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Are software engineers with PhD in demand in Academia?
I'm about to defend my PhD in Computer Science in a couple of months, and I'm struggling with deciding on a future career path. Over the course of the 8 years I spent in an academic environment, I familiarized myself with advances and challenges of formal software development. I also learned a lot about myself. It might sound a bit depressing but right now I don't think that it's my vocation to be a scientist. I feel that there are lots of talented people who will do the research with a lot more passion and way better than me and that a mediocre researcher is of no use for society.
However I think I would love to work with scientists as a software engineer. I came to this point because I like developing software, I have high respect for science and would happily support the research with tools, and implement the research results in software. Being in a research environment I might become more inspired with science someday and will switch to research.
This being said my question is: are software engineers with a research background & PhD in demand in the academic world? Do they allocate funding for such people in universities/research labs? What should I expect from a career of a research software engineer? Would it be considered strange if I applied to a PostDoc position saying that I want to concentrate primarily on software?
I would appreciate any comment or advice. Thank you.

If you are interested in life sciences, there is a high demand for programmers/bioinformaticists.

tl;dr: Yes, some universities do value software engineers with a research background.
University College London (UCL), for example, has a Research Software Development Team (RSDT), which specialises in providing software engineering by programmers with a science-research background.
From the first of those links:

This is a team of professional software developers with particular expertise in designing, constructing and maintaining software for academic research.
Our goal is to enhance UCL’s capacity to produce high quality scientific software, from the simplest scripts to complex simulations running on state of the art high performance computers. We do this by collaborating with researchers who are creating their own software

How is it funded?
The work can be funded in one of several ways. It can be funded through university core funding. The work can be bid for as part of a research funding proposal or consultancy contract. It can be funded as part of a research grant for generic research software development.
What do they do?
The UCL RSDT team work alongside researchers on scientific projects. They co-author papers with them, transfer best practice & skills into the team, and hand over well-crafted, well-documented software (and its version-control history) for research.
The team do have research backgrounds themselves. They help select / develop the algorithms. When starting a new project, they read some of the background literature to the project - particularly that relating to the algorithms - to get enough grounding to enable them to ask meaningful questions of the researchers who they're working with.
And (touching on a comment by dgraziotin), the team host Software Carpentry Boot Camps for research staff and doctoral students. This gives the attendees an introduction to key concepts that they might otherwise not be exposed to, such as unit testing, version control, and working from the command-line.
Do many universities do this?
At the moment, this isn't an initiative at many universities that I'm aware of. However, given the success of UCL RSDT to date (the team is now expanding again), and the growing awareness of the concept of the Research Software Developer ("a new type of hero", as described by Neil P Chue Hong, Director of the Software Sustainability Institute), this is probably an idea whose time has come.
Disclosure
I am a little involved with the research software development effort linked to above.

Interesting answer. Do these software developers have any scientific/research input? Do they help develop the ideas/algorithms, or do they just implement other people's ideas/algorithms? Also, do they typically have a research background themselves?

@EnergyNumbers Thanks, I read about UCL RSDT recently, but this initiative still seems to be quite unique, no? My wishes of best luck to you though, I hope you will successfully promote the RSD idea worldwide.

@EnergyNumbers Thanks for your answer and edits, I accept it with pleasure, still I welcome others to express relevant comments, if any.

There are also various research labs that have (many) such positions. For instance IIRC in ADSC Singapore (http://adsc.illinois.edu), more than half of the staff are considered scientific developers, all of them with PhD and decent salary.

UCL RSDT is not unique, there are groups like this springing up at many UK universities. My university has a strong RSE (research software engineering) team. The OP might be interested in the Society of Research Software Engineers (https://society-rse.org/)

Short answer: it looks ilke it, yes. I don't know where you are in the world but, when I've looked at academic jobs sites in the UK and USA, there have always been lots of ads looking for people to develop software for research teams – especially in bioinformatics but also in any area of science where computer modelling can be applied profitably. I've not looked closely at these ads but my impression is that, unlike the group discussed by EnergyNumbers, these are mostly fixed-term positions within a specific research group, tied to a specific grant. But the demand does seem to be there.

A PhD carries weight in academic environments in a way it doesn't in any other context. Your colleagues will respect someone with a doctorate more, and it will provide opportunities for job opportunities within academia that are closed to people without a PhD. Depending on quirks of college funding, you may even find yourself joining the faculty in capacity (visting assistant professor, research professor, etc.) rather than simply being staff or an adjunct professor. Staff employment is typically grant-dependent, and semester-to-semester contingency the lot of adjuncts.
Software PhD's are probably more in demand outside of universities. Check the salary differences an decide accordingly.


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What's the logic behind the European grading system? Why did they make it so confusing?
The European grading system also follows an ABCDEF system like in the US.
However, an A in an European grading system is worth more than an A in an American system.
So what is the point of using such a confusing system?
Now every American student applying in Europe will present their As and be perceived as incredibly impressive, while an European student with many Bs will go to US and be underestimated because a B in US essentially means "slightly above average", while a B in Europe means "Very good, but with minor mistakes".

what you link to is a "grading equivalent" scale for people wishing to transfer between institutions... Most faculty who deal with students coming from the US, and we get several, are aware of what an A or B grade means and can work out what and where they should then study.

In Germany, which is a federal system like the U.S., the grading scale goes from 1-5, and yet, the grades are not even comparable among the 16 German constituent states. Everybody knows that final A-level grades from Bremen must be discounted, and that a Bavarian 1 counts much more than a 1 earned in Lower Saxony. In short, effective coordination takes more than using the same scale. It's politically difficult, because of the diversity of local traditions, expectations, and institutions. If it's hard in one nation, it's not going to be easier across nations.

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I don't think Europe designed its grading system to be easy for people an ocean away to interpret.

@AzorAhai Some of the universities in EU are much older than others elsewhere... They are probably quite happy with their grading systems...

Maybe it's the American system that is confusing

Actually, you are underestimating the intelligence of American academics. It isn't hard to do the computations and people on admissions committees know these things. In many cases, automatic translations are done before the committee even sees an application.
If you are confused by it, it is really only because you don't deal with it frequently enough. But in the larger world it isn't an issue and people won't over/under value anyone based on different grading schemes.
But for the most part, local practice is local. Most of the students stay fairly close to home, so any consistent scheme will do for most students. For the others, it is just a translation problem along with other translation problems that might occur.
I'll also note that not every institution in the US uses the same scheme in any case, and the "meaning" of an "A" can vary. The translations are needed here too.
It is a normal part of academic life.

+1, especially paragraph 2

And there are some countries where the grading system is even easier than the U.S. Straight A applications from these countries are not very impressive, although straight A+'s are.

Even within the US, colleges may differ significantly in the amount of grade inflation.   People look at class rank and the competitiveness if the school (or even the major) to evaluate.  Also this is one of the rationales for GMATs, GREs, etc. (especially for foreign schools wher people don't know much about it).

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Using initials to promote gender neutrality when publishing as a female?
As I work my way through my academic career (second-year PhD student), I am confronted with many stats and instances of gender bias in the publishing process (see references below). Of course for double-blind peer reviews, this is not an issue, but for others it may be. I’ve also seen stats that indicate that female first-authored papers receive fewer citations, even after taking into account the historical gender lag of fewer female publications.
So the question I’ve been pondering is: Should I use my initials (first and middle) when submitting papers as an attempt to introduce gender neutrality into my work? I am lucky that I have a relatively unique last name (nothing like Smith) so I’m not very worried about identity.
Is this a good idea? Are there any further pros and cons I may not have considered?
References

Michał Krawczyk and Magdalena Smyk – Author׳s gender affects rating of academic articles: Evidence from an incentivized, deception-free laboratory experiment
Erin Hengel – Publishing while Female. Are women held to higher standards? Evidence from peer review
Rachael Pells – Understanding the Extent of Gender Gap in Citations

Discussion about the existence of the presumed effect and answers in comments have been moved to chat. Please read this FAQ before posting another comment.

If you feel at risk in your profession for such things, then, certainly, establish a professional persona for yourself that will help assure fairness. Whether it is necessary or not, or backed up by statistics, is irrelevant. If you feel at risk, do what you think is best.
I would also suggest that you get some advice from a female mentor or professor about this. What have their experiences been? I'd guess their advice would be pretty good.
But I'll add, that you should think about making that a permanent persona that won't change in the future. You want your complete history to be traceable through a single name, even as your life changes. You can be A professionally, and B personally, as long as no fraud is intended.
I once should have changed my name, but didn't. Things would have been better for me had I done so at the time. The issue was completely different, but it had consequences.

