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Can the communicating author remove some of the authors (4 out of 6) when submitting the second revision of a paper describing a database?
Our paper was due submission for second revision at a BMC journal. The communicating author, as I understand is responsible for handling all the communications between all authors and the journal, while also making suitable arrangement to cover any open access charges.
However, the communicating author in our case, without informing any author, removed 4 out of the total 6 authors while submitting the second revision. How should we deal with this? isn't it a academic fraud by the communicating author? Can't we, as students do anything to stop this?

Have you verified that this is something the communicating author has deliberately chosen to do, rather than an error or accidental omission at some point in the submission/production process?

Yes. This is an deliberate act, since she mentioned us all in the acknowledgement when she sent out the 2nd revision of the paper. Earlier, she had even asked us to raise money to cover open access publication charges too.

That sounds ... bad. Especially on this scale (4 out of 6 authors?).

Yes. What can(should) we do about it?

Two other relevant pieces of information: do you (honestly) believe that you deserve to be authors (i.e. did you make significant contributions to the research)? And is this person your supervisor/advisor?

Yes, we all worked as much as the other author included in the authors now. We all did data curation, designed the database and help write the manuscript. 3 of us have passed out from the university. She was the project PI and also served as the supervisor/advisor for 2 of us, while still supervising the fourth masters student. The project was submitted as part of the author's(other than her) minor project during his bachelors. We had been authors in the initial submission and even after submitting the first revision.

Why do you assume it is a deliberate act? Maybe I missed something, but from what you say, it could be a technical error of leaving out names on the author list?

She added us in the acknowledgement after removing from the author list. So, it can't be a technical error.

Have you received an email from the first submission process that lists you as author. If yes, this is the only evidence you need.

@Alexandros I think someone in this situation also needs to be prepared to demonstrate that they did deserve to be an author of this paper. The fact that they were included on the first draft points strongly in their favour, but is not necessarily conclusive. That is, whilst the email you mention is important evidence, I don't think it's necessarily the full picture.

@avid. I agree. The more proof the better. But initially the "bad" author considered them co-authors and then changed his mind (removed them from 2nd draft) is a very strong indication of malpractice. And the initial notification mail might prove it.

Perhaps you and the others were marginal contributors, but after this paper's second revision, you cannot legitimately claim your contribution was great enough to claim co-authorship compared to 1) the advisor who shepherded the paper over its lifetime, and 2) the student who originated the idea/paper/data. It may be that the journal wants to reduce author inflation, and told the advisor to remove the lesser contributors. The advisor may have been remiss in not communicating the matter directly to you, but perhaps you were lucky to be listed as co-author the first time around.

Also consider the possibility that, for once, the journal editor or the reviewers asked about the specific contributions of all the authors and found that some didn't deserve authorship by the journal's standards and should instead be acknowledged. Pure speculation of course.

@Jigg If that were the case, the corresponding author would have informed the other authors about that, BEFORE doing this. And that did not happen. We can all pretend that there is some magical reason for this strange behavior but authors should not "evaporate" between 1st and 2nd submission.

@Alexandros you're right, the probabilities of the first author being an arse are probably much, much higher than an editorial process detecting a case of ghost authorship.

I'd expect the editor to notice the disappearance of the majority of the authors and to ask the corresponding author what's going on.

@All, thank you for the helpful suggestions and the discussions.
Like I said earlier, Yes, we did contribute significantly and the 2nd revision wasn't a major change and nevertheless, we have contributed throughout the revision process. Yes, we did receive an email from the editor on our initial submission.
Had there been any information from the editors or reviewers, we must be aware of that, since we have the mail regarding reviewer comments forwarded by the first author, who in turn got it from the corresponding author.

What did the communicating author say, when you asked what the reason for removal was?

She ain't replying to our mails. And, over the telephone she is being too arrogant and isn't saying anything clearly but just that she might reconsider it when the paper comes for proof-reading.

This sounds like an unpleasant situation.
If this happened to me, I think my starting point would be to ensure I had copies of anything that might be useful as evidence. Then, I would write (formally) to the person concerned, asking for an explanation of why they thought it appropriate to remove you all from the author list. I think this has to be the first step: it is always possible that there is a rational explanation (although it's difficult to imagine what it might be). You might choose to copy the letter to the head of the relevant university department, and perhaps to the editor of the journal - particularly if the paper has not yet been published, and so can be put 'on hold' pending resolution of the authorship dispute.
Of course, you will have to weigh up the benefits of asserting your rights to authorship against any potential cost arising from 'causing trouble'. You are completely within your rights to create a major fuss here, and your department should be entirely supportive. I think you should do something. However, there is a risk that some of the people involved will seek revenge, if they have any power over you (e.g. if you are still a student at the university). I am absolutely not condoning such behaviour - it is quite clearly bullying, and an abuse of power. However, it would be irresponsible to advocate taking action without encouraging you to also consider whether there are any potential adverse consequences.

We recently had an extensive discussion of how to deal with such an issue, should it arise, in a postdoctoral seminar I attended. A number of senior faculty contributed their ideas regarding how to deal with such an incident.
I would recommend a more gradual escalation than others have suggested. For example, I would not copy the editor of the journal or the head of the department on your initial communication requesting more information. I would start with communication just within your author group: for example, an email to the corresponding author asking for an explanation of why they removed your (and others) authorship without notification, CCing all other authors of the paper. This gives you a paper trail but also allows you to first address the issue without airing everyone's dirty laundry.
If the corresponding author's response is not to the removed authors' satisfaction, you should then, together, think about escalating your complaint (for example, by contacting the editor). I agree with avid that while you would be in your rights to do so, there is a very real possibility of a negative backlash. I think as a consequence the other dropped authors should be on board with such a decision, and you should have excellent documentation of your complaint.
Finally, this type of incident is a very good example of why every paper should start with an authorship meeting where everyone sits down, agrees on authorship and order, and what constitutes the responsibilities of authorship at each level (e.g., "first author will be so-and-so, and that means her responsibilities are to do x,y,z...and if she finds herself unable to meet all of those responsibilities, then authorship decisions will need to be revisited", etc.) Concretizing expectations prior to the work tends to lead to better working relationships and can prevent some very bitter arguments.

I see your point, but I think there is something to be gained by having an uninvolved third party cc'd as a "witness" to the initial communication. If there is malicious intent involved, which seems at least plausible, once the author who removed the other authors' names realizes they intend to assert their right to authorship, he/she may attempt to get the journal editor on his/her side preemptively, and it's good to have someone who can assert that this was done in response to e.g. an email.

I say yes, this is academic fraud. I suggest to contact the corresponding author and inform him/her that your are going to inform the editor of the journal about the issue. Depending on the answer from the corresponding author you should indeed write to the editor and explain the case.
However, I am not sure what will happen then. Presumably things will get difficult and it would be much better if you could sort this out directly. Also you should communicate your strategy with the other authors and act open for all involved people.

Threatening as a first communication is a bad idea, makes people uncooperative. It is better to ask nicely, and pretend to be understanding, just in case it actually works.

The initial reaction to your problem is that it is wrong. There are, too many unknowns to say why this has happened, if you are deadling with negligence, absent mindedness, some more serious personality issue or whatever. I would suggest the following

Discuss with the other authors how you all became co-authors in the first place and compare your contributions to see if they fulfil some basic critteria such as those of the Vancouver Protocol (given by for example ICMJE and reproduced at Resources for Research Ethics Education. This will help you gain leverage for your authorship/contributorship. Of course, if you had some form of agreement to start with, then that should suffice. The important thing is that it is unethical to publish someone else's intellectual property without consent so establishing such claims can be important. This is why authorship or contributorship agreements should follow the Vancouver Protocol to begin with (I know they rarely do).
Approach the first author and ask him/her to explain the reduction in authors without prior discussion.
If 2 fails to yield results, write to the chief editor of the journal and describe the problem and that you wish to see the paper stopped. If the paper contains materials that can be attributed to the authors who have been dropped, that should be grounds for halting the process and starting an investigation, perhaps through COPE.

I'm assuming that by BMC you mean a BioMed journal?  You should read the BioMed Editorial Policies page( http://www.biomedcentral.com/about/editorialpolicies )
which lists 4 requirements for qualifying as an author:

to qualify as an author one should have:
(1) made substantial contributions to conception and design, or acquisition of data, or analysis and interpretation of data;
(2) been involved in drafting the manuscript or revising it critically for important intellectual content;
(3) given final approval of the version to be published. Each author should have participated sufficiently in the work to take public responsibility for appropriate portions of the content; and
(4) agreed to be accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved.
Acquisition of funding, collection of data, or general supervision of the research group, alone, does not usually justify authorship.

So if you can satisfy these criteria (especially the first two), you should be an author.
The same page also addresses authorship changes:

In line with COPE guidelines, BioMed Central requires written confirmation from all authors that they agree with any proposed changes in authorship of submitted manuscripts or published articles. This confirmation must be via direct email from each author. It is the corresponding author’s responsibility to ensure that all authors confirm that they agree with the proposed changes. If there is disagreement amongst the authors concerning authorship and a satisfactory agreement cannot be reached, the authors must contact their institution(s) for a resolution. It is not the Editor’s responsibility to resolve authorship disputes.

