable?
P.S.As far as the issue of reproducibility is concerned I like to give one particular example. It's a bit hilarious but nevertheless I believe is on the right spot here :)
Consider the possibility there was some "large scale scientific conspiracy (e.g. a case of fraud)" concerning the results from the Large Hadron Collider at CERN. Now, let's say that every single participant in the experiments done there was part of some "grand scientific kabal" designed to mislead humanity about the very nature of our Universe. (I met people on the Internet who actually believe in this claim. :) Then, how can one be certain there is no fraud in the claims made by the scientists participating in the LHC experiments if there isn't any other such devices in the whole world? I tried to actually argue with "scientific kabal believers" such thing is impossible because there are simply too many people from too many countries doing research there and too many are watching the facility to serve as some "fraud facility" to lie to the poor people, but then I go back the argument that until one can build an LHC identical to the one at CERN in their backyard no one could be certain its results aren't fraud! Hilarious, isn't it? But, then I was dismayed how can one actually argue with someone putting up arguments like that? The funny thing is I couldn't. How can you convince a skeptic like that? And if you can't convince someone for such a big and visible experiment like the LHC how can you convince him other much less prominent experiments aren't fraud, too? But, then, if you can see fraud everywhere how can you discern it from mere sloppiness? What if you have doubts at the status of the very experts that have to do the discerning in itself? Then, what are you options?
The way I see it one can doubt endlessly in anything and everyone, then how can such an extreme skeptic ever achieve firm standards for anything which s/he can't get his/her hands on? And with the state current science is in this is practically impossible. Then, one should never be able to tell when there is a legitimate case of fraud and when things just weren't thought out well enough.

If you so much hate my answer and you're voting it down why don't YOU people write down one yourselves? At least, I made the effort to write an answer to the question-good or bad as it is!

Something is not always better than nothing. While we appreciate the effort, we don't necessarily appreciate the result. Downvotes are strictly an assessment of quality of the answer. They are not an assessment of the person posting the answer, nor of that person's effort.

Most particularly, your answer is lacking in any references or hard numbers that the question is calling for specifically ("Are there any studies ...").

I think it answers the point why such studies are practically impossible to do-it's impossible to get good statistics of the numbers of actual fraud-related cases versus the number of possible cases, therefore the question the OP is asking can't be answered in the context of the modern state of organization of scientific research. This is the message I want to convey. If I don't-please, tell me why? May be I can learn something from this experience. I would also like to see an alternative answer to the question so I can compare it with mine, but in its absence what can I really tell?

therefore the question the OP is asking can't be answered — This is a good reason to downvote the question.

-1 for...a number of reasons. Among them that the research I do requires only the device that currently sits in the pocket of most people in the developed world. Also for ignoring that science in the past was mostly conducted by the idle rich, or those with patrons, and that is perhaps indicative that things weren't so cheap.


text:
Is the conference "ICCTCEEC" a scam?
I submitted a paper about 20-25 days ago in this conference http://ctceec.org/ knowing about IEEE involvement here.
Today I have got an acceptance email for my paper, The astonishing thing to me is, I knew at least 1-2 month is required to review this type of conference paper.
The conference date is 8 September, 2017 which is very near. Is there anyone who can assure me that this conference is not scam?

The relatively short review period would worry me less than the exceedingly unprofessional website and the fact that the seem to accept papers on everything relating to EE or IT. I am not sure if the conference is strictly "spam", but I would bet good money that it is not worth going to.

If you have to ask, it probably is.

Have you ever cited, or even read, a paper from this conference? Do you recognize anyone on the program committee (who is not at your institution)? If you can't answer yes to both questions, you shouldn't send your paper there.

My guess would be: not a complete scam (i.e. there really will be a conference, accommodation will be booked, the talks will happen, etc), but very low scientific quality, since the range of topics covered is so implausibly vast.  The sort of conference where most participants are not really going to disseminate their research or learn about other people’s, but just so that they can list the talk on their CV and tell their department that they are travelling to international conferences.

Anyway, they are probably going to compete for the conference with the longest unpronounceable abbreviation.

What were they thinking when they designed that website?...

@MCMastery At least they refrained from making the marquee text blink ..

Also not in favour: numerous unsolicited e-mails (I have received more than 10!) with ads for this conference have been sent out from different accounts, all on an anonymously registered, now suspended domain (which happens to share the exact name servers with the official ICCTCEEC website), containing dubious shortened links.

