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Can it be disadvantageous to actively publish in completely different fields?
I'm a researcher in a STEM field and work at an institute where research staff salaries (including mine) are dependent entirely on third-party grant money. I've already successfully obtained research grants and served as the PI for a few projects.
In my spare time (i.e., after I go home for the day) I very much enjoy reading and writing about topics in the humanities, and I have recently had contributions on these topics published as peer-reviewed articles in humanities journals. In retrospect I wonder whether having published in these venues was a good idea.
The problem has to do with my current and future grant proposals; some funding agencies require proposals to include a CV listing all of the applicant's peer-reviewed publications in the past n years.  (And even for those agencies without such a rule, the reviewers can easily find all my publications online if they care to look.)  I am wondering how the presence of my non-STEM publications will be viewed by the STEM proposal reviewers.  Are these publications going to be interpreted negatively, as a lack of research focus on my part?  Where feasible, should I include an explanation in my proposal CVs that these publications were avocational (and if so, how should I word this)?  Should I entirely give up my beloved hobby of writing for humanities venues in order to better secure my funding prospects as a scientist?  Or are my fears here entirely misplaced, there being no downside at all (or maybe even some benefit) to having the occasional humanities article in my publications list?
Two further things to note:

I realize that there are a couple possible workarounds that I might try, such as using a pseudonym when publishing in the humanities, or simply omitting the humanities publications from the CVs I include with my grant proposals.  However, both of these necessarily involve some deception or bending of the rules, and in any case won't take effect for the proposals I've already got under review.

There are already a couple of questions here about publishing in foreign fields (Can I publish in a field completely unrelated to my present field?, Is it good reputation for a researcher to publish an article belonging to different research field?), though these are from students who haven't yet started their PhD.  My question is more about how an unorthodox publication list will affect STEM research grant applications specifically, for an applicant that already has a doctorate and some project lead experience.

I can't provide an answer, but just an anecdote: I do mathematics but have a few publications in different areas such as social sciences or measurement sciences. I do not think that this did any harm to my proposals, but I can't know for sure.

@Dirk: Which ones? I am reading through the list of your publications on your university homepage - most seem to be in Arxiv or in math journals

"How to be best in the OECD better life index?" is published in Social Indicators Research, another one is in Microscopy and Microanalysis and yet another one in Journal of Sensors and Sensor Systems.

May I ask, about what two (distinct) fields you speak? It might matter, for example, if it is Physics and Psychology, I think that actually might be a good combination. I can give a lot of examples. Are you applying methods, or modes of thinking, to the other field? Guess then, it would be advantageous. Or, is your main field Biology, and in your spare time you write for some Intelligent Design Journal? Then maybe not so good. But actually any, more serious, combination that came to my mind seems to be advantageous. Btw, do you know S. Eilenberg, the famous Asian Art Collector?

@Dirk: As I understand it, those two papers seem to be "mathsy" enough (one is even in the arxiv!!) and not something completely unrelated (like what I think the OP talks about).

Separate your publications into professional and hobbyist, perhaps explaining your hobby in the latter.

I've looked at a lot of CVs of job applicants, for proposal review, and for promotion packages. I've also sat through a lot of review panels for proposals, as well as hiring and promotion committees. I can't think of a reason why publications outside one's field would be looked at negatively by myself, and I've never heard anyone raise any concerns either, even though such publications occasionally show up on people's CVs. So no, I don't think this that there is any disadvantage to it as long as it is the "occasional paper" and not half or a third of your publication list—at which point it would suggest that you are not focused on the thing you're currently applying for.
Is it viewed advantageously? Not really either: You're generally evaluated for a job or a proposal, and what matters in this context is how well you're qualified for that one thing. The fact that you've published in other areas might be noted as a curiosity ("darn, this person has managed to have a side-line of humanities research -- that's quite a stretch to be good at both!"), but it's irrelevant to your primary area in which the application is, and so is generally just ignored.

It depends.
As a general rule, if your main discipline is X and you also published in discipline Y, as a researcher in X I would be inclined to be impressed by that (assuming I was satisfied that you were doing good work in X, which is the main thing I would care about, e.g., in the context of evaluating your grant proposal). In fact, it’s quite likely that I would be a little bit jealous of you for doing that, and that it would remind me of my own unfulfilled aspirations to someday publish work in discipline Z.
The relatively narrow exception to this rule is that there are specific areas Y which I might take a dim view of, and by association I might hold a not entirely favorable view of people who publish on Y. I don’t mean something like the humanities in general, but some specific sub-disciplines which for example may strike me as intellectual dead ends or being grounded in some political agenda or ideology that I disapprove of. Unfortunately academia does have such pockets of weirdness where all sorts of things get published that I personally would not want to be associated with. I could give some examples, but... let’s not go there.
In either of these cases the effect would be extremely small in any case. Since I am supposed to be evaluating you for your work on X, I would do my best to keep my focus on that and not get distracted by other essentially irrelevant things. But — speaking of the humanities — I am human, so can’t completely ignore the possibility that my judgement would be tainted in some small way by the extra information, for better or in some cases for worse.

von Neumann, Alvarez, Ulam and many others published in fields which were considered distinct even in their day, and history certainly doesn't consider it to be their disadvantage. Josephson and Newton, with their interest in esotorica, might be considered illustrious counterexamples.

@MarkMorganLloyd yes, interesting examples that roughly illustrate my “it depends” claim. (Although since you bring it up, I’m curious: did Ulam publish anything outside of math and physics? Did he go as far afield as the humanities?)

I think that Ulam was limited to maths and physics. However even in the '40s maths and physics were distinct disciplines, and I'd also suggest that his interest in applying simulation (in particular the Monte Carlo method) to areas of physics which had previously been treated analytically created a third discipline which again (these days) is considered largely distinct from the others. Of course another interesting example is Hoyle, who even went as far as writing a bit of SF.

@MarkMorganLloyd sure, Ulam was a legend and a personal inspiration of mine, both mathematically and as a highly interesting person - I didn’t mean to imply he wasn’t broad in his interests. I recommend his memoir Adventures of a Mathematician if you haven’t read it. And Hoyle was apparently believed by many to have deserved a Nobel prize for his nucleosynthesis work (see here). His fiction writing is just icing on the cake, though indeed very impressive. Thanks for the great examples!


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How to properly point out the M.Sc. thesis in a Ph.D. application
Having personally contacted a professor about the possibility of a Ph.D., he asked me to send him a cv and a copy of my M.Sc. in order to evaluate.
Instead, in the online application form of "other" Ph.D. programmes, I have found that I need to include a cv, among the other things, but there is no possibility to attach a copy of the thesis. So, preparing the cv, I thought to imbed an hyperlink to the thesis.

I would ask you: if it is acceptable, or is counter-productive?

Most PhD programs ask for statement of purpose (others ask for Research statement). I believe this is where you should present ,briefly, your research and MSc thesis findings.

You should distinguish between the search for a PhD supervisor and getting accepted to a PhD program. A potential supervisor is likely to be interested in the details of your thesis. However, when applying to a PhD program, the people going over applications will probably not be interested in the details of your thesis, so you do not need to attach your thesis unless you are asked to. In that case an abstract is more appropriate.

I would advise to add the links, because I don't see what you could possibly lose by doing so instead of not doing so.
You can add links in LaTeX using
 \href{link.to.thesis}{My MSc thesis title}

In my opinion, this is a nice way to link to everything relevant that can not be properly adressed nor otherwise included in your CV. You can for example provide references such as the homepage of your advisor, your department, your other software projects etc. - all just by putting links behind their names.

Fill out the application form as far as possible. You could choose to include in your application a link to an online copy your MSc thesis, as you and others have suggested.
However, as your potential professor has explicitly asked you for it, I would send him a copy of your MSc thesis directly, as an email attachment if possible.

