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Is it inappropriate for an author to copy and paste from his/her original paper in an extension paper?
I am currently a referee for a paper.
One of the authors of the paper had written an earlier paper,
which I will refer to as the "original paper,"
and the paper which I am now refereeing is an extension of the original paper,
which I will refer to as the "extension paper."
I have found that large portions of the extension paper
are copied from his original paper.
In particular,
a whole section of definitions is copied from his original paper;
and some paragraphs in the introduction and literature review
are copied wholesale or with slight modifications from the original paper.
Is it acceptable for an academic paper to copy paragraphs and even a section from an earlier paper by the same author?
My intuition suggests that it is acceptable to copy the definition section,
with an acknowledgement that it came from the original paper,
since definitions are standard.
But it seems strange to me for the introduction and literature review
to be too similar to the original paper.

I tend to agree with you. In my experience with empirical papers, it seems totally OK to copy/paste parts about the research methods (that happen to be identical to previous papers), but not OK to do that with sections where you describe the broader significance of your results or where you give a theoretical overview.

Possible duplicate of Attitudes towards self-plagiarism

It's okay to copy definitions, even from other people's papers, as long as you make the appropriate citations.  Definitions are (and should be) standard.

The answer depends on the relationship between the papers, and I'm not sure which applies based on the information in your question.  In computer science, at least, there are two general cases:

The extension paper is the "extended journal version" of a previously published short-form work such as a conference paper, workshop paper, or extended abstract.  In this case, the rule of thumb is typically at least 30% new material.  The extended paper will often contain large chunks verbatim, as it is expected to supersede the original paper, rather than existing as a separate work.
The extension paper is a separate work: in this case, extensive reuse of material is self-plagiarism.  Two exceptions: first, related work, methods, and definitional material may often be reused as long as it is appropriate to do so---the material should be appropriately customized to fit the new environment.  If the author would just be paraphrasing for the sake of paraphrasing, though, it's not necessary.  Second, introductory material may be partially shared, though it should be more heavily customized for the new context.

In all cases except for minor reuse of related work material, the extension paper must declare a clear and explicit relationship with the prior paper.
Note that many other fields do not have the notion of a "journal version" and thus have much stricter standards.

+1 for the 30% new material rule and for "The extended paper will often contain large chunks verbatim, as it is expected to supersede the original paper"

I think there's another relationship worth mentioning, although it's not at issue in this particular question: I have seen cases where journal articles were republished with some revisions in an edited volume.  Often these are not quite reprints because they may include a small amount of new analysis, or altered intro/conclusion to fit the theme of the volume, but the bulk of the paper may be lifted straight from the earlier publication.  Also, the copying is usually acknolwedged with a note saying something like "an earlier version of this paper appeared in Journal X".

@BrenBarn Good point... I've seen book chapters that way too on occasion.

Publishers have concerns about this from a couple of directions.

Copyright.  A publisher will generally not want to publish something without making sure that the copyright is clear.  If you've previously published a paper and then recycle text from that earlier paper into the new paper you need to make sure that you have retained the copyright on the text.  Chances are that if you published your previous paper with a main stream commercial publisher then you transferred the copyright to that publisher and don't have the right to publish the same text in a new paper.
Originality.  Most publishers have policies that say they only publish original research papers.  It's an editorial decision whether the new paper has enough original content to qualify as original research.  Reusing the text of mathematical definitions and standard theorems is a gray area where some publishers are willing to allow some text recycling.  If this is done, it's critical that the original source be properly cited or better yet that the material be treated as a quotation from the original work.

Most publishers now use software to automatically check all submissions before they're sent out for review.  If there's a concern about old fashioned plagiarism or recycling of text ("self plagiarism"), then this is often dealt with before the paper is even sent out for review.
As a referee, I would note the recycling of text from the previous paper and then review the current paper and consider whether the new work is sufficiently original to merit publication.  It will ultimately be up to the publisher to decide whether they're willing to deal with any liability for copyright violation that results from the text recycling.
The Committee on Publication Ethics (COPE) has some useful guidelines on text recycling:
http://publicationethics.org/text-recycling-guidelines

To be a bit more direct.  Although it used to be common to recycle text from "methods" and "literature review" sections, most publishers now frown on this and it is becoming increasingly difficult to publish papers that reuse text in this way.

One thing to consider is to flag it up to the editor/publisher. Most review systems have a way to provide comments to the editor only (not the original author). This is a case where you can flag up and discuss these aspects of the paper. Of course if the paper actually does not contribute anything beyond the original paper (in the same words or new ones) you could reject the paper on those grounds.


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If a reference is applying for the same position, are they obligated to inform you?
If a reference applies for the same position do they have a professional obligation to inform you that they are applying for that same job?

"Reference" means several things in academia.  Do you mean someone who is writing you a recommendation letter?

I am interpreting the question as: does someone who writes you a recommendation letter for academic position X and is themselves applying for academic position X have an obligation to inform you of this?
They certainly do not have a professional obligation.  By that I mean that there is no rule that requires it.  On the contrary a general principle of academic job processes is that when possible they should be kept confidential, so the information that someone is applying for academic jobs and if so what jobs need not be disclosed by them to anyone (except the institutions they apply to, obviously).
As usual, the question of ethical obligation is a bit more interesting.  In my opinion the answer is still generally no: in most circumstances there is no ethical obligation to disclose this information.
I should clarify that in my part of academia both job applications and reference letters are done in "carpet bombing" style: many people who are applying to one academic job are applying to twenty or more, more commonly fifty or more, and not so rarely one hundred or more.  Many of the letters are common to all 20, 50, or 100 jobs.  Thus if the writer happens to be applying for a position at one of the same institutions -- and let me say that whether someone is applying for "the same position" is sometimes well-defined and sometimes a bit nebulous; people of very differing levels of seniority can be treated very differently by hiring committees, and it is not uncommon that in that situation if one really does want to hire both people then one tries to do so and sometimes succeeds -- it is not necessarily a direct conflict of interest.  More specifically, I have occasionally seen an application by a letter writer for "the same position" that the letter writee has applied for, and the letter writer's application did not undercut their letter.
In my circle most letters of recommendation are general evaluations of the candidate that would be suitable across an entire range of institutions: they do not make a specific argument as to why Institution A should hire the candidate.  In fact, in my field (mathematics) we have an extremely convenient automated job applications site (called, reasonably enough, MathJobs), so when someone asks me for a recommendation I don't even know the full list of places in which that recommendation is being used.
I have written dozens of recommendation letters for academic jobs.  Exactly one was specifically targeted to one institution, the one job to which that person was applying.  If I had also been applying for the same job: yes, that would have been awkward and ethically problematic.
As above, I would say that the ethical problem occurs when you are writing a letter which is targeted to a specific institution and you know at the time of writing that you plan to apply for the same job.  Such a situation is the ne plus ultra of conflicts of interest, and the ethical thing to do would be to decline to write the recommendation for that institution.  It is not necessary to disclose why, but if one is willing to write other strong recommendation letters it would be good to say so.
Finally, let me say that one can largely avoid this issue by making sure that your recommenders are much more senior than you.  Thus, if you are applying for a postdoc position, have all your letter writers be on the tenure track.  If you are applying for an assistant professor position, have all your letter writers be tenured.  This turns out to be good advice anyway: senior people have more pull and, other things being equal or nearly equal, are the ones you want writing for you.

As a letter writer, if you are willing to disclose that you are applying for a particular job, it is much better to explain the situation than simply decline. I trust my letter writers (who would be applying at a much more senior level any ways) to put themselves above any conflict. While this is potentially naive, I believe the hit of losing one of my top letter writers is greater than anything they might say about me in the letter in an attempt to get ahead of me.

I'm not entirely sure I agree with this answer, but there is a closely related issue I am sure about.  You do have a professional and ethical obligation to reveal to the readers of your reference letters if you are applying to the same position as your referent.  Conflicts of interest cannot always be avoided, but if they can't be avoided, they must be revealed.

@JeffE: In most cases I have experience with, the readers of the letters are in a better position than you are to know this.  If you think that you might be applying to the same position as someone you are writing a letter for -- e.g. if you know that he is applying for an assistant professor position somewhere and so are you -- what do you advise?

+1, especially for the last part. My first thought on reading the question was "but why are you getting references from people who are applying at the same level as yourself?"

The person did not know the reference was applying, in fact the reference recommended the person for the job, and chose to apply for that same position a few days later....

I was not made aware the reference was applying for the same job, that is my concern.  Doesn't the reference have an ethical obligation to at least inform me that they are applying for the same position?

@Dale: I am not sure that one has an ethical obligation to inform outside parties that one has applied for an academic job.  (How did you find out about it?)  As I said above, if two people turn out to apply to the same job out of dozens or hundreds, I don't see that it is problematic (or even how they would necessarily know).  If you are writing a letter targeted specifically at a certain job at a certain institution and then you later apply for the same job, I would regard that as an unacceptable conflict of interest.

