text:
How common is it for journal to reject a solicited paper?
A guest editor at a peer-reviewed academic journal solicited me to write a paper. I initially hesitated for lack of time. But the editor's invitation was courteous. So I sent an abstract, which was accepted by the editor.
I submitted the 6k-word paper a few weeks later, taking care to comply to the submission guidelines (I downloaded the journal's CSL file for bibliographic references, for example).
I just received a rejection letter. I know an invitation is not a ticket to bypass the reviewers. Still, I am rather stunned. I'll get over it, but I was wondering how common it is for academic journals to reject solicited papers?

I've seen this happen once. A paper submitted for a special issue of a journal  was rejected, not because it was a bad paper but because it was on a topic quite different from the special issue.

Surely the editor and reviewers said why the paper was rejected. It's unlikely that any paper gets rejected after review solely because of wrong template or citation formatting. Unlike content, that stuff is easily fixed.

This is not common, but it certainly does happen.  I know a small number of people who have had their invited submissions rejected.  Whether it is a likely possibility in particular instance will depend on how many invitations the editor(s) send out—and, correspondingly, how well they know the potential contributors and their work.  If the invitations are kept to a relatively small group of individuals familiar to the editor, it is less likely that anyone will submit a manuscript that is of low quality or is not topical.
Whether this is likely to happen also depends on how the submissions are being evaluated.  Sometimes, an expert guest editor for a special issue may take care of all the refereeing themself.  However, this will not work if the topic is too broad or there are too many submission.  I was actually responsible for getting a low-quality invited paper rejected from a special issue once, when I was asked to referee it.  The work was simply too shoddy to merit publication in any venue.

It is not common, but I have encountered one of such case before. The author of the submitted paper is the guest editor of the special issue which this paper was submitted. I sent this paper for peer review and received negative comments from 2 reviewers. Hence, the academic editor decided to reject this paper. Usually what I will do in such case is to ask the academic editor to give the author one chance in revising and improving the paper. And usually this will work. But in this case, the reviewers' comments are too negative and it was unlikely for the author to improve the paper and address their concerns, so it was rejected. I feel very bad when writing the rejection letter to the author, but I have no choice.
My answer to OP question is, check the reviewers' comments. Are the comments negative? Are they valid? If the comments are negative overall, then it could be the reason for the reject decision.


text:
Publisher has changed many terms in section/subsection titles to acronyms
I have an accepted paper which is now in the proof stage. Throughout the paper we define various acronyms, since we use these terms lots of times. For example:
These two acronyms are introduced in the first section:

A Bayesian network (BN) is a well known machine learning technique for (...) The conditional probability distribution (CPT) requires the specification (...)

Afterwards we generally used these acronyms, but not always. For example, at the start of a new section. We felt it is better to start the section with

Bayesian networks were introduced by (...)

than with

BNs were introduced by (...)

I think it is much easier to read the first way. Afterwards we do use the previously defined acronyms.
They have even changed these in the section titles. For example, a section is called

Estimating the Conditional Probability Tables of a Bayesian Network.

They have changed this to

Estimating the CPTs of a BN.

To me this does not look right. The reader who just wants to quickly grasp the contents of the paper will likely be confused.
Is there any convention about this? Do you think I am right to suggest the complete titles?

I agree with you. If the journal insists on using the acronyms once you've introduced them,  I'd suggest that you consider not introducing the acronyms at all. (Your paper would get a little longer, but perhaps careful rephrasing could mitigate that effect.) In my experience, though, journals have usually reverted copy editors' changes if I objected to them.

I also agree with you, and I would go even further and write "Bayesian networks (BNs) were introduced by" at the beginning of a section rather than "Bayesian networks were introduced by". I'd also probably leave off the 's' on "BNs" in the revised version I gave, but my guess is that an editor will put it there no matter what you say or do.

My cynical interpretation would be that it's 'just' a lazy find/replace on the part of the journal after interpreting your deliberate choices as an inconsistency!

I have done as suggested, I have reedited the titles and reverted to the full name at the start of section, including a comment on why I do it. Thank you all.

You should not assume that all changes introduced by the typesetters are the result of enforcing some house style. You should also not assume that these people are particularly competent. If they modify your text in some nonsensical way, you have two choices:

Page 7, line 15: Replace "Estimating the CPTs of a BN" by "Estimating the Conditional Probability Tables of a Bayesian Network".

Page 7, line 15: Please replace "Estimating the CPTs of a BN" by "Estimating the Conditional Probability Tables of a Bayesian Network".

Personally, I'd choose the first variant. This is not a request, this is an order. If they don't comply, escalate to their supervisor.

I think the copyeditors usually do not tell you their supervisor's contact information.

I kind of agree with @AnonymousPhysicist but for a slightly different reason which is that you're probably already doing your correspondence with the (academic) editor. They may not be a supervisor of a copyeditor/typesetter, per se, but they are the right person to work through if you have disagreements with copyeditors.

Please is polite. You also say "please" in a restaurant despite it's you that pay for your "order". It does not change the fact that you as author can insist on the paper being written in a readable way.

@CaptainEmacs I'm German. (Yes, I know that the English-speaking world uses "please" more liberally.)

It could be that they find your titles overly long and verbose (and they may have a point - they do this work for a living). But your point about giving people a fresh start in a new major section is valid too.
An in-between option would be identifying the major/minor terms in your titles and using acronyms only for the minor terms. For example:

Estimating the CPTs of a Bayesian Network

If you're already thinking about Bayesian Networks (and know what they are) then "CPTs" is easily recognized. More easily than

Estimating the CPTs of a BN

But it's less ponderous than

Estimating the Conditional Probability Tables of a Bayesian Network

It's a matter of style, and since it's your text in their journal, you should both have a say in it. Aesthetics and clarity should be balanced against each other as well. Treat this as a negotiating position, and consider the question from both viewpoints.

"they do this work for a living" From several experiences with copyeditors (which, as it seems, are often cheap outsourced labor forces), I can assure that this doesn't mean much in this context.

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text:
How do I cite my own PhD dissertation in a journal article?
I recently finished my PhD, and now I'm in the process of submitting a journal article on the work I did in the final few months of my degree. This work is an extension to some conference papers that I'd published earlier, and so I've cited them in my journal article stating how the submitted work differs from the published material. When I submitted the article to the journal, I mentioned in a cover letter that the same results/algorithms exist in my PhD dissertation.
After submission, I received a note from the journal to also cite my own PhD dissertation in the article, as there is a fair bit of similarity. The note said:

You can resubmit after you have referenced the original article, and explained in your new article how this new work builds on your previous publication(s).

Considering the work presented in the journal article is not really an extension, and is pretty much the same as in the dissertation, how do I properly reference it? In my experience, I have not seen papers where the authors cited their own dissertation in the text.

Maybe a google scholar search for "my dissertation" will give an example, close to your situation, that you can follow. Include one or more general terms for your field if you want something more field-specific.

Wording "the original article" may hint on some confusion. Are you sure you made it completely clear that the work in question is your dissertation and not a published paper? I think some clarification may be necessary

In my experience (Theoretical Computer Science/Mathematical Logic) this issue is typically handled by having the sentence "This article is based on Chapter X of the author's PhD thesis \cite{myThesis}." as a stand-alone paragraph at the end of the introduction section.
Having just the plain sentence is consistent with the article having been edited only minimally to turn a chapter into a stand-alone article. If there are substantial differences, these can be pointed out in addition. Eg "We refer the reader to \cite{myThesis} for a much more detailed exposition of the proof."

In my field this sentence is usually part of the acknowledgement section. Not sure exactly why that is!

In my experience, this sentence is often a footnote on the first page. It's also often slightly extended by appending "written under the supervision of [name of Ph.D adviser]."

Here's an example from one of the top economics journals of using the footnote on the first page: https://onlinelibrary.wiley.com/doi/pdf/10.3982/ECTA6248

If the dissertation is "published" then cite it like any other work. Otherwise cite it by name and authors and mark the citation as (doctoral dissertation, U of the Universe, unpublished).
It might only take a note or a short paragraph somewhere to explain how the present paper is related to the dissertation. "Builds" was just boilerplate. In fact, the note you sent to the editors might be enough if it is incorporated in a "prior work" paragraph or two.
"Published" is a nebulous term for dissertations. It can mean other than "by a recognized publisher". For example, some dissertations are "published" by the university and available via the Library or by ProQuest/University Microfilms.
But, failure to cite the ideas is self plagiarism. When in doubt, cite, even if you think it is over-citation.

Some dissertations are nothing more than a collection of previously published work along with a description of how it fits together as a whole. In such a case, just cite the individual papers as you would those of any researcher. Such dissertations are common in some fields and are also sometimes known as "stapled" distributions.

I disagree with the part about citing the dissertation as a published work. My dissertation was three working papers. I certainly was not expected to cite it when I published that work. I simply had a note in the acknowledgment.