The website has a button that says "IEEE proof", whatever that is supposed to mean, which seems like the equivalent of a folder on your computer named "definitely not porn". Understand: they're trying suspiciously hard to use their (alleged) IEEE affiliation as a marker of legitimacy and quality.
Follow that link and enjoy that delightful prose:

"We believe education is our motherhood and research is our motto. Our intention is to collaborate innovative brains at one place. So, here we are with "International Conference on Current Trends in Computer, Electrical, Electronics and Communication" (ICCTCEEC) platform to share, learn and discuss. We guarantee your pleasure because our city itself mean you what are we."

Let's say the intentions of the people who committed that website are not fraudulent that's still incredibly sloppy and careless not to have it proofread. Seeing this, I would doubt that anything else about that conference can be worth your time and money.
By the way, IEEE affiliation, even if legit, doesn't mean the conference is good or not spam.
The usual advice in these cases: consult with your supervisor and colleagues. There is typically a rather small number (~5) of conferences worthy of attending per field and any half-serious researcher knows which these are.

The IEEE proof shows that this conference has somehow been registered with IEEE, whatever that means, but for example, the deadlines given on the IEEE website for it are not the same than the ones the OP mentioned or the conference website does. So I would say, while it is not strictly a scam, it's probably not good.

The link goes to the official IEEE site, so I think the connection to IEEE is legitimate. On the other hand, the IEEE page about conferences says: "IEEE sponsors more than 1,800 annual conferences and events worldwide". So I wouldn't be surprised if some of those are indeed low quality.

Yeah the IEEE link makes it unlikely it's an outright scam, but I think we can all be pretty sure that the quality of the conference will be on par with their short description of the conference.. "We guarantee your pleasure because our city itself mean you what are we."

"We believe education is our motherhood and research is our motto. "  They believe research is their motto.  They can't confirm that though.  Awesome.

Registration of the conference with IEEE (i.e., 2017 International Conference on Current Trends in Computer, Electrical, Electronics and Communication (CTCEEC)) is a good sign that it is not an outright scam. However, I note that the conference is sponsored by the Bangalore Section but I couldn't find it on their website which is troubling. Within the IEEE community this tends to imply that the section is treating the conference as a very low priority so quality control may also be quite low. Thus, while I doubt the conference is an outright scam, it likely will not stand out much more than a research colloquium for graduate students at a given university on a CV.
To elaborate a bit more on sponsorship, generally high profile conferences are sponsored by international societies (e.g., IEEE Computational Intelligence Society sponsors the Symposium Series on Computational Intelligence) and the conferences tend to have competitive peer review take place. Generally you will want to know what major societies in your field are and limit attendance to their conferences.

Scam = ripping your money off: Probably not.
Scientifically worthwhile to attend: Probably neither. Just check the submission format, which is M$ Word 07 instead of LaTeX/PDF; that usually answers the question.
Touristically cool: Decide for yourself.
List of accepted papers consists of Indian authors, afai can see 100% (which is not necessarily bad, they invented zero and got Primes is in P, amongst a lot more).

-1 Whether or not there are Indian authors is kind of moot given it's a conference in India sponsored by the Bangalore Section.


text:
Can someone interview their sibling?
I just had a job interview (permanent lecturer position not connected to a grant) and, immediately afterwards, I found out that the person who is the group leader and responsible for recruiting is the sibling of one of the candidates.
I made sure that this is actually the case. It is not a suspicion; it is a fact.
Could this be justified under some circumstances? This seems ridiculous. Should I raise a complaint?
This in the UK.

Did this other candidate also get a post?

@DmitrySavostyanov I do not know at the moment, however I know a couple of more things that I didn't write and it seems that it was decided beforehand that they get the position.

The only fact stated in the question is that the group leader and the candidate are related. The title asks about something not asserted in the question itself. Should the leader interview the sibling? No. Should the sibling be prohibited from applying for the job? Probably not, but I think that's the real question here (and the answer should discuss the limits placed on the group leader's role in that application process).

If a decision really was made beforehand, that raises a flag on the entire process, not just the group leader.

Typically, the sibling(/relative/partner) has to excuse themselves from interviewing/discussing that candidate (not the others). Which doesn't make that much difference, as the others know. And if you think about it, ethically not much different from interviewing your ex-students (MA, PhD, PostDoc), which specialization makes rather inevitable. [*I've worked a 0.1FTE finite-term position for my partner at a UK uni... only one other candidate applied.]