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Why isn't pre-registration required for all experiments?
Why aren't all experimental results of any validity required to register the experimental plan used for the research paper in question, ahead of time, giving the understanding that the results will be made known.  Why,
because

The description of the experimental procedure should be untouchable once the experiment commences, and most importantly
it removes the option of simply failing to publish.  This option may introduce bias as there may be myriad reasons why a valid experimental result could be withheld.  Such reasons include those given by the biases of the experimenters themselves or the judged impact of an out-of-the-box result.

By all appearances, if one is to embark on an experimental program, shouldn't one be bound to disclose the results?  Registration seems to be the only way to enforce this.  It wouldn't be taxing... simply emailing a pdf to a database system of some kind would be enough.
I'm guessing many papers undergo this process on an informal level, but I doubt every research paper has some sort of registration like this.
[My background is in mathematics, not the sciences proper.]

From the perspective of biological sciences, some experiments are very straightforward and would work the way you describe. But for many of them it is very difficult to determine the success of an experiment beforehand and the protocol may evolve as time goes on. Even after pilot experiments there are still snags and dead ends that may force you to take the research in direction different than the original protocol. Then there are also issues of timing (e.g. age of animals) that may require protocol modification. It's just not realistic in many cases.

Insightful feedback, thanks.  In re-reading my question, I realize there are no perfect solutions and that my proposal has issues.  However, I certainly think greater care and attention should be given to the "withholding results" problem, especially in the politically charged and controversy saturated world we live in.

Pre-registration is not the easy "cure" for publication bias that you seem to think it is. In short: Who is going to enforce that authors actually follow their pre-registered plan and publish their results (which takes time, effort, and money to check)? What kind of consequences can be imposed on those who don't?
There are no major incentives in place for editors, reviewers, or authors to enforce this, except for their desire to advance the field and enhance the rigor of their discipline. Clearly, this intrinsic desire is not enough to prevent authors from throwing out negative results, reviewers from recommending rejection of negative results for not being interesting, or editors from declining to publish negative results.  Pre-registration alone does not change that incentive structure; changing the incentive structure is not easy to do.

In medicine, pre-registration of clinical trials has been required by many major journals as a prerequisite for consideration for publication since around 2004-2005. However, there is no clear evidence that this has had an effect on publication bias in that field. Authors continue to submit papers in which the primary outcome of experimental protocol deviates from the registration, and reviewers often don't check the registration document to catch this. Non-publication is still common. And many journals are unwilling to take a hard line on pre-registration.
You said,

The description of the experimental procedure should be untouchable once the experiment commences,

In medicine, the pre-registration did not actually achieve this. See e.g.  Mathieu, S., Boutron, I., Moher, D., Altman, D.G., & Ravaud, P. (2009). Comparison of Registered and Published Primary Outcomes in Randomized Controlled Trials JAMA, 302 (9):

Of the 323 included trials, 147 (45.5%) were adequately registered (ie,
  registered before the end of the trial, with the primary outcome clearly specified). Trial registration was lacking for 89 published reports (27.6%), 45 trials (13.9%) were registered after the completion of the study, 39 (12%) were registered with no or an unclear description of the primary outcome, and 3 (0.9%) were registered after the completion of the study and had an unclear description of the primary outcome. Among articles with trials adequately registered, 31% (46 of 147) showed some evidence of discrepancies between the outcomes registered and the outcomes published. The influence of these discrepancies could be assessed in only
  half of them and in these statistically significant results were favored in 82.6% (19 of 23).

You also said,

it removes the option of simply failing to publish

Pre-registration does not, as you seem to believe, compel the experimenter to publish the results.  How could it? Who would enforce this?
Pre-registration can potentially make it much easier for the results to be published than they otherwise would have been; some journals offer peer-review and conditionally accept the article based on the pre-registration, before the experiment has actually been conducted. (Negative results can be quite difficult to publish otherwise.)
But non-publication remains common in medicine, even among registered clinical trials. From Ross, J. S., Mulvey, G. K., Hines, E. M., Nissen, S. E., & Krumholz, H. M. (2009). Trial publication after registration in ClinicalTrials. Gov: a cross-sectional analysis. PLoS Med, 6(9), e1000144:

We examined reporting of registration information among a cross-section of trials that had been registered at ClinicalTrials.gov after December 31, 1999 and updated as having been completed by June 8, 2007, excluding phase I trials. We then determined publication status among a random 10% subsample by searching MEDLINE using a systematic protocol, after excluding trials completed after December 31, 2005 to allow at least 2 y for publication following completion. Among the full sample of completed trials (n = 7,515), nearly 100% reported all data elements mandated by ClinicalTrials.gov, such as intervention and sponsorship. Optional data element reporting varied, with 53% reporting trial end date, 66% reporting primary outcome, and 87% reporting trial start date. Among the 10% subsample, less than half (311 of 677, 46%) of trials were published, among which 96 (31%) provided a citation within ClinicalTrials.gov of a publication describing trial results. Trials primarily sponsored by industry (40%, 144 of 357) were less likely to be published when compared with nonindustry/nongovernment sponsored trials (56%, 110 of 198; p<0.001), but there was no significant difference when compared with government sponsored trials (47%, 57 of 122; p = 0.22). Among trials that reported an end date, 75 of 123 (61%) completed prior to 2004, 50 of 96 (52%) completed during 2004, and 62 of 149 (42%) completed during 2005 were published (p = 0.006).

And authors have many reasons for not publishing, reasons that don't necessarily go away with pre-registration. From Song, F., Loke, Y., & Hooper, L. (2014). Why are medical and health-related studies not being published? A systematic review of reasons given by investigators. PloS one, 9(10), e110418:

We included 54 survey reports. Data from 38 included reports were available to estimate proportions of at least one reason given for not publishing studies. The proportion of non-submission among unpublished studies ranged from 55% to 100%, with a median of 85%. The reasons given by investigators for not publishing their studies included: lack of time or low priority (median 33%), studies being incomplete (median 15%), study not for publication (median 14%), manuscript in preparation or under review (median 12%), unimportant or negative result (median 12%), poor study quality or design (median 11%), fear of rejection (median 12%), rejection by journals (median 6%), author or co-author problems (median 10%), and sponsor or funder problems (median 9%). In general, the frequency of reasons given for non-publication was not associated with the source of unpublished studies, study design, or time when a survey was conducted.

Actually verifying that the details of a manuscript match the pre-registration document involves some overhead for reviewers and editors. See e.g. Mathieu, S., Chan, A. W., & Ravaud, P. (2013). Use of trial register information during the peer review process. PLoS One, 8(4), e59910, which found:

1,136 authors (n = 713) and reviewers (n = 423) responded (37.5%); 676 (59.5%) had reviewed an article reporting a clinical trial in the past 2 years. Among these, 232 (34.3%) examined information registered on a trial registry. If one or more items (primary outcome, eligibility criteria, etc.) differed between the registry record and the manuscript, 206 (88.8%) mentioned the discrepancy in their review comments, 46 (19.8%) advised editors not to accept the manuscript, and 8 did nothing. The reviewers' reasons for not using the trial registry information included a lack of registration number in the manuscript (n = 132; 34.2%), lack of time (n = 128; 33.2%), lack of usefulness of registered information for peer review (n = 100; 25.9%), lack of awareness about registries (n = 54; 14%), and excessive complexity of the process (n = 39; 10.1%).

Finally, publishers and editors may be reluctant to require pre-registration because they fear that authors will simply go elsewhere. From Wager, E., & Williams, P. (2013). “Hardly worth the effort”? Medical journals’ policies and their editors’ and publishers’ views on trial registration and publication bias: quantitative and qualitative study:

Only 55/200 journals (28%) required trial registration according to their instructions and a further three (2%) encouraged it. The editors and publishers interviewed explained their journals’ reluctance to require registration in terms of not wanting to lose out to rival journals, not wanting to reject otherwise sound articles or submissions from developing countries, and perceptions that such policies were not relevant to all journals. Some interviewees considered that registration was unnecessary for small or exploratory studies.

This is an excellent answer.

I'm not sure I've ever done an experiment where what we did that was written up in papers was actually what we thought we would do, except in broad enough terms as to make a 'pre-registration' useless. When trying to do something that no one else has done, you don't really know what you are precisely going to do.

Obviously authors can't be prevented from abandoning pre-registered experiments that go badly; what pre-registration could usefully do, however, is adjust the thresholds of statistical significance.  If someone pre-registers an experiment unlike anything they've done before, the sample size for a statistically-significant result should be smaller than if the experiment is similar to twenty others by the same person that have been pre-registered but not yielded a publishable positive result.

Pre-registration should not be required for exploratory tests whose outcome will never be published as being meaningful evidence of anything beyond justifying that it may be worthwhile to conduct further, pre-registered, experiments.

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Using Cambridge's "short-title reference system"
Does anyone have experience using the Cambridge UP's "short-title reference system" or even just know of a work that uses it. I'm copy-editing for some extra cash but the style guide they have online is really not very helpful.
The very first reference I've tried to come up with, for example, is a translated work, and they have no indication of how to include the translator in the citation other than saying that it should be there.
My best guess is:
Author's name, Title of Work, Translator's name (trans.)(Place of publication: Publisher, Year), p. page number.
I guess the main issue is I can't tell if "(trans.)" should be in parentheses or not. This is just my best guess based on the example given for a book with an editor, which is "Editor's name (ed.)"
Thank you for any advice!