Dear Nicholas, I have already sent him the cv and the thesis as attachments in the response. I was considering also to apply to other PhD, and their online application form has a field for a cv but not for a copy of the thesis. So I thought to imbed an hyperlink to the thesis inside the cv.

I see now. I was confused at the inverted comments around "other".

Send an admissions office the information they ask for. If they give you the option to provide additional information as a text field, then you could list a link to a version of your thesis on Dropbox or on a university web site (or similar) as part of your "additional statement."
However, given the number of applications that a centralized admissions committee might receive, they are probably reluctant to get copies of master's theses and publications—it would be too much extra work to read them all.

I disagree with the first sentence.  Send the admissions office the union of the information they ask for and the information they need to make an informed decision.  If they choose to ignore the additional information, that's their loss.

@JeffE: The questioner was asking about a case where there isn't an option to upload additional documents.

There is always an option to type a URL somewhere.

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Non-Thesis Masters
I am completing my masters in chemical engineering. I have completed my first two semesters but was unable to find a research thesis topic to work upon. Will it be bad to complete my masters degree without a thesis, if I don't get a better option?

Related: http://academia.stackexchange.com/questions/1165/planning-to-do-phd-masters-thesis-important-usa, http://academia.stackexchange.com/questions/8288/how-do-i-plan-for-my-phd-now-that-i-have-graduated-with-a-masters-degree-without

If you're mainly interested in getting a job in the industry after you graduate, it probably doesn't matter too much.  Sure, a really good thesis could be a bonus, but you'll probably have have to get pretty far in the recruiting process before anyone's even going to look at your thesis, and if and when someone does, they probably won't look much beyond the abstract.
The one exception might be if you already have a fairly specific idea of what you want to do in your job, and can arrange a thesis topic that lets you demonstrate the same skills you expect to be using.  But it doesn't really sound like you have that specific a vision for your future yet.
If you plan to pursue a PhD degree, though, things are completely different.  What people looking for prospective PhD students are most interested in is the ability to carry out academic research and describe its results, which is exactly what a thesis demonstrates.  Without a thesis, you're going to have to find some other way to demonstrate your research and writing skills.  It's not completely impossible — for example, you could try writing an independent research paper and getting it published in an academic journal, as suggested in this answer to a related question — but it does have the potential to put you at a significant disadvantage.

(Background disclosure: I'm a PhD student in mathematics with several years of past experience working in the IT industry.  I've also had some experience in helping to evaluate candidates for both academic and non-academic positions, although I cannot really claim extensive first-hand knowledge of that side of the process.)

By the way, this is actually the first time I've even heard of such a thing as a coursework-only master's degree. Around here in Finland, pretty much all degrees, even at bachelor's level, require some kind of written dissertation. No thesis = no degree. Of course, the amount and level of research required depends on the degree, but the only places I've heard of that don't require any thesis at all are vocational schools, and even those typically require a final project that sort of carries the same role.

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How much material can be changed between an accepted manuscript and "camera ready?"
After a paper has been accepted, other than the reviewers' suggestions, how much content can be changed before the camera-ready version is resubmitted?  Is there a general guideline? Thanks!

I vote for reopening, there is a huge difference between "between peer review and final submission" and "between accept and 'camera ready'.

In my (very limited) experience in CS, a lot (if its a conference), but only if you are somehow improving the paper - you can't obviously publish after removing key results that caused the acceptance in the first place!
Anecdote: My first publication happened after I was able to solve one of the 3 open problems posed at the end of an accepted paper by my advisor - this caused the entire paper to be re-written in terms of the more generalized result, and it did not go through any further reviews (only an informal mail from my advisor to the editors outlining what we did!)

Are you allowed to exceed the page limit?

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Teaching while doing a PhD
If I have understood correctly, most people doing their PhDs do their best to avoid any teaching duties while in their programs. However, I think I might want to do some teaching too. Of course, I have a hidden agenda. I would hope that:

Usually, (good) skill to teach is required later on your career, when applying for tenured positions. I would receive good experience.
Giving lectures related to my research topic might get someone interested about it. I could delegate some minor (boring :-) part of my research topic for someone to do as his/her master thesis.

Am I hoping too much here? Any experiences?

My department has a teaching requirement for PhD students; so did the department where I got my PhD.  Sadly, this does not contradict your observation that "most people doing their PhDs do their best to avoid any teaching duties".

I myself am not yet in graduate school so I can't speak from personal experience. But I know a friend doing a mathematics PhD who has a full fellowship, but simply likes teaching, so he has said he'll voluntarily teach a class starting next semester. So other people have been in your shoes, and opted to teach.

There is another benefit of teaching and that is you end up discovering small (hopefully) holes in your knowledge as you start presenting it to others...allowing you to fill those in.

Most doctorate programs have some amount of teaching/ta/facilitator/etc as a requirement of the program. Some people try to do more, some try to do less, but unless you're working in a research lab (with its own endowment :-) expect to do some teaching.

Re 'good skill': if your goal is to find a tenure track position then yes this would be good experience.  Assuming that you enjoy teaching, and who here doesn't grin, this would be a good opportunity to enhance and refine your teaching skills.
Re 'lectures on research': be careful here.  Odds are that any teaching roles you would be offered at this point in your academic career would be pretty low level undergraduate type stuff.  Depending on your area of research you might also run into some problems 'presenting' un-vetted data.  There are always exceptions to the rule but I wouldn't expect for you to be teaching anything so specific that your research would come into play.  YMMV but that has been my experience (since you asked).
Suggestion: Be careful with overloading your schedule. Teaching is one of those jobs that finds a way to embed itself in many aspects of your life that you didn't expect. For example: I expected to spend my middle years sitting on the porch reading books with my wife, not reading term papers.  Oh well.  While it is good to gain experience you don't want to spread yourself too thin and suffer an impact to your research (remember, the reason you're here in the first place :) or your personal life.

Concerning your first point, teaching is a major component of most academic jobs, and in fact is the main part unless you're a superstar, so you should at least try it to see if you like it. I thought I'd hate it until I tried it my senior year, and it was incredible and changed my life. I love to research and have published several papers, but teaching is the reason I want to be a professor. So try it out!
On another note, your PhD institution will probably be much more gentle and helpful if you have any difficulties, while a postdoc or other 'real job' will expect you to already know what you're doing. So you should try teaching now while you have a safety net.

most people doing their PhDs do their best to avoid any teaching duties while in their programs.

Some people. I'm not even sure it's "most". At any rate, many many people do not try to avoid teaching duties, and a sizable fraction even make it a point to do quite a lot of teaching.

Am I hoping too much here?

No, you aren't. In fact, your hopes are in line with what I would consider basic ethics and norms we should be reinforcing in Academia. I suggest that you not also hold on to these expectations, but try to imbue the rest of the system with them: Your colleagues, the teachers in charge of courses, the students, and the administrators which you're in interaction with. Thus even if that's not the reality right now, you would be helping making it the reality.

Any experiences?

Well, not exactly referring to your points, but I'll say I found teaching to be a very psychologically-rewarding activity, and it's what I remember perhaps the most fondly from my Ph.D. days. Now I'm post-doc'ing and don't get to teach - and man, do I miss it!


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Reviewing a revision, after the original review did not reach the authors
A couple of months back, I reviewed a manuscript and recommended a Major Revision. Ten days ago, I received the revision for review, with a note from the editor asking me to expedite, since the review process had already taken a while (not due to me).
However, from both the initial decision letter by the editor and the authors' response, I see that my initial review did not reach the authors (I checked: my review is in the system). The other review, which did reach them, mostly raised points orthogonal to mine, so if I were to review the revision again, I would likely reiterate my original points.
I immediately notified the editor and expressed that I would be happy to re-review, but would appreciate a confirmation that this review would then actually reach the authors. No response. A week later, I wrote again. No response. That was three days ago.
To be honest, I am a little miffed. Not so much that my initial review, which I did spend a considerable amount of time on, was not forwarded - stuff happens. More that I am not getting a response to what to me appears a straightforward question. After having been asked specifically to move quickly on this.
At the moment, I am vacillating between either doing the review ASAP or waiting for any kind of response from the editor first, but this second option seems passive-aggressive to me. Additional info: I know the editor, we meet regularly at conferences. I know that since he has been appointed dean, he is drowning in work.
Questions:

Has this happened to anyone else? How did you react?
Am I overreacting? Should I just review and stop whining?