Interviewing a family member is not permitted. Yes, you should raise a complaint. Do it politely, of course. But in the end, you have to ask yourself whether or not a work group that would even try to get away with this is one you want to get involved with.

I strongly agree with this answer. For what it is worth, when I applied for graduate school, my cousin-in-law was a professor in the department at one school, and he explicitly stayed away from any admissions decisions connected to me. He later sort of implied that he had wanted to stay away from admissions decisions for the entire year's cohort, but he was persuaded not to by the others in the department who apparently had enough trouble finding people to do the committee work already. The idea that someone would take this active a role with a sibling is absurd.

Now I understand more about how things are being done there and I do not wish to join them However, I find it deeply annoying and I believe that someone has to speak up to those cases, then they learn to at least try to pretend to follow the rules.

@JoshuaZ I know, there was an opening in my current department and I sent this ad to someone that I knew through a closed friend. I disclosed that and I was told that I couldn't be part of the recruiting process (which I completely understand)

For what it's worth, I have chaired and served on academic hiring committees in my research institution. Rules vary from country to country, but in the US academy, this conflict of interest in hiring is not permitted.

Were you not asked (on the application) if you know any people at the Institution you are applying to ? I thought this was common at UK universities. In which case, the sibling would have had to indicate the relationship. Which might mean that the group leader might have been banned from the actual recruiting decision. You can ask for clarification, but do not go in alleging mis-conduct. For example, I sit on a panel with my partner of 20 years, this is recorded, and there is a procedure in place for any conflict of interest that may arise.

@Marianne013 No, this question is almost never asked during the application stage in the UK universities. It may be asked from a candidate during the interview. It must be asked from all panel members.

+1. Additionally, their internal auditors may be very interested in knowing about this activity.

@DmitrySavostyanov Imperial College asks for it.

@DmitrySavostyanov I've applied to work to several UK universities recently and quite a few of them asked if I was related to any current employee and, if so, to give details.

@DavidRicherby So did I, but I never saw this question. I always see "have you ever worked before with us?" question, but nothing about relation to current employees. I take back my "almost never" statement with apologies, but I personally never encounter this question.

@DmitrySavostyanov No need to apologise for having had a different experience.

@Marianne013: here in Germany, I'd expect that it is up to the people in the hiring committee to disclose possible conflicts of interest. A candidate applying will often not know who is in the hiring committee. Someone in the institution who is not on the hiring committee wouldn't have a conflict of interest, would they? (And I don't see how knowing someone in the institution is a sensible filter: working in my field for years, I know someone in pretty much every relevant institution in my country, plus in many [most?] in the surrounding countries)

@cbeleites: That's why it's a free form field, it gets accessed for relevance. Knowing someone at the place you are applying at and/or working there (for internal applications) is not a reason for rejection.

From my personal experience, very unsubstantiated and anecdotal, family hire and similar conflicts of interests do still happen in UK universities. It is very frustrating and demotivating for other candidates, particularly when  your skills match the job description well and you've put a lot of time and effort to prepare the application and the interview presentation.
Such conflict of interests are of course unethical and potentially illegal, but it is not easy to prove a case, particularly if HR are inclined to turn a blind eye towards the problem. If you want to raise a complaint, take care not to reveal your identity to your immediate line manager (Head of School) and explicitly request form HR to maintain your anonymity, particularly if you are still on the probation period. It may be a good idea to talk to your local unions. Good luck.

Thanks for the advice. Luckily my line manager has nothing to do with this group and it is easy to keep this confidential. What do you mean exactly that is is not easy to prove a case? I guess you mean it is not easy to prove that hiring was not objective. Does it mean that the universities have a tendency to turn a blind eye to such cases?

I can't draw meaningful conclusions based on my limited personal experience, so I can't say what is a "tendency". But proving anything is not easy, if the other side is reluctant to collaborate. People may say that the head of the recruitment panel stepped out and did not interfere with the assessment of their sibling, and the case collapses from severe conflict of interests to slight procedural mistake, bearing little consequence to anyone but yourself. But you never know which side HR will take.