I can't give you direct advice about the Cambridge short title but there are quite a lot of applications to go from bibtex to different reference styles. I would suggest using one of those to help. I found the easiest way to do this is to add items to zotero and then export as bibliography, they have hundreds of styles based on journals as well as common ones like Harvard and Chicago Manual.

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The exact meaning of the term *Alma Mater*
More often than not, the term Alma Mater is applied to one's place of undergraduate studies.
Would it be reasonable of me to apply this term to a university where I received my doctoral degree?

Usually the "Alma Mater" charge a fees for their alumni to be part of them. It is therefore statistically more relevant to try to aim for the bachelor degree's holders ... there are more of them!

There is literally nothing in the term specifying an undergraduate program. From Wikipedia: Alma mater (Latin: alma mater, lit. 'nourishing mother'; pl: almae matres) is an allegorical Latin phrase used to proclaim a school that a person has attended or, more usually, from which one has graduated.
Sure, you can use it for your doctoral institution. I doubt anyone will notice.


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Bulletized lists in APA paper
I am looking at the APA7 guidebook, and having issues understanding bullets.  The guidance refers to the needs of the document to determine this.  However, I need to format this for APA requirements for my university.
Are bullets doublespaced themselves?  and my second question, what if an individual bullet is multi-lined (ie. longer than one line and word wraps). Is the individual bullet single-spaced? or is everything doublespaced?
Thanks

Does this not help: https://apastyle.apa.org/style-grammar-guidelines/lists/bulleted

Thank you no, it doesn't unfortunately.  I'm not seeing where it says in guidance that bullets and the list are either way.  Right now, I'm counting pixels and guessing.

Please see the examples--bullets are double spaced, but if a bullet goes into multiple lines, those are single spaced.


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Adding notes on my unofficial transcript
I'm in a master's program for astrophysics now applying for a PhD. On my transcript there are two classes that just read "Special Topics in Astrophysics", but one of them is "Radiative Processes in Astrophysics" and the other is "Astrophysics Laboratory". Both are pretty important classes, and some schools do not have a section where you enter all of the physics classes I have taken so I cannot specify what they are. So is it OK that I put notes on my unofficial transcript beside these two classes clarifying what they actually are? Would that be considered tampering?

Typically you won't want to modify your transcript directly yourself, even if it is unofficial. Universities (or the people evaluating transcripts) are very familiar with these sorts of generic course numbers or topics courses that are taught by different professors with different subject matter. It is better to highlight this in other places in your application, including:

In your statement of purpose, where you are talking about the research you want to do and why you want to do it, especially if it builds on material from those courses.

In your reference letters. If you have a letter from the instructors of one of these classes, they can explain the course and how you did.

Depending on the school you are applying to, you may have another opportunity to highlight this elsewhere in free form text.

For a PhD you might communicate with a professor directly, in which case you could explain to them that you've taken these classes.


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Can I write a systematic review as an undergraduate and get it published in a journal?
I am an undergraduate of Animal and Environmental Biology. I don't have much research experience, but I have taken some courses on research writing and have assisted some senior students in their research projects. I want to write a review paper, but I am not sure how far I can go. Is it really possible for me to write a good review without much research experience in the field?
I would also appreciate working with a senior author, an experienced person in the field of Entomology.

This seems like a question for a local faculty member who can possibly help and give you advice.

I'd suggest review articles are not the best use of people's time.

@AnonymousPhysicist Why?

Is it really possible for me to write a good review without much research experience in the field?

I would say "only in exceptional cases", a fundamental component of writing a review is evaluating the material, which isn't really feasible without experience.
I have noticed that quite often students reference review papers written by other students that have been published, and quite often they are not very good review papers (they miss papers than more experienced researchers may be aware of and the reviews are often uncritical).  Unfortunately the students are not in a position to judge whether it is a good systematic review, which rather defeats the object of having a review.  I think students write reviews because they and their supervisors want to get additional value from the work the student must do in learning their field, but in general reviews are best written by people who really know the field.
Perhaps the question is to ask how much the readers would gain from the review paper.  How could you be sure it was relatively complete, fair and accurate in it's evaluation?
There are exceptions, I can think of some very good reviews written by students and early-career researchers, but they are the exception rather than the rule.
The problem is that experienced researchers probably have little to gain by writing review papers...

"researchers probably have little to gain by writing review papers." except citations.

@AnonymousPhysicist yes, however not grants, which is the primary performance metric for most institutions.  Writing a good review paper is very hard work, and it is often easier (and more interesting) to get citations by doing novel work.  I don't recall citations being an issue at any of my performance appraisals ;o)

I think if you were able to find an interested supervisor with sufficient experience in the field and with the review question you are interested in pursuing, then I think conducting specifically a systematic or systematized review can be both a valuable way to contribute your time and energy in answering a pressing question in your field as well as to gain a LOT more knowledge and understanding of the literature in your chosen topic.
Systematic (or to a lesser extent systematized) reviews are meant to be conducted in a scientifically rigorous way that removes some of the biases that might be associated with people who are highly opinionated about a particular topic as well review papers where the citations that get chosen are only reliant on that person's expertise and experience. Both traditional literature reviews and systematic reviews and meta-analyses have value, but as you are a newer reseracher who doesn't have the necessary expertise to be relied on to have an authoritative viewpoint on your topic nor the experience to know what literature to include, then by conducting a systematic review with sufficient and documented methodology, you can create the trust necessary to publish a review paper on a topic that people can respect.
I myself conducted a systematized review in a field that I was very new to and, because it fulfilled a great need in my field and had a sufficiently rigorous methodology that could be validated by others, then it has been well-received by even senior researchers in my field. Because I had to read so much of the literature on my chosen topic, I also gained a lot of knowledge and a publication in my chosen field, which I am now further backing up with other empirical and experimental research projects. The process of undergoing a systematized review has therefore been incredibly valuable to me personally while also helping my field progress in a meaningful way.
That being said, even a systematic review should not be taken on without consulting a whole host of people, including researchers familiar with your topic of interest, researchers with experience working on systematic reviews and the host of protocols they require, and with librarians with expertise in literature searches and databases. I imagine if you were to contact a senior researcher in your department, if you both have similar interests, then they could help guide you throughout the process and contribute the expertise and experience that you might be lacking.
I will warn you, however, as you are considering your options, that systematic reviews can take as much or even more time to do well than a lab experiment or field sampling or other research approach might take from the time of planning to publication, so I would also only recommend undertaking a review if you have certain limitations that prevent other methods of pursuing your particular question or if you feel fairly sure of your interest and motivation to accomplish the task (i.e., looking through hundreds or usually thousands of papers in the case of a systematic review).
This all comes from my own personal experience as an early-career researcher, and some of the other comments and answers you receive might disagree with me, but I hope that my point of view and my own experience with a very similar situation to yours can be helpful in contributing to your descision-making. I wish you all the best in whatever you ultimately decide to undertake!

Go for it!
Trust and follow your interests, especially whenever it involves both reading and thinking.

Can I write a systematic review as an undergraduate...

Sure! Yes! Go for it!
You should follow anything that inspires and interests you, and ignore any comments to the contrary. Trust your judgement; there's no better way to learn about a field than to sample a wide variety of different authors' perspectives, techniques and results.
Most researcher groups can not avoid imparting at least a degree of tunnel vision since they are sort-of by definition mission-driven to publish their own unique results and perspectives.
I had an initially maddening experience with an undergraduate independent project; it was for credit and approved, and I sought out the department expert on the subject. They gave me no helpful information and a single very old reference from 20 years earlier and told me to "muddle through".
At first I was taken aback, but as soon as I hit the journals I had the time of my life! This is back when "hitting the journals" meant carting a new 50 pounds of bound volumes to your desk in the library every hour or two, lots of little ripped pieces of paper marking pages to be photocopied or read, and pages of scribbled lists of what to go look for next.
It was incredibly educational! I saw the drama of reported discoveries, corrections, alternative interpretations, theories, new theories, unfold before my eyes in a way that is almost impossible to see any other way (except for a few cases that make it to TV etc.)

...and get it published in a journal?

Why not!?
Yes as other answers point out, the probability is low that you can just do it yourself for say a semester, then fire it off to a journal and get an acceptance notification the first time.
But if the process interests you, then even a rejection might be an interesting step!
And now that you have this large body of information, you might consider revisiting it again in a year or two, or "marketing" it to potential co-authors who may have excellent ideas how to improve and expand upon it.

It is standard practice in my lab to start your PhD by writing a review on your subject. I was very critical about this at first, but it is an excellent way to boost, organize and integrate your literature search, gather material to populate your thesis later on, work on your writing skills, and deal with the editing process.
As others have pointed, the quality varies widely, and it would be better if actual experts would write reviews, but as they don't, a motivated PhD student is the best second choice, and they sometimes do a good job...