Dumb question, perhaps, but can't you just call the editorial office?

I don't have any phone contact info for the editorial staff, although you are right that I could try to reach the editor himself...

"The authors have not addressed any of the concerns in my earlier review (attached for reference). Therefore, I cannot recommend acceptance at this time."

The combined ignorance of your revision points and the request for 'expedite' review smell like sloppy editorial process to me. What is your opinion of the journal? If I were you I wouldn't do more work on this submission before it's sorted out. Lack of organization on their part does not constitute an emergency on yours.

I strongly agree with @JeffE . I know another case where the comments of one reviewer were either ignored or poorly addressed by the main author, however the article passed to minor revision. this needs to stop.

@thePhDstudent: Do keep in mind that ultimately it's the editor, not the reviewer, who makes the decision about whether the paper is ready to publish or needs more revision.  If the editor doesn't agree with the reviewer's comments, she doesn't have to require the authors to address them.  But it is strange in that case to keep asking the same reviewer's opinion.

I cannot say whether the situation is due to sloppiness or due to some technical issue but it seems odd and something that should not happen. I gather that you were in an electronic review system of some sort and then the review should automatically be forwarded. In a journal not working with an electronic system, something like this is more likely to occur but should be a one off mistake in any case. Problems like these, if they recur regularly, will likely sink the journal reputation in the end. you probably have some sense of the standings of the journal.
The lack of response may not mean much and I would not over-interpret it. It is of course not a positive reflection of the journal.
Anyway, I would recommend you to basically re-use your earlier review. Look through it after reading the paper and authors comments to see if anything can be removed. If you catch anything new that needs corrections, of course, add it. You have done the work once and unless the paper is completely rewritten with significant changes to discussion and conclusions, your comments still stand. You can only reiterate your verdict of Major Revisions, which should lead to a third round. I think, under the circumstances that would b fair, unless the authors fully comply with your suggestions, in which case the editors can use his/her discretion (depending on a second reviewers response of course).
So bottom line: your initial review needs to reach the authors but with corrections for whatever has been changed. Unless you receive some explanation for what has happened from the editor, you have to draw your own conclusions about the quality of the journal and particularly the editorship. Try to form a well-founded opinion, whether you think the journal is worth your attention in the future. One mistake is reason for caution, but not reason for judging.

I had this happen as a reviewer at a journal with a 3+ month review cycle. The journal BCCs the reviewers on the decision letter so I knew my review was sent. I also knew my review was sent as a PDF attachment and the other review and the AE comments were sent as plain text. The authors wrote a point by point rebuttal letter to the AE and reviewer, but didn't acknowledge my review, so I expected they missed my review.
I emailed the AE within a few days of accepting the rereview that the authors seemed to have either missed my review or ignored it (including both typos and major concerns). The AE responded immediately (with 48 hours) saying to just review what I had. So I sent a review back that said "The authors are either unable or unwilling to address my major concerns and therefore I recommend rejection". After that review cycle, I received a 3rd version, with a rebuttal letter that apologised for missing my earlier review.
I would not whine, but nor would I spend any time rereviewing. Just say that your concerns are not addressed.


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Why do PhD take so long in the USA?
(When I finished my computer Sci degree, I decided not do as PhD as I believed that in order to get a programmer position, most employers valued 3 years more experience as a programmer greater then a PhD.)
Reading this site, it seems normal for a PhD to take 5 years, however in the UK most people expect a PhD to take not much more 3 years unless the student is being lazy.
If I saw the CV of someone applying for a  computer programmer job unrelated to their PhD and they spend 5 years on a PhD, I would questions if they were worth interviewing just on that bases.

The question was being closed as a duplicate, and since the answers here seemed to fit well enough the original question, I've performed a merge.


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"Breaking in" to reading papers in an unfamiliar field?
I graduated from my undergraduate degree about a year ago and took a job in industry.  While completing that degree, I did research with a professor related to machine learning.  However, after finishing that project, I don't think ML is where I'd want to do my research if I decide to reenter the academic world.
The advice I've received regarding applications to grad school is to be reading papers of a professor I want to work with, at least with enough understanding to suggest a new idea/direction of my own.  However, I don't really know exactly what I'd like to research, but I do have some general topics I'm interested in (categories on the level of "robotics" or "cyber-physical systems") --- figuring out what areas are still active research and what is ancient history is a bit harder than when I could just turn to my advisor and ask "what/who is at the cutting edge in this field?"
Aside from just "jump in the deep end and keep reading until it makes sense," are there methods or techniques that might help me build context or evaluate the areas I'm interested in?

Have you thought of joining professional societies like ACM? The newsletter would give you an idea of what is current in research and industry. Depending on who you work for (yea my company is a no go as well on this one) you might be able to get them to cover some of the membership cost.

You could use a database, thorough your university library for example, to search for papers in your area of interest (with keywords or author names etc). This will help you see what others are researching and publishing and to determine if that is what you want to do too.
Reading relevant blogs and forums (that deal with same or similar topics as the one/s you're interested in) may also give you some ideas.
Similarly, talking to academics you may wish to work with is a good idea, as already suggested to you by others.
I would also make sure that the academic I am working with is someone who is going to be supportive (and have time for me) to make sure that I get some help (rather than being completely on my own). If this relationship doesn't work, your job is going to be much harder. You can change direction of your research later in the degree or post graduation.

+1 for suggesting the personal contacts, Not so much for the database approach, but that is just opinion. Most profs have posted office hours and most of those would be happy to talk to a prospective student and give a few pointers.

Review articles try to summarize the latest most relevant findings in a field. Read a couple of those and you should at least have heard about the latest results and popular methods

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Leading an Academic "Book Club"
Short form: How should one lead a collaborative "book study group" amongst one's peers, particularly when the leader does not have deep prior knowledge of the book?
Long form: I'm an undergraduate CS student† (rising junior).  In the remaining time before I graduate, I thought it would be a fun idea to read a volume of Knuth's Art of Computer Programming each semester and work some of the problems.  Since I know others in the department might be interested in studying this work, I decided I would organize a "book club" where we read ~40-50 pages a week and then meet up to discuss what we read and/or solutions to exercises that we have solved.
So, my biggest question is: Besides solutions to exercises in the book or clarifications on what we read, what else should or could be discussed during our weekly meetings?
There are plenty of resources online about "how to lead a book club," but they all primarily focus on literature/story analysis, etc., not something suited for scientific writing.  Many book clubs will have a time where they read a chapter aloud, which also is not applicable to Knuth's work.  I feel as though I'm searching for the wrong term when I use the phrase "book club."  Is there a standard term for this form of study group that I could use in searches?
Furthermore, I have not read AoCP before.  Thus, I don't have a strong basis of knowledge upon which I could draw to guide discussion.  Obviously, a great solution would be to get a professor or grad student who has read AoCP to act as a mentor for the group; however, I do not know if any have done so--assume for sake of this question that such a mentor is not available.

†I know that issues facing undergraduates are generally off-topic here.  However, I believe this situation could also be faced by a grad student or a postdoc--the primary difference would be the difficulty of the source material they are studying.  I simply mention my background so readers may understand where I'm coming from.

I just took a best guess as far as tags go... I'm not as familiar with tags on Academia.SE as I am on Math.SE. ;-)

Issues facing undergrads, in my opinion, are completely relevant insofar as professors should be paying good attention to them.