So you need to deal with this in your institution; pointing out that is contrary to journal policy for authorship to change without consultation is a good place to start.

The PI din't acquire funds, neither collected any data, but provided general supervision of the group. So, can she be denied authorship? Yes, we collected the data, designed the database schema and the relational database, made the interface and provided inputs towards finalizing the manuscript. I believe we do fulfill the criteria to be authors.


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Is it hard to get an article published in a journal as an undergraduate?
I'm an undergrad and I would like to publish in a research journal, specifically, ones about chemical pedagogy.
Is it hard to get an article published in a journal?
Are there any other venues which may be easier - i.e. do you know of any say magazines on chemical pedagogy or aimed toward chemistry educators? I'd imagine that the standards for publication in a magazine are lower than in a scientific journal.
Any advice for a beginner at writing and publishing?

Related: Assume an undergrad has something worth publishing: how might (s)he get it published

Thanks. I like to assume that what I have is worth publishing ;). We'll see how well that assumption holds up.

Is it hard to get an article published in a journal? — Well, that depends on the article, doesn't it?

Most articles outline new/original research using new/original data and some sort of experiment and statistics. Did you do anything of the sort, or is it more of a review?

@JeffE: ...and the journal. :-)

@Dissenter: "I like to assume [it] is worth publishing." From what I have seen on (mathematics) forums, many amateurs are overconfindent on the interest of the work. As others pointed, you should ask a professor to evaluate your work. Journals are amazingly specialized these days and the experience of a professor would help a lot to link you to the good journal. Another good test is the bibliography: try to write it on your own and compare to profesional articles. Most articles I mentioned above had a very poor bibliography (if any): Wikipedia is not enough for a research level article.

@Dissenter The main journal for chemical pedagogy is *J. Chem. Ed. and while they do accept publications from undergrads (and I'm sure would be happy to review it), as others have said, you may want help of a faculty member to submit. I expect you could find some on Chem.SE.

I would imagine that your best bet is to talk to a faculty member about it. Find a faculty member who is also interested in the topic. They can probably give you good advice on this and may even be interested in co-authoring the paper with you (which is probably more realistic as an undergrad), and honestly going this route wouldn't be too bad for you since your name would then be associated with an expert on the subject, giving you more credibility.
One thing I've learned in college is that if you have an idea, talking to a faculty member about it can get you a lot of opportunities. And if you talk to someone and they can't help you, they can almost always refer you to someone else who can be of help.

Depends on the journal. You might want to try publishing in your university's undergraduate journal if you don't have backing from a faculty member.
[For an example of a university-specific undergraduate journal, click here.]

"your university's undergraduate journal" What's that?

How is backing from a faculty member relevant?

Having support from a faculty member is relevant because, even if you are a good writer, writing a journal article is a difficult skill to learn on your own. The faculty member can help you learn this skill.

example of undergraduate journal: http://thurj.org/

@David: That's a good answer, thanks.  (I was a graduate student at Harvard not so terribly long ago, but the journal did not exist then.)  I think that if you're not fortunate enough to go to Harvard it is less than likely that your university has an undergraduate journal of its own...but this may no longer be true X years from now.  I took the liberty of editing the link into your answer -- I hope you don't mind.  Doing so also allowed me to reverse my downvote.

@Pete: The Harvard of the South also has its own undergraduate journal: http://juro.uga.edu

@TK Duke has an undergraduate journal?  :) Anyway, I am a little embarrassed by not knowing about your link, but I would be much more embarrassed if I had made the comment in 2010.

If you ask questions "Is it hard to get an article published in a journal?", about journals and in general "Any advice for a beginner at writing and publishing?", etc. then  it is very unlikely you will publish something in a reputable journal, based only on a few lines of advice via Internet.
However:

try looking at student's conferences; very often there are great places to share undergraduate work, and learn how to present results (via posters, talks, sometimes - conference proceedings),
ask someone from your university to look at your work, and guide you through the first publication (a lot of work, but worth it); but since it's chemistry you do it in someone's lab, right?

Yes, it is hard to publish in a peer reviewed journal.
If it were easy anybody and everybody would do it. That should not prevent you from trying.
Typically a magazine is easier to publish in. The real question you need to ask yourself is "Who is my target audience?" The general public? Or experts in the field? If the general public, a magazine might be the best choice.

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What should I put in the introduction chapter of my thesis?
I have to start writing my thesis. My topic for research is work life balance in IT sector - a comparative analysis of male & female IT professionals in Pune.
I need help in writing the first introduction chapter. what all should be included in this chapter & what should not?

Why are you writing the introduction chapter first? Write it later, once you've worked out what it is you're introducing.

then which chapter should i start with?please suggest

Either Literature Review or Method(s/ology). Or maybe both, in tandem.

then which chapter should i start with — The one that you are closest to having already written in your head.  Alternatively: pick one at random and just start.

Talk to your advisor and look into student services provided by your university.  The department should have pretty clear guidance on document structure and format.  You will also learn a lot by reading some of the dissertations of previous (successful) candidates.

+1 for reading older theses. Even better would be to read a few of the theses from past students of your parimary adivsor to get a feel for what specific format s/he likes.

An introduction should funnel the reader from the wider perspective, in which your study is part, to the formulation of your thesis theme or question(s). This means you need to establish the wider perspective where your work improves our knowledge as well as identifying the gap in knowledge where your work attempts solution(s). In terms of writing this can be accomplished in several ways, although similar content-wise.
In a short research paper you start out by writing about the wider perspective leading into identification of and statements about a gap of knowledge where your paper fits. You follow up by reviewing the literature to establish what is known in detail and perhaps highlighting the identified gaps. You may finish off by recapping your work and the main conclusion to the gap(s) identified earlier. Some prefer not to do so in the introduction; a matter of taste or tradition.
You can write your introduction in the way just described as a long chapter (due to the literature review) but you can also choose to split the text into several chapters. You would then have a chapter called introduction which will only contain the wider perspective and identification of a gap in knowledge. Sometimes it can be useful to add a short chapter detailing the aims of the thesis where you can expand on the questions based on the identified gap. You then follow up with a chapter called "background" or something more descriptive, but which contains the literature review.
Since all theses are different, some may have one question to solve, some may have several and somewhat disparate around a main theme, the way to write the introduction will have to be adjusted. for the former case the main template can be followed but in the case of several research questions around a theme some adjustments are needed. Exactly how to solve this is difficult to say since it depends on the type of questions and how they are tied together. But, it is necessary to make sure the place of each question in the greater scheme of things is known and that the literature review clearly shows what is known about each topic. This can in an extreme case mean to have a single short introduction of the major perspective and then have sections for each of the questions, almost like a set of papers (if it is not built from papers/manuscripts); each complete with introduction, methods, results and discussion.

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How is a paper with multiple authors usually written?
I am attending graduate school this fall and one thing that I still could not wrap around my head is that some of the papers are written by seemingly a group of authors (5 people or more). I am curious how this is usually done.
Are each person assigned a small chunk of work and the paper is put together when everyone is done? This raises so many questions such as what if a person doesn't finish his or her part? How do you piece together the paper so that it is coherent throughout (since people may have different perspectives or understanding).
And is there important differences between a paper written by two person and those written by five or more?

I think you'll find that even with multiple authors, it is still "owned" by one or two key people. The others will contribute but the overall flow and structure is governed by that main person. So the other authors may be told "I need a diagram that shows X", or "I need a couple of paragraphs on Y". Using a shared document or LaTeX + source control, development can be quite iterative and the overall structure and flow tends to be maintained nicely.

Did you never have to do group work in class? It works the same way (and, just like in class, it sometimes works great, and sometimes the entire project just implodes - mostly depending on what the chemistry between the authors is).

I think you'll find it much more practical/common to assign one person the bulk of the writing/organization. I usually ended up with the writing task in my Software Dev classes, so I could focus more on big-picture development issues rather than minute debugging details. That, and I actually enjoy writing, so win-win for me.

http://www.phdcomics.com/comics/archive.php?comicid=562

Authorship might refer to the contents of the paper, not necessarily to the writing. That is, the presented work was done collaboratively while the (bulk of) the writing lies with one or two of the authors (typically the first one(s)).

I think that this article from the Research Whisperer covers aspects of how multiple authors can collaborate to get a paper done. It is an interesting and quite brief read that I would recommend.
TL;DR version:

One leads the project and the initial drafting with others
contributing to an almost complete draft.
The team splits the work into broad sections for each collaborator, which then draft, combine and revise.
Decide on all the details and each writes its own section with minor final corrections.

From my experience, the first one would be the most common with an almost final version making it to the very senior people in the article.