I think you are asking two slightly different questions (though you seem to think that they are the same thing):

"Can I write a systematic review as an undergraduate and get it published in a journal?"
"Is it really possible for me to write a good review without much research experience in the field?"

For the first question, yes, an undergraduate student can generally follow a systematic review method and then publish the results in a journal somewhere. This is because there are journals that accept all ranges of quality of work, ranging from very stringent journals with less than 10% acceptance rate to journals that publish almost anything submitted to them (as long as the authors pay the publication fee).
Your second question asks if you can actually produce a "good" review. Obviously, "good" is very subjective. A review that is "good" for student readers might not be "good" for highly experienced researchers, though it might be "good" for the majority of moderately experienced researchers who would like to learn more about the topic. I would suggest that the practical way to write a meaningfully "good" review is to identify a specific researcher whom you consider credibly expert on the topic and then ask them for a friendly review of your completed paper, and then recommend a journal whose selectiveness standards match the quality of the article. If this expert would be your supervisor or even coauthor for your writing of the paper, then that would greatly enhance the chance that it would be of higher quality.


text:
Is it appropriate to add a co-author at the stage revise & resubmit?
Context
I've submitted a paper - it was sort of a side-product of my main project - to a high ranked journal from an adjacent field. Recently I got a revise & resubmit that was close to a reject, but the editor sounded really interested in the paper being multidisciplinary. I'm suggested to contextualize my research stronger within the journal's field. I feel like getting one of my experienced in that particular field colleagues involved in the revision in order to get the paper accepted.

The question
If a person helps you a lot during the revision, are you allowed to include him as co-author?

Absolutely you can add a coauthor in revision, if there is good reason for doing so: in fact, I have recently done so myself on a paper where revision involved some new experiments with the aid of a colleague not previously involved.
Most journals that I know consider authorship changes routine and even explicitly support such changes by asking you to review and, if necessary, modify author lists as part of submitting a revision through their system.

Yes, you can do that. "Revise and resubmit" means that they intend to put your paper through the same refereeing process upon resubmission as they did on the initial submission. So at the very least, the journal can treat it as a completely new paper if their system doesn't allow authorship changes between drafts.

As mentioned in the other answers, almost all journals allow you to change the author list at any time before final acceptance. Sometimes when the reviewer asks for some extra information, additional experimentation/analysis may be needed and in this process new people may get involved. So a resubmission would have an extended list of authors.

If a person helps you a lot during the revision, are you allowed to include him as co-author?

Of course you are allowed to do so. Denying authorship may be unethical but even for that there are no strict rules. You may choose to specify how the new authors have contributed, in the Author Contributions section of the paper. Many journals actually ask for it.

EDIT: this contribution has received downvotes, and I guess I was not clear enough. Even if I do praise probity, academia is not homogeneous, neither do so-called scientific fields. Authorship, work, citation and evaluation habits differ a lot. So I will describe three practices I have witnessed. Completed by the conference Evolution of Scientific Publications: the Point of View of Scientists (in French, Colloque de l’Académie des sciences, 14-15 mai 2007), which I attended.
First, maths. Traditionally, many consider the contributions are equal as soon as people co-author. And the authors are put in alphabetic list. Yet I know a person who gained a professor title from a developing country, and was offered a certain amount of money to add local co-authors to a paper. Who did not have the level to contribute. Which the person accepted.
Second, in my community, some consider the student ought to be first author, even though the student did not do most of the work. The student should find a position, after all. The advisor is often put at the end (even if she/he did nothing). I was once strongly suggested (by a boss) to add somebody else, because "he was important". I was young, and did accept. I do regret that now. After all, rules in our field are not so strict as mathematicians...
Third, in medicine (a close friend's experience). Papers can have much more authors. My friend told me (exaggeration) that the first author writes, the last proof-read, the others are... there, with varying good-will and contribution. Indeed, in the above mentioned conference, I have seen in a row a mathematician claiming that authors are of equal importance, and a biomedical pundit asserting that: the first place and the second are important, and the last and the penultimate too. Indeed, I know at least a ranking in France that rewards services if a member is a co-author of a publication with different weights: w1 for the first and last, w2 for the second and penultimate, w3 for the third, zero for the others. I let you dream about the fights to change positions from 4th to 3rd... And I know an author who often add (his/her) spouse to the co-author list, even if the spouse is not knowledgeable in the field. And the other authors accept that.
So there are habits, conventions, pressures of different sorts. And the borderline is easily crossed, and  fluctuates across fields.
If you are strong enough to make your own rules, do want you want, at the risks of hitting local habits.
So you "can" add a co-author at this stage. A "revise and resubmit" is a new paper. In some fields, this is common practice, but might be borderline inappropriate if you just add a "name" to help the paper go through the next review.
To improve your paper impact, and strengthen your ability to cross disciplinary borders, I would suggest you to re-elaborate the novel paper (collaboration = work with) with your putative co-author, instead of performing a mere scaffolding, probably less painful, but likely, in the end, to be less beneficial.

That isn't "borderline", if the added author didn't add enough to be considered an author.

I have been careful with this opinion, since I have met different practices in different fields. In mathematics, a co-author generally has performed the work appropriately. In medicine, some co-authors are surgeons who do not even bother proof-read the paper somebody else has written with their name on it. In bioinformatics, I will be obliged to add folks in a co-author list, because they have done routine genetic analysis, contractually. Unappropriateness might be field depend.

@Laurent, Thanks a lot for this insight! I appreciate very much that you share your diverse experience.

@Ilya your positive feedback is important to me. Good luck with your revision

authors: Трутень Трутенев


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Grad Application: Research Experience without Letter of Recommendation
I am in the process of applying for graduate school, and I have some past research experience during summer. I am not planning to get a letter of recommendation from the supervisor whom I worked with during that term. (I had been recommended to join their group by another professor, and I joined bluntly without any interest on the subject, and further I had no background education on the topic. As a result, I believe that I did not leave a good impression.)
My question is, would it be bad to include this experience in my CV without a LOR from that specific supervisor?
It was mentioned in here by StrongBad that it is not a good sign, if so should I remove that experience from my CV?

First, note that it is only a red flag if you are omitting the most recent or only research experience.  You are generally only required to get a few letters of recommendation. If you need N recommendations, and have a sufficient set of strong and recent recommenders, then there is simply no reason to get additional weak recommendations beyond your N strongest.
Omitting from your CV, however, is probably a bad idea, because it can be considered dishonest.  In my experience, a full CV should include both your triumphs and your sins, and hiding your sins will only increase your trouble when they come out at a later time.
If you don't have other more recent research experience, but you didn't completely burn your bridges, you might approach this by having a very blunt conversation with your former advisor.  Lay out your concerns like you have here and ask what the professor would suggest is the best path forward.  They may be willing to write you a very neutral letter, e.g.:

X was a member of my group for a brief time.  It was not a good fit, but I believe they have the potential to do well elsewhere.

Then you can lean on the strength of your other letters be essentially evaluated as having not done research.
If you've really angered the professor, though, and have no other research experience, then it may be the case that the only good way to address this is to get some more research experience.


text:
When do you stop mentioning your dissertation in the cover letter?
I am re-drafting my cover letter for the tenure track faculty positions in the U.S. While I was finishing my dissertation, I quickly moved to a new research direction. Although I can make the case of how my new research direction grows out of my dissertation, I wonder when do people stop talking about their dissertation in the cover letter? Or must the cover letter contain a dissertation paragraph?

My usual advice about cover letters and vitas is to include everything that you can include "with a straight face". A some point you stop putting your high school awards, because it's too embarrassing to mention them; at some later point you stop putting minor honors from your undergraduate studies; etc.
If you are a recent PhD and are applying for tenure-track positions, you should certainly mention your thesis, unless you have so much other research that it is no longer relevant.
But you do not necessarily need an entire paragraph. Just now, I looked up two successful cover letters of mine. One had a single sentence about my thesis (for a research post-doc position). One had two sentences, the second of which just said that my work could be suitable for undergraduate research (this letter was for a tenure-track position).  At least in my field, we usually submit a longer "research statement", and so there is little need to go into depth about research in the cover letter.

In the cover letter, equally important to a summary of your thesis is the fact that you have already earned your PhD - that you are not in some nebulous "ABD" situation. That is something the search committee is likely to be interested to know.

You are mostly hired for what you are doing now, so you should avoid the impression that you are unsteady, and your interest shift every other year. However, there will be some members of the committee who are not from your current area. If one of them is interested in your Ph.D. topic, this might be a big bonus for you. So you should mention your Ph.D. topic unless your results are mediocre, or so much time has passed since your Ph.D. that a faculty member interested in that topic and not your current work would not see an advantage in having you in place of someone with a different Ph.D. topic. How much time this actually is depends on the subject area. In many branches of pure math this could be "never", while in applied areas of CS this could be 2 years.