I would just say that it seems to me that reading a volume of AoCP, as an undergraduate, in one semester, in your spare time, with any reasonable level of depth, seems...ambitious.

@NateEldredge Since when do I let hard work stand in my way? :P /teasing. Seriously, though, I am aware it is ambitious, but I'd much rather try for it all and find out I need to slow down than play it safe and not be stretched.

I would call it a Study Group.  Perhaps you could circulate some discussion questions or points to the members a few days ahead of each meeting, as an ice breaker or skeletal structure.

I ran one of these a few years back. Here's what we did:

Start by publicizing the idea with your friends/colleagues and setting up an initial meeting. You'll get a sense prior to the meeting whether there's interest. The more advertising you do here the higher chance you'll actually have a showing at the first meet.

At the first meet, re-state the purpose—group of people working through the ideas in the book—and decide the meeting cadence (weekly, biweekly, monthly). This is important; reading through books like this take time, and for the group to work it's critical that people actually read the content and come prepared to discuss questions. You need to give enough time to let them read, and not so much that they'll forget what they read.
On this note, we also split the book up by chapter (we were reading [Elements of Statistical Learning](http://statweb.stanford.edu/~tibs/ElemStatLearn/, chapter splits made sense there). You may decide to split by topic or whatever else. The main idea is to ensure that everyone's on the same page, and comes to the next meet prepared to discuss the same content.

During the break, read up on content. As the group leader/organizer you may want to take notes on what you read to prompt discussion (itemize points covered, questions you thought of, points for discussion). Send out one or two emails reminding them about it.

At the first meet, come with discussion points and be prepared to lead a discussion, as it's likely no one else will take the lead. You don't have to be an expert, you just have to lead the conversation and bring up talking points. If you're not comfortable in this role, find someone who is and make sure they come to the meeting.
I recommend you keep the meeting at 60 minutes or less. If the first one is a success the rest then just wash, rinse, repeat.

Agreed.  Any time I tried to go in some "new direction," the best way to start is get the team together and come to a set of shared goals.  From there...

One more point: make sure that the workload of reading, doing problems, and meeting to discuss fits everyone's schedule and energy level.  Don't assume that just because you can do this, on top of your courses and social activities, doesn't mean other people will be.  Start with modest work load and increase if everyone agrees.

While I did not lead a book club, I was second in-command in two and I, currently, lead a study group as an undergraduate. Here's what I learned in both experiences.
On Recruiting
You should always keep in mind how many members you want. Maintaining a book club with 4 to 7 members is easy because you can get to know each member individually, and you can keep tabs on who's coming to the meetings and who isn't. Larger groups take more work, and inevitably attendance will drop because each member will be contributing less and less as the group grows, so they don't really get attached to the group.
Some people have great intuition, some don't. Follow yours if it has yielded good results before. If it hasn't, find someone on whose intuition you can trust.
Example: In one of the book clubs I assisted, the leader was easily influenced by flattering. I met one of the possible recruits and I was immediately struck by how unsettling he was. He did not seem trustworthy at all. Later I discovered he had many rape accusations on him, among other illegal activities. He took over the discussion and derailed the entire group, and after I left all the female members left because of how unsafe they felt around him.
Quality is harder to achieve than quantity. Once you have achieved a number of members slightly higher than the ideal, cease recruitment and focus on improving quality of the research/debate.
Some people will drop out and that's OK. It's inevitable.
On the Group's Structure
Ideally, you should at least have a second in-command. Someone who can share some your responsibilities, who understands the group's missions and objectives, who can recruit and evaluate members, who can take decisions in your absence.
Each member will eventually show his or hers personal skills and tendencies, and you'll have to watch out for that. You might have a member particularly prone to joking and changing the subject, and that can be good if he or she raises morale when everyone is tired of debating. You might have someone who likes cooking for the group, which brings many benefits. Someone might have a great place where you can bring everyone to discuss the book. And, of course, everyone has negative points and you have to deal with that as well. And so on.
Example: I recruited a young man to my research team. I already knew him for some time, and knew that he struggled with a deep depression, that he had a terrible family environment and that, while hard working, he struggled with his grades.
At first, he lagged behind and was a constant drain on my time and resources, which made me reconsider my decision of accepting him on the group. As of now, though, he is our most dedicated researcher and one of the few people I always seek when in doubt about how to manage the group. He is, now, my assistant and most loyal researcher.
You don't need to know everything about the subject, but it's unforgivable if you come across as knowing more than you really do. Set your boundaries, clarify how inexperienced you are. You are an undergraduate and no one should forget that.
Still, you absolutely need to know how to lead a discussion so that people expose their thoughts and experiences. You'll need some charisma for that, and it often helps if you know each member individually, even if superficially.
Example: I am an undergraduate and I lead a research team. One of our members, hierarchically inferior to me, is someone with years of experience in the area. She alone has more publications than everyone else in the group together.
Still, she has never questioned my authority. Because I lead the group well enough, because we work great together, and, mostly, because I know when to shut up. She knows more than I do, so I let her talk without interruptions.
Get to know you book club members. Some will be shier, some more vocal, and that has nothing to do with the quality of their contributions. Learn how to make the shy genius speak, and control the vocal minority who often derails the discussion. Control the debate so that everyone contributes, otherwise you'll be bleeding members after some sessions.
Eventually, every group develops a culture. Respect and cherish it.
Example: On my research team we often organize lectures. Our marketing is often humorous, it's our opportunity to joke about our research. Most of our attendants comment that our relaxed approach to the subject matter was a deciding factor in attending our events.
On the Meeting
Prepare a list of subjects to be discussed and send it to the members some days before the meeting. After the meeting, send a summary of what was discussed and decided.
If the meeting is going for too long, make a short break to drink water, eat something and use the facilities.
Try to make the meeting someplace where you won't be interrupted or bothered. Be there some time before the expected time so you can make sure everything is there (number of chairs and tables, for instance.)
If someone is not taking part in the debate, ask for their opinion on the subject. Try to make everyone participate.

One of the topics not covered by other answers is the importance of food and departmental support. Fortunately they can be one and the same.
I would ask your department chair or director of undergraduate studies if you can have funds to help support your group.
For example, in my department we want undergrads to take these kinds of initiatives and provide a small amount of money to make sure that you guys are well fueled with pizza and soda during these sessions.
US$50/session would not be a terrible burden for most department budget lines but would likely help increase your sense of camaraderie (and perhaps productivity). Happy undergraduate majors attract other students to the major and it's a win:win for everyone.

An alternative format to a book club that is well-suited for what you want to accomplish is that of a reading seminar/reading course. You may even be able to arrange to get credit for it, depending on your department/university.
The organizer of the seminar distributes the content you want to cover to the participants. Each participant is responsible for learning his or her content deeply enough to teach that material to everyone else at the assigned meetings. However, ALL participants are responsible for reading ALL of the material prior to every lecture to gain at least passing familiarity, and their role when not lecturing is to ask questions to the lecturer about anything they don't understand. Solutions to the associated exercises could be discussed immediately after the lecture, or at the beginning of the next meeting, as you prefer. My personal recommendation is to meet multiple times a week, since it's too easy to neglect readings if you only meet once a week or less.
Keep in mind:

The benefit of the lecture is primarily to THE LECTURER. Teaching material to others forces you to internalize it more deeply than simply discussing exercises would. To that end, the lecturer should take the opportunity to learn how to develop simple examples to illustrate and clarify concepts and definitions.
The point of asking questions, beyond learning the material, is to promote discussion, foster a collaborative environment, and, well, to learn how to ask questions. Treat this as a mandatory exercise.