In my field (math) one person is generally in charge of a specific section / result. They write the rough draft of the section they are responsible for, and then like Samuel pointed out in the comments, one person is usually more in charge. That person puts the pieces together in the correct order and writes the introduction and transitions (this is also sometimes simply the person who has the best English). After that, (in the papers I've worked on) the file is put on ShareTex and edited by everyone until everyone is happy with it.
As for what happens if one person doesn't finish their part: the same thing you do in group project when one person doesn't do their share. That material is either cut from the paper, or someone else has to take on more work.

This is certainly common but I'm not sure it's a general rule.  It's also pretty common for one person to draft the whole paper, and then pass it around, or back-and-forth, for coauthor(s) to edit.  I've done both of these in my collaborations as well as a sort of mix: one person writes most of the paper, but a small part will be written by other coauthors, then pass back-and-forth to edit.

In my field (Atmospheric Science) you will find papers with dozens of authors.  That doesn't mean there are dozens of individuals who have all contributed equally.  There may be one or two people leading the research, needing little bits of data from everyone.  For example, one might describe a major intercomparison study between 10 datasets.  Suppose that each dataset is prepared by a PhD student or postdoc; then for each dataset this person is a co-author, and perhaps also their supervisor.  Their contribution is small but significant — provide data essential to the paper and assist in the discussion as to why/how their results are different from others.  In this case, having 10–20 co-authors is not unusual at all.  The actual writing, however, might come for 90%+ from the first author.

The dataset example is one of the arguments for data citation vs. co-authorship.  Especially for cases where you're acknowledging use of someone's data, but they might not agree with your conclusions ... or they might've passed away years ago.

@Joe I would say it depends on how much the owners of the dataset are involved.  In the case I had in mind, they would be actively involved in the discussion of why the different datasets are different.  Presumably, the creators have a better understanding of why that may be than anybody else.

Yes, ideally you'd contact the creators of the data to ensure that you were using it correctly ... but for some larger, well documented datasets (eg, MODIS, Hubble), trying to run everything through the PIs would cause a major bottleneck in puplishing.

@Joe Right, so it depends on the dataset and on context.

My publication history crosses disciplines and the multi-author papers range range everywhere from two to thirty-two authors.  Across all of these publications, I have seen two main modes of multi-author paper-writing, which I will call "collaborative" and "pedagogical."

Collaborative is the typical mode of writing that I have seen in scientific collaborations.  Authors generally tend to fall into three rough categories:

Primary authors are one or more people who take responsibility for organizing the writing of the paper, and who produce the vast bulk of the text.
Secondary authors contribute specific pieces to the writing at the direction of the primary authors, most often figures, examples, and experimental methods.
Tertiary authors are people whose technical contributions rise to the standards of authorship for the field, but who are not needed to contribute any writing.  This is highly field-specific.  These range from common in experimental fields like biosciences or experimental physics to practically unheard of and possibly unethical in more theoretical and mathematical fields.

In fields where author order matters, the category of author and their responsibilities tend to closely mirror their order in the paper, according to the customs of the field.  In formulating the manuscript, the primary authors tend to form a writing plan, often dividing responsibility for sections, but sometimes having one do a first rough pass and then "passing the token" around for further refinement.  Towards the end of the writing, when the secondary authors' pieces are integrated and the primary authors are satisfied, the paper will typically be sent out for commentary and feedback from all authors, and after a few further iterations there are no significant objections, the primary authors are satisfied with the paper, and they submit.
Pedagogical, on the other hand, is when you have a clear split between junior and senior authors, where the junior is a student or postdoc and the writing of the paper is also being used by the senior(s) as a part of their training.  In this case, the text is typically generated primarily by the junior author (either one section at a time or all at once), and then submitted to the senior for feedback and instructions.  This may go on for many iterations.  Eventually, if there is a fixed deadline, or if things are dragging on too long, the seniors may seize control and "finish" the paper between themselves in collaborative mode.
Occasionally, there may be more than one junior author, in which case the partition of their responsibilities are typically dictated by the senior.  Likewise there may also be secondary and tertiary authors, just as in collaborative authorship.

Collaborative writing differs from article to article. First, it may be useful to say that in at least some cases, all authors may not be worthy of author or contributorship according to the Vancouver protocol (here exemplified by ICMJE). If we disregard such issues and assume all authors deserve authorship the following cases seems most likely. Since I reside in a community using the ordering of authors to signify importance/impact on the final product, the use of first author a co-authors should be seen from this perspective.

All authors have contributed a significant part of the manuscript (MS). They are all specialists required for the research and provided vital input on their specific field of expertise. Typically, one person will take charge and make the first draft to which the others add their parts and comment on and add to the parts common to the MS. This case probably means all authors have similar intellectual input to the MS. Review and cross-disciplinary articles may be examples of types of articles written this way. Who will be first author could be a matter of who initiated the work, who took on the task of coordination or a matter of the alphabet.
One or a subset of the authors have a more leading role and essentially write the MS on which the other authors provide specific input and comments. This is perhaps most common when contributions vary in importance and where a few have a major intellectual input on the science whereas the other authors provide smaller but crucial input on aspects of the MS. This is likely the most common case in most collaborative research involving groups of researchers. The first author will vary from publication to publication produced in such a group where all have provided sufficient input to fulfil the requirements for authorship/contributorship. Author order will be determined according to contribution.

Regardless of which way one goes, it is necessary for someone to take on the chore of being "secretary" and actually get common ideas into text. It is possible that a single authors can provide a section or two to the MS which is included verbatim but usually some editing is necessary to make the reading uniform throughout the MS and that would be the role of the "first author". It is therefore common that the "secretary" makes a first draft asking others to add both specific parts and commenting on the text from the others. The MS will be passed around until all are satisfied. So most multiple author articles have been produced in some fashion along these lines.

Image credit: phdcomis.com
For entertaining purpose. Don't take this cartoon as a serious answer or generalization, just however it resembles pretty much my experience, especially the last 3 positions: the second-to-last, the last, and the middle one.
The first ones are not necessarily true. In my field (CS), the first name is still the most important one, normally a PhD student working on his own sub-problems towards his thesis; and having his name at the first place is important for his overall thesis evaluation.
When I have to review paper, I often frown upon papers with many authors, especially short papers. One extreme was a 4.5-page paper with 8 authors (gosh...)
To my experience of having read a lot of papers in the field, the most beautiful and important papers are normally the ones written by 2 authors, then papers written by only one author. Never seen a great one with 7 authors... ;)

Note: this experience may be different in other fields, for example my friend for once said that in his field (earth sciences), each part of the task is already a huge work (collecting 40GB of raw data (1 person), preprocessing it (1 person), sharing expertise on the configuration setting (1 person),...) and they all end up in the author list. For sure, anyone with contributions should be given credit, but in the case of my friend, perhaps an Appendix or Acknowledgement section seems more appropriate.

While I appreciate the humor in this sarcastic cartoon, it does not faithfully represent how things really work.

No surprise :) No way a first year student who did all the things and got the third position, etc. The same goes with the first too. But... it's just exaggeration, comics purpose.

According to the FAQ of "Piled Higher and Deeper" permission is necessary to reuse their comics.

In my view, the division of labor would be between the individuals involved, and cannot be answered as a industry standard. As for unfinished work, I doubt that the other authors who have contributed to a finished work would leave the unfinished portion incomplete. So either the contributing authors will finish the incomplete work (giving credit for what work the author of the unfinished work did) or they group would cut out the author who failed to meet the dead line by doing his work from scratch and simply not include him or her as a contributing author.
As for coherence in thought and readability, I would believe this is solved during the editing process. Often times, one of the authors (the best skilled) would take the job of editing the work and working with the other authors to smooth over the rough edges.
The only difference between papers written by one person and papers written by multiple authors is that the work and credit is shared by all who are involved. All the basic steps are still involved, their simply altered for the piece being done. Or so that is my understanding.

My field is theoretic Computer Science, and I don't want to speak in behalf of the whole field but personally (and this is probably a very individual) I like collaborations where a lot of the work is done while sitting together throwing ideas to the air and discussing them and then thinking (everyone together) later on solutions or new ideas for problems we encountered then calling everyone again for a followup meeting.
(The writing is a different story, but who cares about it anyway?)

"who cares about it anyway?" ... um the OP ... did you even read the question?

I think (and if so, agree) that he ment to say that the writeup stage is the secondary part and not what the attention should be put at...


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Consult on the submiting format of PNAS
I am now learning about the submitting process of PNAS. The instruction says that the authors are encouraged to submit the article in a single PDF file. However, I am wondering how could I create this PDF file. Do I have to transform a word into a PDF, or I should get this PDF file created by the Article Sizing Tool, which is a tool provided by PNAS to estimate the total length of the article. Moreover,could I just submit the article by using a word?