Based on extensive anecdotal evidence, not stats, I'd recommend, yes, using first two initials and then surname, if your surname is sufficiently unusual so that (e.g., if/when you google yourself with those parameters) you are "unique".
Yes, be sure to set up ORCID and similar, as mentioned in another answer, to disambiguate yourself, and to allow for future modifications.
I say this based on long-term observation, in math in the U.S., of perhaps inadvertent presumption about gender and such... Better to avoid it entirely, even if things are not as wildly prejudicial as decades ago. Dodge it.
Yes, I know there is a big issue here, which my advice might be seeming to ignore. In effect, later, when you are established, you can make the professional-ideological point that you were ... who you are ... all along. On practical grounds, I'd tend to recommend against too-aggressively mixing ideology and professional issues, for a beginner, since you'll tend to not get your foot in the door at all, and be dismissed as marginal. Get a little credibility first, and then you'll be better able to do something about the (visible, if subliminal to many people) inequities that exist in the system.
EDIT: Thanks to @DanRomik for some insightful comments... which among other things made me think that a fuller explanation of my rationale for the advice would help people evaluate it.
So, first, yes, in general, short-term, when one is acting on one's own as a not-so-powerful person, it may be best to try to "stay under the radar", unless one chooses to risk martyrdom of some sort. I cannot give advice about nuances of self-immolation, so I tend to give advice about how to avoid it... which may not be the universally correct choice, I understand.
In mathematics, in the U.S., in my observation, the biggest bias issues are not about overt, explicit bias (though there is quite a bit of that), but unconscious bias. That is, I know very many good mathematicians on hiring committees who would never consciously select against women, ethnic minorities, etc., ... but nevertheless mysteriously functionally do so. If accused of somehow being biased, these honorable people would be hurt and absolutely deny any intent of discrimination.
Yet they do discriminate. Wow, how to make a policy to prevent this? Obviously it is easy to prohibit overt bias, etc., even tho' people with conscious biases can figure out how to circumvent such... but how to outlaw (acting upon) unconscious biases?
For that matter, people without conscious bias, but with unconscious ones, and who otherwise strive mightily to behave ethically and with a good social conscience, will (apparently!) have extreme difficulty understanding that there does continue to be a problem ... since, supposedly, biased behavior is illegal... "Equal Opportunity"... "Affirmative Action"... and so on... ?!?!
In my own case, in general social terms, I had not really thought of the possibility until my daughter explained to me "beneficent sexism": guys hold doors open for gals, all that. Nothing overtly mean about it, but, duh, yes, lotta problems.
And, no, not "equality", but "equity".
Now and then I think about the semi-voluntary martyrs of the Civil Rights movement in the U.S. c. 1964. My question in that case is whether that's what it really took? To read LBJ's memoirs, it probably did. What's the analogue for gender equity?

So, you would “recommend” to all women, in any academic discipline (I didn’t see you qualifying your recommendation with any specifics), to hide their gender when they are trying to publish? Without passing judgment on the recommendation itself, I’d like to call attention to just how big of a deal this is. You are in effect saying that there is something so horribly wrong with academia, that all of us should immediately get off our chairs, and... do nothing, except for the victims of that wrong, who should discreetly modify their own behavior to avoid harm to their careers. ...

... Do you see how it might be a bit problematic for you to be offering this advice, especially as someone who does not belong to the group of people who would have to live with the consequences of following your recommendation (in either direction)? Even if the problem you are pointing to is as bad as you make it out to be (I don’t feel qualified to enter that debate, frankly), isn’t the action you are advocating simply a cop-out, or a work-around that obviates the need for you and other senior people in academia to create mechanisms that would ensure women don’t suffer unfair discrimination?

(For example, you could be advocating for all authors, male and female, submitting papers for peer review to be required to initialize their first names - this seems more fair to me than just telling women to do this.)

If you use only your initials, readers and reviewers (in non-anonymous refereeing) will either default to assuming that you are a man or, less likely, make no assumption about your gender.
It is plausible that this strategy will protect you from being discriminated against. Without being able to guess your gender from your name, readers and reviewers can't take your work less seriously just because you are a woman.
You're asking whether this strategy will "promote gender neutrality". If by this you mean whether using initials will promote gender equality in science, the answer is clearly no. To the contrary, one more woman scientist will become invisible; prejudiced people will have one less chance to correct their false assumptions; and, to generalize a bit, it will appear as if only men produce publishable research.
I am not arguing for or against hiding your identity; I am just pointing out the implications, so you can base your decision on them. As to what consideration should be more important, that is for you to decide. Regarding the strategic question of picking your battles, Paul Garrett's answer is good advice.

As an author, you can choose any variation of the name you will put on your manuscripts. People use initials instead of full names for a variety of reasons, including very long names, names which are hard to write using English letters, names which are hard to read correctly, etc. If you want to abbreviate your name for whatever reason, do it.
It is a good idea to stick to one form of your name to keep build your publication track record. However services like ORCID help you maintain your track record even if you change your pen name later for any reason.

Even if there is an impact, I suspect it is very minor.  And then you are giving up some of the benefits of having your name out there to begin with (harder to search).  Given your statements, it seems like cites and thus notability is a motivation for you.  So I think it is counterproductive to cloak your name.
My guess is gender is immaterial or if anything a positive.  (IOW, I don't buy that a stats difference must be the result of discrimination.  Of course we would have to do really controlled experiments to see that...blind/unblind, not just factor controls).  I suspect that biased judgment stemming from prestige of university is much stronger.  Even ethnic bias is, I suspect stronger than sex bias. Both of these of course are much harder to cloak.
But in any case, I believe your mindshare is better spent on the work and doing it as well as possible and promoting it as well as possible versus contemplating injustices.

Why you are getting downvotes: The effect isn't merely presumed, the question quotes three studies; that other biases also exist doesn't  make the bias in question go away; other answers explain how it is possible to work around the problem you mention in the first paragraph; your 'advice' in the last paragraph comes across as rather arrogant and dismissive.

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Does an advisor owe his/her student anything? Will an advisor keep a PhD student only out of pity?
I know what imposter syndrome is. But, believe me that's not the case with me. I have worked hard for the 4.5 years of my PhD, but I feel that my research is absolutely mediocre and as a result my self-confidence has taken a toll.
Now, my advisor is a brilliant person. She is well known in her field (computational mechanics) and has many high-impact publications (IF>10). I had my undergrad in materials science and was exposed to computational mechanics in my masters. I was fascinated by it and wanted to study and work on it. However, when I joined my PhD, I was asked to learn and use a different modeling technique and a different length scale which was not in the realm of my advisor's expertise. I work in continuum while she works in nano scale. Yes, the impact-factors vary in the journals for nano and continuum. But, all I am concerned with is the quality of my research work.
Post qualifiers and research proposal (my committee seemed happy with my theoretical knowledge, preliminary work and plans), I published one paper in a decent journal. But, my work was nowhere near that being done by my colleagues. I kept on working and completed three more manuscripts which are to be submitted soon. But still, my work is just mediocre and most likely will end up in average journals (IF <2).
I feel that I should not have pursued PhD and I was not fit for producing good research. I also feel that I have screwed my chance of doing anything significant in academia.
I also feel that I am still being funded and not fired because my advisor is a good person and is allowing me to stay regardless of my average performance out of pity.
Does my advisor owe me anything? Could it be that she keeps me only out of pity?

Adding to the answers below: think about the skills you've acquired.  You are now equipped with a new modeling technique or tool.  Can that tool be used somewhere else?  Just imagine every research field as one giant jigsaw puzzle, and waiting for someone to walk up with the right piece of the puzzle.  Your supervisor may have thought that the technique he/she suggested is that critical piece.  Just continue to explore, and with some luck, you may find that you are just the right person holding the piece required to yield information that leads to a breakthrough.

From a supervisor's perspective, I would say this: we make 'bets' when we do research; e.g., we suggest a direction or ask our students to explore area/tool-X.  It may not pan out.  We do not punish students.  It is part of the research process.  If it was not so, then every researcher would be guaranteed a breakthrough every time he/she thinks of an idea!  Instead, the student's experience (failures or successes) helps us make better 'bets' going forward; yes, some bets will have a big payoff, but most of the time, no.

maybe interesting to you concerning the aftermath of a PhD https://academia.stackexchange.com/q/12767/41661

Medicore may in fact be good enough.

I know what imposter syndrome is. But, believe me that's not the case with me. – Honestly, the rest of your question makes this very difficult, i.e., it strongly suggests that you are suffering from the impostor syndrome. I strongly recommend that you seek some external assessment of your progress and qualities.

@Prof.SantaClaus: Please do not answer in comments.

It sounds like you're on track to get 4 of your own papers out of your PhD.  In many fields that would be regarded as very successful.

"my work was nowhere near that being done by my colleagues". What makes you think that? The impact factor of the journal where they published? The IF is a good indicator of the potential quality of a paper, but you can find very good papers in IF<2 journals, and there exist average paper in IF>10 journals. Also, some fields are inherently less likely to lead to publications high impact journals, keep that in mind.

If your performance is average, you are performing approximately as well as others.  While everyone wants to be above average, statistically, that is unreasonable. :)  I think you are likely being too hard on yourself.

Most research is, by definition, mediocre. And very much needed (also by those who excel). What you suggest would be a very expensive form of pity :)

Don't worry so much. Mediocre can be good enough for getting a PhD if it is so important for you.

@speedymcs but money is not the problem. The problem is lack of good people in the right positions.

So, basically you are measuring the the quality of the research done by the IF of the journal that that work can be published ?

