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Why add a minor to a PhD?
As an undergrad I had a couple majors and a couple minors...no big deal. Ultimately all it meant was I took a lot of classes all over the place and went through the time and effort to declare them.
As a PhD student, though, declaring a minor is pretty uncommon. Hell, a lot of schools don't even offer the option. My understanding is that minors are usually for highlighting a certain amount of coursework in a closely related field to the one you're studying. Seemingly obvious pairings would be a PhD in Math with a minor in Statistics, or a PhD in Classics with a minor in Philosophy. However, unlike in undergrad (and really even at the Masters level), during a PhD the emphasis is primarily on research, not coursework. So why is a PhD minor a thing? Does it serve any purpose more than just another notch in your academic belt?
Personally, I am thinking about adding a Math or Statistics minor to my PhD in Computer Science, but I can't come up with a good reason other than "I'm interested in higher level math/stats and it's really applicable to the area of CS I work in." That's enough to satisfy me, I guess, but is there really any other reason to do this?
EDIT: I guess I should add that *in my case* I'm not thinking about a minor for minor's sake, but rather that I'm already taking a bunch of courses in that area so it just means an extra course or two. The question still stands though: why is it a thing? And, furthermore, does it carry different connotations in different areas (e.g. the humanities vs. applied sciences)?

I've never seen someone declare an official minor for a PhD (I didn't even know it was possible). People (including me) usually just take the courses they are interested in and or are related to their work.

@AustinHenley I know. As I said, it's a rare thing. But people do do it. That's why I'm curious.

Is it actually called a minor where you are? In the places I went there were types of certificates you could get for say adding medieval studies to your history or philosophy degree.

@AustinHenley: it's actually required at my school to declare a minor. Typically, people just minor in the same department as their major, but it's not so uncommon as you might think! :-)

To be honest, I've never heard of a minor for a PhD. However, not all PhDs have courses. My PhD was 100% research, no coursework involved, so the option for a 'minor' was mute, and the 'major' was dependent on what school you were enrolled in for funding.

In addition to the laudable goals of actually advancing one's education in a structured way, as several of the other posters have mentioned, it does serve to credentialize you in the minor department. Someone with a PhD in Math with a minor in Statistics potentially reads to me as very different than someone strictly doing a PhD in Math, even before I dig into their CV. That is one function - essentially keyword recognition of "I belong amongst both groups".
As someone who works in an interdisciplinary field, that can frequently helpful.

A minor gives a grad student the option of diversifying his/her learning experience. Much research is interdisciplinary (like stats and CS), so taking a few classes in another department can be very beneficial. It also gives a grad student an excuse to take courses in something that isn't directly related to their research. (Minoring in a foreign language or business can be generally useful, for example.) In my own experience, most grads minor in something closely related to their research.
As far as I know, very few people look at a graduate student's minor. The biggest reason I can see for having a minor outside one's home department is to diversify one's educational background.
I looked around to see what universities said about this. Georgia Tech states that "The purpose of the minor is to encourage a wider interest on the part of the student and to provide a broader basis for the evaluation of the student's capabilities." (source) Stanford requires a minor for its Education grads (source).

Per what jvriesem says I can verify that Georgia Tech, and I would expect other universities, does indeed encourage a PhD minor in order to broaden one's education. In fact, it is a requirement for graduation to get a minor, by taking something like three courses outside of your department. I would encourage a PhD student to pursue a minor for this reason, if it wasn't already requirement.
I ended up taking EE courses which were pertinent to my physics research area, which I may have taken anyway. I did find content to be directly helpful for my research, so it was a net gain. Outside of satisfying the graduation requirements, it may be useful to some potential employers, even if it is only a small part of the consideration for a job candidate. In my case the engineering knowledge proved helpful for landing a job, since my core area of study was physics.

I have a PhD in Education specializing in adult literacy. My minor is in Non-Profit Management. I'm sure you can see that the two disciplines are perfectly suited to each other.