The author instructions state that "A single PDF file is acceptable for initial submissions of all research articles except Contributed papers". Further down it is also stated that "Publication-ready file formats include Word or LaTeX."
This means that depending on what type of manuscript you are submitting, different rules may apply. Word and LaTeX (the latter must be accompanied by a PDF file) are fine but for a few forms like their "Express Submissions" require a single pdf to be submitted initially. Only of the manuscript passes the initial stage will it be required to provide editable files.
You should generate the PDF from your Word document or LaTeX class files according to the instructions.

Thanks for your reply, I will check it.  What puzzles me is that why do the jouranl provide a tool to create a PDF file which combine all materials together. If I don't use this created PDF, will the journal reject me?

@caliant, as long as you follow the instructions to submit one PDF, it shouldn't matter what tool you use to create it. The important point is that you submit one file in the PDF format. The PNAS tool is provided for the convenience of folks who cannot otherwise create the PDF file from their source materials.


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Should supervisors read acknowledgments before the printed version of the thesis?
I'm finishing my M.Sc. thesis and I sent it to my supervisors so that they can read it.
In the final version, I would like to insert an acknowledgements page where I thank them. Should I include it in the last draft that I will send them, so they can read it? Or should it be included in only the final version, without their knowledge?

Have you included your supervisor's name in the acknowledgements?

Yes I did, thanking them for their willingness and support.

There is no need to remove the acknowledgement in the final version. I know students have done so and for very different reasons, they want to "surprise" someone, they are not on friendly terms with an advisor and does not want the advisor to see it before it is printed. etc. The "surprise" aspect is, I would argue, greatly overrated. To not provide it because of a conflict is not likely to help the conflict. So, even if the reason is non-controversial, not including it might raise an eyebrow of a sensitive advisor. In the end, this is something that should not matter but some people are overly sensitive so ask yourself, are you confident that you will reach your intended effect by doing what you suggest, then go ahead, but if you do not feel so, avoid it. You will sometimes be surprised how much is read into a benign text such as an acknowledgement.

Yes, maybe I just wanted to surprise them, or maybe I did not want that they might see it as an attempt of flattery...
I will follow your suggestion and add it in the next version I will send them.

I would include the proposed acknowledgements in the last draft. I would also include those that net-positively helped you even though you may not be on the best terms with them. By doing so, you will be taking the "high ground".


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Complete stranger asking PhD student to review paper before submission
I am a PhD student and I have been contacted today by some other PhD student with a very odd request. He is from a different university in a different country and I don't know him at all. He is asking me to review his own paper before submitting it to some journal. Is this a common thing to ask? What is the best response in this case?

"He is asking me to review his own paper" - is it just that, or is he providing some explanation as to why he has picked you of all people for exactly this paper of his? This could provide some insight into whether it's a case as described in Dave's answer, or one facet of mostly undirected academic spam.

Part of the job as a phd is to make as many contacts as possible in many different places: so congratulations, you just gained one for free :)... don't waste it.

I find the etiquette about these things can be very different from one area of research to an other. I would ask my advisor and/or fellow phd students within your field.

papers are included or not in to email. Do you have published works, by your self or here you one of authors. If papers included are they correlated to your field of work. Why to not write "not interested" if you are not and ignore if this is a scam.

I'm not surprised to hear this.  I often encourage my students to reach out to others working in their specific field.  Do it if you have the time, interest, and expertise.  Ignore it if you don't.  Don't think there's more to it than that.

Isn't it a bit weird to reach out to another PhD student though? I don't have an academic background, but this seems weird to me. Or is it simply because another student is good enough and likely has more free time than a graduate?

Sounds like a nice plan and might end up in a collaboration or "professional friendship". But in that case this should be reasonably well explained in the mail. As in "I know you don't know me, but I like your work and do similar stuff, so what do you think about helping each other out?"

@skymningen is that similar field or same field - can be seen from paper, less then 30sec to judge.

@Kevin not sure what's so weird about it.  A lot of academia is collaboration.  In theory, anyway.

If he's a complete stranger, I can understand the situation feeling a little creepy to you.
I suggest you ask him how he chose you for this role.  Ask him where he's studying and who his advisor is.  Look up the advisor online to see if everything looks above-board.
His response to a short email with a couple of neutrally posed questions may help you figure out if you are comfortable with his initiative.

But see that's just the thing...why all the back-and-forth?  If you want to do it and you think it could be useful, do it!  If you couldn't care less or think there's some bad mojo behind the request then ignore it and move on.  I certainly don't pay attention to or act on every e-mail that comes to my inbox or call or piece of mail that comes to my house.  There's not some magic equation that's suddenly involved because this other person purports to be a PhD student.

@DaveKaye - Agreed, a lot of back-and-forth would not be worthwhile.  Very good point.

From a social and scientific standpoint, you should agree if you have time and interest in the paper. You may get a contact who works on similar themes and you may collaborate in the future. As others have noted, the person will also likely be on the hook for reading one of your future manuscripts as well.
There is, however, another perspective, which is that of someone who is concerned about intellectual property. Many large companies have strict "no unsolicited ideas"-policies, because they do not want to risk future disputes. Something similar may apply to you: Say you are already working on a new method for solving problem X, that you have not currently published. You recieve a paper from a stranger who has had the same idea. Suddently, by accepting the manuscript, you may in the future be accused on plagiarism of the same idea. The reasonable thing would perhaps be to collaborate on a joint paper since you have the same idea, but people in the academic sector are not always reasonable.
This depends highly on the nature of your field of research. In my experience, these types of issues are likely more prevailent for research with commercial applications. Universities are increasingly becoming concerned about intellectual property rights as well.

Since you don't know him at all, it can be a little weird, but the ice can be broken if you exchange some e-mails. As others have said, you can be more comfortable with him if you talk more. Also, you can ask if you two can collaborate on a project. You didn't give any details on the particular paper, if it seems a good idea, and also his publication record. If the paper seems good(even if it is not perfectly written yet), IMHO you can start a collaboration.

Barring the less-likely (and nefarious) reasons (he wants to make contact with you for some other reason, he is spamming all phds at your university) such request is perfectly legitimate.
You did not say if the paper is from your area of research, or whether he refers to some of your published work - that may be important in determining the reason why he is asking you for review.
Actually, checking the quality of one's paper with your peers (other phd students) is a very common advice given to phd students by their supervisors (if they are any good). True, this mainly refers to the other people in a lab, but there is no reason that people would not go beyond this.
What does he gain by you doing the review? Well, if you will criticize his paper, he can fix the problems and has better chance to be accepted first time around or with minor revision. The reasoning is, even if you are only phd student, if you can find problems with his paper, the more experienced reviewers will find them too (and probably some additional problems you will probably miss). It is not called "peer review" for nothing (check the definition of the "peer" in the dictionary).
What do you gain by honoring his request (although, I should stress, you are in no way obliged to do the review, especially if it is far from your own area of research!)? Well, first, you will get insight into what your peers (your competition perhaps) are doing. You may get a invaluable chance to peek into the good paper which will be officially published in 6 months or even longer (although, until it is published, you will be bound by the confidentiality). Yes, you may find out that the paper is worthless and that it was all waste of time, but hey, welcome to academia and the world of peer reviews. It will not be your last time.
So, I would suggest, that you ask him why he contacted specifically you. If he is following your publications, then perhaps you will be interested in what he is doing. If you find out that his research is unrelated, politely decline and say that you are not expert in his area.


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Valuing Proprietary Research for Grad Admissions
I am a second-year Math and CS undergraduate in the US. I am beginning to consider my prospects for graduate school, or possibly industry research.
My research experience thus far is from an internship at a private company.  I do not participate in client work, only in proprietary/confidential R&D. In terms of demonstrating results, my work is at best reported in an internal whitepaper or two. Otherwise it's strictly confidential. The only thing I have to show for my work is a cleaned/approved resume blurb.
Thinking about my application from the perspective of a University, I feel like my research experience really just looks like I'm hand-waving results without anything to point to. I really enjoy the work, but I am worried that its lack of visibility will hurt me in the long run when applications roll around and I have nothing tangible to show for it.
Is this a typical concern? Or is this enough of a reason to request to participate in research presented at conferences or switch to research at my University instead?

What type of grad school are you applying to? I ask because there are parts of CS where the top grad schools will have a much higher bar for published research than most other fields, so general answers could be misleading.

If you apply to graduate programs in the US, little in the way of research will be expected of you as few undergraduates have any serious experience.
You can mention proprietary research in your CV, mentioning the name of the company if possible.
If you want it verified by a reader you have a couple of options. One is to use a researcher at the company as one of your letter writers, they can verify that you have been involved. The other way might be better, actually, since letters from academics are a bit more useful. Ask a researcher at the company for permission to give their name (& email) as a contact to verify your participation. If you get permission, then include that information in the CV.
But a professor who knows of your industry work might also be able to put a line in a letter. It wouldn't need detail.
Note that things that others say about you can have more weight than things you say yourself.