Did you ask your supervisor feedback on your performance? What does she say? I'm asking this because putting aside impostor syndrome and Dunning-Kruger effect, it can be very hard to judge your own performance, particularly in a first-time experience. I remember one of my final exams that (even with all those oral exams I had before to "calibrate" my feeling on how it went) felt like going horribly wrong - to end up with the 2nd best mark. The professor explained afterwards they judged the performance by adjusting the difficulty of questions to where I was getting ≈ half right, half wrong.

@mathreadler Could be, in any case my point was that it's unlikely OP has the position out of pity

@smcs yep. more likely that the institution knows they will lose money for every non-finish.

Having 4 papers published or submitted during a PhD period is actually quite substantial. Which journal they go to may be secondary, and there are many considerations. For example, at your stage of your career, getting anything accepted and published is more important than trying really hard to get that one paper into Science or Nature -- which entails a far greater risk of rejection and consequent delay, something one might be willing to accept as a well-known researcher in a field for whom one publication more or less makes no difference, but that you can ill afford.
But that's maybe not the question you're asking, so let me address that as well in the form of a story about myself: When I was a graduate student, I had always wanted to work at MIT or Stanford or a similar place, and to make breakthrough discoveries. Indeed, I know this to be true for many of my academic friends. But the longer I've been in academia (I've been a professor for 13 years now), the more I've come to realize two things:

By and large, science progresses not through discrete breakthroughs, but by continuously grinding problems down through the work of hundreds of people until the rare new ideas have been put into forms that can be used widely. Think about gravitational waves: yes, the follow from Einsteins equations and were theoretically well understood not long after, but then it took a hundred years until a whole community of hundreds or thousands of people had made the materials, detectors, and computational tools to actually use gravitational waves observable. All of these people made valuable contributions without which this would not have been possible, even though few of these contributions were published in the highest impact factor journals. What I'm trying to say here is that there is honor and value in doing good science, even if it never rises to the level of breakthroughs.
About breakthroughs to begin with: Of course, every grad student also wants to be the next Einstein. But few of us actually get to be. In fact, if you stay in a community, even if you're really really good, you will come to realize that there are people that are just so much better than you are. So not only do we not get to be the next Einstein, but almost all of us will actually never be at the top of our small sub-disciplines. But that doesn't mean that we're worthless -- there is honor in doing the everyday work moving science along and contributing to the scientific enterprise as a whole. Academia is composed of the high end of the ability scale, which is quite rarefied, and one has to learn to live with the fact that there are always people better than oneself. Take solace in the fact that the proportion of the general population who gets a PhD is already quite small, and you're in that fraction.

Remember that some of Einstein's contemporaries were developing the foundations of quantum mechanics. I sometimes suspect even if he wondered if he was in the top of his field when surrounded by other luminaries like those.

@TimothyAWiseman: It's a legitimate thought for sure and it would be hard to believe that even had moments of doubt. At the same time, the work that made him famous in the physics community (and would eventually earn him a Nobel) was done in 1905, when he was 26. Few of us can say that of our own careers.

Researchers which regularly publish IF>10 are in my experience not keeping any student just for pity. Usually they are also extremely clear in the communication about missed expectations if you ask directly, which is what you could do in a meeting discussing if your PHD work is ready to be written down or not and how to proceed later.

+1, Pity earns the advisor exactly nothing. Nor does it give the student anything of value. Good, simple, advice here.

The decision of your advisor/professor on which PhD student to keep and finance further not only depends on (# of papers) x (impact factor). Towards the end of my PhD I wrote 4 funding proposals for internal university funding and national foundation funding, although my advisor pushed me to bring further mediocre results to paper format after one top-tier publication. 2 have been granted luckily. Even if not funded finally, my advisor was impressed I made contacts to postdocs in other groups, developed ideas and managed common funding projects. This impressed my advisor more than writing another low/medium-impact research paper which is the current "sport competition" among PhD students in the light of publish or perish, who gets the higher # x IF product on researchgate.
And while there are always smarter people in academia as Wolfgang wrote, academia also needs managers, organizers and idea-givers with broad interdisciplinary knowledge apart from savants and specialists. A scientific community only consisting of Einstein alikes would be a very inefficient one. So don't make yourself smaller than you are and don't think your scientific career is already over. But also be aware it is a poker game and you have to play your cards as long as they are uncovered, it even was for Einstein, also with a smaller luck factor because the truth always wins in science in the end :-)

There is something called "diminishing returns". And there can be a good argument that the amount of bodies and money being thrown at science experiences this.  In other words, 10 times the Ph.D. students does not give 10 times the results.  Because the last tenth (or half, or even 9/10th) of researchers are not as strong.  In addition the later slew of problems may not be as tractable (less "sweet spot").
So it is completely rational to consider that half of the Ph.D's are below average (this is not Lake Woebegone.)  And this is definitely something that hits students as they experience difficulty or as they near finishing up.  They ain't gonna be Dick Feynman.  They may not even end up being Joe R1 Professor.
This doesn't mean anything miserable.  Life goes on.  Do good work and look out for your own interests.  Right now, you are almost done.  Get it finished and collect the sheepskin.  Even if you are a subpar Ph.D., it is still much better on the resume to have one, than not to have one.  Especially as you move away from the hothouse of academia, into industry, into flyover country, into the long decades of your productive life.  Just get it done, grab the "union card", move on.
Maybe you will never be the end all be all of next gen computational mechanics.  But that doesn't mean you aren't a smart guy/girl/thing in certain domains.  Consider applying your skills in applied mat sci (yes, even experimental work...you don't have to be Hermione Granger in Potions class...deciding what experiments to do is way more important than technique).
There are also huge opportunities, cool problems, and a willingness to try things in the US shale oil/gas industry.  Get a gig with Halliburton.  Yes, it's boom bust, but live for the moment, have fun for a few years and keep your resume updated.

Or, for my two cents, don't work in a field which contributes directly to climate change making the planet uninhabitable for our descendants, even if it's the most profitable one.

I agree with most of this, but while diminishing returns is real, there are also things like network effects. While I have no proof, my suspicion is that at current levels 10 times the P.h.D. students in hard sciences is likely to give more like 11 times the results because it means more community, more opportunities for collaborations, and simply more people slowly working away at the edges of the big problems to open the pathway for the big results.

As a journal associate editor, I can tell you that mediocre work does not get published. I agree with many of the previous contributors that having a paper already published and another 3 in the pipeline is great for a PhD candidate. No one will ever think less of you for working on something different and/or difficult - quite the contrary!
Remember that this is a time for you to learn: learn techniques, yes, but also (and maybe more importantly) analytical skills, writing skills, organizational skills, maybe some teaching skills too. These do not depend at all on how "hot" your research topic might be. Remember too that for many Faculty positions, the search committee will look for interpersonal skills that show you would be willing to collaborate with colleagues. Even if (and that's a big if) your research is indeed only "average", this is only a tiny piece of what makes a successful scientist.
I would like to suggest that maybe the work you are doing now might not be your true passion? In which case, I would strongly recommend that you spend some time thinking about what questions you find really interesting, and see if you can't pursue a postdoctoral fellowship in this area.
Maybe also, have a heart-to-heart conversation about your feelings with your advisor, and ask her to be brutally honest, if you don't think she would naturally be. As an advisor myself, I have been blind-sided by issues I didn't know existed, thinking that everything was good because the student was always upbeat, and didn't want to "bother" me with problems. If I had known earlier, I could have done something about it. Personally, I think it is part of our role as advisors to address some of the emotional and/or life balance reality of graduate work and work in academia in general.
I hope this helps,

Don't give up, reinvent
My father got a PhD in economics--he was somewhat pressured into this, I think.  He wanted to do math, but someone showed him how much math there was in econ, he was convinced or gave in or whatever.  He ended up really bored with economics, but he got really into production management (statistical quality control, queuing, inventory control, etc in factory production).  So, he basically reinvented his career by doing good research in that area, and taught that all his career.  He couldn't get tenure since his PhD was in another field, but his articles were hot (he's really smart) and he was able to get good jobs because colleges with production management programs wanted the guy that wrote that stuff.
I think you are in at least as good of a position.  You got pushed into working in another modeling scale (I have no idea what those words mean, just going by your question) that isn't what you were really interested in.  If your advisor is keeping you funded after pushing you into doing work you weren't interested in, it could be guilt, or a sense of responsibility, instead of pity [I'm being somewhat harsh here, I don't know you or the advisor, but I think you should consider that you were not wanting to go in the direction you were pushed in, and, if anything, the advisor owes you].
This is the beginning of your career, not the end
Finish your PhD, and then figure out how to do the research you really want to do.  If my dad could have a career in an entirely different field, you can definitely have one in the exact same field, working with a different scale.  You are not tied to what you are doing now for the rest of your life, and you will not have the disadvantage my father had in that he was really working completely outside his PhD.
My advice is that feeling guilty or inadequate is using up your emotional energy in a completely useless way.  You don't know yet what you would be capable of, working in the field you really wanted to work in.  Learn from this experience for your future decisions--don't let people in power push you in a direction you don't want to go.  Take the negative aspects of what is going on now and use them as your rock in future negotiations.  "I'm not going to get into that situation again, because I know how badly it turns out."
Don't compare yourself to others when the playing field is not level
Your colleagues are working in the field of your advisor, for an advisor with a lot of expertise in that field.  You are working in a field outside of your advisor's expertise and outside of what you were personally interested in (if I'm interpreting correctly).  It's unfair to yourself to compare the impact of your publications, when they had a huge advantage over you.