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How to handle dislike of/lack-of-interest in sub-specialty of research area
I am a PhD student studying in a field that I enjoy. Furthermore, I enjoy the area within the field that I am specializing in. However, my specialty generally has two major application arenas, which in some ways are disjoint. I came to the program knowing I would be working in one of them, sub-specialty A, despite having no prior experience in it. I did have experience in the other, sub-specialty B, but the faculty in my department who work in sub-specialty B either didn't have openings or didn't see me as a fit for their group (i.e. they didn't support my application).
I arrived planning to give sub-specialty A a fair shake, as I honestly knew little about it and for all I knew I'd enjoy it. After a semester, I am finding it hard to stay interested in the research, and this feeling is compounded by the frustration of feeling like I have to start over in the field. It's also tough watching my peers work on problems of sub-specialty B that I find so much more interesting than my work in sub-specialty A.
I know a PhD is the start, not the end, of a career, and that what you do during it is not what you have to do for the rest of your life, but, that being said, I do have to spend 4-6 years working with this material.
How does one handle this sort of situation? Is it appropriate to bring up my concerns with my adviser? Could trying to bring in a co-adviser from sub-specialty B be a feasible way to bridge the gap between the sub-specialties? (NOTE: It's worth mentioning that this is literally the only problem I am having with my PhD; the school is great, the cohort is great, and my adviser is great) Have other people been in these circumstances? If so, what did you do about it?

But he was very clear with me coming in that I'd be working in the arena of problems related to sub-specialty A. The issue is that I overestimated how much I'd enjoy that sub-specialty. I don't really want to bring it up if the response is just going to be "Well you knew that coming in." Because that's true, and all that the conversation would have done is make me look bad to my adviser.

That's a valid point. A follow up question though: when is the appropriate time? Is a semester long enough? Should I wait until I've published a first-authot paper in this sub-specialty first, so that I can veritably say that I have definitely given it a shot? Or is after a semester of assisting others with their projects (essentially apprenticeship-style learning) and taking coursework enough time to have a leg to stand on in this hypothetical conversation?

when is the appropriate time? — Today.

How does one handle this sort of situation? Is it appropriate to bring up my concerns with my adviser?

YES. That is exactly how one handles this sort of situation.
Try something like the following:

I knew coming in that I'd be working on A, and I thought I'd enjoy it. But after a semester, I'm feeling.... How do you suggest I move forward?

and see where that gets you.

Should I wait until I've published a first-author paper in this sub-specialty first, so that I can veritably say that I have definitely given it a shot?

If you believe you've given it a fair shot, there's no reason to wait to voice these concerns (in a professional manner). There's no "milestone" at which point you can say "I definitely don't enjoy this area" - there will always be more things to try. The reason to speak to your advisor is that he may be able to advise you on what to try next.

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Applying to religion affiliated universities: how to write Statement of contribution to mission
There is an opening for an assistant professor position at a US university, that I really want to apply to. However, it is a Catholic university and the application requires a "Statement of Contribution to Mission." I have read the university's mission statement which, besides the usual academic missions, includes quite a few religious missions. I am not Christian; in fact, I am an atheist. From the answers to this related question, and that the job posting states clearly Equal Opportunity, I understand that I can still apply to this position. But I have no idea how I should write such a statement. Of course I won't lie in the statement to pretend that I'm Christian. But having no clue and personal connection to those religious values, tradition, and missions, I find it impossible to write even one word.
Is there any suggestion for writing such a statement? Or should I not apply?

How have things worked out for you? Your experience might be useful to others, so likely worth sharing.

I think you should certainly apply, as long as you have no personal opposition to Catholic education writ large; the previous question you link is a great source if you are uncertain.
As to your question, for an example, I pulled the mission statement for Marquette University in Milwaukee, WI.

Marquette University is a Catholic, Jesuit university dedicated to serving God by serving our students and contributing to the advancement of knowledge. Our mission, therefore, is the search for truth, the discovery and sharing of knowledge, the fostering of personal and professional excellence, the promotion of a life of faith, and the development of leadership expressed in service to others. All this we pursue for the greater glory of God and the common benefit of the human community.

Following this broad statement, they have four subsections on Excellence, Faith, Leadership, and Service. Of course the mission of your university may differ but I presume it will paint similar broad strokes.
I would write a statement that addresses the primarily non-Faith elements of the mission. Quoting again from Marquette, on Excellence they state:

education must encompass the whole person: spiritual and moral as well as intellectual, the heart as well as the mind

Without aligning with their religious beliefs, you could certainly contribute to education encompassing the whole person, particularly in intellectual pursuits.
Most U.S. Catholic universities that I am familiar with belong to either the Jesuit or Franciscan orders, though there are others as well - it might be worth spending a bit of time researching the order of the university you are applying to. Painting in a very broad brush, Jesuits tend to value intellectual pursuits as valuable contributions to society, and lean quite a bit more liberal than official Church policy on social issues. Franciscans are particularly concerned with service to the poor, and as such their universities try hard to accommodate students with financial difficulties. Even if you disagree on the religious aspects, you can probably find something in the general mission of these orders you also support.