Yes, I think lack of visibility hurts a bit - university researchers mostly value the open disclosure model of university research.
Yes, I think it would add value to your resume to be able to show the research you've done in an academic setting. Really, what grad schools are looking for is your potential to do academic research. Nothing can substitute for evidence of doing good academic research to speak to that potential. You're early enough in your undergrad career that you have time to do academic research, so if your goal is academic research I'd definitely recommend getting involved on the academic side now. The purpose of this isn't just to build a resume, though, it's also to find out if you like doing academic research.
However, not all applicants will have academic research experience, and PhD applications are judged as a comprehensive whole, not a single criterion. I think the best thing you can do with your application is to have strong letters of recommendation that speak to your aptitude for research. These letters are best from university professors, but your industry superiors (especially if they have academic credentials, at least a PhD of their own) can also assist you to move your research background from "hand-waving" to "tiral's boss says they're a great researcher and would do well as a PhD student". They need not describe the specifics of a project to speak to your skills.
Of course, some companies may forbid this sort of honest letter-writing, which is very unfortunate for you and I have no solution to that problem.

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How do you judge the potential of a newer journal?
I'm in a fairly niche field that is still in the process of organizing itself. As such, there are a number of existing professional societies that are spinning off journals along with newer societies that are getting into journal publication. Since some of the usual metrics for judging a predatory journal may not apply, how do you judge the potential of a newer journal so that the publication does not end up being a wasted effort?

To expand upon part of Dave Everitt's answer,

look at the founders of the journal - did they start it primarily as a platform for their own publications, and do these authors and their associates make up the bulk of the authors?

I would also look at who is publishing and editing the journal.
Is the publisher affiliated with a scientific society? Sometimes scientific society will launch new journals (e.g., the Ecological Society of America launched Ecoshpere to be their open source journal).
Or another is a new journal from an established publisher? Established commercial publishing companies are launching new journals. Although people argue about the ethics of publishing with them (cf What are some examples of negative effects on a career for boycotting Elsevier journals?), my own experience has been that their products are usually scientifically sound (presumably because they are afraid of hurting their brand image). Additionally, journals such as Nature now have spinoffs (and spinoffs of spinoffs, e.g., Nature to Nature Methods to Scientific Reports) to catch paper that do not fit into their flagship journals.
Also, who is the editor-in-chief and other editors? Do you know them in your sub-field? For example, when the journal Theoretical Ecology launched, the they had Alan Hastings as the EIC, a highly respected Ecologist.

Then again, established publishers like Elsevier sometimes publish things like Chaos, Solitons and Fractals...

@StephanKolassa - but I don't think they set out for it to be quite what it is - once launched it may just not catch on with the intended audience, leaving it to fend for itself...

@StephanKolassa I'm not familiar with that journal or the story behind. Would you care to elaborate? (or if you don't, I completely understand as well).

"...presumably because they are afraid of hurting their brand image" —this is a double-edged sword at best; from my viewpoint it is wholly a negative trait for a scientific journal.  Accurate scientific observations can and should challenge common assumptions.  "Worry about reputation" has no place in a search for truth; accuracy, not politics, should be all that matters.

@RichardErickson: the editor-in-chief, Mohamed El Naschie, published a large number of his own articles in that journal, some of which were, ahem, not judged as of high quality by peers. The section in the Elsevier Wikipedia article hints at this. There was much more at various academic blogs. Frankly, I'm a bit amazed Elsevier didn't discontinue the journal after that, like airlines retire flight numbers after crashes.

@StephanKolassa Thank you for sharing that story. I had never heard of that occurring before. (I believe it,  I've just never had never saw it before).

Is your niche field organizing it?
If you are in a fairly niche field, then you should know most of the significant people in that field - and preferably actually know them, not just their names.
I strongly believe that a new niche effort (no matter if it's a journal, conference or association) can be successful and worthwhile only if it's done by those people (or a significant part of them) in order to fill their own niche needs. No matter if they come from different organizations (of course they do) or they haven't a single specific association (which most new fields don't have), there is a "virtual community" of people interested in that field and working on it.
Are the key people you know involved in that journal?
Regardless of that, maybe ask them directly about that journal? In the end, it's their opinion that will determine whether that journal will be successful, not any arbitrary metrics.

A suggestion checklist for new journals

check who has been published in the journals - are they notable contributors to the field, or all from one research group?
circulation - try to find out how many copies they print (if printed) or readership numbers
look at the founders of the journal - did they start it primarily as a platform for their own publications, and do these authors and their associates make up the bulk of the authors?

Having said that, although most fields have their primary journals, and new ones have to start somewhere, you can still use the above to litmus-test a new journal (as well as the vanity journal tests e.g. would they accept your paper without any peer review?).
Finally, beware of the new swathe of bogus journals, promoted by well-disguised spam targeted at academics via their university email addresses, for example, see: Journal accepts bogus paper requesting removal from mailing list(!) and Murky world of 'science' journals a new frontier for climate deniers


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What are the main differences between undergraduate, master's, and doctoral theses?
When I did my undergraduate thesis, my adviser was expected big on students expecting them working really hard, so it ended up as a reduced master's thesis (most of the reviewers said that it was an overkill for a B.E).
So because of this, I did my master's thesis pretty much in the same way I did my bachelor's thesis; the PhD dissertation was a different story.
What are the principal differences between these three pieces of research?

Leon: I've removed the second question, "- What are the mistakes students coming from a master or undergraduate may do when preparing this publication just as an extended part of their previous research?" This really should be asked as a separate question.

In a Bachelor or Master thesis, you have to show that you are able to apply the knowledge of your field to solve a typical problem in your field.
In a PhD thesis, you have to show that you are able to extend the knowledge of your field to solve new problems.
The distinction between a Bachelor and a Master thesis may be a bit subtle. Generally I think a Master thesis should show a significantly greater level of independent working. While for a Bachelor thesis your advisor could tell you which methods to use to solve a specific problem, for a Master thesis you could be expected to choose the methods on your own, and maybe adjust existing methods to better fit the problem at hand.
These are the principle differences I see, but of course its also depending on the specific student. A good Bachelor thesis can be better and include more independent work than a bad Master thesis.

I would see the differences as follows:

Undergraduate thesis demonstrates the capacity to apply basic research skills in an area of interest to you. At this level, the focus is on gaining broad competencies (akin to an overview of what research is all about).
Masters thesis demonstrates the capacity to apply advanced research skills (i.e. move beyond basic research skills) in an area of interest to you so that you are able to incorporate some critical insights in your study. At this level, the focus is on developing critical thinking in a subject area.
PhD thesis demonstrates the capacity to apply specialised research skills (i.e. expert knowledge of a particular concept or method) in an area of interest to you so that you can make significant and original contribution to knowledge. At this level, the focus is on identifying a 'gap' in knowledge and addressing it, hence you advance knowledge in a field of study.

These are are arbitrary descriptions as there are overlaps (i.e. all levels require critical thinking); however, the three levels are distinct and require difference level of competencies.


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When Applying for Postdocs Should GPA be on your CV?
Lets assume your GPA is very high, say 3.95 or higher, at both your undergrad and graduate school institutions. I have always included it while applying to summer research programs and internships while still in my PhD program. But this is probably inappropriate on the postdoc market right?
Perhaps this question is somewhat subjective, but, after checking out some other questions on this exchange, I didn't think it was overly subjective.

Mark Meckes's answer only considers academic postdoctoral positions. In such cases, he is correct: undergraduate and graduate GPA's do not matter.
If you are applying for non-academic postdocs, however, the situation is very different. At large research centers—particularly those managed by corporations, such as essentially the entire US Department of Energy laboratory system—hiring is done by corporate employees, and must be approved by several layers of management. Several of the national laboratories even have strict GPA cutoffs for their employees, regardless of the length of time they've been working post-graduation!
Consequently, if you're applying for positions only in academia, then there's no need to include GPA. However, for anything outside of an academic setting, it can actually help to do so.

Good point.  I was indeed thinking only of academic positions.

Will including the GPA for academic positions actually net you negative points, i.e. make you look like you are holding on to the past, or don't understand academic culture etc., or is it truly a doesn't matter one way or the other kind of thing. My inkling is perhaps the former.

It won't hurt you, but it won't help much, either. After your postdoc, however, it will look even stranger.

For academic positions I'd say rather, it won't help you, but it won't hurt much, either.  After your postdoc, however, it will look very strange.

No (to the question in the title), and yes (to the question in the post).  For postdocs no one cares about your grades.  They're only interested in the quality of your research.

Also for faculty positions.

Post-doctoral and staff positions at non-academic settings work very differently. See my answer.

Huh, this contradicts all the advice I've heard about preparing a CV.

@DavidZ: All the advice you've heard about preparing a CV (when applying for academic postdoc or faculty positions) says to include a GPA?  If so, I'm curious what the source of this advice was.

Well... I guess it would be more accurate to say that some of the advice I've heard says to include your GPA, and none of it says not to include your GPA. This would be based on web searches, other people's CV examples, and a few of people I've talked to, though it's been long enough that I don't remember specific sources.