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The importance of the title "Mathematical Physics" vs. "Physics" on one's degree for grad school/jobs
I've got a question for anyone that cares and knows how to help. I'm a third year physics student, currently enrolled in the "regular", straight-up physics stream. However, since I've realized I don't want to go into the experimental side of physics, I am trying to avoid having to take a lab course. This isn't possible while staying in the stream I'm in right now, but due to my elective and other choices in regards to the mathematics courses I took thus far, I am still eligible to switch into Mathematical Physics. I've looked at the requirements and the courses I'd now need to take when compared to the ones I'd need to take if I stayed in the regular stream are basically the ones I would use up my electives on anyway. Thus, the only qualitative change arising from switching the programs would be that I would be able to avoid that final lab course, and could take another course, say, biophysics or a maths course, instead.
My concern, however, is what impact would this have in regards to my going to grad school or looking for jobs? As far as grad school is concerned, I would assume it wouldn't have much of an impact due to the importance of actual classes I took and not the name on my degree, but what about jobs if an academic career doesn't pan out? Does "Physics" look better than "Mathematical Physics" in certain cases? If so, when would that be? In other words, is mathematical physics looked down upon as being esoteric?
Any other advice in regards to this switch would also be appreciated.

@ChrisWhite Oh, no, I'm not avoiding all labs. In our first year, we had two courses with labs already, and in the second year I took two courses, consisting entirely of labs. So I would only be avoiding the final lab course. I also have two summers of research under my belt, where I was involved with an experimental group, so my work there also consisted mostly of nanofabrication and experimentation. Granted, this was in condensed matter physics, so data analysis wasn't as rigorous, though (hah!). With that extra background info, do you still have the same position as before? Thanks!

@ChrisWhite Yes, diminishing returns is what I'm afraid of, and I've already got one extra lab course under my belt MaPh and Astrophysics majors don't have to do. There are only so many courses left, and I don't want to waste another one on this, as I feel at this point I'd gain more from others for what I want to go into (chaos theory/dynamical systems/fluid dynamics). But your reaction was exactly what I feared, people seeing Mathematical Physics and thinking what you thought. Given a chance to explain, I can always do that, but could there be occasions where I won't be given such a chance?

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/


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Publish in ArXiv/Munich Personal RePEc Archive/SSRN
I have just finished my paper on case study in quantitative finance, and thinking of publishing my work. Although, I am an undergraduate student and getting published in a decent academic journal requires both funds and many months until the final decision after a potential acceptance. My thought was to share my work in a repository such as ArXiv, Munich Personal RePEc or SSRN Electronic Journal to share the results.
My questions are:
1) whether I am eligible sharing in the aforementioned, since the paper is not a working paper and I am not willing to get into the publishing process.
2) Is my work safe and equivalent in terms of copyrights as a published paper in a peer-review journal?

Why do you think "getting published in a decent academic journal requires...funds"? Also, did you do the case study under the supervision of an academic?

In the cae of ArXiv:
1) Yes. However, your paper needs to be endorsed by an established academic. See ArXiv's help on the endorsement system: https://arxiv.org/help/endorsement
2) You need to give ArXiv a perpetual license to distribute your work. But otherwise you retain the copyright. With a traditional subscription-based journal, you would typically have to give your copyright to the journal.


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What to write in CV when transferring between schools?
I'm transferring between two PhD programs, same program two different schools. I have done 4 years of study in the first school but have not (and will not) receive any degrees and I need to complete 1-2 years of study in the new school to get my PhD. Assume that the new school is more prestigious. I wrote this piece in my CV.

2010-Expected 2016 PhD in Compute Science from New University

PhD Student at Old University (2010-2014)

2007-2010 MS in Computer Engineering from Another university
...

However, the second line is kind of small and doesn't catch eye but if someone wants to read my CV it's there. The problem is I have not been student at New University since 2010 and I don't want to say that I'm a first year student. Also since I didn't get any degree from Old University I cannot have a separate entry for it.

My advisor told me to remove the years (2010-2014) and change phd -> phd student as I haven't received my phd yet :)

The problem is I have not been student at New University since 2010 and I don't want to say that I'm a first year student. Also since I didn't get any degree from Old University I cannot have a separate entry for it.

Why does it matter whether you got a degree from Old University?  There's no rule that says the education section of your CV can only be organized by degree.  You just need to be clear and honest.
What you propose doesn't seem inappropriate, but I think this might be slightly clearer:
2014-2016 (expected) PhD in Computer Science from New University
2010-2014 PhD student at Old University (transferred to New University)
2007-2010 MS in Computer Engineering from Another University

May this format help you:
If "university major" is the university which is going to give you your degree and "university minor" is the one in which you have studied about four years;

2010 - 2016 (expected) PhD in Computer Science; university major
[some space here] 2014 - 2016 university major
[some space here] 2010 - 2014 university minor

However, I think that as you are not receiving any degree from your minor university, and its name is not going to be mentioned anywhere in your certificates; there is no need to bring it's name in your CV too, because you don't have any proof that you have studied there.

Disagree that you have no reason to list universities unless they awarded you a degree. An academic CV is a timeline of your whole career. If you spent four years studying in a university's PhD program it should be there.

it's listed somewhere else in my research experiences section but not in the education section.

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How do I get editing help for technical (mathematic/statistic) paper publishing?
I have several topics that I would like to publish. While I can get a paper, in technical terms, 100% of the way done I am not an English major. I don't do great at speaking human, or dotting my "i"'s. I could be much more productive if I had help.
I am currently not affiliated with a university or academic institution. I work and on the side I sometimes do some thinking or work on (statistically) fun problems. I would like to share the results in an approved and excellent forum.
How does one go about finding someone with that strength to help edit (or is it co-author) articles with the intention of publishing them in decent to great peer-reviewed publications? Are there any culture-known "best known methods"? Are there negative repercussions of having non-mathematical technical help? If so, what?

I suggest these four steps:

Identify your research community. The problems you are working on should have some connections with previous works. If not, it will be hard to publish your work anywhere, because it is harder to draw the attention of other researchers on your topic. You can use search engines such as Google Scholar for this purpose.
It is likely that the authors of these papers use the same notations, publish in the same journals and use a similar article structure to describe their work. Become familiar with the format by reading related articles.
Write down a draft, following the usual format of your field. If your English is weak, you can ask someone to fix your mistakes (he/she should not need to be familiar with your work, but it is easier if he/she has some scientific background).
Contact a researcher working on close topics, asking him/her for feedback on your draft. If the feedback is positive, a collaboration might be possible.

I have followed these steps and this has lead me to my first research paper (co-authored with my "mentor"). It takes a lot of time but it is worth the effort.

I said that I knew the technical content well.  I have a degree in the field.  I can write so that another engineer can understand it.  I just don't write pretty and often miss the every formatting detail that journal formats require.  I'm looking for 1) help speaking human and 2) help putting my octagonal peg in the circular hole by shaving off the rough edges.

@EngrStudent: Yes, I have understood that you knew the technical content. (Otherwise why would you try to write a research paper?) I still recommend contacting a researcher, because I don't see where you could find a copy-editor. Moreover, if you are new to academic research, it is likely that there will be more changes to do than just formatting issues. (Hence a real collaboration could be possible.)


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I'm RAing for a friend who's a professor at my school. How should I address him in conversations about the research?
I returned to school a few years ago to earn the grades I needed to get into medical school; consequently, I'm the same age as some new professors. One of my acquaintances from a sports club I belong to is approximately my age  and is a professor who researches something of interest to both of us. A conversation about his research lead to me volunteering as an RA for his lab.
Given that we were friends first, I worry that addressing him as as 'Dr.x' might feel weird for both of us. Moreover, it seems that few professors are comfortable asking to be called 'Dr.x' when someone asks them what they want to be called (even if they would prefer it), so I don't think asking him will be of much help.
Lastly, I don't worry about calling young professors 'doctor'; I wouldn't have much of an issue calling someone older, or even younger, than me 'doctor' even if we met outside of academics, It's the fact that we're the same age and that we were introduced outside of academics that makes it, for some reason, weird.
That said, using his first name doesn't feel right either.
I'm considering using his first name in private conversations and 'Dr.x' in public ones.
How should I address this person?

If this is in the US, first name is usually the norm for a lab member addressing the professor. But you can just ask him.

Where in the world are you? In the UK, I've never addressed anyone as "Doctor" or "Professor", even back when I was an undergrad. This is completely normal; some undergrads call me "Dr Richerby" when I'm teaching them but I always tell them that "David" is fine. I can't think of any occasion on which I've heard PhD students or postdocs address staff as "Doctor" or "Professor".