Why are you encouraging OP to lie when (to use the example you gave) "the promotion of a life of faith" is part of the institution's mission?

@user76284 I don't see any encouragement to lie. The university's mission contains A, B, C, D, and the answer suggests detailing how OP can contribute to A, B, C; they clearly can't contribute to D, and they shouldn't claim otherwise.

@user76284 Federico Poloni has it right, it seems like you've inserted some false understanding that does not exist in my answer.

@BryanKrause Are you suggesting that OP give the impression that he will promote the university's mission?

@user76284 Read the answer.

Hopefully the OP has found and had a successful career since this was asked.
As a former student at a Jesuit University, let me add to the answer of Bryan Krause that there is little difference in the ethical and service beliefs of Catholics and Secular Humanists, who might indeed (as myself) be atheists.
There would be, in my view, no need to mention your religious (non) beliefs in application. Indeed, my university had at least one Jewish professor. In chemistry (his field) or math (mine) or history or most other fields, religion and/or belief systems of students and professors never comes up. There were religion professors of course, and the philosophy department was generally Thomistic, which is actually quite secular in many regards: "Truth is where you find it.". Even there, however, modern, non secular philosophers were taught.
Focus a "contribution to mission" statement on ethics, education, service, philanthropy, and such, not on the acceptance or rejection of faith or any particular belief system. And be honest in every way.
You would be expected, I suppose, not to be a proselytizer for some non-Catholic system, but I also suspect that if you were asked by a student and answered honestly that no one would object.
Note that there are some religious schools that have very different requirements, but I haven't found that to be true among Catholics in modern times. Most academic disciplines are taught in Catholic universities in exactly the same way as in non-secular institutions. Even when the professor is, for example, a Jesuit. They tend to require precision of thought, not some particular belief system. Math is math.

One of the things I ponder about is how many priests are actually atheists. I think I knew at least one who wound up that way. And he was actually a religion professor. But his real dedication was to growth and to service.

"there is little difference in the ethical and service beliefs of Catholics and Secular Humanists" That's complete bollocks. And Thomism is not "secular".

@user76284, I claimed that the philosophy faculty were generally Thomas's, not that it was secular. Most were priests, actually. Nor do I claim or think that Thomism is entirely secular. Thomas was a priest, of course with belief in God. And many secular humanists agree with the teaching of the  Eight Beatitudes. FWIW, my minor in college was Philosophy and I've kept a life-long interest.

The Eight Beatitudes refer to God and the Kingdom of Heaven. They are intrinsically incompatible with secular humanism.

I know this question is old, but there is one glaringly obvious answer that does not appear.
If you know nothing about a topic, read a book about it.
For example, Mere Christianity by C. S. Lewis.

I was not talking about getting into an argument about faith, I don't think religious people are more stubborn than atheists, and I didn't say OP would have to become religious in order to apply. I was just addressing OP's main point that he/she felt no connection to religion and didn't know what to do.

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Bigger question- why would you apply to a college or university that is based in a belief system that is fundamentally opposed to your view of the world? The Catholic Intellectual tradition is based foremost in a belief in God. You do not believe in God. How can you teach from a prospective you do to believe in or understand? Is that fair to the students who are going to that university to learn from that prospective? Is it fair to the administrators and religious of that school who build programs and collaborations based in the perspective? Is it fair to others who may want the job who do hold the same beliefs?

I'm confounded by the -2 or two people who downgraded my response. The response is based in simple logic and is a clarifying question as to motive and eventually the happiness and well being of both the applicant and the institution. I would like one of the people who voted the comment down to help me understand the logic behind their opinion, or is this just anti-Catholic or religious mind set showing?

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@user104446 "applicants of other beliefs need to get a job so they can get on with their lives" And they can do so elsewhere. It is not the institution's obligation or responsibility to provide them with employment.

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How often do people find mistakes in papers and not tell anyone?
I found a significant error in a paper with 1000 citations.  My advisor agreed that it is a significant error, but discouraged me from telling the author.
It occurred to me that maybe other graduate students also found the error, and never told the author, or they did tell the author and he just never corrected it.  I think an author would have very little incentive to correct his own work, especially if they were famous for that work, and readers are strongly incentivized against writing a correction paper, because the author would be mad at them.
How often does this sort of thing happen?  Can we really trust the literature?