@DavidZ, yep I saw similar advice online, and sensed it was incorrect. That's why I asked the question. I think that most websites focus on industry jobs, since that's mainly what people do with their degrees (this is probably even true with PhDs these days)


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What are appropriate questions for a closed-door (non-public) part of a PhD (or master's) defense?
There is a related question about questions to expect for PhD defenses here: What questions to prepare for PhD defense?, but the question (and answers) are referring to the public oral defense.
Generally, at least in Biology in the U.S., there is a "closed-door" or "non-public" part of the defense where the committee "grills" the student about all types of things. I am wondering what types of things are appropriate. It seems that sometimes questions are not related to the thesis or dissertation specifically, but general questions in a large field / body of knowledge. If committee members do not provide you with reading material or potential questions, how would one even go about knowing what to expect? Is it appropriate to fail someone for not answering seemingly random questions - as if they are to have encyclopedic knowledge?

Do you have any personal or anecdotal evidence backing up your "it seems that many questions are not related ..." statement ? That's not typical in my experience.

Anecdotal evidence from other students that I can not attest to whether or not there is a link to be made - but at least they felt like it wasn't there, and personal evidence from my own qualifying / comprehensive exams (which I understand is not the same). I will tone down the language though - you are right to point out that this isn't everyone's experience.

"questions in a large field / body of knowledge" was pretty typical at my institution (engineering, Germany). However, you could expect the committee members (4 including the supervisor) to ask questions about their field of expertise. So when the "energy professor" was nominated to my committee, I set off to get myself a copy of his lecture notes. However, people usually wouldn't fail for not being able to answer those questions, but would not score perfect grades, either.

As the norms and rules vary enormously from institution to institution and department to department even within the US, ask your supervisor.
In my experience the supervisor and committee do give at least broad outlines of what's expected/what topics will be covered. (My personal opinion is that we [academic supervisors] give way too little guidance about what to expect, making the process far too stressful.) You can and should at least ask for this guidance.
Also in my experience, the broad "anything goes" questioning you describe in your question applies more to comprehensive or qualifying exams, where the goal is to find out if the student has an adequate level of foundational knowledge etc. to begin a research program, than to the defense. The PhD (or master's) defense is usually much more focused on the material in the thesis/project itself, although it can of course stray into related topics (see the answers to the question you linked about PhD defenses for more discussion of the typical scope of these exams).
As for

Is it appropriate to fail someone for not answering seemingly random questions - as if they are to have encyclopedic knowledge?

When you put it that way, of course not. But ... a student's and a professor's view of "seemingly random" is often different. A professor might legitimately feel that a researcher in field X should know about topic Y, even if that seems unrelated to the student. Again, I think it comes down to reasonable expectations being set and communicated before the student starts to study for the exam. (As I say in my third paragraph above, that applies to comprehensive/qualifying exams. Students usually shouldn't even have to study for their thesis defenses — the defense is about exploring details of a topic that they've just spent several years immersed in ...)
I agree with @Buffy's points that making any reasonable effort to answer the question will count in your favour (e.g. "well I don't know that but it seems related to ..." or "let me start working that on the blackboard and see how far I can get ...") Again in my experience your examiners are actually on your side and want you to succeed, they will usually provide hints if you make a good-faith effort to tackle the question.

The part about "anything goes" is very field- and location-specific. In some fields, Germany still has a "Rigorosum", a form of doctoral defense that includes questions about the general field, beyond the scope of the doctoral thesis.

@Roland, things vary. When I was still "in the game" our defense was private and quite informal. We sent a few candidates back to the drawing board to do more or fix serious issues. Most of them eventually got over the wire with a bit more guidance. So, it wasn't failure in the sense that "you are done here", but rather "major revisions" similar to that of a journal reviewer. But the questions asked were about the work, not general knowledge of the field. I think we would have treated real failure as a failure of faculty to guide properly along the way.

According to this link  https://www.discoverphds.com/advice/doing/phd-failure-rate , 3% of UK PhD students fail their viva (thesis defense). I've never seen or heard about a failed PhD defense in my career (95% US/Canada with a smattering of UK/European)

@Roland I personally know two people who have failed their PhD defenses in the United States (Ecology / Organismal Biology). One at least was given a masters degree instead, and I am not sure what happened to the other.

Generally speaking anything and everything is on the table unless you are told otherwise. There are no limits. It is up to individuals what is asked and up to those and other individuals to evaluate the answers. The candidate may not be able to answer everything.
But it probably isn't required to answer everything. What is required is to say sensible things, including "I never studied that".
But for the foundational knowledge of your field, you'd better be able to give pretty good if not absolutely ideal answers.
The (second) worst story I ever heard, though it may be apocryphal, is one in which the candidate in biology or chemistry gave his dissertation presentation in which he repeatedly mentioned pH. There was an outside member of the English department on the committee who said she didn't have any real questions, not understanding the subject, but would like some layperson's explanation of pH from the candidate. The person, who had long ago studied it formally and was able to use, froze up and gave no answer. He failed.
But maybe that was just a horror story told around grad students to scare them into working harder, something like a campfire ghost story.
In a private oral exam of my own I was asked a question and started to develop an answer (math - algebraic topology) and it went nowhere. I stopped and admitted that I wouldn't be able to finish it, but was able to say exactly what the flaw in my argument was. This actually impressed the examiners more than if I'd given the correct answer immediately, as they told me later.
So, you don't have to be perfect, but you do have to make sense. Do that and you will probably be fine, subject to the vagaries of personality.

This begs the question - what's the (first) worst story you ever heard?

@Greg, thought you'd never ask. There was a story of a failed candidate killing his advisor. I guess I'd rank that first.

@Buffy: did he kill the advisor before or after failing the exam?

@st01 after of course

@Buffy oh my - that is much worse

When I was a Masters students, we used to attend the PhD defenses. We'd sit at the back and remain very quiet. After one candidate finished his presentation, a professor asked a question about one of the slides (this was way back in the day before computers). The candidate fished out the slide in question.  The Prof asked about the second bullet point. A literal reading of it obviously violated the 2nd law of thermodynamics. All the candidate had to do was go "Oops, that's obviously a typo", but he didn't. You could hear the wings of the vultures as they circled the room. He never backed down.

@st01 it would be difficult to fail the exam if you are in prison.. of course I suppose they never got caught.. but then how would we know the story?

One of the best pieces of advice I have received is to defend only what you have done. That means that you have to be an expert in your thesis and to a reasonable level in the field as a whole. This perspective enables answering tough questions:

Why haven't you done X? We thought about doing it, however after analyzing our case specifically we opted for Y because of A, B, and C.

Why X is missing? Agreed! It would be good to have it. I did Y instead because it seemed the right way at the time because of A, B, and C.

Your result X goes against state-of-the-art! True, however we take into account A, B, and C that others have overlooked.

Any tough question can be turned into a silent agreement and "selling" what you did instead of defending what you could have done.

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How do I handle academic references for US PhD program, when I have been out of academia for a (very) long time?
I live in the US and have been working as an engineer in industry for over 10 years. I graduated from a top UK University, with outstanding grades in a Masters degree and several university-level prizes.
I have decided that I want to pursue a PhD, as I have a strong desire to be doing more advanced and challenging work. So, I am planning to apply to the PhD program of the best university that is in my area (which happens to be a top-tier US institution). My family and I are fairly settled in the area and we have no desire to relocate.
The institution has an admissions requirement that I have to provide three recommendation letters, two of which should be academic. Therefore, it seems that I have little option but to reach out to some of the professors that I worked and studied under during my undergrad course 10+ years ago. I am planning to provide one industrial reference and two academic; however, I am concerned that my undergraduate course was so long ago that the professors will struggle to remember me, given the hundreds of undergrad students they interact with each year. So, at best, even if they do generously agree to write a letter, it will probably be fairly generic and unspecific. And of course, it won't be in any way a good reflection of the more experienced and mature person I am now.
At worst, they might simply refuse, given the amount of time that has passed. I wouldn't blame them, and in a way I feel bad asking, after all this time.
So, what should I do in this situation, given the amount of time that has passed? Is there another way I can approach this?
The irony is that, given my industrial experience and personal development over the past 10 years, I think I am almost certainly a stronger candidate for a PhD program now than I would have been straight after I finished my undergraduate degree; however, given the amount of time I have been out of academia, obtaining strong recommendation letters is going to be much more challenging.

Have you asked the university if, in your situation, they will accept all industrial references?

@PatriciaShanahan I haven't, no. That probably would be a good thing to try. Even two industrial and one academic would help me a lot.

I faced a similar, but more extreme, problem applying to a PhD program 25 years after my last college education. I used all industry references: two managers who had supervised me (hardware and software), and my employer's CTO who did not know me quite as well but had very good academic connections.

@PatriciaShanahan ok, thank you for your advice. I will contact the school and see if I could do something similar.

When it comes to references, rules get bent and broken all over the place. Just provide what references you can get.