I'm not a CS person, so forgive me if I'm wrong, but a quick look at the table of contents leads me to believe that the content is relatively basic and fundamental. I would expect probably any of your professors to be proficient enough at the material to mentor such a reading course, even if they haven't read this specific book. If a mentor really truly is not a possibility, you may consider having pairs or small teams of participants give each lecture, so no one gets stuck during preparation without having anyone else to talk to about their problems.


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Applying for post-doc, how to mention mutual acquaintances?
I am applying for post-docs, and there is a professor I would very much like to work with. I would like to e-mail him and see if he has any open positions in his lab.
I have never met the professor before, though I am friends with several of his former and current graduate students. I feel like this is an important thing to bring up. What is the best way bring this up in a brief e-mail?

Another possibility is to frame the email using "X suggested I speak with you."  I'm not sure how much difference it makes to the reader, but I certainly find it easier to write emails to people I don't know if I can create a similar context.  It is better if the suggester is someone with higher stature than a current graduate student, though.

@VahidShirbisheh of course i will discuss mutual research interests, i meant in addition to that. i have worked in the same department as his former students, so while we don't have any research projects together we have discussed science ad nauseam. i believe these students are capable of providing a character reference in addition to vouching for my technical expertise

that should be "of course (comma) i will discuss..."; re-reading my comment, it sounds unintentionally brash

Is your interaction with the students purely social or academic ? If the former, then the "X suggested I speak to you" construction is sufficient. If the latter, then you can briefly spell out the connection (one sentence or so)

I'll answer with a view from the other side (I.e. as a recruiting professor). Getting mention of a mutual acquaintance in an application email (or cover letter) is not so common. Most often, I find out about those from reading the CV (former student of mine was PhD advisor, for example) or by getting a separate recommendation (or follow-up) by email directly from our mutual friend.
But, I did recently receive such an application mentioning a common acquaintance, and I must admit it was a nice touch. I definitely will bring up the subject with said acquaintance in the net future, checking for his views on the candidate.
The wording was "light": "I heard a lot of good things about your research group by XXX, who is an officemate in my current group".

Thanks for this response! I think that your sentence construction is perfect, I much prefer it to "X suggested I speak with you" (suggested in the comments). However, beforehand I will see if my friend could alert the professor to my interest, to help him make the connection (assuming he/she can do this is a fairly casual/natural manner).


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Should I list talks on my CV given by co-authors?
On my CV, I have a few talks listed where I was not the presenting author (though I am a co-author on the work).
I have left them on my CV because as a graduate student, my CV is pretty slim. However the work in question was recently published in a journal, which now appears on my CV.
Should I delete all the talks where I was not presenting author? I'm not sure adding length to my CV is really appropriate since the information is fairly redundant (all the same line of research and similar talk titles, just different conferences).

What could the possible justification be to include them? Because the talk was based on your work, which you already get credit for as a publication?

The simple answer is no. You should not list items that you have not performed. In this case it would be listed under "talks" (equivalent) and that would be wrong. On th eother hand it represents work that you have done and as such it can be listed but probably under a different heading. The important thing is that it represents what has actually happened. I can see a heading called, for example, "Other work presented at conferences" and then list the talk and state that you was part of the work but that it was presented by someone else. Again, the importance lies in formatting it so that the actual conditions are very clear.
When the CV is short, I think such additions may make sense, later in a career these posts will lose their importance relative to other headings.

I agree with Peter: unless you're at a very early stage in your career, don't list talks given by others. It clutters your CV, and it looks like you're desperate to lengthen the list (at best), or you're claim credit for others' work (at worst).
However, in this age of scientometrics, you need to keep a list of these things, separate from your CV, as they may be required of you in the future (as I learnt to my misfortune): by your employer, by a funding agency, etc.

I would go further: Even if you are at an early stage in your career, don't list talks given by others. Your CV is supposed to list the things that you have done.

@F'x, I think agreeing (and even your second paragraph) would work better as a comment.

@aparente001 This answer adds some substantial information: That for an early scientists, the things can be different since even working on a project that was presented somewhere (by someone else) is an achievement that can be worth mentioning.

@JeffE I would list these talks under "Local Proceedings", listing all co-authors, not under "Talks", which makes a difference and is not lying anymore.

In general no, but the main issue is that the information in your CV is transparent and accurate. Therefore, you must clearly separate talks where you were the presenting author from those where you were not, so that there is no ambiguity.
To add talks where you were not the presenting author would be largely redundant, especially if the work is included in published articles. However, on a short CV it can make sense, and (to me) it can also be reasonable if you e.g. contributed a lot to producing the actual presentation (writing, constructing graphs, poster layout etc). But as the previous answers state, adding these talks could also be seen as you trying to pad your CV


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Discussing work in progress
I am about to begin my hunt for post-doc positions. As such, I will be discussing my dissertation work in some detail with potential post-doc advisers.
I am currently in the data collection phase, and none of this research has been published. I am somewhat worried because, as a requirement for my PhD, I have to contribute novel research to the field. I hope to submit a part of my dissertation to a conference; however most relevant conferences are not until next summer, and submissions are typically due early next year. In other words, this research will not be published for a while.
Is it appropriate to ask for some discretion when discussing my dissertation with professors who do similar research?

If you're looking for post-doc, you're near completion of your PhD, and thus your results will be published soon, as you will have to write (or have already written) your thesis (and possibly defend it). Or are you in the system where the thesis is not public?

i hope to graduate roughly a year from now, and its been suggested that now is a good time to look for postdocs. writing time for the phd is minimal in my field. where i am, students are not expected to publish their dissertation until after they defend. at that point i hope to already have a post-doc position. my thesis will absolutely be public, but not for another year-ish.

As a converse to this, one could ask whether it is ethical for a researcher to make use of non-public information learned from a job candidate in the context of an interview or application.  I would say "certainly not".

Thanks Nate. So I guess the answer is that it's implied, so I shouldn't have to say anything.

I think the following won't apply to you, but may be useful for people in other fields with the same question.
If you work in a field where putting preprints online is an accepted practice, then write up your work and upload a preprint.  In this way you clearly establish priority without needing to wait for the article to be refereed.
For instance, in Physics, CS, and Math, most researchers put preprints on arXiv.org.

Note this is only applicable once the project is finished. In this question it is still in data collection; much too early even for arXiv.

You are right to be cautious. better safe than sorry. But as Nate said there is an ethical responsibility on the side of the recruiter to keep things you said during the interview confidential. And since you are considering working for him, you surely do not have reason to doubt his honesty, or else you would have ran away!
So: you should speak about your unpublished work and results. Be careful to mention that it is unpublished, though, to be sure they get it and do not mention it inadvertently to someone else.

Is it appropriate to ask for some discretion when discussing my dissertation with professors who do similar research?

Sure, why not. The correct answer is "certainly". If it doesn't come, run away.
On the other hand, to me it sounds extremely early to look for a postdoc job when you do not yet have any publications about dissertation project (and while you are still collecting data).


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Should one apologize in response letters to reviewers? If not, why not?
A student co-author drafted a response letter to the reviewers in which they apologize numerous times.  I found this strange, but I can't pinpoint why.
Question: Should one apologize in response letters to reviewers?  If not, why not?
I'm not sure if this is just my personal feeling, or if there are some underlying, tangible reasons for not apologizing.

Would you clarify what  the student co-author apologized for?

It's a weird habit that is extremely common in my community. I would say one should not (especially since 95% of the time one isn't actually sorry), but it is nevertheless standard to do so.

Here's an example:  "[blah blah blah] should be discussed and evaluated."  "We are very sorry for our negligence..."  (It's a computer science paper, by the way.)

I think it would be very awkward to apologize in this way.  The correspondence should be purely professional.

Never apologize for anything.  It's everybody else's fault!

What culture does this student hail from?  Some cultures are very apologetic, and consider it proper manners to be effusively apologetic.

Definitely a cultural thing. In some cultures you apologize for everything, in others you say "thank you" for everything, in others you reply bluntly.