The fact you are stating you wouldn't have an issue calling someone "even younger" than you a doctor, is a bit strange to me, as if your age is an indication of the appropriate title for someone based on their degree.  If you are friends as you think, you ask the person.  If you are not friends, you follow cultural norms.

@user1938107  In a context like the one I described, I'd want to use a title for a younger person so that he wouldn't wonder whether, on account of my age, I didn't appreciate the fact that he's the boss (so to speak). With the person I described, who's my age, and who's professionally senior to me, there's no reason for him to believe that I might be mistaken about who the boss is in that context. So the question becomes, might it feel uncomfortable for him if a friend of his were to begin expressing his subordination.

How should I address this person?

You should ask him how he would prefer to be addressed, and then follow that.

Listen to what other people say. How do the other people in the lab address him? We cannot answer without this crucial bit of information. There are three possibilities:

First names, everyone. No problem in this case!
Everyone calls him Dr Whatshisname. Then you'd better stick with the unwritten lab rule and address him formally in a work context.
Generally Dr Whatshisname, but some of the more senior colleagues are 'allowed' to use his first name. In this case, I'd suggest using the first name, too. The fact that you are his age will make this look more natural.

Every research group I have been to used either 1 or 3 (but I can imagine 2 being used in other fields and cultures).

As mentioned in the other answer, it is always the best to ask the person how he prefers to be addressed.
In my opinion, first look at the etiquette in your country and university. In some cultures in the universities and companies, people call their workmates, professors, colleagues, etc. by their first name, regardless to their level of education or their place in the system. In this case, calling that professor with his first name may not be that much trouble and will be considered a polite manner.
If it is an etiquette to formally call people in your university, for instance Professor Enthusiastic Student; it may be a good idea to call your friend Professor Enthusiastic Student when you are in a group of students and other researcher, in the classes or in the lab meetings; and call him by his first name when you are alone and you have private meetings in which only you two are talking to each other.
I have the impression that this is the right way to address that person, because in the academic environment he is not considered your friend, he is your professor and you are his student, so calling him in a friendly manner may be considered impoliteness; also in your private meetings and sports club, you are fiends and he does not have any teaching or research role in this occasion, so calling him with professor title is probably considered inappropriate and unfriendly.

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text:
How can I find open physics postdoc positions in Europe?
What are the most common ways to find open postdoc positions in physics, in Europe?
I use inspires and academicjobsonline, but on both sites, there almost haven't been any new positions in my field (4 in total since december).
Are there any other sites / tricks I'm missing?
(EDIT: my subfield is theoretical QCD)

Many jobs are only advertised on the website of the respective universities. Often professors post positions on their home pages or group pages, so it may be a good idea to keep an eye on them. Sometimes job openings are also mailed around to colleagues, so it is a good idea to let people know you're on the market, so they can forward these announcements.
Depending on your particular subfield there may be other relevant websites as well.

My subfield is theoretical QCD

I don't have any specific suggestions there (apart from inspires, which you have already found), but maybe others can chime in.

@freddieknets that would be useful information to edit into the question.

From my experience, most postdocs in high-energy physics have application deadlines anywhere between the previous September and the end of December. That is, for postdocs starting in fall 2014, you need to be filling out applications in September-December 2013. At this time of year, though, there are just not many people listing open positions. It's not just you; I've been looking at the listings as well and very little has been posted since the first week of December.

Perhaps you should also look at http://jobs.physicstoday.org/jobs/work_function/postdoctoral-research , http://www.jobs.ac.uk/jobs/physical-and-environmental-sciences , http://www.eurosciencejobs.com/jobs/physics , and http://jobs.sciencecareers.org/jobs/europe/postdoc/ .

Open positions in public institutions often will & have to be announced on a public job database, not so likely on private job databases where you find mostly industry positions (e.g. in Germany, Austria, Switzerland, Netherlands).
Often higher academic positions are listed in printed newspapers in Germany.
Another option is to look on the sites of the national phyiscal societies (e.g. http://www.pro-physik.de/phy/stellenmarkt/jobsHome.html)
In this answer I gave some tips how to find websites of research groups specializing in field X, you can add here "positions".

There are various listings of jobs and sites where open positions are advertised, for example
http://de.physnet.net/PhysNet/physjobs.html
The sources listed in other answers are also available. For your field, there is also the HEP Postdoc Rumor Mill
https://sites.google.com/site/postdocrumor/
that should be starting the 2016 version before too long.


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Is Obama's JAMA paper OK?
As some of you may have heard, Barack Obama recently published a paper in JAMA describing the US health care reforms (link). First of all, I am not trying to start a discussion on the validity of the content of the paper.
Maybe I am overreacting, but as an academic, that specific publication raises a number of concerns. Within scientific research and publishing we have a number of ethical principles that should always be adhered to (e.g., authorship, conflicts of interest, plagiarism, ...). When I look at that publication, I can't help but wonder about a number of things, such as:

Authorship: Obama is listed as sole author on the manuscript. I personally highly doubt that he has done all of the research and writing himself. That constitutes a problem in publication ethics, as is often discussed at length on this site. He does name a couple of people in the acknowledgements, but in my opinion these people should have been authors while Obama should've been in the acknowledgements. Quoting the acknowledgements:

I thank Matthew Fiedler, PhD, and Jeanne Lambrew, PhD, who assisted with
planning, writing, and data analysis. I also thank Kristie Canegallo, MA; Katie Hill, BA; Cody Keenan, MPP; Jesse Lee, BA; and Shailagh Murray, MS, who assisted with editing the manuscript. All of the individuals who assisted with the preparation of the manuscript are employed by the Executive Office of the President.

Conflicts of interest: the paper essentially "finds" that the reforms done by the Obama administration are a good thing. Of course Obama will say his reforms are good, yet this was not explicitly disclosed in the conflict of interest statement.

Political papers: the article is published as a special communications, which requires prior inquiry before submission. I feel that this type of paper does not fit into a scientific journal. It's fine to do politics, but I feel it should be done elsewhere.

I am genuinely left wondering whether papers like this one are good or not. While I applaud the idea of scientific papers coming from policymakers, the above mentioned issues (and others) are significant.
My question: are such papers in scientific venues OK or not?

"While historians will draw their own conclusions about the broader implications of the ACA, I have my own."  This statement alone reflects that this is not a scientific article.  I think the difference is that this article is classified as a "special communication" vs. "original investigation" and therefore isn't purposed to be 'scientific'.

Has JAMA previously invited contributions from other non-scientists?  What about other top journals, like Nature?

While this is certainly a worthy question to debate, it seems better suited to a blog or other discussion-based platform, and not a great fit for a Q&A site.

@GEdgar: every issue of Nature has "popular" articles written by staff and freelance journalists. As does Science. JAMA in a similar model also includes view points and editorials, as well as other infographics presentations many of which are not prepared by "scientists".

Of interest: the JAMA editor-in-chief's published discussion about this.

One might imagine that none of the parties involved cares much about the highly artifactual rules about authorship, etc. Nor "impact factors", citations, or anything else connected to academic games and status. Arguably, they transcend those rules in purpose and in their own professional situations.

"I personally highly doubt that he has done all of the research and writing himself." Based on what? I would a assume an Ivy-league educated former law professor was capable of composing a peer-reviewed article. We have no idea how long he has been working on it.

Indeed I too wonder what is exactly meant by "Is it OK?" OK to whom exactly? Obviously, it's OK to the journal. The question doesn't invite any true question about actual rules and goes off with vague accusations: I cite "I personally highly doubt that he has done all of the research and writing himself." and "I feel that this type of paper does not fit into a scientific journal." ...

Whilst its a really interesting subject, I can't find a question here. The OP list things they "wonder" about, and then asks if it's "OK". Lets be honest, the only reason we're discussing this paper is that the author is Obama, and the OP is implying unfair treatment due to the author's reputation.
You can literally taste the irony. I don't have an opinion on Obama, but I know criticism without evidence leads nowhere.

@TomášZato questions about ethics are always going to be a discussion as no black and white answer exists. Publication ethics are explicitly on topic for this website. Given the amount of votes for both the question and its answers, I would hardly dismiss it as irrelevant. To answer your question: I was referring to "OK" for the scientific community. The answers and many comments indicate that the publication does raise eyebrows and (clearly) conflicting opinions.

@WillieWong hits the nail on the head.  A 3-word quote from the editor sums this up: "Three other editorials" (my emphasis) - i.e. this is to be treated more like editorial content than research content

The JAMA editor said it's an editorial, and even if he hadn't, it's clear enough Obama's connected to Obamacare and not the scientist behind a new study. Academics having a two-way interaction with policymakers is a good thing; without it they lose an opportunity to help craft better policies. Given JAMA decided to support that sort of interaction, the rest follows: they made clear it's a special case, followed norms of political writing re: authors etc. Also note the editor extended an invitation to other similarly situated folks who may disagree (future presidents, the candidates).

Surely the President of the US can always just do whatever he wants? /joke

As a side note, I would suspect that there's few people who have reviewed more information regarding the ACA than Obama (and those that have likely work for him). As such, it would be very foolish to ban him from sharing his findings with the research community, even with his very obvious bias.