For a "cumulative" dissertation as you describe, @Dawn, it is enough to cite the individual papers as you suggest. The dissertation isn't really a new thing, taken in itself. The OP here didn't describe it as such. And I assume you mean three "published" working papers. Edited to clarify

No, I am suggesting the reverse. The dissertation was working papers. When publishing, the convention is to write something in the acknowledgment like: “The present research was originally conducted as part of the author’s dissertation work at The University of Research.”

@Buffy Out of curiosity, is it common in the US that PhD theses are not published? At least in Germany (and I think in many parts of Europe), in general they must be published. Of course, traditionally this just meant handing in 30 or so copies to be deposited at some main libraries, and nowadays it means publishing it at the university library's website + 5 or so copies handed in.

@Buffy as an example: "PhD dissertations are published or otherwise made available for distribution as proof of the candidate’s achievement, echoing a traditional European idea that the candidate for a doctorate must make a contribution to knowledge and cannot have a degree for making a discovery that is kept secret. Because of this, restricting access to dissertations or delaying the release of the work (i.e. “embargoed”) only occurs in very exceptional cases." https://gsas.harvard.edu/degree-requirements/dissertations/publishing-options

@user151413, some places all that is required is to have it sent to ProQuest which is a "sort of" publishing. It isn't that things are held as "secret", but just that formal publishing may not be required. But graduates often "mine" their dissertations for papers after the fact. And "published" is a fuzzy term. Is available via ProQuest "published"? No peer review.

@Buffy What do you call "sort of" publishing? (I mean, what would be "real" publishing?) Is submitting 30 copies which get placed in some national libraries "sort of" or "real"?

@user151413, as I said, the meaning is fuzzy. Some would say yes, since it is probably available. Some would say no since there is no independent review. Fuzzy. In the US universities have their own rules. There is no national system.

@user151413 I believe the issue is about the generic sense of the word "publish/publication" and the specific academic sense. I am in the Netherlands; a PhD thesis would be "published" in the sense that a definitive version of the thesis is formally disseminated both in print (with dozens of copies) and digitally, but it is not expected to count as, e.g., a "prior publication" when submitting to a journal or be listed under "Publications" in the CV.

@jnanin I agree that it is subtle to ask whether this constitutes prior publication if you want to publish the result again (I agree it doesn't, which however doesn't mean it shouldn't be cited).  On the other hand, if someone published a result I had published prior in my PhD thesis, they had to cite it, because it was published prior.  So in that sense, it is just like any other published result.

@user151413 But that's equally true for working papers that are "published" on, say, Arxiv or SSRN. They can and should be cited as necessary, just like any other works, but that does not mean that the final peer-reviewed version of the paper has to cite its own earlier working paper version.

Traditionally, PhD theses constitute a public proof of your abilities and therefore need to be published. (This is certainly true in the places in Europe I know, but a quick search revealed e.g. the same for Harvard, and I assume it is true for more US places as well).
The traditional way of this publication process would be to print a certain number of copies and hand them in at your library, which would then distribute it to some central libraries (national library etc.) which hold a copy of anything published in a country/region. There is no need to be able to order the thesis with a publisher, for it to have an ISBN number, etc.. (Semi-fun fact: When people started chasing German politician who plagiarized their PhD thesis, in some cases all copies were borrowed from those libraries and were never returned.)
These days, the publication process (at least in natural sciences) often consists in submitted an electronic version which is made available on the website of the university library.  (It might be that a reduced number of printed copies still needs to be handed in.)
In either case, this constitutes a publication which can be cited.  It should be cited like any other book, i.e.,
High Voltage, "On current and resistance", PhD thesis, Tesla University, Berlin, 2021,
or corresponding to the journal style.  If it is published on the library website, it makes a lot of sense to add the URL or (if existent) DOI.
Of course, if the PhD thesis is not published, this is different, and it need not be cited. (In fact, one might argue it cannot be cited, as it is not a publication.)  In any case, if you are unsure you should check with your university, most likely either the library or the graduation office.

True for some US places, certainly. But there are no universal rules in the US.

@Buffy There are no universal rules e.g. in Germany either, in the sense of centrally imposed rules. Typically, each university makes their own rules for awarding PhD, and possibly departments can modify the rules. But I'm rather sure that all of those rules say that a PhD thesis must be published. I think this is simply the traditional perspective on a PhD thesis, see also the Harvard quote - that it is a publication, publicly demonstrating your qualification.

And, again, certainly true for Harvard. The US is not Germany.

@Buffy No doubt about that!  I guess in the US pretty much anything can call themselves a university and award degrees.

So, chauvinism now? Please. The standards here are pretty high generally.

@Buffy Sorry, this came across wrong. I know that the standards are pretty high in general. But there are also some rather mediocre places. So I was generally curious whether there are some official conditions to found a university, or in essence, anyone could open a place which can call themselves university and award degrees. (Whether people would pay for that, or anyone would take those degrees seriously, is a different story altogether.)

Seems https://en.wikipedia.org/wiki/Category:Unaccredited_institutions_of_higher_learning_in_the_United_States  and https://en.wikipedia.org/wiki/Diploma_mills_in_the_United_States provides some information.

Quote: 'In 2004, a housecat named Colby Nolan was awarded an "Executive MBA" by Texas-based Trinity Southern University.'   ROFL!

When I submitted the article to the journal, I mentioned in a cover letter that the same results/algorithms exist in my PhD dissertation.

The editor made a mistake.  Very probably an automated plagiarism check was performed without viewing the cover letter or examining the type of document the plagiarism check located.  The editor thought your dissertation was an article, which it obviously is not.
Are you sure this is a good quality journal?
How do I identify predatory and low quality journals? With Beall's List gone, how can I tell if a journal is spam?
It is perfectly normal to cite your own dissertation the same way you would cite someone else's.
Once you have cited your dissertation and determined this is a good journal, you can write in your response letter that the submission is a portion of your dissertation and it is not previously published in any journal (assuming that's true.)

If the dissertation is published (which can mean many things - basically just that everyone can go and look it up in some library), then it should be cited.

I agree that this is a mistake by the editor. Obviously you can use the text from your dissertation with a minor note or citation somewhere in the article.

@Dawn But isn't that precisely the point, that it should be cited properly?

@AnonymousPhysicist Hm, the editor might just have been sloppy or in a hurry.  In the quote, it also says "build on previous publications" (not: articles).

You could try pre-printing it and citing the preprint. Benefits are short time to `publication' (a couple of days, maximum, and only on a weekend) so very short delay to resubmission, moreover, the citation still counts for h-indices etc. I am sure that arXiv does theses as I have definitely read some there.
A proper citation could simply be a sentence like ``[type of result] [number or name if applicable] was developed in [citation], and is [restated/extended/some other word] here."
[citation] Your Name, Year, Your Dissertation Title, Dissertation from [your univ.]
This citation may be adapted if you do indeed arxiv it.

Putting the dissertation on the arXiv does not help with the OPs issue at all.

Not only was that not the sole content of my answer, but had you read more carefully, in combination with the rest of the answer it absolutely does aim to help -- here is a place to cite it from, and here is how to cite it, together following the conventions of normal self-citation practises in academic literature.

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text:
Can a hypothetical question be chosen as a research question?
Suppose, can I choose "what would happen if the USA doesn't exist" as a research question? Would this be still acceptable by a wider researcher community?

It's a terribly broad question. In what context are you asking it? Are you asking with reference to a particular group of persons? Are you asking about implications to global political dynamics? Global military dynamics? Regional military dynamics? Regional political dynamics? Economics? This is far, far too broad of an individual question IMO.

Thanks. @tonysdg
Sorry, it's a broad question. But suppose I want to discover the implications to global dynamics...and would it still be a research question?
My question is...is there any problem for a hypothetical question to be a research question?

Not at all - in a sense, every research question is a hypothetical question - or a hypothesis. Your job as the researcher (as I see it) is to offer credence to that hypothetical question and convince others - both in and out of the academic community - that (1) it's a valid hypothesis, and (2) you have some insight to offer into it.

One would need to be careful that your hypothetical was actually relevant to, and useful to, your particular community. In History, I suspect such a question would be deemed irrelevant. In political sociology, perhaps not (but your work would need to be based on that discipline). Just asking random counter-factual questions is not a good use of your time, and will be rightly rejected by your peers. Astrophysicist will scoff at my long detailed paper on the implications that the Magellan Cloud is made of Cheddar.

@JonCuster - I just want to point out that you missed a great opportunity to have a detailed paper on the implications that the Milky Way is made of caramel and chocolate.

@tonysdg - but NOT coconut - I hate coconut...

At least in the hard sciences your question would not constitute a good research question. A scientific theory is considered a 'good' theory, if it makes falsifiable predictions (i.e. predictions which can be compared to observations of the real world) and has not been falsified despite comparing it to lots of observations.
Suppose in researching your question you come up with the theory "Hotdogs would never have been invented if the USA did not exist". This is not a good scientific theory, since it can not be falsified by comparing it to observations.
Things would be different, if it would currently not be known whether the USA exists or not. If in this case you can logically argue that "Hotdogs would never have been invented if the USA did not exist", this would constitute a valuable scientific contribution, since it would provide a link between the observation of Hotdogs and the existence of the USA.