My rule of thumb, generally in life as much as any specific aspect of it, don't apologize for something you haven't done wrong. This is of course highly debatable but an apology is a formal acceptance of a mistake made, not a figure of speech to be polite. So I'd say don't apologize for something if you don't believe you "f*ed something up".
It does have a cultural component however, as a British friend of mine once put it:

buying a bag of crisps in England involves 4 "Excuse me"s, 7 "Sorry"s
  and numerous "thank you"s.

In this scenario specifically, I think it'd be an insincere apology, and might even be taken as mockery to apologize in response of a comment made by a reviewer. I'd rather advocate for a respectful and appreciative response, something like:

Re: "[blah blah blah] should be discussed and evaluated."
We would like to thank the reviewer for pointing out the lacking
  discussion on [blah blah blah], this has been added in the revised
  version of the manuscript, see page X, paragraph Y.

or, if you disagree with the reviewer about that particular comment because it's not missing

Re: "[blah blah blah] should be discussed and evaluated."
We would like to thank the reviewer for pointing out the lacking
  discussion on [blah blah blah], however this topic has been covered in page X, paragraph Y.

OR, if you disagree with the reviewer about that particular comment because it's not necessary

Re: "[blah blah blah] should be discussed and evaluated."
We would like to thank the reviewer for pointing out the lacking
  discussion on [blah blah blah], this topic has been omitted because reasons A,B and C.

Of course these examples are grossly simplified and generalized, usually a bit more context regarding the proposed changes would be appropriate to give in the response. Remember the response is aimed primarily at the editor, not the reviewer. If you can convince the editor, you might even bypass a second iteration to the reviewer.

I would add to the point about doing something wrong also that if I have caused in inconvenience to the Editor or other persons involved I would apologize

@arkiaamu I'd say if you have actually caused any serious inconvenience to the editor, you'd be rejected straight off the bat. But that's an opinion more than a fact.

I do not understand how thanking the reviewer for something that you do not feel thankful for (pointing an omissions which is not actually an omission, etc) is better than apologizing for something that you are not sorry for.

@BorisBukh good point, however you can angle it like this, you can be thanking for the attention they have given to manuscript and the comments to make it a better. You don't necessarily need to say "well, thank you for your useless comment" :)

I do not suggest to be rude. No commentary is best in this case.

I agree with this answer as modified by the comment from @BorisBukh.  Apologize if you're actually sorry; thank the reviewer if you're actually grateful; and otherwise just explain what you did (or didn't do) in revising your manuscript.

I agree with Boris.  A single "Thank you" at either end of the response letter is sufficient, if and only if you truly feel thankful.  Otherwise, respond directly.  For example: [blah blah blah] should be discussed — This topic is covered on page X, paragraph Y.

But you should consider that written word in E-Mails don't convey tone as good as speaking to someone. I've read that in many cases a written mail will be received a lot harsher in tone than intended by the writer (and can easily be misinterpreted) - so you should usually write your email a lot nicer and with more politeness than a normal conversation. So an additional thank you doesn't hurt at all.

I think there is an important distinction to be made between acknowledging mistakes and apologizing.
Reviewers often notice genuine problems with our work, and I think that it is entirely appropriate to acknowledge the mistakes that we have made and to express (genuine!) gratitude to a reviewer for pointing out the problem.  For example:

Whoops - you're right, figure 3's legend and caption don't match.  Apparently, we forgot to update the caption when we changed the figure presentation. Thanks for the catch; it's now fixed.

Apology, however, should be reserved for the places where one has actually caused problems and/or pain for a reviewer (as opposed to just problems for one's own science).  For example:

We are sorry that our original description of the method was apparently so difficult to understand.  We have revised and clarified and believe that it should be much more intelligible now.

Given this, I find that gratitude is frequently appropriate, while apology is sometimes (but rarely) appropriate.

We are sorry that our original description of the method was apparently in some way we find difficult to understand so difficult to understand.

@Michael Yeah, that's not apology territory. But I've certainly had times where I agree with the reviewer, as I come to realize something was written with way too many assumptions about reader knowledge.

Ah, I may have misread the intent of the second statement to suggest that sometimes "apologies" are less than sincere due to the writer of said apology not really understand why they need / are supposed to be apologizing.

"I apologize for failing to explain clearly enough why we found your description of how our original description was difficult to understand so difficult to understand."

That you are writing back to the journal suggests you got an "accept with revisions" or "revise and resubmit" response.  You are writing to the editor, not the reviewers.  I would suggest an overall appreciation to the reviewers for their time and attention (reviewing papers takes a lot of time):  "We offer our thanks to the reviewers for their suggestions and corrections.  A list of revisions follows," and then do a list coded to page number or section.  Don't apologize, unless one of the criticisms was that your proofreading wasn't good and you had errors throughout the paper.  That kind of inattention drives reviewers nuts and it's worth acknowledging that you could/should have done that better.
An editor doesn't want to wade through a lot of blah-blah apology stuff.  S/he wants to know whether you've improved the paper enough to make it acceptable.  Get to that point.


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How many times should one proofread their paper before submission?
When I did my PhD in mathematics, I would proofread my papers maybe 10 times before submission.  Moving into computer science has changed my attitude, since reviewers frequently ask for major revisions (regardless of how careful I am).  Now also pragmatic matters (e.g. not having enough time before conference deadlines) enters into things.
I'm fairly sure 0 is not an appropriate number of times to proofread one's paper, but I'm not sure how many times suffices.  I don't know what is "normal" when it comes to the number of times one should proofread their paper.
Question: How many times should one proofread their paper before submission?

π, e, or maybe φ.

There is no global maximum.

There is no global constant q such that more than q proofreads are required. It depends on your writing style, the topic, your mood and many many other factors.
A comment though: In my experience, no matter how many times you personally proofread the paper, there are cases where it is not enough and you need a second or a third person to proofread your paper to catch mistakes for which you have a blind spot (i.e., no matter how many times you read you won't be able to catch the subtle mistakes and this is more true if you are not native english speaker or you are younger researcher.)

Too add, you may want to (i) leave the paper alone for a few days before coming back to it, (ii) read the paper from back to front, (iii) read it aloud, (iv) print it and comb through it line by line, and/or (v) start reading from random paragraphs.   These will help you identify blind spots.

@Prof.SantaClaus Good points and they definitely help. But in my experience there would still be some things that only a 2nd pair of eye would catch.


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How to be effective at desk research
I have just graduated from a masters degree in information systems, and I'm due to begin a role at a large IT consultancy firm in 6 months time.
For the interim I have arranged a period of desk research with one of my old professors. I cannot go into specifics but to give you a taster my research will be around small/medium IT firm strategies.
I will of course receive direction from my professor on the detail, but some general advice for someone wanting to shift into an appropriate mindset for being effective at desk research would be very helpful.
What strategies would you use to tackle a desk research role?

What do you call “desk research”? I can imagine, but maybe you'd rather be explicit about it…

I need to find answers/insights to two main topics, and I will be able to use specific databases and the wider internet to do so

Sounds like you're doing a literature review on two topics in management strategy.  I assume you've been trained to conduct research from your Masters.  Grab a (post-graduate) textbook on business research methods and go forth and conduct your literature review.  Given you're planning on using publicly available documentation it sounds like a "discourse analysis" of "business strategy."  You may want a (post-graduate) textbook on social science discourse analysis.

Set clear objectives and deadlines as early as possible to force yourself into a practical mindset. Don't do it for your supervisor, do it for yourself. Try to funnel your thoughts and ideas into a confined key focus point .
This prevents you from procrastinating (which I consider to be a big threat in desk research).

So, if what I get from my supervisor are a couple of major topics (the main 2 objectives), would you advise the objectives I develop are answering sub-questions to that?