In contacting your old professors you might start by reminding them of what courses you took with them and what grades you earned in those courses. It would also be appropriate to supply a copy of your full academic transcript.
I frequently get requests like this from students that I haven't seen in 10 years or more.  I comment on the students transcript and grades in my courses and whatever I can remember about the student.  This isn't ideal, but it's better than nothing.
Another common strategy for students who've been working in industry for a long time is to begin graduate study by taking a few courses on a part-time basis at a local university.  It's much less of a commitment by the department to allow you to take a course or two than it would be to admit you as a full-time student and provide you with financial support.  If you do well in those courses then you can ask the instructors for academic references.

Personally, I would find it very helpful if the student came to visit me personally to talk over their past and future. It would jog my memory about them and our former interactions in a way that an email contact would not.

Thanks for your helpful answer, I will request a copy of my transcript today. I also like your suggestion of part-time courses. If I don't get accepted during this cycle, I will look into those and see if i can do something to build up some fresher academic references for next year.

@Buffy thanks for the suggestion. I will try to meet them in person, if I can.

I believe you should look for industrial references with academic experience, of at least industrial refs who have a PhD and can comment on your likely success in that endeavor.
Unless you had some special experience with a prof that provided reason to remember you, a recommendation from a generic source will not help an admissions committee.  Let your transcripts speak for themselves, and find references who can help lay out your reasons for a career change to the committee.
You are an "atypical candidate".  You should embrace that.

Yes, letters of recommendation that primarily comment on transcripts are rarely helpful. Anyone can read transcripts.

Thanks for your helpful answer; however, looking back at my time in industry, I can't think of a single person I've worked closely under in 10+ years that had a PhD (unfortunately).

In my case, with a gap of well over 40 years since my last academic work and having been out of employment for 7 years, I first talked it over with my intended supervisor and the university relaxed its requirements to one industrial reference. My referee did not have a PhD but was an engineer of international repute.

@Time4Tea Then find someone to attest to your ability to learn complex subject matter, your ability to handle large projects, your determination to finish what you've started ....

Ok, thanks for the advice.


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What can I do one day before admissions deadline, if I believe my recommendation letter writer will not submit in time?
One of my professors this term promised to write me a recommendation letter for grad school. However, tomorrow is the deadline and her letter is not on the application website. She really liked me, so it's probably a case of her forgetting about/misremembering the deadline.
However, I can't reach her via e-mail, and she's the kind of person who puts absolutely no information online (phone, travel plans, etc). Perhaps she's on some sort of trip to a conference or something.
What can I do (with respect to the graduate programs I have applied to) to resolve this? Is there usually some sort of university policy regarding this situation? I really don't want to be unable to apply for grad school because a professor forgot to check her e-mail.
This situation is different from What can I do if a professor agreed to write a recommendation letter, but never sent it?, because in my situation the deadline has not yet passed.

Is your question "How to reach this professor?" or "How can you explain the situation to the graduate programs you applied to?" (See "Here's my situation, any suggestions?" is not an answerable question). If the latter, it appears to already be addressed in What can I do if a professor agreed to write a recommendation letter, but never sent it? and this question would be a duplicate.

It's the second situation, the difference being it wasn't "years ago", but "multiple times over the past few weeks" that the professor promised to write me a reference letter. She clearly just misremembered the deadline and went on doing something busy.

OK, do the answers in the linked post address your question? (I understand there are some differences with respect to when you asked the professor for a letter, but the part about how it affects your current applications is essentially the same). If not, can you [edit] your post to explain why you think the answers would be different?

@ff524: The most important difference in this question is that the deadline has not yet passed, and that the applicant has not yet been rejected.  For instance, would it be worthwhile to contact the departments where they are applying and explain?  They might be willing to wait a little longer.  Or maybe a letter from the letter writer's department chair would be helpful?  I don't know, but answers to this question could consider it.  But those would not be relevant to the other question, in which those ships had long since sailed.

Call the school you are applying to, state that the prof who is supposed to give you the recommendation is out of her office and unreachable, and ask for a one-week/two-weeks extension of the deadline; 2. It's your responsibility to try to reach her. Did you talk to her department and find out when she is expected to be back?

@NateEldredge Good point, thanks, I've updated the question to highlight this difference.

@ff524: I've also edited the other question's title to indicate that it asks about what to do long after the fact.

I have contacted a close colleague of my professor, and he says that she's currently very busy, but will finish the letter just in time. Apparently, my professor has a bad habit of not looking at her e-mail frequently.

I would try the following:

Contact the department(s) where you are applying, and ask them if they have received the letter.  (It's possible that they have received it, but for some reason it has not yet been logged in their online system.)  Explain that you would ask the professor herself but you cannot reach her.
If they say they have not received it, ask if they would be willing to keep your application under consideration, pending the arrival of the letter.  I don't know if this will help, but it's worth a try.
Contact the professor's department chair and see if he/she knows anything about the professor's whereabouts.  It is possible that something unusual has happened (e.g. she is in the hospital), in which case the chair may be able to write a note to the admission committee explaining the circumstances and asking for their patience.
If it seems that the letter may not be forthcoming within a few days, consider seeing if someone else can write you a letter.  Be sure to explain to them the circumstances, so they understand that it is urgent for reasons beyond your control.

Hopefully someone who has been on an admission committee will add an answer saying how they normally handle such situations (which must be rather common).


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My PhD went over time - advice for explaining this on a CV
It is a concern to me that I may look unattractive to potential employers because I went so far beyond the original budgeted time for my PhD (50% over time). I am currently searching for a job in industry, where there may be no understanding of the difficulties of my research and I expect to recieve no sympathy from prospective employers.
I feel that on my CV I must somehow find a way to hide that it took me so much time to finish my PhD. However I will not blatantly lie on my CV. Does anyone have any advice? Or any suggestions as to how I could explain this extra time on a CV? I hope I am not the only one to have ever been in this mess?
The time I studied for my PhD went to 6.5 years, which is far beyond the typical 4 years for PhD studies in Europe (I study in London). In growing desperation (for applications to jobs based in Europe) I consider replacing the first two years of my PhD with a job, possibly titled "research assistant" or something similiar, and placing it under employment history. On the CV it would then appear my PhD took 4.5 years, a more typical length. Any thoughts on doing this? Is it correct that in the United States and Canada that 6.5 years is close to the typical length (or time required) for a PhD and therefore I would not be discriminated against?
Any advice and suggestions are appreciated.
PS it genuinely took 6.5 years to finish this PhD, it was impossible to finish in 4 years.

If you published good research, nobody cares.  Six and a half years is the average length time to complete a PhD in the US.

Whatever you do do not fabricate or conceal the truth. I am not sure someone would worry about finishing "on time" as much as looking at the quality of the work you have achieved. In my system there is also a 4-year research time limit (in terms of calendar time it can be extended by including teaching, maternity/paternity leave or whatever is applicable). Regardless of whether you apply for a job in academia or industry the criteria for the employment will be much more than finishing on time. So issues like quality, number of papers published, social skills, other relevant skills will be measured. If you have a reasonable explanation for the extended period of your PhD, just spell it out. Do not make a big story about it, just cleanly provide an explanation that makes the period understandable and reasonable.

I’d also add that if you explain away (aka lie about) a 2 year research assistant position, you can expect questions in the interview about this position and that might lead to a tangled web and a stressful interview. Plus, stats at my UK based institution imply that a majority of students actually exceed their 4 year registration period.

I'm not sure I understand (and this might be a US centric thing). What does it even mean for a Ph.D to go "over time" ? It takes as long as it takes, and that's pretty much it. While taking inordinately long (8+ years) might raise some eyebrows, 7 is still within the "normal" range, albeit on the higher side.
In fact, I've often suggested to students that the benefit of staying an extra year to strengthen their CV (if there's a path to doing so) far outweighs the potential cost of taking "longer" to finish, in terms of future job prospects.
I suspect Europe (or parts of Europe) is different.

Yes, the system(s) in Europe has strict time limitations but mostly concerning financing. It is still possible to complete a PhD later although there is likely less support from the university/department once time runs out, for example, you may not have office space.

There's a typical PhD duration in Europe depending on the country (e.g. 3 yrs France, 4 yrs US, 5 yrs Sweden). I have a working contract with the salary based on my funding, that states I'm employed for 3 years. It is extremely hard to get further funding for a long period of time - in France, if your team has money they might pay you for an extra 6 months, and I've even hear of people using the unemployment support (very good in France) in order to defend later, or getting employed as the team's engineer if they wanted to significantly postpone the defense.

@penelope The time allotted for a PhD in Sweden is normally 4y, but that excludes teaching or other duties. Therefore many end up with e.g. 5 years, including 25% teaching.

@fileunderwater Sorry, looks like I was miss-informed. But I think the point is still valid.


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Who is to decide the main idea(s) of research in a PhD Proposal, the student or his/her supervisor?
I'm a pure math phd student and the supervisor gave me two papers so as I find an idea to research but the subjects are unrelated and I can't concentrate on one of them and can't decide which one is likely  to be a fruitful subject, What should I do?

Talk to your advisor!