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Changing an experiment due to preliminary data
I'm writing a paper comparing the performance of 2 algorithms (lets call them A and B). A performs better than B, however preliminary data suggested a way to significantly improve the performance of B. I made the changes to B and sure enough now B outperforms A. I've verified that it's not just a fluke of the specific inputs I was testing against, making the changes to B leads to consistently better performance.
What is the best way to write these findings up? It feels an awful lot like cherry picking to me (especially since I didn't know when I started that I could improve B and for all I know there are improvements to A that could make it better than the improved B)
But despite its questionable origins the modified algorithm does perform the task faster and I want to include that information in my paper.
What is the best approach to take?
Call the modified version Algorithm C and just add it to the paper?
Add this information to the appendix?
Something else?

I haven't written enough papers on my own to offer a definitive answer, but I can say that you are most certainly not cherry-picking. Cherry-picking would be ignoring certain inputs where B is slower than A (and not reporting that). In fact, presumably you've got a paper here on how to speed up algorithm B. That said -- you should check to see if there's any past work on speeding up that algorithm, and you would need to rigorously check that you haven't made any additional assumptions or affected corner cases.

Consider this:
What question is your paper trying to answer?
This is the real question to consider. If I were writing a paper about average milk production of cows and my question was "How much milk does the average cow produce in a year?" and then I only selected the 10 best cows, then I am really answering the question "How much milk do the 10 best cows in my selection produce in a year?".
If your paper's aim is to compare two or three algorithms, then there's no problem. If you write a paper about A and B, it's no different from writing a paper about A and C or A, B, and C. How you arrived at the algorithms does not change question you are answering.

I would comment instead of answering, but I can't, so here it goes. What I would do is state what has actually been done, which is a project in two steps: (1) enhancing the algorithms as much as possible [you have already done this to B, but not A yet, so do it] and (2) testing for efficiency. This is consistent and clean, and looks perfect even though you started with something else in your mind. (If a research project could predict everything one would find during research itself, no research would be needed.)

So you have A, B and B'. If A and B have been already presented in the literature but a comparison has not been made, an article presenting B' and comparing it with A and B seems useful.  There is no cherry picking, since you are not ignoring data. It may be helpful to include your thoughts on potential improvements to A or B that you did not pursue.

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Ethics of using public and illegally obtained databases for academic purposes
I'm on my senior year of college, and my professor and I have decided on an independent study where I will analyze and develop some method(s) for screening valid data sets for the 'selection' phase of data mining, where spam bots, dead accounts, and other irrelevant data sources are omitted from machine learning analysis.
The problem i'm running into is that I really want to use a data set that is from the real world, so I could truly discover something meaningful from the data that hasn't been discovered before.
My initial thought was to use the Ashley Madison hack dump from the summer of 2015, but I wanted to consider the ethical implications of using such sensitive data. Alternatively, I was thinking I could manipulate the data before analyzing it to provide some sense of anonymity to the victims of the hack (for instance, replacing all full emails with the first and last character of the name, as well as the @ and suffix).
My question is NOT whether you think these practices are ethical, but whether there has been some professional work done in the past anyone is aware of that can serve as a model for my current work.
For example, Facebook was caught manipulating the content of its users' Facebook feeds in order to measure the emotional reaction of the content on their future posts.

There are a lot of publicly available datasets and even more available to academics. While the Ashley Madison set would add a certain excitement to your work, I'm sure you can find a more legal one if you're worried about possible consequences.

Note that the database is not necessarily (probably not at all) illegally obtained by you, it was illegally obtained by the person who posted it online. Your question title suggests you might hack some website and download their DB to use in your research.

Relating to just the AshleyMaddison data, there is a plethora of articles on your exact question. I will summarize the main talking points and provide links at the end.
1. Can I download it?
The data is probably public-domain, but it depends on where you live. In some countries like the US, the data itself is publicly accessible and part of a wider conversation about personal rights to privacy, whilst in others like Canada, is has been explicitly decided that AshleyMaddison still holds the copyright and downloading the data is akin to acquiring stolen property (note, AM is owned by AvidLifeMedia, a Canadian company, and people have said that this decision was to offer some degree of protection to ALM, as hacked users cannot use the data dump as evidence in court). Other countries say that fundamentally nothing that can be downloaded can be stolen, so this doesn't even apply.
2. Can I share portions of the data with others?
If you are in a jurisdiction that allows you to download it, you can by default share it - and many (perfectly legal) sites exist for just that. You type your name or e-mail address in to see if you are part of the hack (or your spouse was). For better or for worse, there is no crime for making public-domain data easier to access.
3. Can I process the data and share summary statistics?
Oddly, unlike the above 2 issues, this is legal in every country which offers protection for journalists and researchers - including Canada. Many researchers, particularly those researching infidelity, have asked lawyers this question, and they all say the same thing - yes it's legal. In fact, top US lawyers have gone as far as to say that journalists are probably in the clear if they publish a list of names of celebrities who appear in the hack, for whatever little public good/interest there might be there.
Many articles also point out that there is a big difference between the legality of this, and the ethics of this. Both the law of the land and what is considered ethical behaviour changes over time, and they don't always have to be in sync. Some say that in using the data you are condoning and even encouraging the hack - which may lead to more hacking/data dumps in the future. Other's say that your research may be the only grain of good to come out of the whole debacle.
I will summarize by saying what I would personally do, which is use the data, get the outcomes, then way up the pros and cons of those outcomes with the example you will be setting for others in using this data. Legality is really not the issue here at all, because even if it is illegal, you are incredibly unlikely to find yourself going to court from either Ashley Madison or hacked users, as both parties would have a very poor case. Those aren't my words, those are the words of Jennifer Granick, a law professor at the Stanford Center for Internet and Society.
So if the real question here is the ethics, then this is something that is ultimately up to you to decide on. There may be all manner of real repercussions from your department - particularly if someone in the department turns up in the database... - but that's a very different question.
http://www.huffingtonpost.com/entry/ashley-madison-hack-creates-ethical-conundrum-for-researchers_us_55e4ac43e4b0b7a96339dfe9
http://www.al.com/news/index.ssf/2015/08/is_it_illegal_to_download_the.html
https://onlinejournalismblog.com/2015/07/20/ashley-madison-ethics-journalism-hacked-documents/
http://fortune.com/2015/08/19/ashley-madison-media/
Finally, there are many stories that people have posted online detailing their experience at the hands of the hack. Some say it wasn't really them, some say it was. Some are outraged, some are just numb. I would suggest reading one or two of the longer blog posts to really get a sense of what this data means to some people. It's more than just a resource. People have committed suicide due to the shame or discrimination they faced as a result - most notably people from the LGBT community - so it's really important to not shy away from that when deciding to proceed, or not, with your research.

What's your basis for saying that, "Downloading copyrighted data is akin to acquiring stolen property"?

That many people have been found guilty of downloading copyrighted works which they did not legally obtain? If your setting up a "but in Spain/Switzerland/Cambodia/etc it's legal" trap for me, I refer you to the sentence after the sentence you quoted.

Regarding point 3  -  there is a difference between the process of how journalists can use the data, and how an academic/researcher can use the data. (I am pretty sure that an Academic/researcher in US (and Canada)  will need to go through an internal IRB (or IRB like-body) to get approval of their plans for how they will handle and report on this kind of data.

@Carol It's going to be jurisdiction-specific, but in the US at least, there is an exemption for using data that is already public domain "Research involving the collection or study of existing data, documents, records, pathological specimens, or diagnostic specimens, if these sources are publicly available..." - http://www.hhs.gov/ohrp/regulations-and-policy/regulations/45-cfr-46/index.html#46.101

@Wetlab_Walter, thanks - aren't those regulations written under assumption publicly available databases/records were generated so that they already satisfied the human subject issues. However, I acknowledge that this is way outside my field, my jumpy sensitivity is from listening to discussions within university committees charged with keeping our research misconduct/ethics policies. The main message I got out was, always in good faith put it in front of the IRB if it involves human subjects, even if it is to say that it falls under the NIH regulation.

@WetlabWalter: Your conclusion does not follow from your premise, unless "akin" is in the sense of "also being illegal in some cases". Also, have many Canadians been found guilty of this? (I'm asking because I honestly don't know). Finally, what about fair use, even in Canada?

Thats a good point Carol - the power handed down from the US government to IRBs (and the exceptions to their jurisdiction) as laid out in that linked document probably was written with the assumption that publicly available data cannot illegal and thus not ethically ambigious... however as you rightly go on to say, thats not for us to decide. The law is the law, even when its unfair, which is why both of us have in-house ethics committees who say "before you do anything, check with us!". And thats a very good point that I totally overlooked - the OP must check if they also need such approval.

I think you're conflating "public domain" and "publicly published"; to be in the public domain is to have no copyright, and just because something is public doesn't mean there is no copyright attached to it.

On the one side i've got einpoklum criticising me for suggesting that the works are protected under copyright (I know AM has sent out lots of DCMAs and many think these notices aren't legal, because databases of facts on their own often aren't copyrightable), and i've got Geoffrey on the other side telling me I'm conflating "public" with "public domain", suggesting I've failed to grasp that the works are copyright. I can't win :P

Very thorough - by far the best answer I see on here. I also agree with your suggestion for modeling the study (analyzing the data, then determining the precedent I would set by releasing it).