Thank you for the response, Jan-Christoph. My dissertation topic is a narrower research topic within my larger research interest. In my cover letter, I am also stating that I am expanding my research program by moving to this new research area. I am not abandoning my dissertation topic, but I do have a much larger research program.


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Researcher with Startup Company - Conflicts of Interest?
Looking for your advice on best practices on how to avoid conflicts of research.
The facts:

Researcher is a director of a research institute on campus.
Researcher has a start-up company involved in same research as his    university research.
Researcher uses this company as a way to get Small Business Innovation Research/Small Business Technology Transfer (SBIR/STTR) grants to fund    his lab under subcontracts.
Researcher has company located on campus in university sponsored    incubator.
Researcher employs a post-doc and shares this post doc with his    company – funding of post-doc is 50/50 between the company and his research center.
Researcher's lab members go between his lab and the company lab space freely.
Researcher is interested in submitting closely related grants through his research center and through his company as SBIR/STTR.

What are best practices or rules to put in place to minimize conflicts of interest in such a scenario?

At the institutions I'm familiar with (large, public R1 universities in the US), there are institutional conflict of interest (COI) policies and procedures in place which must be followed to handle various situations that come up, including the situation you describe. I suggest you contact your COI office for more information about navigating your specific situation.

Thanks... we are in the process of updating ICOI policies and was looking for suggestions to include.

I'm no expert; I just know where to go if I have a COI problem. :) You may find some useful links in this Google search I threw together.

Also, it is my opinion (others may disagree, of course) that helping you sketch out COI policy updates is out of scope for this site.

Thanks MadJack - I appreciate your time and help. I agree about the scope of this site. I misspoke above - I was looking for how others in a similar situation navigated the waters.

@Conflicted -- Without more information, I don't actually see any glaring conflicts of interest. Both the faculty's employer (the university) and the faculty himself are stakeholders in the startup, so they have similar interests. I can only presume (since the federal government requires this) that any conflicts of interest are also disclosed to the sponsoring agencies and are managed according to the usual best practices. Can you state concretely which part you find troublesome?

possible duplicate of Is it ethical for a professor to get masters students to work on open source modules related to the professor's profit-making company?

I think that general suggestions for COI policies can very well be on-topic – though it may take some time until somebody answers them. However, What are your thoughts on this scenario? and Have you navigated through this before? are poll-like questions and thus no good fit for this site. I am therefore taking the liberty to remove them. (cc @MadJack)

First of all, you should know that this sort of setup—a researcher has a side business very closely related to his research—is quite common. It does sound like there are a few unusual details in your story, but the overall picture is standard fare for most universities.
The only direct answer that I can think of is to work very closely with both your advisor and whatever department your university has set up to handle this sort of thing. I went to Pitt, which has an entire department set up to assist with questions like yours. My advisor had a very good working relationship with the university, and I found these people very helpful. You should be able to find this within your university (if it exists) by talking to your department chair. On a very similar vein, Pitt, had a distinct Conflict of Interest department set up for these types of matters as well. They can answer questions.
NOTE: talk to your advisor before doing anything!!! The chance that the university is unaware of this is pretty slim, particularly if he has an SBIR grant. He has probably worked out all the necessary details a long time ago. If you go around raising alarms where none should be raised, you'll end up seriously annoying your advisor and looking like an idiot. You don't want to do that.

I agree that it is common, but that doesn't make it right. It certain cases it is ok, but often they are used as cost mitigation in for profit businesses. This is wrong since graduate students are paid low wages and provided almost none of the typical legal protections of a normal employee since graduate students are students not employees in the United States. I've seen a lot of outside contracts come into my department, for projects which employed graduate students, and which were not worthy of a thesis and some of which restricted publication entirely, which really is just exploitation.

@daaxix - What you are describing is definitely a problem, but that is by no means the norm. Anecdotally, I know that both my advisor and two other advisors in the department had their own companies, employed their students, and kept everything very fair and appropriate; pay was split, time was split, and resources were separated appropriately. It can go both ways.

and where they paid a market wage for the work done for the outside companies?

@daaxix - In all instances that I was aware of, including my own, yes.


text:
Is it OK to send email to journal asking for extension for a revision?
I am in the process of sending the response to reviews to a journal. It looks like it will take some days for the revision.
In the reviews, the associate editor had commented the following

Finally, I would appreciate if you could submit your revised paper by Jan 12, 2018. If you cannot meet this deadline please contact us (xxx@elsevier.com) to request an extension, otherwise your paper may be withdrawn.

I was wondering if it was OK to write to them asking for an extension or should I somehow submit the revision by Jan 12?

The answer is literally written in those three lines you quoted...

Ask for an extension. This is quite common in case more extensive changes/analyses need to be done.
Submitting a subpar version would waste their and their reviewers’ time, and may even end in a desk rejection for you.
When asking for an extension, shortly explain why you need more time (ideally, related to the reviews you got – show them you are working on the paper), and make a good estimate on when you will be able to resubmit. You don’t want to ask for several extensions during the same round.

I agree strongly with almost all of this, but don't really think you need much in the way of an explanation.  Apologizing for being busy really should be enough.  Definitely make your new estimate an accurate one though!

You quote the associate editor specifically asking you to request an extension, so it’s a bit weird that you’re not taking them at their word. What I take from the wording is that not submitting by Jan 12 would cause them inconvenience, and you should take that into account in how much effort you make trying to finish it by Jan 12, but they will accommodate those who request an extension. If you don’t keep in touch with them, they won’t know whether you’re still working on it, and they may withdraw your paper if you don’t keep them apprised of its status.

The associate editor specifically said you can request an extension, so absolutely feel free to do so. There is usually no harm with such a request and it will not affect the future decision; the journal wants to publish your paper or they’d have given a reject decision. It’s really easy for the desk editor to extend the deadline – just modify a box in the editorial management system. In fact it’s possible the desk editor will simply grant the request without checking with the editorial board.
For context, journals usually give these deadlines because they want to keep the author thinking about the manuscript, and are hoping for a timely revision. The last line about your paper possibly being withdrawn is because there are authors who, after a revise decision, decide not to revise their paper but do not inform the journal. If you exceed the deadline your submission gets marked as inactive. When the journal decides to do spring cleaning and remove all the inactive submissions, that’s when your submission might be withdrawn.


text:
How should I handle reviewer comments when grammar makes the meaning unclear?
I have received reviewer comments on a paper that I had sent to a journal. Now although the reviews look good, there are lot of grammar mistakes in it making it difficult to understand some of them.
How do I handle these kind of reviews? Is it okay to write to the editor’s office for clarifications? I guess that way, the process would take a long time.

@thomas It doesn't get easier to understand bad grammar when your own grammar isn't that good either. In other words, a (near) native speaker can easily understand broken language, but a broken speaker will have a hard time to do so.

@Thomas another way to look at that: lack of English fluency on either side impedes communication in English, so if the OP isn't a native speaker that may explain why they're finding this review harder to read than some of us might.

@Mark "all perfect English is alike; every imperfect English is imperfect in its own way".

I think Dawn's suggestion of how to deal with these comments is excellent, both getting a second opinion and restating your understanding of the comments.

First, work through the comments with someone else to parse their meaning as closely as possible. A native speaker might be able to explain what the reviewer was trying to say in his/her comments. If several people are not able to understand or do not agree, then you may contact the editor for clarification. But try not to reach this point--nothing in the snippet you have provided seems that problematic.
Next, revise and resubmit as directed by the journal editor. In your response to reviewer comments, I would create a numbered list of comments. Before stating how you addressed each comment, you should briefly restate your understanding of what the comment was conveying. If you have not adequately addressed the comment because you did not understand it, then this should at least prompt the reviewer to clarify their comment, rather than become annoyed at your response.


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Consequences for publishing final-version PDF, in violation of publisher policies?
Are there consequences that are typically enforced when an author puts the publisher’s PDF on a personal website or social media (e.g. ResearchGate) in violation of the publisher’s policy? I see many journal policies which prohibit uploading the final-version PDF on repositories (see Sherpa/Romeo). But at the same time, I see many final-version PDFs freely available if you look on ResearchGate, Academia.edu or an author’s website.
If these are cases of technically breaking the publisher’s rules, are there typically consequences for researchers?

In the context of academic publications, a "publication embargo" is a time-limited period where you can't share the paper. See e.g. What exactly is an embargo for a journal?. I don't think that's what you meant, so I edited your post to clarify. Please let me know if I got it wrong.

FYI How often do publishers sue researchers for copyright infringement for putting their articles on a personal website?

There's a distinction between a preprint, a version that is effectively final (a version after the peer review), and the publisher's version. Could be that those authors you're talking about actually have the right to make at least one of these versions available on their websites or elsewhere.

Meta discussion about this post, and in particular about arguments to reopen.

Much of the answer on this question is dependent on the specifics of copyright transfer and the specific policies of the journal. Here is a journal article about copyright and author self-archiving. Among authors, the topic of copyright transfer is not very well-understood.
What consequences are typically enforced:
According to this article by chroniclevitae.com , the typical consequences for authors who publish their site to a social media site (Academia.edu in this example) is a notice to the violating website to remove the copyright'd content, However, even this action is somewhat limited, as academia.edu received a peak of 2,800 requests over a few week span for a site that hosts over 2.3 million journal articles.