First, it depends on the country you're in, the type of funding you're applying for, and probably to a smaller extent on your field of research.
In case you already have an agreement with a supervisor, then you should probably look to him for advice on choosing a topic, but make the choice yourself. Given that he sent you papers on these two topics, you can probably assume (absent any evidence to the contrary) that both would make a good and fruitful subject. Thus, choose with your heart: what problem is most exciting to you?

This is a tricky question. In principle, of course, it's best if one comes up with one's own question/project. However, it is all too easy to accidentally, from inexperience, choose a too-hard, or boring-to-experts, project, or, more subtly, a project in which neither you nor your advisor has any special insights to give you an edge over anyone else.
Especially if you are hoping to make a run at the "research post-doc" game, you'll want to have done Ph.D. work that is of interest to experts in that field. A novice has the obvious difficulties ascertaining whether a given topic might be of interest to experts, but your advisor should be able to clarify this. I have seen examples of people working enthusiastically on a PhD topic, and finish the degree, only to have no one care at all, and no job offers result.
Also, I don't think it's the case that a "smart-enough person" can pick random problems (that are of interest to experts) and expect to make significant progress merely by wanting to. While it's true that "fresh eyes" can be helpful, literal inexperience is rarely useful. I tend to think that one's advisor should give "insider advice" about un-obvious possibilities for progress.
Thus, in reality, I think that the true choices available are something like first choosing an advisor based on their expertise. Then ask them for guidance. Presumably they will not dictate a project, but merely suggest, giving you choices... but it is very important to continue the iteration of "getting advice", rather than just privately making a choice and assuming it is wise. Lacking the information and experience your advisor should have, it is essentially impossible to make good choices on your own. Tentative choices, to be discussed with your advisor, yes.

I understand your situation because I recently started my PhD.
You do the following:

Try to come up with ideas from those two papers
Apart from that try to come up with own ideas of yourself
Take all the ideas with you in a meeting with your supervisor and tell him frankly what you want to work on.

I think in general the role of the PhD should increase trough the course of the project. In the beginning, the supervisor will have a significant role, both in selecting the subject and performing daily duties. This is needed imo to get the unexperienced PhD going. Later, the role of the PhD increases, and the supervisor takes a more passive role.
In the Netherlands, it is customary to write four journal papers as a PhD (4 years). While the first might be an idea that your supervisor came up with, your last should probably be your own idea.


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Editor didn't invite for a second review
I recently reviewed a paper and recommended Major Revision. I provided a referee report with some detailed comments on what the revision should address. I can see from the system that the Editor gave a decision of Major Revision, the authors of the paper have been notified and they already submitted a revision four months ago. However, the Editor did not invite me as a referee in the second round. I have been refereeing for over seven years and this is the first time that I experienced such a situation. I have been obsessing that the Editor found my report incompetent or not useful. But, the overall recommendation was the same (Major Revision) and the same journal asked me to review other manuscripts in the same time frame. What do you think the reason could be?

Maybe the review assignments haven't gone out yet for the second round from four months ago. :) Or maybe they got your contact information wrong. Once my advisor asked me, "I need that review, where is it?" and I was like, "What review?" "The one I invited you for a few months ago." When we looked into it she typoed my email address and so it went into the void and I never saw it.

I downvoted this because the question seems to be about a personal case and invites guessing about the editor's intention. However, the more general question "When is a reviewer activated again by the editor?" would be more appropriate (and also a very good question).

There are always difficulties second-guessing from what others actions result from. The fact you did not get re-invited, is not strange in my experience (as reviewer and editor). First, I assume you do not know what the other (I assume the journal uses more than one reviewer) reviewer provided in a second review. It may have been minor revisions and the editor could make a decision to provide a major revisions verdict but go directly to accept if he/she thought the corrections were good enough. This is an editors prerogative.
It is always possible that an editor chooses a different reviewer for the reason you mention but given that you have done many reviews before, I sincerely doubt this is the case or reason. Another possibility is that the editor felt someone with different expertise was needed for some aspect of the manuscript, perhaps based on comments by the second reviewer. But, you will never know the details of the story and I would not think twice about the event. The fact that you keep getting requests shows your expertise is in demand.

The most common reasons not to invite a previous reviewer for a second review are, in my experience:

The reviewer wrote a poor review the first time (probably doesn't apply in your case).
The reviewer ticked the "I do not think it's necessary for me to check the revision" box.
The editor decided to make a decision immediately, without consulting reviewers. For example, the author's response to reviewers might be poor and the editor feels further reviewing is a waste of time.

In your case, I'll suggest a much more benign explanation: the editor noticed that you have already been invited to review another article recently or perhaps already have an ongoing review, and decided not to invite you again for fear of taking up too much of your time.

My guess would be that when the editor saw the revised manuscript and the comments from the authors, he deemed the revision to be less major than he initially thought, and decided to not send the manuscript out for review a second time.

The editor thought your comments were sufficiently addressed in the revision and made the decision to publish.


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How to quote a draft in my thesis?
For my bachelor thesis I needed a certain source. As it wasn't accessible neither on the net, nor in my library, I decided to ask the author directly. She was kind enough to send me a draft of the text in question, explicitly allowing me to use it for private academic purpose.
Now I'm in the middle of my thesis. How do I cite a draft that doesn't even have a date? If I had the published version, I'd simply cross-reference, but I don't, and adding the page number of a word document that my supervisor doesn't have seems utterly useless. Do I simply leave out the page number (it's a very short paper), or do I add the paper as an attachment?
I know this is something I'd normally ask my supervisor. Unfortunately, communication with her is not something I'm interested in, for personal reasons. I'm therefore looking for a reasonable advice that has nothing to do with her preferences.

If it has been published, ask the author for a pdf of the published version (from your question I got the feeling that the paper has been published). This would also be easier to share with your supervisor later on. It makes no sense to cite or quote a draft version if the paper has been published. At least ask if the draft has identical content as the published version. If so, you could maybe get away with using the draft but citing the published version in your reference list (not ideal though).
Otherwise, cite it as a working paper/draft, by including author, title, and the date when you recieved the paper, see e.g. Chicago manual of style online or MLA style guide.

It's not clear from your question what the status of this "source" is --- i.e., whether it has been published, will be published, or may never be published.
If it has been published, but you just didn't have access to the published version, I would cite the published version.  If you have a quote where you need to cite the page number, I would go ahead and cite the page number from the draft.  Although others might disagree with this practice, I've found it's not uncommon to find page-number citations that are off by a page or two due to citing different versions of a paper, different editions of a book, etc.
If it has not been published but is "in the pipeline" (i.e., has been submitted to a journal), you can cite it as "forthcoming", or as "to appear" if it has been accepted.
If it is unknown whether it will ever be published (i.e., it is just a work in progress that may or may not be submitted for publication at some later date), you can cite it as "in prep", "unpublished ms.", or "personal communication".  Personally I tend to view "in prep" as meaning "the author intends to publish this at some point but it's far enough in the future that we don't know where or when", "unpublished ms." as meaning "there is little chance this will ever be published", and "personal communication" as "this was not even written as an article-type document but just information conveyed to me via email, conversation, etc.".

I know only two ways:

you write "Author, private communication" in your references;
you publish the unpublished material and add its author as an author of your paper.

"you publish the unpublished material and add its author as an author of your paper." Say what?

@xLeitix. I meant "you publish the draft, partially or entirely" and of course add the name of its author to your paper.

You can't just publish somebody else's draft, no matter what you do with author names. Especially since the draft in question apparently is already published, just not available to the OP.

Also, please don't add people to your author list without consulting them first. I would be furious if that happened to me.


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How to send end-of-the-year wishes in academic environment?
Currently I am working in a research group where there is much emphasis on the interpersonal relations.
I want to write an email and send it to my direct supervisor, with whom I have closer relations compared to the others. But, I also want to send my wishes to the whole group included the head of the group, but I want to do it in a fashion which will sound mildly formal but with a sense of respect and hierarchy in it, and not friendly and too informal.
Any suggestions, or nice emails that you have received?

There are many options which can be made by themselves or in some combination.

You can design a "card" to attach to the mail which could be informative or aesthetically pleasing (but do not make it a huge file).
You can, as I and my former adviser do, make a "Christmas letter" that summarizes the year both academically and private. You need to adapt to your audience here since the private section should not be too detailed if your are not really close friends, but comments on travels with a nice shot is never a bad idea.
You can divide the send list up into different categories but the backside of this is that if you group people and group them wrong (from their perspective, it can become embarrassing).
The previous point is also true for listing people in some order; so alphabetical, even in the way you list the e-mail addresses, is probably wise.

Do not emphasize Christmas and New Year per se since not everyone may be celebrating these primarily Western holidays. Use something more neutral formulation such as "Best Holiday Greetings" or "Best Wishes for the Holiday Season". Again, know your audience and adjust.

You can send a general more formal greeting to a larger group and then follow up with a more personal greeting to specific people you wish to share more personal greetings.

So, think about the options and combine to taste.