The answer of @dan1111 covers very well the ethics/legality of using this particular data set. To answer the question: are there standard methods of handling the human subject aspect of the proposed research? (with respect to your instinct that you should anonymize the personally identifiable data in it). I will assume you have a similar public dataset that was legal and that you did get the permissions to use.
The answer is yes. But at least in US universities, what you propose is classed as human subject research because of the personally identifiable information. Your research plan would include strategies on how to protect the human subjects, (protecting the the personally identifiable data). And it would  first be submitted to the university internal review board (IRB) before you touched anything. They might expect a plan that ensured that the PII be anonymized even before you get to 'view' the dataset. What you propose might be enough, but they may require more steps or protections in place.
There are several questions that are similar on stack exchange and the answers will also mostly jump to quickly point out the equivalent of IRB approval.
Ethics of scraping “public” data sources to obtain email addresses, Sensible measures to ethically use freely available, but personal web-based comments in research?, Is it legal/ethical to use data grabbed from a Stack Exchange site in a paper?


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What is the purpose of getting good grades once in college?
So, I understand good grades in high school, you use your GPA with your application to college. Once your in college, is there any reason, like putting your college GPA on your resume, to get anything greater than a C(unless to fulfill prerequisite grades)?

The Dutch Wikipedia has an article on exactly this: Zesjescultuur.  Google Translate may be of help ;-)

You don't go to college to get grades, high or low. You go to college to gain specialized knowledge, and grades are a reflection of your mastery of such knowledge. Given the same college degree, applicants with an average A grade will invariably be preferred to applicants with an average C grade, on the good grounds that they have superior knowledge.

[continued] As in, if you need to have brain surgery, someone who graduated top of the class from Stanford Med School would be an obviously better choice than a bottomer from a provincial university. If you are having legal troubles, a top graduate from Harvard Law would be an equally obviously better choice than Lionel Hutz. This is not because grades are important in and of themselves, but because they reflect breadth and depth of knowledge.

There are several reasons to aim for good grades:

You will probably want either a job or graduate school admission after graduating. The better your grades, the easier it is going to be and the more choices you will have.
You are in college to learn. Why waste your time and the college place on not doing your best?
Think about those prerequisites. If you only just make the grade to go into the next class in a sequence, you may not be able to keep up and may fail some of the later classes.

On point 2: unfortunately, learning subject matter and learning to the test are more often than not quite different.

@gerrit If a test does not measure understanding of the subject matter, it is a bad one. I cannot recall ever taking such a test myself, at least not in post-secondary education.

@fkraiem A test can only measure a distinct subset of understanding of the subject matter, namely, the testable subset.  The ability to perform well in written tests does not equate the ability to perform well when applying knowledge and skills.

In my experience as a student, good grades do not in general indicate a great understanding of the material, but bad grades do in general indicate a poor understanding of the material.

@user28375028 I agree. There are several strategies that can lead to good grades. One of them is to really understand the material. That is the one I'm recommending.

@gerrit If your primary goal is learning, grades can be a useful indicator of understanding. If you just want good grades, you can probably figure out easier ways of achieving them than learning. All systems can be gamed, but a system can still be useful, if you decide not to game it.

Kind of disagree with this.  I've only been asked for my college transcript by an employer exactly once since I graduated.  This includes working in three fortune 100 companies and holding a teaching position at four different universities and earning a tenured position twice.

The other answers give the standard practical reasons why one should aim to get good grades, but I prefer a more idealistic explanation, which is that good grades are not the real goal one should focus on, but rather a side effect. If you focus on the real goal of learning the material at the highest level possible, good grades will follow automatically. So, good grades do have their practical uses, but philosophically speaking, they are just a distraction.

As the other replies already make many important points, I'll just add a few that are not listed yet:

During college special programmes might be accessible only if you have a good GPA. Look up "honours programme + your college name" and something might pop up.
In some cases you might be able to compensate for certain grades by scoring higher on other subjects, this also varies per college.

The purpose of high GPA (good grades) as an undergraduate in college is to demonstrate to future employers, collaborators and professors your ability to complete a certain amount and level of work in a satisfactory manner. Many factors in your life will be influenced by your undergraduate GPA:

many scholarships have a minimum GPA and academic progress which must be met.
Graduate school admissions are largely based on undergraduate GPA, class schedule, and letters of recommendation.
Many Future Opportunities are only available to those who achieved a high GPA, for example, I have seen Ph. D. programs which require a 3.0 minimum undergraduate GPA.


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work doesn't show on paper
I was on vacation when a senior PhD student wanted me to help with his project. I rejected and my advisor sent me an email to check whether I wanted to co-author this project a few weeks later. I accepted because he is my advisor and It'll be nice to have a paper for graduation since I just got into the PhD program. I worked on this project for about 3 months with full commitment(including weekends) so that the tool built by the senior student was able to run on some platforms.
But the result turned out to be not very good so the senior decided to remove the part I worked on from paper. But I did all the tasks like analysis and it was not my mistake for the result. He told me my contribution for this part was probably equal to or lower than polishing the paper. The reason is that the paper is the final product for submission. I asked him how to count the contribution and he told me by feeling. I'm really frustrated. My advisor told me to come to his office with the senior maybe talk about the project. I know there is nothing I can do. Maybe someone can help me to overcome my mental issues.

Your advisor is the best person to decide whether you should be on the paper.

Is there any mention of your work in the article? E.g., "we investigated blah but the results were inconclusive"? If so, definitely. If not, then I still think there is value in your investigation showing that the researchers that their direction was wrong. Your authorship is payment for your work. You deserved to be paid.

You have learned that research is a process without certainty of result. If your work doesn't appear in a paper, you have no claim to authorship, though it would be polite and professional for the authors to acknowledge your work in the paper.
However, what you did isn't necessarily lost and can be, perhaps, worked on in the future, expanded, and possibly result in some future publication.
But there is no reason to "beat yourself up" over such an issue. It isn't a failure on your part, but just in the nature of scholarly work that not everything reaches fruition or the result we wish. Don't give up.
Even if there is no visible result of your work, however, the goodwill of your advisor can mean a lot for your future. Even the NY Yankees occasionally end up in last place. (Sorry, local reference)

Those ideas that didn't pan out or make it to publication always have a funny way of popping up in future problems. Digging into a topic is rarely fruitless if you wait long enough.

Different fields will handle this situation differently. If something doesn't work, then the fact that it doesn't work can still be a valuable contribution. However, if your advisor agrees that your work shouldn't be included, you have no reason to doubt his judgment.
Unfortunately, in research, you have no guarantee of success whatsoever. If you ask around, you will probably find that everyone with sufficient experience has at some point spent three month or much longer without getting a paper out of it.


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How can I find if a certain study has been replicated or the results reproduced?
I am trying to find additional research about a certain topic.  I have found one study that is specifically about this topic, and the results are very interesting.  I would like to find out if any additional studies have attempted to reproduce the results.
I have tried searching online using several ID numbers found on the nih.gov site where I am viewing the original study.  There are very few search results, and the search results seem to all be referencing this same original study.
I have tried emailing the author of the original study as well.  To my surprise, I actually received a response, but it was short, contained merely a list of some links to "more information" about the topic (these websites were just general information), and did not respond to my question about additional studies. (To be fair, this author is an active professional, so I understand that they may not have time to email with me.  I have not attempted to reply asking my question again.)
Perhaps I am not finding additional studies because there have not been any.  It may also be that I am not using the correct tools/resources.
Is there an established way to find if a particular study has been replicated?
This question is intended to be generic enough that it is relevant for any study.  However, for my particular topic, I have managed to find one study that repeated the original in another country.  I am currently looking for more.

Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.

@Community I'm afraid I don't understand your request.  The question seems very clearly put to me, "Is there an established way to find if a particular study has been replicated?"

Look at any article that cites the study.

@JonCuster How do I find these articles?  Also, is this a recommendation to check other citations within the article?  So far, what I've read that refers to the original study refers only to the original, and not others that have attempted to replicate it.

Your friendly local research librarians can help you, either directly or by showing you how to use various search engines (Web of Science and the like).

Was the original study pre-registered?

No way around it, this is a difficult issue, and there's no truly reliable way to solve the problem. But we can approximate searches by things like "Web of Science". Beware, many things are not indexed on WoS...

@BrianBorchers I'm afraid I'm not sure, sorry!

@JonCuster and @.paulgarrett Thanks for the tip about Web of Science. I'm not familiar with that tool and will try it out soon.

The “Community Bot” is so stupid. HOW MUCH MORE SPECIFIC DID HE NEED TO BE

Whoever tried to reproduce the study and published about their attempt would surely cite the original paper, as commented by @Jon Custer. So looking through papers that cite the original could be a start. I found that "Cited by" in Google Scholar has good lists of citations for a paper, including preprints. However, there would be a delay before publications appear. Also, some reproduction attempts, especially failures, might never be published.