Remember: As Bledsoe points out, this is still murky territory. Publishers, journals, and scholars are all feeling their way around.

Possible extent of consequences:
When an author agrees to publication from a publisher, the publisher receives not only the words and graphics, but also (sometimes) the copyright from the author. If the publication required a copyright transfer, a copyright violation is being committed by uploading a published paper, even by the author of the paper. The possible consequences are as diverse as typical copyright violations, but can be up to and including paying money to the publisher for loss of revenue.

Money damages in copyright infringement actions are commonly awarded under three legal theories, actual damages, profits, and statutory damages.

Source for additional reading and understanding of copyright infringement and the possible monetary consequences from a legal point-of-view.

"can be up to and including paying money to the publisher for loss of revenue." - Do you have any sources to support this statement? Do you know of any example where an author was required to pay money to the publisher for loss of revenue after posting the final version PDF online? Do you know of a specific statute which specifies this kind of consequence in this scenario? Or are you just speculating (in which case, you might want to say so in your answer).

According to the source you cited, the publisher could only recover compensatory damages due to loss of revenue if they had suffered "provable financial loss directly attributable to the infringement". This is almost impossible to prove in practice. Statutory damages are easier to recover, but these require that the publisher "registered a work with the U.S. Copyright Office before the infringement (or within three months of publication)" which rarely happens in the case of academic documents. If anything, your citation suggests that the consequence you mention is very improbable.

You're right, and the original question asked 'what consequences are typically enforced'. My answer is some of the extreme measures which can be enforced by publishers.

In that case you might want to make it clear in your answer that the extreme measure you refer to has never been enforced by an academic publisher for a journal article (as far as you know), and that even if a publisher did sue an author, it would be difficult for them to recover monetary damages due to the legal requirements. In its current state, this answer is somewhat misleading (It clearly does not represent "typical consequences" for authors who post papers online.)

Created Distinction in my answer and included 'typical enforcement measures'


text:
Is there position statement on academic research workplace
I wonder if there is any professional research organization (like Society for Neuroscience or National Academy of Science) that released an independent position statement or an opinion piece published in reputable journal that addresses best practices for research workplace.
I am looking for a written document that answers the question:

In what conditions academic researchers want to work?

Conditions include paid family leave, building quality, office space, infrastructure, budgeting standards, how students are treated, benefits etc.
For this question by "academic researchers" I mean tenured and research professors, maybe postdocs at R1 universities. But other similar answers are encouraged.
Here are examples of existing statements, but they don't address institutional policies or workplace enough:

Building a Culture of Research: Recommended Practices
How to build a better PhD
Key Strategies for Building Research Capacity of University Faculty Members

This, from a UK academic union, is definitely not "independent", but might address some of what you're after? https://www.ucu.org.uk/media/2748/Hot-desking-open-plan-offices-and-space-utilisation---UCU-factsheet/doc/hsbrief_hotdesk.doc

@Flyto Yes, that is somewhat looking like what i wanna see.


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Is supervisor bound to clarify the technical queries of a Ph.D. researcher?
Summary: are PhD advisers obligated to help with technical questions / tasks that PhD student is trying to solve?

This question arose due to my confusion regarding the role of a Ph.D. supervisor.
I am aware that, nowadays, plenty of platforms are available for a researcher to ask their questions. But receiving a proper answer mostly depends on others' will. Suppose I opt for a stack exchange site to ask a question then the possibility of receiving a solution depends on the response by members of the community. If I ask on GitHub or email the author then also it is optional for them to answer my query.
Some tasks during Ph.D. are expected to be completed in a stipulated amount of time. There may be negative consequences if it takes so much time for a Ph.D. researcher to get her query solved.
It is optional for colleagues, teams (if any) to solve a query of a Ph.D. researcher. Although the Ph.D. researcher tries hard to get an answer by reading books and thinking much about the problem, my question is regarding the role of the supervisor in this context.
Is a supervisor bound to clarify the technical questions of her Ph.D. researcher?

I request down-voters to comment the reason for down-voting, Whether it is about the quality, presentation, intention etc,, of the question.

This seems an entirely reasonable question to me.  It is not in the best interests of students at any level to have all of their questions answered directly.  Part of being a good teacher is the ability to help students learn to answer their own questions.  This is especially true of research students as when they gain their doctorate they should expect to be working at a level where there is nobody to answer their technical doubts as they are at the cutting edge of their field.  IMHO, you don't have to answer if you don't think it is in their best interests.

@DikranMarsupial: Good comment! I suggest that you turn it into an answer.

@alephzero If I could downvote your comment, I would, since your interpretation of the question is based on overly negative assumptions. Giving answers to technical questions is not the same as "doing all the work". It could mean that the supervisor is much more familiar with certain technical circumstances and is able to guide the student in the right way, for example, by helping them to ask the right questions and look in the right places.

@lighthousekeeper he basically gives what OP asked - a reason why people might downvote and a hint to how this can come across. I wouldn't put it like that (hint: the life experience bit sounds arrogant), nor would I downvote, but the question does read insecure to me and wanting assurances you cannot fail or like it tries to shift blame (pre-emptively?) to others for potentially failing. At the least it can be read like that. If it isn't coming from that place then it's a good hint at perception and how to rewrite if OP cares about that perception or feels it might taint the answers.

obviously it's fine to struggle with a PhD (or being the supervisor as the question could also be written by a supervisor^^) and the exact boundaries of what one can expect and cannot expect, what the normal challenge level is supposed to be etc. and to question the personal situation and assistance of the personal supervisor!  Another issue for that perception might be that it focuses on "technical" questions when many might perceive those to be exactly what the PhD student is supposed to solve themselves. Perhaps specifying the field could help to clarify in that regard.

@lighthousekeeper You can call us negative, but it is very vague where OP limits her/his “technical questions”, and this question very much reads as if OP think that the job is to ask others to help out, and the supervisors job is to be a timely source of answers when SE or Reddit is insufficient.

The down votes are presumably because nobody would accept the obligation to help with all technical questions.  So it's not plausible that the answer would be yes.

What do you mean by technical? "How do I use this instrument?" "How do I do this model in R?" "What does this theory mean?"

The supervisor may not know the answer either, and there may not be an answer (yet); hopefully in that case the supervisor can offer guidance towards how to approach the problem and how to work around it if an answer can't be found in reasonable time

No.
The role of supervisor is understood in a number of ways by a number of people, but supervisors are not bound to clarify technical questions.  They should provide reasonable guidance (for instance by suggesting possible solutions paths, references to similar material, appropriate training on equipment, course selection).
Now reasonable guidance means different things to different people, mentoring takes many forms, and supervisors have different styles, but good supervisors can and will gauge the amount of guidance needed on an individual basis.  Other supervisors may choose to let the students sort themselves out.

It is not in the best interests of students at any level to have all of their questions answered directly. Part of being a good teacher is the ability to help students learn to answer their own questions. This is especially true of research students as when they gain their doctorate they should expect to be working at a level where there is nobody to answer their technical doubts as they are at the cutting edge of their field. IMHO, you don't have to answer if you don't think it is in their best interests.
It's also quite possible at PhD level that the supervisor doesn't have the answer (and nor might anybody else), which is what makes research fun.
I view a PhD as being an apprenticeship to be researcher in some particular field of research, so the aim is to learn the skills required by working with (hopefully) a master.  Learning how to address doubts or solve problems for yourself is part of the progression to a journeyman (journeyperson?) that can work on tasks independently.  Your job is to get your apprentice to that stage by the time they finish.  Sometimes that is by directly teaching them things (e.g. how to use a chisel), sometimes it is having them work with you on something, sometimes it is letting them make their own mistakes and helping them to learning from them.  I am learning to make musical instruments as a hobby, and I learn more by thinking about things for myself and trying to work out what I am doing wrong than I would if my (truly excellent) teacher just demonstrated how to do everything.

Very nice. Every teacher/professor should keep this in mind. "... at any level..."

The additional paragraph (...no one knows...) is also important to remember. Can't vote twice, though. Sorry.

I think there are some more general underlying questions in this, implied and necessarily precedent to the question asked. Answering them, answers the question.

Is a supervisor bound to entertain every question a researcher might ask?

I'd argue no.
I feel it's ethically fine for a supervisor to set well-defined boundaries. An extreme might be "no more than 10 questions a day, by email, before 10am. In each, show what reasonable effort you made to find the answer yourself" - I've laid down similar boundaries myself, albeit far less stringent, when mentoring large numbers of people.
It'd also be ethically fine for a supervisor to fail to respond to questions which were clearly asked to large numbers of people at once; were abusive or personal; were asked through a weird medium; were not on the topic of the research; or were otherwise in violation of commonly-implied social boundaries for expecting a question response.
So the supervisor is not ethically required to even respond to every question from a researcher.

If an appropriate question is appropriately asked, is the supervisor bound to respond?