See What should you do if you spotted a non-trivial error in a highly cited paper?, How to deal with errors in well established papers

Did your advisor give a reason for not wanting to contact the author?

@Kimball He just said it wasn't a high priority and that maybe we could bring it up next time we saw him (which would probably be never).  I assumed he didn't want to lose the friendship or something.

This surely happens all the time.  And no, you cannot trust the literature.  I don't think anyone would seriously claim that you can.  Neither authors nor reviewers are infallible.  If the result is important, you have to check it yourself; or weigh the effort needed against the risk of it turning out to be wrong.

There are a lot of errors where technically what is written is incorrect, but an experienced reader who is carefully studying the paper would notice the error and be able to recognize what should have been written instead.  People often don't bother to correct errors of this kind: not so much to avoid embarrassment, more just because it's a big hassle. It may be that your advisor thinks that's the case here - maybe it is obvious to her what is meant, even if it isn't to you.

It would help if you could indicate the field of the paper - different fields have different kinds of "mistakes".

When I was a post-doc, I came across an error in a paper by some very famous researchers.  One of the intermediate claims in the paper was clearly wrong.  In fact, it was so clearly wrong that I assumed that they authors had merely made a mistake in how they were phrasing the claim, and that the main arguments ought to be correct.  Although I knew one of the authors fairly well, I didn't contact him about it.  However, the paper was part of a lengthy back-and-forth between two sets of authors, and about a year later, the other group published a strong rebuttal, based, in part, on that error.

@NateEldredge if indeed it's a "forgivable error", I think it's a good teaching moment for the advisor to then explain to the student why that is. And so it's reasonable for the student to ask for some clarification.

It does happen. During my PhD, I replicated the work in a modelling paper analytically and then numerically, and both times demonstrated that there was an error in the original well-cited paper. My advisor insisted that I must have made a mistake myself but wasn't interested in checking my work.I hadn't made a mistake: the error was there, but I didn't feel I could do anything about it. In my later career, I met the author, but still didn't say anything because I would have needed to redo my calculations to demonstrate it and it was too much work.

True, scientific literature is littered with papers that have errors in them. This article raises concern over the issue of uncorrected errors in scientific literature: http://retractionwatch.com/2016/05/19/retractions-arent-enough-why-science-has-bigger-problems/

Closely related: http://academia.stackexchange.com/a/48228/20058

How is this question possibly answerable as posed?

If it is "a significant error," then presumable it appears in a central argument. Hence, the central argument is flawed. You could present a paper that highlights the issue and gives a valid argument. You could ask the original author to co-author your paper.

@user2768 That is much more difficult than you would suggest.  Sometimes the errors are very subtle and extremely difficult to nail down. This is one of the subtle and major issues of the cutting edge of modern mathematics. There are threads on MO asking "what is the error in this paper" in some form or another, and there are rarely any definitive answers.  Just heuristic insinuations, or appeals to alternative proofs/disproofs.  None of them can point at the exact issue in the exact paper and go "Here, this is the problem."  Just "this seems like it is questionable/much harder than suggested"

@zibadawatimmy, user56416 claims to already know the error. In any case, pinning down the details is surely a part of mathematics.

@user2768 Easier said than done sometimes.  Voevodksy had a multi-year spate when Simpson published a counterexample in 1998 to a theorem Voevodsky and Kapranov had published in 1991.  But Simpson couldn't point out what the flaw was.  And nobody could find a flaw in the counterexample.  It wasn't until 2013, 22 years after he published, that Voevodsky conceded his result was false.  I'm not sure if anyone knows exactly where things went wrong to this day.

@zibadawatimmy, now I understand your point. Although a counterexample suffices to show that a result is wrong, it does not show where the result went wrong (i.e., no particular hole/mistake in the proof is identified). For user56416, presumably knowing the error means knowledge of sufficient evidence (counter-example or otherwise) to show there's a problem with the original work.