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How to cite Nature's "Supplementary Information" papers?
In one of my works I cite several times this kind of publications, but I don't know the recommended procedure to refer to them at the end. For articles I usually take bibtex code from Google Scholar or a similar site, but these papers do not figure there. I'm not sure even whether the best writing practice is to cite them or just to cite the main article, when referring to some specific information that is not published in this main article.

Supplementary information is always part of a paper. Just cite that paper as you would normally do. If you want to specifically mention in your text that you are referring to supplementary information you can just call it by its title, something like "(Supplementary Figure 2)".


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What constitutes a declarable conflict of interest in gender studies?
From Wikipedia:

A conflict of interest (COI) is a situation in which a person or organization is involved in multiple interests, financial interest, or otherwise, one of which could possibly corrupt the motivation of the individual or organization.

Question: In the context of gender studies, what constitutes a declarable conflict of interest in gender studies?
As some hypothetical examples:

A woman scientist is writing about male violence against women, and is herself a victim of such violence.
An LGBT person is writing about an LGBT topic.

In both cases, the work will likely be influenced to some degree by the author's personal experience, i.e., one could argue that there is a conflict of interest.  However, it seems unreasonable to insist that a victim of violence declare the fact.  Similarly, it seems unreasonable for an LGBT person to declare their LGBT status, and possibly face discrimination as a result.
In these scenarios, there's a conflict of interest in declaring a possible conflict of interest.

A bias does not imply conflict of interest; though conflict of interest usually implies bias.

"A study of average heights of males in Swahili. Disclaimer: Author is male."

Usually, these relationships are financial.
For example:

In a paper talking about how Twitter has failed to police harassment, a professor who's an investor in an early-stage social network competitor would have to declare that.
Similarly, board memberships, speaking gigs, etc. are things that would have to be declared. For example, while writing a paper about abortion access rights, a professor should disclose if she was a paid speaker for a pro-choice advocacy group.

Generally, "I really care about this" for personal reasons doesn't so much count as a conflict of interest. I cannot imagine, for example, a journal intending for those writing in gender studies to disclose if they had been victims of intimate partner violence.

+1.  More generally, I would say the question is whether the author stands to receive a tangible gain from the work, and that usually means money.  Intangible gains like personal satisfaction, increased attention to a demographic group, etc, are beyond the scope.

In addition to being conflicted by people who pay you, you're also usually conflicted with immediate family and current or former romantic partners, or with anyone who those people have a financial relationship.

Thanks.  Judging from the votes, this seems to be the consensus.

@NateEldredge: I would argue that publishing is tangible gain and therefore, we need to refine what we mean by "gain" in this context.

Trying to think of a strong edge case for demographics disclosures: if you're part of a very small group on which you're doing research, say you're studying residents of your own Island and come to the conclusion that they're statistically ridiculously honest, skilled, smart and are fantastic lovers compared to the general population.... should you mention that you're talking about yourself and your own ingroup and or highschool friends even if you don't stand to gain financially directly.

disclosure: I am passionately in favor of this topic.

Note that financial gain can be potential, not necessarily actual, as in the Twitter example.  Further, it can be "second order" potential gain.  The professor in the Twitter example need not be the investor; it could be the professor's partner/spouse/parent/etc.

Another good example would be policemen. (it's often seen in police shows) They're not allowed to work on cases where they (or close relatives) are involved because it could impair their work/judgement. No money involved here though.

As a matter of nomenclature, I would say that a conflict of interest is related to material gain (aka financial gains) that hinge on the results of your work going a certain way. @Fomite does a good job of describing this.
What you're talking about is probably better described as bias. All researchers have some bias for their own work, this is normal and expected. For example, at the low-end you have "I spent two years on this work and don't want it to go to waste", and at the high end you have "I have a deep personal connection to this work" or even "I really think this is the right theory, even if I can't quite find the right evidence to support it". Having a strong connection to your work is a good thing! As long as it doesn't affect your objectivity...
Conflicts of interest are easy to identify and disclose (do you own shares of a competing company? Yes / No?), while biases are more subjective and much harder to spot - and in many cases would be silly or a violation of personal privacy to declare. Good researchers / authors are expected to recognize and control their own bias in their writing, but sometimes it leaks through and this is where editorial review and critical reading come in - don't take everything in a paper at face value!

I think you hit the nail on the head. Bias can affect how we interpret results, but is usually not (expected to be) declared.

How would bias not influence results in the exact same way as financial gain? A good researcher/author should be equally able to recognize and control their "conflicts of interest". I think it is probably even far easier to control and be more objective in that case than when the person has a personal bias. I actually think it is close to impossible for a person to ignore their personal bias and present "fair" evidence against their bias because then they'd probably not have the bias. OTOH it is quite easy to be fair and ignore potential financial gain, if the person so chooses.

@Drunk yeah, I think the point is that in the case of "you will lose your funding if you publish a negative result about us" the researcher doesn't want to ignore their conflict of interest.

You are confused between a conflict of interest and bias.  A conflict of interest is when it is in your personal best interest if the results are interpreted in a particular way, regardless of whether that way is correct or not or supported by the data you have gathered.  As others have said, that is most frequently financial, but there are other *consididerations.  Bias is more or less having an opinion.
What would non-financial conflict of interest be?  Say you were doing a study on recidivism rates of convicts that earn degrees while in prison, at the same time you were about to come up for parole...clearly it is better for you personally for people to believe that you are safe to let out.
Bias would be if your childhood best friend was studying for his degree, while you do the above study -- you may unintentionaly bias the data in favor of convict-students, but presumably there's no danger of you deliberately corrupting the data to get the result you want.
You are expected to recognize your own biases and guard against them unduly influencing your results.  Bias is too pervasive and too nebulous to require reporting, there is simply no end to the things that could conceivably cause you to lean one way or another when gathering and interpreting the data.
A conflict of interest is much more concrete, and you are required to disclose a potential conflict of interest so others can judge whether you are cooking the books and/or are likely to be doing so.  If you don't disclose, and the conflict is discovered, the assumption is going to be that you were.

Not directly financial conflict of interest: Is it ethically justifiable to conceal a fatal conceptual flaw in a thesis to avoid an unaffordable 2-year setback if the flaw is the advisor's fault?

Mere influence of personal experience on a topic is not enough to constitute a conflict of interest; if it was then arguably every belief on everything would be a conflict of interest.  Conflicts of interest generally occur when there is some direct causal connection between a cause one is pursuing and some personal benefit; something more direct than a mere influence on a general topic or idea.  Thus, a woman who has been a victim of male violence would not generally be considered to have a conflict of interest when writing about the general topic of male violence, but she might be considered to have a conflict of interest if she were writing directly about a police matter or court case she is involved in (e.g., a journalist writing about a court case where she is a witness or alleged victim).  In the latter case the conflict should be declared in the interests of informing the reader.
When dealing with topics like gender research, it is notable that everyone is in some category that may have an interest in general outcomes of the research.  As a general rule, if a purported source of bias would apply to everyone then it is probably not something that needs to be declared.  For example, if being female is a purported source of bias when writing on gender theory, then presumably so is being male.  Similarly, if being LGBT is a possible source of bias when writing on LGBT issues, then presumably so it not being LGBT.  In such a case, it seems unlikely that every author should have to declare their gender/sexual preferences merely because every possible category might have some indirect interest in the cultural outcomes of the matter.