I'd argue yes.
If the researcher has shown reasonable effort in their search for answers, and found none, then they've likely encountered a "blocker".
It's arguably the whole point of mentoring, to hear and respond to problems encountered by those we're helping: without such interactive guidance, we're just a YouTube video on legs.
Are there those who won't fulfill this ethical responsibility? Absolutely. There are crap supervisors in academia, just as there are crap managers in business. And unless there's some explicit rule in place in the institution you're working at to force them to take a greater interest in helping, there may not be a lot you can do about that.

What form of response is the supervisor bound to give?

Any of the following would be fine:

"I don't know how to help you with that."
A partial answer, acknowledging that it's only partial.
A full and complete answer of the question, maybe even raising additional issues that might be relevant.
Proposing a reframe of the question, if it seems based on a deeper knowledge failure. Arguably the best help a mentor can give is to see beyond simple questions to deeper issues.
A pointer to likely sources of the answer.
A suggestion of other avenues of inquiry or research approaches that might lead to an answer.
... and so would many other approaches.

And as others are said, answering every potential question is neither the only, nor the best response to every question anyway, since we're trying to teach people to fish, not give them a coupon for unlimited free fishsticks.
I suspect that's why the OP didn't say "answer", but rather "clarify".
TL;DR: For any reasonable question, asked reasonably, and within any explicit boundaries set by the supervisor, YES, but only a response, not necessarily an answer. It's a mentor's role to give support and advice.

Your supervisor is usually someone fluent in the research field you are doing your PhD in.
But it does not have to be the case: my supervisor was maybe 40% competent in my research (a novel one at that time) and I was not expecting reseach help from him.
He was a wonderful supervisor, though: he helped me to navigate the muddy waters of Academia, was keen to listen and to challenge some of the points, and was very helpful in the logistics of my PhD.
We had an extraordinary relationship but

Is a supervisor bound to clarify the technical questions of her Ph.D. researcher?

Certainly not. Besides the slightly demanding "bound" (or at least this is how I read it, as a non-English speaker) they may simply not know the answer (it is research after). I would say that if at some point you do not discover the answers to your questions on your own your PhD is not that great (in terms of learning how to do research)

Indeed, there should come a time when you know/understand some things better than your supervisor, and are in a better position to answer the questions - you have been studying them and they have not.

@DikranMarsupial: yes, I would argue that this point should come quite fast, for things you have a common understanding of. If someone does not make the effort to understand something that is on the way to their PhD then there is something wrong. The further you go, the fewer of such cases where you want someone to explain things to you (generally speaking)


text:
Is it common to attend to conference of past postdoc during a new postdoc?
Summary: I have finished postdoc #1 (it was negative experience) and started postdoc #2. I have been invited to present work performed during postdoc #1. Is it normal and expected, since it will take away time from my current job?
I have finished a postdoc a few months ago. It wasn't a pleasant experience both from a perspective of human relationship with my supervisor (a fake, hypocrite, toxic and stressful person/experience, nothing like I had faced before in my whole life) and from a research project (too little challenged mentally, left alone most of the time, and badly managed: set to work on non priority tasks most of the time). I will start another postdoc in a few months, in another research group, in another city, in another topic (which I personally find much more interesting).
However, I have been contacted by the 1st postdoc research group, asking me whether I would attend to a conference, to present some of our work. This would be for a few days during the 1st month of my 2nd postdoc, which would start in a few months from now. On a personal level, I do not think it would help me much to present this work (I am not involved in this topic anymore), I would rather work in the new laboratory (every working day will be extremely precious and valuable, since there aren't many). If I were to attend the conference, it would mean the 2nd postdoc would have to pay me a full salary while I would be "working" for the other laboratory.
I would rather not give more details, at least for now. I am wondering whether it is common for people doing several postdocs, to "work" for previous postdocs, or attend to conferences related to previous postdocs, while it removes working time in the new postdoc.

Yes, it's common. Of course nobody can force you to do it anymore at this point ...

I feel that the question you really want to ask is "even if it's common, is it okay if I decline?" The answer is an emphatic "yes, it's ok to decline". You get to choose how to spend your energy; it's a healthy choice not to spend it on a bad relationship and work situation when it won't even really help your career.

This is very country specific. Not the same in France, USA, Germany, Spain

Just be sure the invite isn't from a predatory conference

If there is a chance you would be interested in presenting at the conference, consider discussing it with your 2nd postdoc supervisor. One of the goals of a postdoc position is career development, which is not limited to the specific project you were hired for. Even if the 1st postdoc topic is different, the experience of giving the talk may be useful (and also could be noted on your CV, although this may be minor if you have several other publications).

If I were to attend the conference, it would mean the 2nd postdoc would have to pay me a full salary while I would be "working" for the other laboratory.

This is not necessarily a problem. Again, your 2nd postdoc supervisor can provide guidance, and may be more than willing to support this as part of contributing to the academic community and developing you as a "whole researcher". It is routine that some "mopping up" from a previous position is done early in a new position; supervisors are often fine with this (within reason) because it enhances your general record/reputation and maintains useful connections/goodwill.


text:
Restricting details in privacy-related research to prevent abuse
I'm starting to do research in machine learning on sensitive datasets, which sometimes seems like a double-edged sword. For instance, some projects involve showing how a company/organization/government can infer sensitive information about you and abuse it. I feel that this has to be published as it may already be abused somewhere or will be soon. At the same time, if I publish too many details then some corporations etc. may find it easy to implement and start abusing.
Do some conferences/journals accept papers that have scarce details on some parts of the modeling such that it may hinder abuse? It should be noted that while the code may be sent to the reviewers for a check, the data is sometimes of a sensitive nature such that it cannot be handed over.

You must read the related literature and not speculate on your own (as you seem to do now). All methods for extracting sensitive data from datasets are well-known. Thus, privacy research aims to propose ways to transform the datasets for providing sufficient protection against those attacks (e.g., k-anonymity). So, read the corresponding papers and follow their lead.

I think that I may not have expressed myself clearly enough. I'm not doing what you seem to define as privacy research. My works concerns modeling sensitive datasets using machine learning methods (I've updated my question). Here I would definitely disagree with your statement saying "All methods for extracting sensitive data from datasets are well-known". Almost everyday, there's research published on new methods yielding better results on identifying your personality from facebook likes, mental illnesses from mobile phone data etc. This is the kind of research I'm talking about.

I think there are a couple of unrelated question being asked. What data need to be given to the reviewers is very different from how functional the code needs to be.

I think now your post is better. Your focus is on machine learning and data mining. Every paper must always provide enough details for anyone (in this line of research) to be able to replicate your results. If you do not want your method to be abused, do not publish it (that would not stop anyone else publish a similar method though). You cannot get a paper published that proposes a new method for "breaching" privacy and hide the necessary detail to block other people from using it. This is not how science and papers work.

while your intentions are noble, your desire to restrict the flow of information to prevent potential abuse will likely also hinder your own professional interests. essentially it will prevent other researchers from expanding on your work in a fruitful way. one possible compromise may be to offer scant details and in the methods section, include a line such as "full dataset/model available from corresponding author upon request." this will allow you to disseminate to your peers in a meaningful way.

If you don't show the info, it is hard to justify publication.  Applies in other cases (market entrance, national security) also.  Science publication is not suitable for secrets.

From a practical perspective, even if you omit the implementation and mathematical details from your paper, large companies like Google and Facebook, or state agencies have significant amounts of manpower and talent. And if they really wanted to they could probably get very close to the results that you are obtaining in a short period of time.
So it is unlikely that any obscuring on your part would halt these entities from following through with whatever agenda they have. On the contrary, omitting too many details will only make it harder for you to publish.
On a more philosophical note, any machine learning model can be used for good or for evil. Linear regression models I'm sure have helped people to win wars as well as eradicate diseases. As a result, one can easily argue that any attempt to prevent abuse is equally preventing progress in other domains.


text:
Using a paper under review as writing sample for PhD application
I am submitting a PhD application, for which I am required to include a writing sample; either a publication or a class report. I don’t have publications but I have a submitted paper authored by me and my advisor which I already submitted to a conference but was not yet accepted (results are due in 2 months).
I was thinking of submitting this paper for admissions as a writing sample because I think that it is well written. I know that I have to get my advisor’s permission.
In case my advisor agrees, is doing that appropriate? My yet to be accepted paper will be reviewed by professors in the department I am applying to.

As far as I understand it, the writing sample is supposed to demonstrate that you can write well. As such, it will not be a problem that it is seen by the people where you apply (they are not going to review it, they are just going to see if it is well written). What will be a problem, however, is that is has not been written solely by yourself, so it does not actually demonstrate your own ability to write.

So maybe the real question is "Should I submit a joint paper as a writing sample?"