Researchers/authors are human.
Humans make errors.
Thus Researchers/authors make errors (if we assume transitivity is given).
So, can we trust literature? Well, being an agnostic I tend to never blindly trust any statement. I found dozens of errors in the lectures I attended and made the experience that lecturers respond very different to criticism. There are some that feel attacked, or those that simply do not bother, but there are also those that will really think about your criticism and will correct you or themselves after having carefully checked the issue in question again.
I think, that a researcher's duty should be to allow and work with criticism as this will lead to an even better understanding of the topic for all involved sides. Also, your criticism shows interest which is actually a good thing and should be rated as such.
A good criticism should focus on the research itself and leave out personal-related stuff.
So my conclusion is, that you shouldn't just do nothing because of those strange unspoken rules society has built up to underline the higher status of academic people. Remaining silent for social fears is a bad thing that leads to a vicious cycle and harms research in my opinion. You should be free to question whenever you feel like it is necessary to question. Consider for yourself for when it makes sense to consume someone else's time. If you are not sure about your criticism, make some own research. If you are sure your criticism is right, if you ask me, for research itself this is the best one can do.

Slightly tangential (doesn't answer "can we trust the literature?"), but:
On several occasions, especially when working with a class of students to work through a paper line-by-line and replicate its results, I/we have found errors — nothing that changes the qualitative conclusions of the paper, but definitely large enough to be confusing to students. These kinds of errors are overlooked by most readers because they aren't going through the paper as thoroughly, but setting the record straight can save a lot of time and trouble for future readers — especially students, who won't have the courage of their convictions and will think that they must have made a mistake/be misunderstanding something.
It helps of course that (1) I was already reasonably well established in the field and knew/was known to the authors and (2) the authors were reasonable people who saw the value in correcting their minor (but confusing) errors.
For example:
Yates A, Stark J, Klein N, Antia R, Callard R (2008) Correction: Understanding the Slow Depletion of Memory CD4+ T Cells in HIV Infection. PLoS Med 5(1): e11. https://doi.org/10.1371/journal.pmed.0050011
In another case, where there was a typo in a single equation that didn't propagate downstream, and the paper was older (>10 years from publication), the author confirmed the error but said (and I agreed) that publishing a correction probably wasn't worth the trouble.

Can we really trust the literature?

Let me point out here that "can a paper be trusted" and "all of the calculations in the paper are exactly correct" are not necessarily related. This is something that people get wrong about research, and in particular single papers, all the time. Academic papers are useful dialogue. They are not necessarily 100% accurate or unimpeachable.
Peer review is designed to catch methodological errors. It confirms that the authors followed sound scientific principles as appropriate to their field. Most peer review does not check for errors in calculation, and typically could not even if they wanted because the peer reviewer does not have access to all of the paper's data. However, peer review does confirm that a group of experts all read the paper and agreed that the methods and conclusion make sense.
A paper published in a good venue is not strong because it is guaranteed to be 100% accurate, it's strong because the expert community of reviewers thinks it is accurate. I would assume, though I can't cite any evidence, that academic papers at good venues have a much lower error rate than similar documents that do not go through a rigorous vetting process.
As to whether this error should be reported- it really depends. If this is a purely theoretical result, if it is empirically in doubt, if it substantially changes the result of the paper, then the error should really likely be reported. If the calculation is wrong but the intuition and the model are solid, and there is strong empirical evidence for the model, then the calculation error probably isn't that meaningful.
Here's a practical yardstick: if reporting the error substantially advances the scientific conversation, then it is a publishable result that should be published, just like any other publishable result. If reporting the error is just fixing errata and not substantially contributing to the body of knowledge, then it's not publishable and probably nobody cares.


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My manager wants to be the lead author for a paper which I have done all the work for. What ethical reasoning should I use to dispute this?
I work as a research scientist, and I am about to write up the work I've been doing for the past year. I have done all of the big data formatting, set up, edited and run a complex ecosystem model, wrote analysis code, calculated the statistics, produced graphs and map outputs. My manager wants me to pass the final graphs, maps and statistics to him so that he can write up the paper. I have sufficient post graduate research experience and analysis skills to analyse the final data myself and do the write up.
My manager has a good scientific overview of the work but doesn't have the technical skills to run the model or do any of the coding/ statistical work himself. I feel like he should encourage his staff to write up their own work, but he said he needs more papers as first author.
Do you have any suggestions for the points I can raise when I discuss with him that I'd like to be first author?
I want to stay on good terms with him as far as possible, while also asserting my belief that I should be first author. A former colleague done some of the base work for this project, and I think his name should also come before that of my manager's. My manager's supervision of the project has been minimal (a 5 minute rushed catch up conversation every month or so).

What kind of organization is this? Academic or commercial?

Have you read through COPE's guide on authorship issues (see bottom of this page)? Some of it is admittedly not helpful right now (for example, one of the best suggestions they have is to have the authorship discussion before you start the research).