That's a good point about some attempts not being published.  I agree that looking through papers that cite the research would be good, but that's kind of begging the question.  I'm trying to find those very papers; however using the "Cited by" in Google Scholar is a good tip, and I'm going to give it a whirl soon to see what it can turn up.

It boggles the mind how Academia has encouraged NOT publishing replication studies with a null result. Madness.

It is not a general way to check if any study has been replicated, but the journal ReScience X publishes replications of experimental studies and its sister journal ReScience C publishes replications of computational studies.
These could be a place to check for possible replications.


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Is graduate school still an option for me?
I am a senior in Electrical Engineering. I always wanted to go to graduate school to at least get a Masters but I am now starting to doubt that it is even an option for me. GPA of 3.4ish with a major GPA of 3.2ish.
I have a very weak background in Math and Physics (and Chemistry) (grades ranging from 1.8 to 2.7) and I took them during my first 2 years in college. The only explanation I have for such bad grades is that because I was very unmotivated in my first 2 years but to be honest, that just sounds like excuse to me. I also recently just failed a Stats class due to the same reason. I'm embarrassed that I actually failed this Stats class, so I am determined to get A as I retake the class. Apart from that, most of my grades are at least 3.0 or above (Only got one 2.5 in an intro to EE class).
Is grad school still an option for me, even for less competitive programs? If I study my butt off in my final year to get as many As as I can, have strong letters of recommendation, would that increase my chances/leave a better impression? Any advice on what I should do to improve myself and to prove that I am capable of handling graduate school?
(Below are information that would probably help answering/giving advice)
Outside of school, I hold several engineering related clubs officer positions and have more than a year of research experience. I also recently got invited to another research group based on my performance in one class (on track for 4.0). In general, my grades are very tilted, if I'm interested in the topic, usually it will be 3.5 or above.
If there are any professors here, how do you feel about students like me? Do you see me succeeding in graduate school or do you think I am bound to fail as an engineer?

https://academia.stackexchange.com/questions/38237/how-are-ph-d-applications-evaluated-in-the-us-particularly-for-weak-or-borderl You might be interested.

That post is very helpful, thank you so much!

I doubt we can add much to the above post (and evaluating individual profiles is not our role in any case). A 3.4 is not so bad, and it sounds like there is a positive trend, which is good. But, multiple Ds and Fs will indeed count against you, as you know. In any case, it is not a matter of people assuming you are "bound to fail as an engineer"; it's just a question of selecting X candidates from Y applicants with X << Y. All you can do is read the linked page, do the best you can in your final year, make a large number of applications, and see what happens. Good luck.


text:
Transitioning, First Name Change
I have begun my transition (MtF) and my PhD. This includes, once I have jumped through all the legal hoops, changing my given name. I already have a publication, its very minor, but still I would like to reduce as many mentions as possible of my previous life, so to speak.
Can one contact Elsevier and ask them to change the name on a publication?
I also want to be as thorough as possible in changing my name, because historically trans rights are not a permament thing, so if the wind changes in 25 years I will hopefully still be alive and only a few ppl will know I am trans.

Note in particular the recently updated answer there which shows that Elsevier should be receptive.

One can certainly contact Elsevier, explain the situation, and see what they say. However, generally any change to published work generates a paper trail, such as publication of an Erratum notice in the journal. This is likely to be contrary to your aims, as it would create a public link between your two identities.
Given that this apparently affects only one paper, the best option may be to quietly drop it from your publication list, so that there is no definitive evidence of a link to your new identity. Perhaps the author was your brother, or just a random stranger who happened to have the same surname.

This answer: https://academia.stackexchange.com/a/195062/63475 indicates that Elsevier is part of a program that limits this paper trail for exactly the purpose OP is asking about https://www.elsevier.com/about/policies/inclusive-author-name-changes


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Should I escalate concerns about the format of an unfair assessment?
I have an upcoming assessment worth 45% of our final grade which I do not think is fair.
We have been allocated into groups of twelve, which is further split in half. Each sub-group is to prepare a report on a topic which is broadly related to the other sub-group's topic. Material co-operation between the two sub-groups is optional.
However, the whole group receives the same mark. I cannot fathom why this would be and why the sub-groups wouldn't receive seperate marks. I think it is unfair that we will be given very limited opportunities to appropriately vet or contribute to the work of the other group yet are still marked for it.
I asked my professor to change it, and she refused. Should I escalate this to the department chair? I don't want to come off like someone who is complaining without merit, nor do I really want my professor to know I complained against her.

Don't escalate to department chair
Upon closer inspection , this assessment is nothing special : You have 11 groupmates , report on 2 similar topics . The ‘sub-group’ part is just telling you to distribute the work .
Poor combination of the 2 topics , poor corporation etc. may lower your grade , like any other group work this should be no surprise .
The department chair is very likely to see you as a non-team-player if you complain to them .

General etiquette :
In general , you’re not in a position to "ask my professor to change it", which may even come off as rude .
It's your professor's job to decide how to evaluate your performance under university's policy  .
You can escalate if there's obvious policy violation , be sure to collect strong evidence . False accusation may backfire on you .
If you're just uncomfortable , you may kindly address your concern to your professor/school counselor , don't make demands or accusations . You may also provide honest feedback e.g. via the "end-of-course evaluation survey"  .

It is an interesting grading concept, I think. It introduces a positive  but competitive aspect, a goad to good work. Under those rules you do best by doing a superb job to make up for the possible failings of the other half of the "team". They have the same incentives. So, I find it hard to condemn.
Many competitive teaching aspects are, IMO, unethical, but this one doesn't seem to be, since you aren't graded against one another, assuming I'm reading it correctly. You each get to support one another by doing good work.
But, yes, if you think it unfair and the professor disagrees, then you can escalate it, though I doubt you would be successful. Most likely, the head or dean or whoever, would seek advice from the professor, using your name or not, and some of the above reasoning might come out.
If you do, escalate it, don't make it about the professor, but about the scheme itself.

I disagree regarding the first paragraph: Giving the same grade to twelve (!) different students essentially decouples the grade from each individual student's performance. Even if a student chooses to work extremely hard, it's more or less impossible for them to ensure by their individual efforts that they will receive a good or very good grade. (Very good advice in the last sentence, though.)

@JochenGlueck, grading all members of the team equally is common in some fields. It is the very meaning of a team. Of course, teams require guidance in how to work effectively together.

@JochenGlueck: this type of exam requires a task that can only be completed if all team members contribute and help each other. I think Buffy's first paragraph is great as long as the exam task is chosen well. I have had really good experiences with this type of examination, though the initial reaction of the students was similar to that of openherring.

@Aolon Can you give an example of a task that 'can only be completed if all (or at least most) team members contribute and help each other'? All reasonable undergrad tasks for a group of 6 that I can come up with are usally done by 2 or 3 dedicated students (sometimes only one) plus minor input from the others.

"Under those rules you do best by doing a superb job to make up for the possible failings of the other half of the "team".  that seems at odds with the purpose of group projects, which are usually to do with being able to work as a team.  Excelling to make up for others is a bit of a slippery slope and easily leads to being exploited, which is a sign of poor management.  This is not exactly unknown in academia, so I don't think it is something to be encouraged.  The question is, why are they working as a group?  What are the learning aims?

@DikranMarsupial, some projects in CS are naturally divided into two parts, servers and clients, for example and building vs testing. Without details it is hard to judge, of course, but not all "competition" is bad.

@Buffy, I wasn't referring to the two parts issue, but why it was groupwork rather than an individual assessment.  I teach in CS, and one of the reasons we use group projects is so that students can learn to work as part of a team as that is what they are likely to do in industry.  Also for programming, programming with other people helps you to understand why it is best to write "good code" rather than just "well, it works doesn't it?" ;o)  Gnerally we could make everything an individual assessment, but that would not help students to gain management, planning, communication skills.

@DikranMarsupial, now I'm confused. Why not group work?

IMHO if a project that was aimed at covering these skills ended up being dominated by one student doing a brilliant job, they would all deserve a low mark for not meeting the learning aims.

@Buffy, sorry, I don't understand your question, is there some subtext?   There are some skills that are best assessed by individual assignments (basic coding skills) and others that are best assessed by group work.

If someone dominates a group, then that is a failure of the group as a whole, as it effectively isn't being managed by any of them.  Grading group work is always difficult, anything that involves people rather than just computers is always asking for trouble ;o)  Often even if the learning aims etc. have been explained and management issues taught, students are often very focussed on marks and getting the code working.  I don't think there are any universally good solutions to this problem, but it is a very important set of skills in CS.

I reckon I have another 10-15 years left in me ;o)

@DikranMarsupial I remember at least one group project in one CS class that required weekly reports from each group member on who did what this week, and an overly inequal division of work would result in reduced points. However, most of our projects were in groups of 3-4; the larger the group the more likely 1-3 people do all the work.

@quarague Sure. Critical analysis and presentation of a research article where each team member has to present and they can receive any questions during their part of the presentation. It means they cannot simply split up the article, do their part and present separately. They need to put the pieces together, teach to each other what they learned and then they can create a coherent presentation. They get a shared mark based on the weakest link. In six years, I have only had one group that failed, all the other teams worked together and did wonderful presentations.