Background
Some countries, and I don't know about the UK specifically, have requirements at state-funded universities when it comes to hiring.
One such requirement is that someone cannot be hired directly. The position needs to be opened and announced in some public medium, and kept open for at least X time so everyone has time to apply. Then interviews, etc., are carried and the best candidate is hired, if one is found.
Another requirement is that those with a conflict of interest with any of the candidates should state so. And hopefully excuse themselves from the hiring committee in order to not influence the result, independently of whether this is mandatory.
In practice, sometimes a candidate has already been chosen in which case the position requirements are tightened, if possible, to ensure their champion is the right fit for the position. This leads to positions, which have already been filled, being opened with the sole purpose of meeting hiring regulations.
Consequences
This is the most important part. I'd like to speak of consequences.
Raising a complaint brings you little or no benefit, but might gain you an enemy:

The end result may or may not change, but complaining will ensure you're not hired. The group leader is the accused here, sounds unlikely he'll hire you to his group after your complaint.
The group leader might affect others' impression of you, not only on this particular group but on other locations as well where he might know someone. If he didn't bother excusing himself from interviewing his sibling (which is morally reprehensible, if not illegal) then this seems a possibility.
Between two prospective candidates of equal competence, I'd guess the one most likely to be hired is the one not known to be a troublemaker.

There might be some degree of privacy when presenting a complaint, but I don't know how these are processed. Meaning there's a chance the accused party would not know who presented the complaint. In this case in particular, you're simply pointing out something that is easily proven. You don't have to present a lengthy justification.
Complaint without complaining
A simple email to the right person asking whether such behavior is allowed by the institution's regulations might be all is needed for someone to look into it. You could add a note stating you'd like your identity to be kept private for fear of reprisals. But without an official complaint it's possible they'll ignore it.

Thanks Daniel, your answer is very informative. I have considered your points and I decided it's a safe bet. There are certain things I cannot really comment on. I did consider the points you raised and I decided that on one hand I don't want this job any more and on the other hand they cannot really affect me beyond that (as I said, there is more background I cannot tell). Things are already in motion, I will update my post next week when I know more.

By the way, the position specs were rather broad because everyone else that was invited for an interview was more qualified than than the sibling. So narrowing down the position would have excluded the sibling.

You describe a situation as you see it, but you have no way of knowing or understanding what's going on behind the scenes.  My own assumption would be that if you know about this, than others know about this, including members of the home department that work with the group leader in question every day.
There is an obvious appearance of a conflict of interest, but there are ways of managing conflicts.  My own assumption, which can certainly be wrong, is that this is so obvious that they must be managing the conflict.
So, should you complain?  I don't know laws or procedures in the UK, but I'd first ask, who do you plan on complaining to??  Next, keep in mind that you don't know the whole situation, a complaint might be impugning the integrity of a person when the whole conflict might be handled behind the scenes already.  This is a fairly serious accusation.  You'd also be impugning the standards of the department, questioning whether they'd let such a conflict stand unchecked.
Next, lets say the conflict is unmanaged.  Would you really want to work in an environment where such obvious conflicts are left to stand?  Not getting the job may be a blessing.
With all this in mind, and the possible harm to your own reputation this may cause, I wouldn't recommend complaining.  There may be nothing improper going on, and if there is, it just doesn't seem like you have any options that can improve your situation.  I'd move on, and see if you get the job offer.

I have talked with the person from HR that was present during the interviews and I was told that the conflict of interest was declared and managed because independent people were on the panel. Subsequently I spoke with an HR manager who was shocked to hear what happened and said that no matter what paperwork was submitted this is never ok. I'll see what happens next week

Regardless of what the outcome will be, I do not plan to try to get a job there. I prefer to work somewhere where there is no bad blood with existing members of staff

Is it ridiculous, maybe. Is it justified, yes. Should you raise a complaint, no.
It is ridiculous when HR gets in the way of a group leader not being able to hire the person that the group leader thinks is most qualified. HR would probably prefer the group leader to not be involved, but then you lose a key person, possibly the only person, who can evaluate the technical competency of the candidates. Realistically HR will probably be happy with an independent observer of the interview and might even be happy with documentation that the selected candidate is the best candidate.
Either the process has been approved by someone, in which case you are not going to get anywhere and just come off as a complainer. If it hasn't been approved, then you just made an enemy of the group leader, which is not helpful either.

I'm curious, how can this be justified? It was a rather broad position, not highly specialised.

"It is ridiculous when HR gets in the way of a group leader not being able to hire the person that the group leader thinks is most qualified." Is it always ridiculous, then, for HR to get in the way of any decision, as long as the group leader thinks that choice is best? Besides, OP is not claiming that the hire should be stopped, only that leaving the decision to someone with such an obvious conflict of interest is improper.