The linked question is about faculty job application, but the answers (2nd especially) generalize. Unless you change the question as @Nate suggested, in which case we'd reopen this one.


text:
Somebody made comments and suggestions on my drafts – can I be reasonably accused of plagiarism?
I am a bachelor student. I have been working with a PhD on an article. So the article was supposed to be co-authored; however, he was mainly going to edit  my draft so it can be published. This is, the content of the article was actually my work, while the edition was going to be his part. I have e-mails with all the drafts I have sent to him until the final draft of the article. In these e-mails, one can see that he mainly suggested me to clarify some ideas or was trying to understand the ideas I was pointing out.
On the other hand, we have stopped working together. Thereby I sent him an e-mail, by recommendation of a professor, asking him if he had any inconvenience if I used my drafts for my bachelor thesis (in my country one first obtains the bachelor degree and then one must present the thesis). He answered that my drafts remain my work and that because of this I am free to use them.
The question which I would like to ask is if there would be any inconvenience if I wanted to publish this draft in a journal as long as it is actually my work. People have told me that as long as I have this e-mail where he is recognizing that my drafts remain my work, I would have no inconvenience, however, I wonder if this is enough for I did not ask him about using my drafts for publishing but just for my bachelor thesis.
I am wondering if he could accuse me of plagiarism if I would publish my work. I think that he could not do so because he has written to me that my drafts are my work and thereby I am free to use them. Besides this I have all the e-mails wherewith I could prove that the drafts are totally my production and that his contribution was mainly motivation and making me some suggestions or comments so that I can better clarify myself. Would that be enough in order I can publish my work without any fear of being accused of plagiarism?
Sending him an e-mail asking him directly is not really an option, for the relationship of work has gone deadly bad.

Could you please add a few linebreaks in your text to create paragraphs? As it is, this text is not very readable.

in my country one first obtains the bachelor degree and then one must present the thesis – Just curious: What is the motivation for people who do not plan to stay in academia to present the thesis then?

Your question sounds fine until the very last sentence the relationship of work has gone deadly bad.. It seems to me there is some context missing. When did it become bad? Why is it deadly bad?

I think you are mainly trying to figure out how to cover your A.  Which is a very sensible question....  One thing that might help would be to take the high ground, and write a gracious acknowledgment mentioning him by name, in both the thesis and the journal article....  It's a small world, and you don't know when this guy might come back to haunt you in the future.

@scaaahu, Without entering in too much detail, after some disagreements, he sent me two insulting e-mails and I have never wrote such type of e-mails to him.So it is useless to ask him anything else.

@Wrzlprmft, in my country, people who do not want to stay in academia have the chance to give an exam.

Your issue is rather one of authorship than of plagiarism and thus accusations of neglecting the PhD student in terms of authorship are what you should be worrying about.
First, you should ask yourself whether the PhD student’s contribution qualify him for authorship. For this, he would have to contributed intellectually to the science behind the paper – improving the explanations and writing does not count. Note that general ideas of what to research may be counted as this. For further information, I suggest that you browse authorship. What you are describing sounds very much like the PhD should not be an author, though.
If you come to the conclusion that the PhD student should be an author, things become difficult, as most standards and journal policies require him to affirm the manuscript you will be going to submit, which may lead to all sorts of problems given your bad relationship.
If you come to the conclusion that the PhD should not be an author, you should only acknowledge him for “critical comments on previous versions of the manuscript” or something similar. You are doing nothing wrong in terms of laws, regulations or ethics when publishing the paper without him as an author¹. However, you taking some precautions to defend against possible accusations of stealing authorship may be a good idea:

If the PhD student makes any claims of authorship, he has to back them up somehow. If those claims are wrong, he should only be able to do so by witness accounts of his alleged intellectual contributions. Probably the only plausible source of such accounts is your immediate research surrounding, i.e., supervisors, colleagues and similar. Thus you should ask yourself whether it is possible that they side with the PhD student on that matter.
All your e-mail correspondence is certainly helpful as it should very well document that the PhD student was only involved in writing, e.g., if he asked questions on the actual content of your research.

¹ A problem may arise, if the PhD student actually wrote entire sentences. In this case, he could qualify for legal authorship in terms of copyright. However, my understanding of your question is that this is not the case. Even if it is, his contract or specifics of the relevant copyright laws may solve this issue.

Based on what you said I have the impression that you are the main contributor to this work and he only had some editorial comments. Therefore, you publishing this work, cannot be classified as plagiarism. (If you think his contribution was sufficient for him to expect you to give him some credit (e.g. second author) then you have to be careful because it may cause further complications between you and him. Besides, it is your responsibility to make sure he gets the credit he deserves)
Most of the times people won't actually act against each other in situations like this. I remember a few years ago, I was stuck in a situation where someone decided to publish a team work with his name as the first author, while it was clear to everybody that he was not the major contributor. My adviser sat me down and told me to let it go (and I accepted because he had good reasons). What I'm trying to say is that in cases like this your supervisor would usually mediate and smooths things out before it gets serious.
However, I think the chances of him even trying to accuse you of plagiarism are very slim. But even so, if you publish this work before him, he needs to have enough evidence that he had major contribution to the work. I assume that this is not the case and it is clear from the emails that were sent to you.
I suggest you to simply let your adviser know that you will try to publish this work and don't worry about the PhD student.

It is irrelevant whether you have any emails from anyone permitting you to use text. If you publish your bachelor's thesis and a journal article and there is text overlap between the two, someone may notice and may publish a review -- either in a journal or online -- noting that this can be construed to be plagiarism. One must strive for the utmost transparency in scientific writing. You could either publish the paper first, and then include it as part of the thesis, or you submit the thesis first and refer to it in the journal article. In that case you do not want there to be text identity. You are summarizing in your journal article.
Do make sure that you are not publishing with a predatory publisher that does not do rigorous peer review but only takes money for putting an article online.
The PhD you mentioned is not an author, and should not be listed as such, if they are only editing. You thank them in the acknowledgements, but only those who did the research and the writing should be listed as authors (see the Vancouver protocol).

The scenario you mentioned could probably better be called self-plagiarism. In any case, the author should check with the journal's policies to see if such a "double" publication is allowed.

I don't buy the argument that there cannot be text identity.  In many fields, students' PhD theses are essentially first drafts of eventual journal publications. The journal publications should ideally cite the thesis, of course, but I think that few would consider this an example of even self-plagiarism. The real issue in this question is the relation with the collaborator.

I strongly second @Corvus' viewpoint. In many fields (e.g., mine, mathematics), indeed, a thesis is often a verbose draft of an eventual journal article. Nothing is "claimed" about the thesis to "gain status" that would compete with or be double-dipping with a journal article, in mathematics. In other fields, I don't know how people interpret things. It's certainly not an absolute, no matter how strongly held or widely held various viewpoint may be.

To add to this: The central issue about self-plagiarism is that you claim texts to be independent and new that actually aren’t. Such claims are usually implicitly made by one accepting the journal’s conditions (which disallow publishing something that has been published before) or the exam regulations (which disallow using one piece of work for two degrees). Except for the unlikely case that the thesis was actually published, this does not apply here. And even then, many journals make exceptions for such cases. It’s no self-plagiarism for the same reason that publishing a preprint isn’t.

Just because in some fields it is "common" to reuse texts, one should always make the effort to demonstrate where the texts originated. A journal article is usually condensed, and thus will not have text identical to the thesis, although diagrams may be re-used. They should still be correctly referenced. @Corvus, in what field does one obtain a PhD for what is, in essence, a journal article?  MatthiasDiener, self-plagiarism is also plagiarism.

@DeboraWeber-Wulff In physics and biology, the thesis is commonly a collection of journal articles (already published, in review, or in preparation) prefaced by a brief introduction. I'd imagine that many other domains of the natural sciences work similarly.

@Corvus, that is not text reuse - that is a collection of clearly delineated journal articles. This type of cumulative dissertation is becoming more common, although it is also troubling, as there are so many open access predatory journals that make it difficult to evaluate how important the publications are. And even traditional publishers sometimes shame-facedly have to admit that they accepted bogus papers: http://www.nature.com/news/publishers-withdraw-more-than-120-gibberish-papers-1.14763 Back to the topic: Text re-use must be transparent and sources cleanly given.

@DeboraWeber-Wulff I don't see how a dissertation composed of papers that went through peer review at a legitimate journal could possibly be more troubling than a dissertation that was seen only by a dissertation committee who may or may have read it.

@Corvus, how do you know what the peer review process was? How can you determine what a "legitimate" journal looks like? There are so many "junk journals" today that say that they do peer review and they don't. You can't tell from the outside how rigorous that was. The list of such journals grows every year (http://scholarlyoa.com/2015/01/02/bealls-list-of-predatory-publishers-2015/) Here's an example of what good, open, transparent peer review looks like: http://www.biomedcentral.com/1471-2334/9/49/prepub

@DeboraWeber-Wulff Seriously? After this many decades in the field you think I don't know the journals in my own field? Even from a distance it's not hard: What is the history of the journal? Who publishes it? Who is on the ed board? Is it on Beall's list? When in doubt ask a colleague in that precise area. Etc. In any case, while I agree that peer review is no panacea, my point was that it certainly doesn't hurt and often is a substantial improvement on the cursory scrutiny offered by a dissertation reading committee.