This grading method is unfair and difficult to defend. Grades are meant to assess your individual work and abilities — that is their whole purpose. Now, it’s true that this principle can reasonably be compromised in a small way in some project-based courses that have as their secondary goals the acquisition of “soft skills” such as teamwork and collaboration. That means that it’s defensible to give the same grade to small groups of 2-3 students working on a project, since this is a situation in which a student can reasonably stay informed of what their team members are doing and help ensure that the final work being submitted by the group is at a good level (by cajoling their team members, or stepping in to help as needed) even if there are some differences in the abilities and work ethic of the team members. The ability to collaborate with others and bring a collaborative project to a successful completion is a very valuable real-life skill, and it’s reasonable for a professor to want to encourage developing it.
However, in a group of 12 students, there is no realistic chance for a single student, however talented and hardworking, to ensure that the final work of the group as a whole is at a satisfactory level. If all the students in such a group get the same grade, that means some of them will almost certainly be unfairly penalized for the lackluster performance of other students. And some of them will almost certainly get a grade that is much better than they deserve. For a professor to willfully implement such a grading system seems to me deeply misguided at best, and unethical at worst.
I don’t know if you should complain. If your university and department are reasonably well-managed, I’d say yes, since it does not take a genius to see that this is not an appropriate pedagogical practice. But plenty of places in academia aren’t as well-functioning as we would like.
Even in a well-run department, grading policies traditionally fall under academic freedom (up to some limits of common sense, which are not frequently tested), so if the professor is a senior faculty member and will stand by her grading system, it is not guaranteed that there’s anything the department chair can do about it. If a direct complaint to the department doesn’t work, you could perhaps explore other avenues, like complaining to the student union, university ombuds office, etc, but as some point a cost-benefit calculation may make such steps seem not worth the effort.
In the end, the only thing we can say for sure is that if you don’t complain, the situation will not change. Good luck!


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What do you do when your PhD student is spending too long on a problem?
I am in math and I am fairly new in supervising PhD students, so I need some advice. I have a fairly good student who has made very good progress initially. But after a promising start, he's been stuck at the same problem for over one year, without making any progress. I have at a few occasions suggested that he should try another problem. He would then spend one or two weeks on another problem, but then he would always get back to the original problem with some new approaches/ideas (which still haven't turned out to work). He seems to have grown attached to this problem and feels that it would be a waste to abandon on something he's been working on for so long. I obviously admire his persistance and I always feel bad to discourage him from working on something he feels passionate about. But at the same time, I am worried that the longer he spends on this problem, the less likely he would be willing to move on and eventually give up altogether. What would you do in this situation?
Thanks in advance.

What would you say is working closely? At the moment, we have regular meeting about once a week and we would discuss for maybe one hour. It's very hard to say whether an accessible solution can be found. I have suggested a few possible approach but we haven't been able to get anywhere...

I think it would be better if you approach another ideas and problems, and also not giving up this problem. Perhaps after a few months working on another problems you came back to this particular problem fresh.

Are there ways of weakening the problem, such as instead of proving something for all integers, it's proved for infinitely many integers or for a set of integers whose limiting density is bounded above zero? Without knowing anything specific about the problem, I don't know what to suggest, of course, but I find it hard to imagine a problem that can't be weakened in various ways, and perhaps some of these weakenings have already been proved by your student, and if these proofs are sufficiently nontrivial, perhaps they could form a contribution to the final dissertation.

When I posted this question, I certainly expect so many answers. Thank you so much to everyone for their suggestions. I have indeed tried to help my student to savage this problem, but we never managed to get anything interesting. Some of the observations can go into his thesis, but nothing too significant unfortunately. So, I have come to the conclusion the problem is too hard. Like some of you said, it will be a great problem for his future. As an advisor, I take full responsibility for letting this drag on for so long. I have certainly learnt my lesson, I am hoping that he will too.

To flesh out user37208's suggestion, you could try thinking about the problem yourself for a few days (outside of meetings).  After that you may either have a better suggestion or a more convincing argument that the problem is definitely too hard.

Recommend him to read George Pólya's How to Solve It.

This is one of the hardest questions a math PhD advisor can face.  (Perhaps it is the hardest question.  It is certainly the one whose failure to adequately solve has caused me to feel most, um, inadequate as an advisor over the years.)  Here are some ideas:
1) You say the student is fairly good. I'm not sure exactly what that means.  For me, a good student can make substantial progress on problems of interest if the advisor sets things up very well: by choosing the problems well and by providing help when needed.  You don't want to watch a good student waste much more than a year working on something that is not going to come to anything.  Within this category, a better student will be faster, more successful and independent, and a worse student will need so much help from the advisor that although the student does solve his own problems, the advisor must put at least as much thought and energy into the situation as would be needed to solve the problems herself.
So for me, "fairly good" would mean a student who can be quite successful with a very hands-on advisor.  I would not want such a student to spend a substantial amount of time on a problem that I didn't have some idea how to solve.  That's a strategy for a higher grade of students (a really excellent student can carry the risk of failure of working on truly difficult problems and can also learn from the experience of choosing the wrong problem).
2) One year is too long for almost any mathematician to work on a problem without making any progress.  Certainly I have never done anything close to this (although I have spent many years writing certain papers: progress was being made, just slowly and there was always more to do).

I obviously admire his persistance and I always feel bad to discourage him from working on something he feels passionate about.

To be honest, I don't really feel the same way.  Working on something for a year without any payoff sounds irrational, maybe a bit obsessive to me.
3)

But at the same time, I am worried that the longer he spends on this problem, the less likely he would be willing to move on and eventually give up altogether.

To be honest, you don't sound quite worried enough.  The fact that he has nothing to show for a full year of work is already a problem for him and his future career.  A student can no longer graduate with "one theorem" and expect to be competitive in the academic job market: increasingly, successful graduates already have a body of work.  Moreover, most successful graduates draw on the knowledge and skills of their advisors in very deep, substantial ways: without enough of this access, they may not be competitive.
For a student who has been spinning his wheels for a year, I think you need to step in and give him a new problem in which you know exactly how to solve some initial segment of it.  Starting in a place where you are essentially telling them what to do seems like a good remedy for the situation: even implementing exactly what your advisor is telling you is more than one or two weeks work for a good student.  If you make clear that you do expect him to work and make progress on this new problem -- with your help -- he is likely to do so.  If you have a meeting with him in which he tells you that he worked on the other problem instead, reiterate what you want him to do and schedule another meeting only a couple of days later. If you can keep on him closely enough, he'll get the idea: you fully expect him to make progress on this new problem.  If he wants to work on his own problem in his spare time, great, but you are making sure that doesn't interfere too much with his new day job.
I hope it doesn't sound like I am scolding you.  As I said, advising is such a hard job that most people I know don't feel they are doing as well as they should.  Anyway, good luck.

Very nice answer from Pete as usual. I would add however that if the student doesnt want to stay in Academia after the PhD, then actually it might be better for him to stick with it to the end, even if it takes another year.
Another consideration, which i find to be true for programmers but maybe less so for mathematicians, is that the more you re-write your work from scratch and discover alternative/better ways to do something, the more you develop as a programmer. In a sense, it's always good to dive deep into 1 thing. From a learning perspective at least.

@WetlabWalter: "I would add however that if the student doesnt want to stay in Academia after the PhD, then actually it might be better for him to stick with it to the end, even if it takes another year." What makes you think the end will take only one more year?  What makes you think he will ever solve the problem?

@user58865: "But wouldn't you say that this student's obsession with the problem is a good trait - and welcomed / admired, even expected by thesis advisors?" No, I am a thesis advisor and don't expect students to be obsessed.  Very committed to a problem is great...if progress is being made.  "A least initially, before he learns his lesson that one can obsess over a problem and still make no progress on it and must move on." Hang on -- we're not at initially anymore; we're one year later with no progress.  You are really changing the question.  But yes, I agree with what you end up saying.

Is it something he can set aside and come back to later, when he's completed his PhD?
It might help to remind him that he doesn't need to accomplish everything he wants to research as a graduate student.  If there are areas more likely to bear fruit, he may be well-served by focusing on what will get him to his degree and into a research position first, then coming back to his unsolvable problem, when it's not holding up his career.  This way the work he did actually isn't wasted time.
You might also tie that into issues of funding and such, although you didn't say anything about whether that's a constraint.

Is the problem solvable?  Maybe it isn't, and the student just needs to stop working on it.
Is the problem divisible?  Taking any problem and breaking it down into multiple steps can help.

From the student perspective, and also a teacher. It would be good to have an informal meeting along with tea and discuss the matter. You can tell your honest opinion about the problem, the timeline and the progress. Ask him that instead of working in this problem it will be better if we go for that problem so that we both have interest as this probkem is taking too much time and i feel bad that you are working alone on that problem and my supervision is of nonuse in this case.
Dont tell him that you wasted time with no result/progress on this problem as he will try to prove his self and work on the same problem just to prove that he did it or will give up considerin him self a low performing student.
The more friendly environment you keep the better results you can expect and control as well.