Authorship: This one is messy. The JAMA instructions say Authorship credit should be based only on (1) substantial contributions to conception and design, or acquisition of data, or analysis and interpretation of data; and (2) drafting the article or revising it critically for important intellectual content; and (3) final approval of the version to be published based on the acknowledgements, I think there is a case that Matthew Fiedler, PhD, and Jeanne Lambrew, PhD could be authors for their contributions to planning, writing, and data analysis while those who only edited the manuscript fail the test.
The difficulty is that the JAMA requires written permission from everyone named in the acknowledgements. For whatever reason, the contributors did not feel they deserved authorship. It is possible that they were bullied out of authorship. Universities, and I am hoping the White House, have systems in place to handle this type of bullying. In the absence of any evidence wrongdoing, I think we need to assume that credit was fairly given.

Political papers: This is also a little messy. I think good scholarly journals should include non-research papers (as long as they are clearly mark something like special communications) that likely have broad appeal to the readership. I think journals should strive to keep readers up to date on important issues in the field, even if it is not original research. I also think journals should actively engage in activities that will bring wider attention to their respective field. I think the specific paper falls well within the scope of JAMA which includes all subjects that relate to the practice of medicine and the betterment of public health worldwide. What makes things messy is that in addition to Special Communications JAMA also publishes Controversies in a point-counterpoint and Health Law and Ethics, both of which may have been better fits. Given the partisanship surrounding obmacare a Controversies may have been a fairer way to present the issues.

Conflicts of interest: The JAMA instructions say A conflict of interest may exist when an author (or the author's institution or employer) has financial or personal relationships that could inappropriately influence (or bias) the author's decisions, work, or manuscript. and I don't think that being the originator of an idea counts as a personal relationship that would qualify as a conflict of interest.

I might be completely wrong but he has done more than beeing the originator of the idea. Thus he has a personal relationship with it.

@Llopis All researchers have personal relationships with the theories/projects they develop.  I think conflict of interest here would mean something like the author or a close personal relation has stakes in a business which would profit from the ACA.

For better or worse, most journals effectively have the view that any conflicts of interest that arise from your primary affiliation are "obvious" and don't need to be explicitly stated. (e.g. not reporting that tenure is contingent on publishing). Only non-obvious conflicts (e.g. an academic's side business) need to be reported. Given Obama's affiliation as President, the policy and legacy "conflicts" should be obvious. It falls under the same "of course an academic thinks their new methodology is great" and "of course an industry person thinks their drug is great" bin.

You seem to think that the others wanted their name on the paper. I'm inclined to believe they explicitly didn't want their name attached to the paper and were probably not at all amused that they were given credit in the paper anyways.

@Dunk: We've had a question related to the ethics of that.

@Dunk That's a stretch. What would make you think so?

@xLeitix Dunk is probably not a fan of the PPACA.

@Dunk In JAMA, you must expressly get permission to name people in the acknowledgements section. Beyond that, "Worked at the White House" is going to be way more prominent in someone's career than "Was acknowledged in Obama's JAMA paper." If they didn't want to be associated with the administration, that ship sailed long ago.

@Fromite - Working at the White House looks good no matter who the president is. Having your name attached to a document that plays games with the truth is another matter. Of course, what are the people supposed to say if the president wants to include their name on a document?

The fact that he's term-limited seems like it has bearing on the conflict of interest part.  He actually doesn't have much of anything to gain, other than "legacy" type things, which is true of anyone doing research on an idea they played a role in originating.

@Benjamin - Tell your boss that you don't want your name attached to the work they assigned to you and let me know how that goes for you over the long term.

The link to the JAMA policies appears to be broken; presumably it's moved here. Alternatively, a Wayback Machine version is here.

@Dunk "Working at the White House looks good no matter who the president is." How's that feeling on the other side of 2016?

My thoughts:

Authorship: This is probably the most problematic one, as it seems unlikely that this was entirely written by the President, especially given the acknowledgements. But it's also possible that the framework was written by the President, and what's being acknowledged is editorial assistance, talking over the idea with experts, etc. Especially for a position piece, I don't think that's overly troubling - the piece is clearly "President Obama's perspective on things".
Conflict of Interest: This one I think is a non-issue. "Cares a lot about something" isn't a conflict of interest. Even "considers this the major accomplishment of his career" isn't a conflict of interest.
Political papers: "the article is published as a special communications, which requires prior inquiry before submission." What makes you think it wasn't? I doubt the White House just sent off a paper to JAMA on a lark. If your objection is that JAMA said yes...well, I don't think there's anything inherently wrong with that. JAMA is the journal of an academic society - one that takes political stances. Public health and medicine are inherently political fields - an editorial calling for more preparedness for Zika is political, as an example. This is part of a series examining one of the largest changes to the American medical system...what venue is more appropriate than the Journal of the American Medical Association?

I ignored it in my answer because I agree with you, but I don't see anything in the author instructions that say special communications require a pre submission inquiry.

@StrongBad Indeed, it's expressly not in the heading for that, even though commonly for medical journals I might expect a pre-submission inquiry. But there's no way this isn't a coordinated effort.

In fact, I would suggest that the 'prior inquiry' was JAMA asking Obama, not the other way around.

I've been working on several research project these years, and it looks like a normal position paper[1] to my eye. A very well written one, given the standards. Regarding your specific concerns:

Authorship
This one is the more intriguing, as the norm usually is quite the opposite[2] and you'll expect to find one author from each strong University/Research Centre involved to be listed. But talking about strength, Who's at the level of the POTUS individually and the White House as an organization? Being all of them part of the same "Research Centre" just confirms the rule of listing one (THE one in this case)
Conflicts of interest This is very normal. Position papers are written by the people that are funded to research about the topic.
Political papers I wouldn't surprise if I found position papers on every journal, not only in JAMA. At least I found some examples in CS conferences (I know, proceedings are not journals) where the "next grant research project" are presented.

[1] "A position paper presents an arguable opinion about an issue. The goal of a position paper is to convince the audience that your opinion is valid and worth listening to. Ideas that you are considering need to be carefully examined in choosing a topic, developing your argument, and organizing your paper." https://web.archive.org/web/20070316023144/homepages.uhwo.hawaii.edu/~writing/position.htm
[2] mandatory joke: http://researchinprogress.tumblr.com/post/73499257618/authors-popping-up-to-be-listed-for-a-project

The authorship and conflict of interest problems are very troubling to me.
I see authorship questions as a matter of academic honesty. To not include an author or add an unearned authorship is an implicit lie about how the research was conducted. "Who actually did this?" is a critical question in any study, as only those people can actually say the methods or valid or that the study was done at all. From the perspective of scientific witnessing, only the person who actually did the work can say what was done, or if it was done at all. To have an author who didn't actually do the work saying what was done reduces the paper to heresay, it's just someone saying what they heard was done.
So to have a single author on this paper implies that Obama personally did the majority of the work in this paper, which seems likely to be untrue and thus, academically dishonest.
Also, Obama lists himself as the corresponding author on this paper. Which means it seems that he will be personally handling requests for materials. I somehow suspect that it might be difficult to get a timely response to requests for materials and data.
The conflict of interest issues are also important, but others have already addressed these better. He clearly has a vested interest in the outcomes of this work, and they don't even bother to mention it.
What makes me a bit angry about this is that it reduces something serious that scientists work hard to do right to something which is just PR. Authorship comes with responsibilities, and I have doubts about how seriously that's being taken.
Let's all hope this doesn't become a trend.

Given that it's a single-author paper, how could anyone else possibly be the corresponding author?

@aeismail: The fact that there can't be other corresponding authors does not mean that the single author actually will be the corresponding author.

Also, perhaps you should emphasize you're not suggesting Obama did not do the "health care reform work", but rather the work of authoring this report.

"What makes me a bit angry about this is that it reduces something serious that scientists work hard to do right to something which is just PR." - but writing articles in journals is exactly PR of your work. I write how great and important my results are in every paper and so does everyone else.

"seems that he will be personally handling requests for materials" -- is it the convention that an academic who has a personal assistant who helps with correspondence, would list the assistant rather than themselves as the corresponding author? A President has a lot of people who help with their correspondence, and I suspect Obama will continue to do so once out of office, and those people will change over time. So listing one of his current secretaries would seem... counterproductive. His address is the correct one to contact, albeit he doesn't read all his own mail.

I don't know many academics who have assistants who can handle detailed scientific questions about their studies, but I suppose some may exist.
Obama though is taking personal responsibility for the timely and accurate sharing of materials and questions though. Do you think he will fit it in? If these requests are handled entirely by another person, with no input from him, then well, he's not the corresponding author. Also, if a mistake is made in this process, he'd be responsible for it.
I just don't buy that he's the single-author here.

@ccoffman: I've been working in institutes where the convention was to usually list (one of) the most senior authors as they are far easier to track down years later than the PhD student who is first author - implicitly assuming that they can forward questions to the right quarter. So the idea with that is that corresponding author addresses are not necessarily the email of the student deepest into the details, but an address that makes sure communication is possible/can be started.

@SteveJessop No. The corresponding author is the author to whom correspondence should be sent. The correspondence may well be dealt with by the author's staff, rather than personally by the author, but the correspondence should be sent to them.