As others have said, the conflict of interest is about money.
But also we should not pretend that there is no difference
between studies measuring height of people and studies measuring,
for example children well-being in LGBT parenting.
Any result of height measuring is probably not going to affect
social organisation of countries, etc.
I will stick to this example, because I made some preliminary studies
into LGBT parenting research methodology (disclaimer: I'm not a social
sciences/psychology researcher).
LGBT communities have certain goals that they want to achieve.
For example, many of them want LGBT parenting to be universally accepted,
which is currently not the case.
So, in my opinion, it constitutes a conflict of interest if they
financially support research into LGBT parenting. For example,
as we can read in CV of David Brodzinsky, he received 20000$
from organisation Rainbow Endowment (which promotes LGBT agenda).
In my opinion, this constitutes a conflict of interest, which extends
not only on the research programme that was directly financed by
the organisation.
You could argue, that you can always analyse the methodology,
to ensure it is proper and the studies are not biased. If you look
into 71 abstracts of positive articles listed here (I haven't analysed
3 newly added), you can see that they have many faults,
for example researchers use convenience samples (lesbian researchers
look for other lesbians to be objects of their study in their own,
well-educated, wealthy community), strange variables being analysed
(flexible view on sexuality as an indicator of a child well-being),
etc. I haven't yet found a single study that contained no methodology flaws
(based on abstracts that describe methodology).

Unfortunately you've asked right in the middle of the gray area.  For most publications and journals the conflict of interest has to be one which directly benefits the researcher in a financial or similar way. For instance receiving a job offer or being paid to do the research by the company producing the product under research.  Note that these might not invalidate the research - but the conflict must be clearly stated so the reader can take it into account.
Within social sciences, however, the conflicts may become a little more subtle.
When in doubt, consult with your ethics board and the journal you plan to publish with.  Reputable journals require a signed statement that includes wording about conflicts of interest such as

any real or apparent conflicting or competing interest is clearly stated on submission of their paper (this would include funding assistance) (source)

As you can see this is still quite ambiguous, and the responsibility belongs to the author to disclose any potential conflicts of interest.  When in doubt, including such a statement per the journal's guidelines will give the journal the ability to make that determination themselves.
Do note that many, many social science research papers are authored by people that are close to the subject.  For instance many male researchers study male violence, many women who are mothers study the impact of motherhood on children.  It's natural to study those things that affect us personally.
Being a possible part of the group you're studying doesn't indicate a conflict of interest, but in the interest of transparency it's worth mentioning even possible conflicts of interest.

Interesting - two downvotes.  One might be just a drive by, but the second suggests something is wrong with this answer.  I'm open to suggestions and edits - consider improving the answer or leaving comments pointing out weaknesses in the answer in addition to your downvote.


text:
What is an example of a journal based in China which "warns authors that they are not affiliated with any paper-selling companies"?
Regarding the following quote:

... editors say an increasing number of journals based in China warn authors that they are not affiliated with any paper-selling companies.
Mara Hvistendahl, China's Publication Bazaar, Science, 2013.

Partly out of curiosity and partly because I work in China, I'm interested in finding a concrete example of this.
Question : What is an example of a journal based in China which "warns authors that they are not affiliated with any paper-selling companies"?
Ideally, I'd like a web link to a journal based in China showing this warning.  Or perhaps someone received such a warning in an email as part of communications with a journal.

Have you tried asking around colleagues in China? Usually Chinese journals work chiefly in Chinese, getting submissions of local authors.

What is a "paper-selling company"? Is that like a paper mill?

Is a "paper-selling company" a company that churns out academic writing (e.g. like an essay mill), or is it a company that literally sells physical paper?

@einpoklum While working as a postdoc in China, I have noticed two interesting phenomena: (i) some service-providing companies (e.g. genome sequencing) for academics would offer data-analysis packets that could go anywhere from providing stats to full-blown results description and discussions; (ii) a few colleagues who definitely displayed poor writing and reasoning skills would often come up fair & sound manuscripts out of the blue. I strongly suspect there are companies in China selling seemingly-acceptable manuscript-material.


text:
Does a journal retracting a paper also renounce copyright?
Every now and then, a journal retracts a paper for some reason or another.  I'm wondering what impact retraction has on copyright, assuming the journal (or its publisher) was given its copyright.
Question: Does a journal retracting a paper also renounce copyright?
The notion of "retracting" a paper implies "we don't want it" to some extent (particularly if it is a journal-initiated retraction), which I feel may be interpreted as renouncing copyright altogether.

In general (i.e. when considering non-US jurisdictions), copyright may not even be possible to renounce.  Take Germany for example.

@BenCrowell I don't think it is, because publishers still distribute retracted papers - often behind the usual paywalls.

@Kevin It’s more subtle than that because the concept of copyright does not map directly to German law: Urheberrecht (= authorship) cannot be renounced or transferred, but the journal doesn’t have that in any case; it merely has exclusive or non-exclusive publication rights. And the journal is entirely within its right to renounce its publication rights.

Technically there is also the strange case of plagiarism. Say Bob copies Alice's work and submits it und his own name. If he is found out after acceptance, the journal will have to retract it, but has no copyright to renounce in the first place, since Alice never transferred any to them...

You can, of course, as the author, request that the copyrights be returned to you. Such a request might be granted, or not.

Good question. As far as I can tell, the answer is "no" and the journal retracting the paper still retains copyright (if it was given the copyright in the first place).
Here're some retraction policies: one, two, three. Although the question you ask is not discussed, two things can be noted:

Even if a paper is retracted, the publisher still distributes it (as in, it's still available from the journal's website). What changes is that the publisher makes it clear that the article is retracted.
The publisher only stops distributing the paper if they are legally obliged to do so (e.g. if the copyright is actually held by someone other than the authors, and the authors had no legal standing to sign the copyright to the publisher).

Since the publisher needs the copyright (or permission from the copyright holder) to distribute the paper, the logical answer is "no".

Quick clarification on the last sentence. The publisher needs the copyright or authorization from the party who has it. (This is why some publishers can get away with not taking copyright in the first place. As part of the submission process you sign agreements to give them the rights to distribute.)

The publisher absolutely does not need the copyright to distribute the paper. They merely need the permission of the copyright holder, which is much easier if that means "they merely need their own permission."

@DavidRicherby Absolutely correct, though its noteworthy that type of permission is almost always referred to as a license.

Not automatically. Assuming this is a journal where authors assign them copyright, then the author has signed over the copyright and the article "belongs" to the publisher now. Whether they choose to publish it, retract it, or make and market paper aeroplanes from it is none of the author's concern.
However, copyright transfer agreements sometimes (usually?) have a clause stating that if the journal doesn't publish it, copyright will revert to the author. I'm not sure whether that would apply in the event of a retraction, but the only way to tell would be to check the wording of that agreement.
Disclaimer: IANAL, and this is not legal advice.

In general, no, but there is a lot of nuance to the question.
First, you did not specify your jurisdiction. While many international treaties provide a degree of uniformity to copyright questions, there are significant differences between jurisdictions. For example, the U.S. is notorious for having very limited and weak "Moral Rights" while they are quite strong and significant in Canada. I am not actually aware of any differences in any jurisdiction that will make the answer to this question differ, but I cannot guarantee they do not exist. The best advice is that if you face this question in a way that will have real consequences, you should consult a qualified attorney in the jurisdiction in question
With that said, nothing about retraction inherently relinquishes copyrights. In fact, under most circumstances, the copyright holder may elect to not publish something while still forbidding any others from publishing. In other words, a copyright holder may choose to use copyright to prevent any publication.
However, this ultimately comes down to the contracts and specific statements involved. While I haven't ever seen this happen, a publisher could elect to disavow copyright (or release to the public domain) at the same time as they retract.
Its also possible that the publication never held the copyright at all, but only held a license to distribute. This is in fact what I granted with my last publication rather than a transfer of the copyright.
Even if the copyright is transferred to the publishers, there may be a clause that transfers it back if it is not published within the specified time or is withdrawn within that time (2 years is common).
TLDR: Retraction does not by itself change the copyright and it is likely the publisher either continues to retain the copyright or an exclusive license to the article. But that is a rule of thumb rather than an absolute and you will have to evaluate the circumstances around any particular article individually.

+1; I've taken the liberty to correct what looked like typos.