I think that in every work we should consider the deadline. You can set a deadline and if your student won't progress, change the thesis topic very quickly.
Based on "fail fast" strategy, you should always have an alternative plan and if the primary plan didn't work, fail fast and go to alternative plan.  It could save you a lot of time.


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Need advice on applying for new jobs as a tenured associate professor
I posted this on reddit, but I thought I would post it here as well in order to get as much advice as possible. I hope it is OK.
I am a tenured associate professor who is applying for new jobs at other universities. I have a lot of questions and I would like to hear some of your opinions.
I am at the stage where I can realistically apply for full professorship at my home university soon. This is actually an important reason for me to apply for jobs now because I feel that once I become a full professor, it will be a lot harder to get a job in another university because most openings in my area are at the assistant/associate level.
Already, one of my contacts in a university I am applying to already told me that they might not have the budget to hire someone with so much experience, even as an Assoc Prof (the salary there is calculated based on the number of years in service). But at the same time, some more senior colleagues told me that I should ask for full professorship (maybe not at the aforementioned university, but at the other places). I am worried that it might come across as greedy. But I also heard that being bold can pay off. In one of the openings, it says that "full professorship will be considered at exceptional cases". In others, only assist/assoc. What is the best strategy?
Another thing that I wonder is what I should do with my grad students and postdoc (there are 5 of them working with me at the current university). Should I ask the new school whether I can transfer them with me? Is it something I should mention at the interview stage, or only when an offer is made?
I am also supposed to be on sabbatical next year. Will it come across badly if I ask for sabbatical leave in the new school too early? Alternatively, how would it be perceived if I ask them whether I could start in the new school one year later, after my sabbatical leave with the current school?
Thanks in advance!

Careful. At some (many?) places, taking a sabbatical comes with the requirement to stay for one additional year afterwards.

Do you have a reason for wanting to leave? Are you a superstar - leader of your field? Is your advancement to full an obvious outcome?

Thanks for the comments. In our school, we would have to pay back half of the salary if we leave straight after a sabbatical. I will have some external funding, so in balance, I will come out even.

The resason why I want to leave is simply to go to a better school. My current school is OK, but I can fairly say that I am a big fish in a small pond. I am not at all a leader in my field, but given the school's policy, I think advance to full should not be an issue.

If there is a condition that absolutely must be satisfied in order for you to accept a job offer from a place, then as a matter of ethics, common sense and professionalism, you should mention it at the time you are applying. Otherwise you’re just wasting people’s time.

I definitely agree with you. Regarding sabbatical, I am thinking either ask the new school to give me an early sabbatical or I start with them one year later. I am just wondering from the new school's perspective, how they will see the two scenarios.

I don't think this is a full answer, but let me raise some issues. Not knowing more, I'd think that, on balance, you'd be better off advancing to full where you are and then searching for a different place. And taking your sabbatical in normal order.
Note that I was (twice) hired at the rank of full already in hand. On to the issues:
Many places, especially in the US, are constrained from hiring without a wide (national, at least) search. This can be finessed to some extent, but you may not be able to avoid competition for any position. If you have skills that are a bit unique and that fulfill a specific need at a new institution (my case) then it can be made to work more or less. Some job adverts are very specific in the requirements, tailored for a specific individual.
If you move to a new place, expect there to be a period of probation, probably about two years (not seven). Expect there to be a vote of the faculty at the new place on your tenure. This is probably pro-forma if you are collegial and do the job, but not always the case. In one of my moves I wound up with a very hostile chair/head, resulting in the second move. So, a bit of caution. But, moving as an associate leaves you with both a future tenure decision and a future promotion decision perhaps. You might be able to get them combined in to one decision.
I'd guess that a quick sabbatical at a new place is out of the question. They need to know you are a good colleague and productive before they want to take a risk. Starting a year late might be reasonable if you have the funding for it as well as a solid (research oriented) reason for doing so. A year in the south of France or Spain won't do (nice as it might be).
The students are a bigger problem than you suggest. Even if the new place has room (and funding?) for them they may not all want to move, leaving them with problems and potential setbacks. If you move on to full where you are, while also reducing the number of students you are responsible for, you can reduce this problem, maybe to zero.
Anyway, I don't see a big difference between getting hired as associate and wanting to move quickly to full vs getting hired at full. I think decisions are more likely to be made on what specific role you can fill that no one else is able to at the moment. There would be a difference if there are any quotas at rank or if there is a feeling that the faculty is already top-heavy.
Alternatively, some places might feel it more appropriate to provide an upward path for an existing faculty member than hire an additional full professor. And the question, then, occurs, would you be that existing professor due for promotion. That is why I suggest you need to be able to fill some specific sort of need to make a smooth move.

Thank you so much for the advice. It's great to hear about your experience. My worry of applying after becoming full is that it's very rare in our field for a full to move to another university unless you are one of the tops. Our research is rather individualistic and people tend to just do their own things. Usually a department would look for someone who publish, supervise who can get external funding and teach well. The specific topics of our research is not so important. So, if I am full, it would be expensive and they may prefer someone younger, who will cost less.


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Publishing while working for a drug regulatory agency
I am a recent MD-PhD graduate in the field of clinical pharmacology. While searching for post-doc positions (which are quite rare in my country), I came across several job offers from a drug regulatory agency. I would meet their profile requirements.
Although not my first choice, I am considering this option until I find a suitable post-doc position. Of course during my time at the drug regulatory agency, I would keep a link with academia with my current research group and would like to continue publishing (on topics not directly related to pharmacology).
Could it be a issue for publishing if an author has an affiliation from a drug regulatory agency? Would this take away some credit to the paper? I am asking this question as I understand that these agencies may be associated with some controversies (1).
Selected reference: (1) Carpenter, D. P. (2010). Reputation and Power: Organizational image and pharmaceutical regulation at the FDA. Princeton University Press.

Note that some companies will contractually prohibit publishing by employees without approval.

The answer will depend on the particular agency and its policies.  It might for example be the policy that any publication requires approval by the agency but that publications not related to your work for the agency are commonly approved without difficulty.


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Best Practices : Having your PhD Supervisor as your co-author?
I am in the process of writing a paper. I have done the data collection, and am in the process of analysis. But somehow my supervisor does not show much interest in my work or my research topic (i am in 2nd year, this is my first paper ), we meet once a month to review my overall progress.
I have a paper submission deadline approaching, Should I mention my supervisor as a co-author?
How should I ask my supervisor, if I can add their name as a co-author?
The thing is that I don't mind either way, adding them or not adding them,
I am just too awkward to start this conversation with them.

Please have this conversation with your advisor rather than with us strangers on the Internet. Independently of what you choose, there is a chance that guessing wrong may have severely negative consequences for your future relationship with your advisor. Adding somebody as an author without their knowledge is a big no-no, but on the other hand you can scan our archives to see what fallout may happen if you submit the paper without your advisor if they expected co-authorship.
Also, there is absolutely nothing awkward about this conversation, and you should learn to discuss authorship with your collaborators sooner rather than later.

Hi thanks for the reply, Yeah, I absolutely agree with you. I will bring this topic up in the most genuine way as possible.

This varies by field and probably by place as well. In math it isn't usually the case that the advisor is a co-author unless they are a true collaborator. In some lab sciences (and elsewhere) it is common, even expected, that supervisors (PIs especially) will appear on nearly all work.
By rights, if not by custom, if you are the sole source of the intellectual ideas in the paper, then you should be the sole author. Author should mean that the person has an intellectual contribution. But in those lab sciences, that contribution might be there in fact, but somewhat remote.
For example, I don't appear as an author on any of my student's work (CS), though I gave them considerable guidance at times. But they were the intellectual drivers so get sole credit. Likewise, my doctoral advisor doesn't appear on my dissertation (math) or resulting paper, though he is the (attributed) creator of the proof of one of the key theorems (I had a different, less interesting, proof).
If you need to know, you need to ask directly. It isn't likely that this would be the first time the question has come up for them. And you need to learn the conventions of your field in any case.

Hi Buffy, thanks for your perspective, it really helps. I will ask them directly.

If you send them a draft, say that you are about to submit this draft, and this draft does not have any authors listed, I would expect your supervisor to bring up the question of authorship themselves.

That is a pretty passive-aggressive way to 'deal' with it. Much better to be up front.

I don't think it's passive aggressive at all.


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Mathematics MSc Dissertation - Referring to myself and acknowledging own work
I'm in my last week of my mathematics masters dissertation and I don't really know how to refer to my own work and to myself in the dissertation. To refer to myself I'm using "this author" but it sounds a bit hokey, but obviously I feel like using "I" is a bit too informal.
Likewise, I'm referring to own workings, as an example, as "we will complete this proof ourselves" which again sounds odd (and I've put in my introduction that this is how "this author" will refer to own workings). I don't particularly want to refer to all my work as "this author's work" as I feel like it's a bit pretentious for just a masters diss.
In my undergrad dissertation I just omitted this phrasing and stated that all work without a citation is my own, but my referencing style has changed since then and it would be easy for the examiners to mistake my own work as something from a source.
On the flip side, my writing style is pretty eloquent for a maths student so perhaps using more pretentious language isn't out of place?