@DavidRicherby: indeed, I think ccoffman has unrealistic expectations of the corresponding author.


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Asked to tutor in a class I am currently taking
I am in an accelerated Master's program in Engineering, we are taking a Probability course. At this time the class is review for me (I have a B.S. in Mathematics), we are moving very fast though.
One of the other students asked if I would be willing to tutor them, and offered to pay me for the time.
My main worries are that 1. I will get to a point where I am trying to summarize information I have just learned, 2. That I will have a good mathematical explanation but miss the point in plain English, and 3. that tutoring will cause me to not have enough time to study myself.
With those misgivings in mind, would it be more ethical/reasonable to just give some advice for free or to set up payment plan? I am not just going to say "No, I won't help" but if I was charging I would want to be able to give their money's worth.

Set up an arrangement where you help, where you get adequate compensation, and where it is made clear what the limitations may be. (One of them may be a backout clause, if you or the student feel it isn't working.) If the student is cool with that, go ahead.  You often learn more when you have to explain it, and you and the student might benefit by having the student explain it to you.

You do not really understand something unless you can explain it to your grandmother..

Worry #3 should be invalid in most cases. You will be studying the same material as well, it can even help your own study, as @Wrzlprmft pointed out.

Like most things in life, being open and honest is a good policy.
Since you (presumably) are not close friends with this individual, and he is asking for assistance it is reasonable to request compensation as a tutor.  Every person on this planet has finite time and resources.  Having a near stranger request time should result in some kind of compensation, mutual friendship, or you should decline.
You can tell him that you're happy to catch him up to where you are while tutoring him, but if the topic advances faster than your learning, either work through the problems with him at a reduced rate (or free if you feel like it's equal contribution) or simply suggest finding another tutor at that point.

Fair enough. I honestly would have responded positively to offering to study together. There is added benefit as well to having a reason to keep ahead of the topic, as well as learning by teaching.


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What if someone else published an article on the same topic as my accepted unpublished article
I submitted my paper to a journal in July 2017 and I received an email of acceptance on May 2018 but it hasn't been published yet. Suddenly, while I am searching on my topic I found that someone else through another journal published an article on the same topic of mine (same basics and main idea with some little differences) and I found that his paper was received in January 2018, accepted in July, and published in August 2018.
Is there any risk that the journal will not proceed with the publication of my article after acceptance?

https://academia.stackexchange.com/questions/31018/how-can-i-timestamp-my-paper-without-violating-double-blind-review

Congratulations!  Someone else thinks your research is interesting!

You submitted the paper in July and it was accepted in May of the same year?

After a journal has accepted an article, they're ethically bound to publish it unless there's an egregious error or abuse on the author's part. Some examples could be:

They discover that you actually submitted your paper without acknowledging a critical person who contributed so much to the work that she should have been a co-author;
They discover that you plagiarized significant sections of your paper;
They discover that the reviewer they invited for the paper was actually you, using another name.

In your case, the journal will need to show that you must have known about the other paper before you submitted yours. If they can do this, then you are acting unethically, and they can retract your paper. If they cannot, then they'll go ahead and publish, and you can claim to have discovered the result first while the other authors discovered it independently.

By the way it's quite surprising that your paper was accepted in May and still hasn't been published. If you have not heard from the journal, I would ask them what's going on.

Maybe it is just a fake journal with no intent of publishing but their job is just fishing for ideas.

It is a popular scientific journal with a good impact factor. I already sent them an email asking about the reason for the delay in publication, but I haven't received any response yet.

Comments are not for extended discussion; this conversation has been moved to chat.

I'm not as comfortable here as the other answer writers. I can't be as certain as they seem to be that "all will be well."
I think you should take some action, actually. First, find out why your paper is delayed from your own editor and point them to the "duplicate." (See below for a caveat, however)
Second, try to determine if the other paper is an example of parallel research or a possible plagiarism. In mathematical subfields with a lot of research interest, parallel work is very common. Everyone has access to the same background work as everyone else.
But it is also possible that you were plagiarized from a public preprint and you should explore that avenue as well. It isn't impossible, in fact, that a reviewer has acted unethically here. Those are both reasons for pointing your editor to the other paper. If there is evidence of plagiarism they can help you with the response.
However, if you have already paid fees (or your grant did, or your institution) or if you have already transferred copyright to the publisher then you can insist on it being published. I'm still not assured that you would win a dispute with your publisher, however, as they can return both fees and copyright. That may, itself, be unethical, but probably difficult to fight.

I note that there is some risk involved in pointing your editor to the other paper, if they take the existence of the other publication as a reason to back out of publishing your work. An alternative is to first ask the editor for a publication date. If they tell you they are reconsidering, then ask why. If it is because of the other article, point out the history of the two papers. I agree that you should have priority here, but resolving it can still be difficult.

Are you worried that the journal won't publish? It looks like a completely normal case of different journals having different lead times, to me. Obviously, the asker should check the other article to see if it looks suspicious but what do you think is problematic about the status of the asker's article?

@DavidRicherby, I don't think anything is problematic other than the difficulty involved in finding a resolution. I think the OP has a very valid point, but needs information to proceed. The delay from acceptance to publication may mean something or not. I'm just not comfortable advising the OP that all is well, it will sort itself out.

I agree that you should have priority here, but resolving it can still be difficult. — I don't.  This looks like a standard case of parallel discovery.  In the absence of other evidence, neither paper deserves priority over the other.

@JeffE, I based the statement on submission dates, but agree, it looks more like parallel research than anything.

But your paper was both submitted and accepted before the second paper. So, anyway, I think, you have the priority.  Once the paper was accepted I think you have no reasons to worry. Something really extraordinary should happen in order that the paper is not published. It is not your case. I believe that the papers with similar findings are constantly published in parallel in competitive fields.
As to the delay with the publishing: in some journals it takes time. I suggest that you check already published papers in this journal with regard to how long it takes from acceptance date to publication.

Journals usually indicate time stamps for reception and acceptance of the manuscript: thus it would appear (according to your chronology of events) that you will be recognized as having priority, irrespective of publication date.
There is a slim chance - I’ve seen this happen - that the “competition” was in fact a referee for you work, and that this “competitor” has somehow pushed his/her work to a journal with faster turnaround.  (I’m assuming you did not present this work at a seminar or a conference, in which point the work is fair game).   If you think this might be the case you might want to contact “your” journal, politely indicate your concern and let them do the remaining legwork of checking their files to see if something’s afoot.

How is it "fair game" for me to turn your conference presentation into my paper?

@DavidRicherby conferences are considered public presentation.  If you have the idea for a paper from a conference or a seminar, you can publish (unlike refereeing or grant review, which have explicit clauses against using ideas contained therein).  I don’t do it (and don’t approve of it) but it does happen.  In fact I know personally of people who we scooped of their ideas this way.

@ ZeroTheHero If the new paper does not acknowledge the source of the ideas, it is still plagiarism. (And yes, I also know people to whom this happened, and it was still plagiarism.) However, that said @DavidRicherby it can be "fair game" to take the part that was presented in a conference, re-construct the rest, and publish, including only a buried citation to the conference presentation. That pays lip service to the strict plagiarism concerns, but it still measurably steals the impact of the original authors' later publication.

The aim of publishing is to share new knowledge with the world after a peer review process.  It looks like the world now already has access to the knowledge that was in your paper, so all is well.  I recommend then contacting the journal to let them know your article no longer requires publication, allowing them to focus on disseminating knowledge to the world that hasn't yet been published.

I must respectfully disagree. 1. Even in completely unselfish terms of spreading knowledge, the fact that two independent researchers came to similar results is meaningful and significant (possibly slightly less in mathematics than more experimental areas, but even there it is meaningful if the proofs are not identical). 2. From a more selfish perspective, publications are significant on CVs and resumes so saying simply "drop it" requires a bit more justification than someone else's article came out slightly earlier.


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Sweden admission deadlines
I have researched a few Swedish universities such as Uppsala, Lund, and Stockholm, and the Ph.D. admission deadlines vary a lot. When I go to ScholarshipDb.net and search for positions each has different deadlines too.
I have finished my MSc. in Geography and want to apply for Geography Ph.D. programs. I have a time shortage because in our country six months after graduation the student will face two years of mandatory military service. I am confused right now because there are lots of different deadlines and admission dates.
Are Swedish programs deadlines have a typical norm and are on fixed dates such as U.S. (Nov, Jan, Feb) or they're based on the advertising dates and are somehow unique?

I don't understand the question, really. Any university that publishes deadlines will adhere to them. If they are all different, then they just are. I don't think this is any different in the US, actually.

If the Swedish Institutions have published their admission deadlines, which you have obviously found, why do you think there are different dates available?

The announced positions have different deadlines than the university's deadlines. But typically, in the U.S. they are consistent.

A supervisor may have sourced funds for a particular post and is now in a position to make the post available which means it will have its own dates for the applications.

Are Swedish programs deadlines have a typical norm and are on fixed dates such as U.S. (Nov, Jan, Feb) or they're based on the advertising dates and are somehow unique?