So I'm using "this author" in the context of referring to myself inside the thesis, eg, "in this report, this author does not claim any original results". As for the "we will complete the proof ourselves", yeah, that's why I'm hesitant to use it because it's a bit confusing - it's basically a way to say (in the proof of a theorem) "I did these calculations myself without the use of another source"

It is ok and IMO important to refer to yourself in the first person in this situation.  You are presenting your work in person before a live and for attribution purposes you need to make this clear.
Doing so also also makes it clear when you refer to work done by others, or when you refer to work done in collaboration.  In the former you can use “the author(s) of this or that work…” and in the latter you we use “we”.

I find both "the author" and "we" to be acceptable.
Note that there are two interpretations of "we". The first is the "royal We" indicating that the speaker is somehow superior. This is rarely the intent, so don't capitalize "we". See: pluralis modestiae.
But the other interpretation is an invitation by the author to the reader to come along for the ride as the proof/argument develops. We implies both the author and the reader. This is, of course, quite informal, somewhat like a conversation. But it seems, to me, to fit well with a variation on your example: "we will complete this proof as follows".
"The author" treats the work as something in itself, external to its creators. It is more formal. "We" treats the work (more) as a human construct and is more informal. But either can work.
I prefer not to use "I" for the same reason I don't like the "royal We" interpretation. It is a bit pompous. And referring to yourself by surname may be too formal and does (IMO) seem weird.
Your advisor can probably give advice valuable in your local context about how formal your writing should be.

@AnonymousM, For multiple authors "we" is pretty natural. And the cases can be confused. But that is a result of the fact that English doesn't have sufficient simple terms to distinguish those cases. We make do with what we have.

Try using "the present author"
In this answer, the present author is suggesting that you use the attribution "the present author".  The present author feels that this attribution gives the requisite formality and critical distance of the third-person, while still reminding the reader that the writer is talking about their own work.  The present author uses this assignation occasionally in academic writing, with pleasing results.

The "present" or current author in contrast to some hypothetical future author? Or is there another sense of "present" in use here?


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Do professors get notified when someone in their research group sends in a publication?
I am a new PhD student, and worked on something with a postdoc during my master's degree, and we will send it for publication in the upcoming few months. Even though the work was done during my master's, I was going to put in my current email address and research group information on the publication. Will my professor / supervisor be notified of this? It's not research that I have worked on here, and is something I probably will not want to work on again, but since we have the results we are going to publish them regardless. I would not mind anyone knowing of course, since it's public information anyhow, but I am just curious as to how this works. This is the first paper I will be submitting.

Be notified by whom?

Why not tell them ahead of time you are working on this?

By Arxiv or similar platforms where the work is submitted to. I have not informed because the subject matter is not relevant to my PhD.

It's relevant to your PhD progress that you're working on something else right now. This should be totally okay, though - projects in academia rarely begin and end perfectly at the transition point between jobs. You'll probably be doing some work post-PhD finishing up publications of work you did as a PhD student just like you're now finishing up your masters work. Talk to your advisor. Your advisor is a human scientist who you should be comfortable talking to about science. You can even talk to them about non-science sometimes! If they're too scary for that, they aren't an advisor.

It isn't like there is a large easily-accessed database of who is working for whom at the moment.

I hold it's a real mistake to be sending anything in without notifying the leader of the group the work comes from in advance.

Some research groups may have a mechanism for notifying the group of such things.  But, aside from something specifically set up and administered by the group, it is unlikely to occur.

No, no one will officially notify anyone else, for no better reason than they don't know who they are and have better things to do with their time.
There is no universal database of working group members and there is no incentive for someone at arXiv or at a journal to seek out the possible associates of a submitting author and make judgments about relationships.
However, if you publish (say on arXiv) it is likely that someone will see it. It is possible that someone who sees it will know your PI and will mention the paper to them, perhaps (hopefully) in a congratulatory way. Publishing is, of course, making things public.
I doubt that you are breaking any rules or norms in your group that would make a conversation with your advisor uncomfortable. You could have that conversation. You could also send them a copy of the work more or less simultaneously with your submission. It is one way to build collaborative relationships in (not dysfunctional) working groups.

If you include the name of your current research group in the paper, it is recommendable to inform your advisor about this. Some heads of institute may take offence if a publication is associated with the institute without their knowledge. And in some cases, departments receive funding depending on the amount of papers they publish, so they will want to count your publication if it has the department's name.
Your advisor will normally not be notified if you submit a paper without including them. However, it happened to me once that I submitted a single-author paper and the editor of the journal asked my advisor if they were aware of that (they were, of course). The editor and my advisor knew each other personally, which may or may not have played a role. In any case, you can never be sure.
And of course, even if your advisor is not notified directly, they may have one of those tickers that periodically sends them an email with "potentially interesting" recent papers. In this case, they may anyway get an email with your name and the title of your paper.

Many journals allow you to list the address where you did the work and a current address where you can be contacted.


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Emailing physics department professors for a PhD position in condensed matter/ atomic and optical physics
I am currently working in the field of my undergrad study in "computational systems and microelectronics". I have pursued my graduate masters project in Quantum Transport which have gotten me an A+ along with a Frist Class CGPA and the praise of my professors for laying the foundation of quantum transport simulation in the university in addition to publishing the quantum transport simulation paper in a high impact journal.
Now I am interested to pursue my PhD in quantum information/condensed matter/atomic and optical physics. I have emailed around 40 professors all around the world so far, around 10% of them seem interested and have called me for a PhD interview in renowned Universities (a good sign I suppose) but then they all have rejected me after the interview so far, citing a preference for more experienced candidates in the field. 20% of them outright respond back to the email enquiry, saying that I do not have the necessary background for their research. While a vast majority of professors don't even respond back (I assume they send the email to trash on sight).
I am autodidactic and have been ameliorating the courses that I didn't undertake in school such as Statistical mechanics, Optics etc. However I do have the necessary background in the mathematical and physics framework such as Tensor Calculus, Abstract Algebra, Electrodynamics, Quantum Mechanics, Solid State physics etc.
Is this a "fools errand" for a person of my background attempting to pursue the PhD in condensed matter/ atomic and optical physics or should I power through the rejections and continue approaching professors via email until one eventually hits ? I have met and seen people with my background pursue a PhD in these fields, one or two professors (no PhD openings unfortunately) on consultation even have said that my background is not an issue at all, which gives me hope.
I am currently lost and I wonder is the rejection rates I'm facing normal for PhD applications ? Should I even attempt trying or is this to be expected during the application phase? I have a preference for American or UK universities as these places offer more opportunities post graduation. I hope people who are from these fields and academics could advise me on this dilemma.

The answer for US and UK would be quite different, I think.

So 4 interviews, if each considered 2 candidates and flipped a coin, 1/16 people would be in your spot; that's a fair number, p>0.05, not enough power to reject the null. Even less unusual if they interview more candidates. Could be that something about your interview personality is off. Presumably someone has supervised your masters work? What do they think? Broadly, in the US PhDs are longer and it's expected that incoming students still need some courses; in Europe it's expected you more or less have a project ready to start.

My friend, a Bostonian professor, may be looking for a PhD student, to do research in AFM (atomic force microscopy). Please drop me an e-mail, if interested.

Dear @Michael_1812 thank you for the swift reply and the offer to help :) . Yup I am indeed very interested. I have sent you an email. Thank you for the assistance Michael

The following applies to the US, but, possibly not UK.
As an undergrad, you can contact a professor at a doctoral institution for advice and to express interest, but it will be very (very) unlikely to affect any admissions decisions.
The same is true even for those with a masters, to a somewhat lesser extent.
In the US, admissions is by committee of faculty who look at all the applications in a cycle and make decisions based on formal application materials.
Also, because of that custom, the most likely answer you get from a professor, is "I encourage you to apply." Even if they are on the committee, outside communication is unlikely to affect anything.
The first task of a new doctoral student, in most departments and fields, is to take the advanced courses that help you pass comprehensive exams. You don't need a dissertation advisor for that. Even with a good masters, you need to be aware that comps are usually an gate that must be passed through.
Some other places than the US requires you to apply to a professor who will ultimately be your funding source.

For a physics Ph.D. application in the US, you are generally expected to take the subject and general GRE tests, and the TOEFL test if English is not your native language. Furthermore, the complete application includes a letter of intent describing your background and the kind of research you want to pursue. Additionally, you need an undergraduate GPA of 3.0 or above (preferably). Beyond that, any research publications you might have will help your cause. The system works that way. A committee then decides on the applications and offers positions according to the department's needs which are related to funding. So cold emailing as you do might not help you get into a program I think.

There are many universities, and in my experience a majority of the top schools, where the professor will rarely if ever formally commit before the student has spent some time at the institution.
Basically, they want to see how you will perform in their program, irrespective of previous achievements in other programs.
The default position is for you to apply for admission, get accepted and then set the stage on fire during your first year (usually coursework) when you get there.