The most common way to announce PhD positions is on a case-by-case basis with unique deadlines for each position. There are no fixed dates that universities have to adhere to. You will see an increase in the number of available positions during the first quarter of each year since big funding bodies like the Swedish Research Council decide on grants in the fall.
(I'm a PhD student at Karolinska Institutet).


text:
Do I need to cite a source when defining terms?
In my research paper, I have set aside space to define terms (each having a bullet point). My confusion is how I go about defining these terms. Do I quote a dictionary, another research paper in the field, or do I paraphrase either one? I found one paper giving definitions, but the author doesn't cite any source. Does this mean the words fall under 'common knowledge'?

The purpose of defining terms is to make it clear to your readers how you are using these terms, for example because:

there is no consistent use of these terms in the existing literature,
because your paper’s audience is not familiar with these terms, e.g., due to coming from another field,
you created a concise term for some concept that you introduce in your paper.

First of all, this is not a case of common knowledge: If it were, why define at all? However, that does not mean that you must cite somebody. Instead cite somebody if:

You rely on a specific piece of work.
If you had to look up the definition instead of coming up with it yourself, this almost certainly applies.
Keep in mind that coming up with a useful definition of some things is a challenge and deserves credit.
On the other hand, as a rule of thumb, you do not need to cite if you would not know whom to possibly cite in the first place (possibly after a short literature search).
You want to affirm that you are adhering to some standard.
Using established definitions does not only make your work easier to read but also may make it comparable to other works or reüsable.
If nothing else, providing a source for your definitions may calm down Reviewer 2.

Some examples:

I would not cite in the following statement, which is essentially clarifying a well-known conflict between two common definitions (whose history I do not know):

We here define the natural numbers ℕ to include zero.

I would cite in the following example, not only for giving credit but also for affirming my approach:

We here define epilepsy as […].
  This is equivalent to the definition by Fisher et al (2008), except for […].
  This difference is due to the practical reason that […].

Do I quote a dictionary, […]?

Regular dictionaries reflect the common non subject-specific usage of terms, which is by nature often broad, fuzzy, context-dependent, and different from academic definitions (if they exist).
This usage is also what you have to expect readers to understand if a term you use in a paper is not specifically defined and there is no established use in your field.
With other words, the dictionary definition is the fallback default anyway.
Therefore quoting a dictionary for definition is pointless in my opinion: it changes nothing and clarifies nothing.
If you think that a dictionary definition is the best guidance you can give to your readers, you may as well skip it.
(Note that field-specific dictionaries are a completely different thing.)

Do I quote […] another research paper in the field, or do I paraphrase either one?

This may depend on your field, but I would refrain from paraphrasing definitions just for the sake of paraphrasing.
If I rephrase definitions, I risk changing it.
Therefore I would only do so with a good reason and when I can be confident that my changes do not affect the outcome, e.g., I could change symbols in mathematical definitions to match the conventions of my paper.
In all other cases and particularly in fields where exact words are important, I would rather use a huge quote than paraphrasing.
Still, conventions here may vastly differ between (sub)fields, so best check what is common in yours.
Either way, once you build upon somebody else’s work like this, you should cite.

I fully agree with everything except the part about quoting a dictionary. Under some circumstances, quoting and citing a dictionary can be entirely appropriate. It lets your reader know precisely which definition you are using for words that can be defined in multiple ways. In some fields, such as law, citing the source dictionary can also matter since some dictionaries will be viewed as far more authoritative than others if you want to argue that the definition you selected is the one that should be accepted broadly.


text:
Should I use ‘adapted from’ in an illustration of conclusions based on the results of others
Suppose, you cite some particular ideas, analyze them, and come up with a few conclusions, which you illustrate in a figure that is totally yours.  The labels or conclusions represented in the illustration are neither other people’s work nor my own primary empirical findings. They are somewhere between: my own conclusions, yet based on the data of others. In the caption of the figure, should you write adapted from to show that the figure was ‘sourced’ from other studies (i.e., the conclusions and analysis were built on other resources)?
For example, assume that Study X claims:

Helping people leads to profitability.

Based on that, I conclude that companies should adopt the notion of social responsibility. Among other conclusions, I represent social responsibility in a schematic. Should I write adapted from Study X to say that the conclusion of social responsibility was built on the material from Study X?

I am confused as to what your actual situation is. Did you re-use data from another study or not?

I will put it in this way: the labels or conclusions represented on the graph are neither other people's work NOR my own primary empirical findings. They are somewhere between; my own conclusions (primary?), yet based on others data.

I edited your question to reflect my understanding. Please check that everything is still in accordance with your intentions, in particular that your figure is not showing any data but a mere schematic.

Yup, that's fine. It generally represents what I am trying to ask for. All in all and since I have to present my essay tomorrow and since I can write whatever I want to write in the caption under the figure, I explained in detail that the figure and the conclusions are mine, yet they were built on the below list of sources/studies (without using the exact words of 'reproduced from' as they can be misleading). Do you think that such a way is fine?

I say 'generally' because my conclusions are from my own analysis of others studies (not their direct results).

What's wrong with "my own conclusions based on others' data"?

@JeffE could you please elaborate?

Disclaimer: As the answer to your question could be field-specific, my answer is from an (electrical) engineering point-of-view.
I think the general consensus in my field is that "adapted from" in a figure caption is to be taken very literally: it is to indicate to the reader that a figure from a previous publication has been adapted for use in the new figure1.
Since you are not adapting a previously published figure for use in your manuscript, it seems, then, that the situation you describe does not warrant the "adapted from" disclaimer in the figure caption.
Instead, you should use the main body text to stitch the various references together [with appropriate citations] to support your position, call out the figure in question in the text, and [depending on how much additional detail your figure caption needs relative to the development of the idea(s) in the main body text] an appropriate figure caption.

1An example of using "adapted from" in a figure caption in my field might be the following:
Your competitor's paper A incorporates top-level circuit schematic B in figure C. Your follow-on paper D utilizes circuit B, but you redraw the schematic to highlight the points more relevant to your paper D in new figure E. In this case, the caption of figure E would indicate that the figure was adapted from paper A.

What I've done: Before the figure, I presented it as summary of my conclusions + arguments (references) are provided below fig 1. Then, in the caption of fig 1, the full story is showcased as how such conclusions and figure are mine, yet they were 'built' and 'concluded' from various studies and sources (as listed below) and explained in detail throughout the essay. Yet, before the actual list, I introduce it by saying that these sources are my arguments for choosing the conclusions and then ask the reader to refer to where a conclusion was 1st mentioned to see how each reference was used.


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Including Patients' Pictures in a Manuscript
I am going to include some pictures of patients in my manuscript, which will be submitted to a scientific journal for peer review. In order to keep the subjects’ identity and following the data protection act, I need to hide their faces.
My question is to know whether to put a black rectangle over their faces, especially their eyes or pixelising their faces. I have been told that putting a black rectangle is not recommended for this purpose, but I have never been told the reason.
Could somebody please let me know first that:

Which method is better?
Is that the case that blackening the face is not recommended. If true, why?

Rather than identifying the better method, it is perhaps better to identify the method that is acceptable to both your institute (in particular, your ethics board) and your publisher.

@user2768 And your patients.

@skymningen I like to think institutes only consider methods acceptable when they are acceptable to (their) patients. Similarly, albeit (in light of the above comment) perhaps more likely, institutes should only consider methods that comply with the country's legal system. Institutes are more powerful than their employees and should be better positioned to make the right decisions regarding acceptable methods. Of course, mistakes might occur, but mistakes should be rare. If mistakes are common, then employees should (rightly) be questioning their choice of employer.

@user2768 Exactly because of your arguments I would suspect that the publisher and institute will already have been much more vocal about their preferences regarding anything in this publication than the patients, who often don't know enough about their rights to investigate for example how exactly their anonymity will be protected. Also, institutes or publishers should have a rule set somewhere in writing applicable to all publications, patients do have separate wishes and needs that need to be inquired for each patient separately every time.

@skymningen your position seems to be that a patient's personal preference is more important than any legal or institutional requirement.

@user2768 The patient's preference IS the most important legal requirement (at least in the most countries). If you do not adhere to their preferences, there is no consent, so there is no way for you to use the data. If your patient does not want their picture to be published with a black bar you either choose pixelation or remove the picture. Or let your legal consultant know there might be problems coming up.

@skymningen If "[t]he patient's preference IS the most important legal requirement," then institutes will surely only consider methods acceptable when the patent's preference is considered, so I do not follow the point you are trying to make, it is already covered by my earlier response(s).

The BMJ Publishing Group suggests a very simple reason for the change:

We no longer publish pictures with black bands across the eyes because bands fail to mask someone’s identity effectively.
We will need the patient to sign our consent form, which requires the patient to have read the article.

If you can "blacken out" the face, then why not just crop it out altogether?

If you are in the United States, HIPAA regulations require that no identifiable information about the patient is published without his/her written consent. This includes photographs showing the face (fully or partially) or any other distinguishing features (tattoos, etc.). At the very minimum, you should cover the entire face with a black rectangle, or crop the face out of the picture. Alternatively, you can request written permission from the patient.