Authorship issues basically boil down to "did X do enough work to be an author? Did X do enough work to be a first author?" You only end up with "ethics" discussions if your manager admits that he hasn't done much work yet still demands first authorship. Is that the case? That would be a different issue from the more run-of-the-mill problem of you disagreeing with your manager on how much his contribution to the project is worth.

I'm voting to close this question as off-topic because was edit-deleted.

See How does deleting work? What can cause a post to be deleted, and what does that actually mean? What are the criteria for deletion? for an explanation of why you can't delete your own question. You can, if you want, ask for it to be disassociated from your account by raising a moderator flag and asking for that (see this post for more info on that option.)

Say no, submit the paper, and start looking for another job, not necessarily in that order.

I think an important distinction to retain in the title is that your manager wants to write-up the paper. I'm not saying this is ethical. I'm just observing that this is a fundamental feature of the context that should probably be captured in the title of your question. I.e., it's different to the situation, where the manager wants you to do everything including the write-up and still wants first authorship. In most fields, the write-up is a large component of the authorial contribution. And thus, the question is more about a manager who wont let their employees make that contribution.

Also note my answer here, which deals with a similar thing (from a mostly german perspective, but probably applies to other countries as well).

Who is "the risk-taker" behind what the research is trying to determine? You may have done a lot of brainy, fantastic work, but who is the risk-taker in this case? I've read everything you wrote, and the sense I come away with is that your boss is the risk-taker behind it. You are the brains, but your boss is the risk-taker. Your boss is brainy too and had an idea of where the research would lead and pointed you and others to the correct path. I think you should worry more about preserving your relationship with your boss.

I feel confident in my answer because, although norms differ between fields, you are in exactly my field.
You are absolutely correct that it is not ethical for your manager to ask for first authorship on this paper. From the work you describe, this is your paper. He may need more first authorships, but so do you, and even aside from the ethics of relative contributions, his role should be to help you to progress your career.
Managing this situation is going to be very tricky for you. This happened to me during my PhD -- my PhD advisor was first author on all my publications -- and I did not confront him over it. Obviously, this wasn't good for my career. It wasn't great for his career either, because it meant I was unwilling to work with him after I finished my PhD and so he lost the opportunity to be a coauthor on several more papers that followed on from my PhD work.
On the other hand, having a blow-out with your boss that puts your ongoing work in jeopardy or results in your work not getting published at all is also not going to be great for your career.
I suggest you do try to change his mind, but keep it very polite and civil. Mention the benefits to him of having you do well: it will boost his reputation as a successful PI and mentor, it will increase the likely success of future collaborative work with you, and it will reduce the amount of work he has to do on the paper himself so that he can concentrate on getting more of his own work published. If this fails, it may be worth involving a third party -- in the first instance someone you mutually like and respect, if possible, and not his boss -- to facilitate a discussion about setting some more formal guidelines around how authorship order should be determined.
If all else fails, you could appeal to authority - his boss or the journal editor - but be warned that WILL get messy and bitter.

One compromise to consider is to give him last author placement. This is an honorary ordering that is often used for the person who provided the idea, guidance and resources for the study. It's similar to opening film credits that end with "and", followed by an old, famous actor who does little more than provide gravitas to the work.

The ICMJE guidelines recommend that authors should state their contribution to the project: ‘authors should provide a description of what each contributed, and editors should publish that information’. Journals may publish this information but in most cases it is for the benefit of the editor,who wants reassurance that the criteria have been fulfilled.( see section II ROLES AND RESPONSIBILITIES OF AUTHORS, CONTRIBUTORS, REVIEWERS, EDITORS, PUBLISHERS,
AND OWNERS of the 2015 recommendations)  I'd simply ask via email that each authors contributions be clearly stated per guidelines adopted by ICMJE. Put yours and any other authors in the email and ask him to add his. It doesn't matter that the field you are in isn't biomed, you simply like the idea.  If he refuses you can at least submit the email thread and his refusal to the editor and let the chips fall where they may. I'd be a little surprised if I was an editor and the lead author couldn't say what his role was.

You'll learn from this experience. It's a good idea to discuss authorship at the outset of a project, and perhaps again throughout the process. Generally, the person who writes the paper receives first authorship, followed in order by amount of intellectual contribution, with the last author (in some disciplines) being the main PI/lab head. If your superior now insists he/she must write the paper, he/she is probably entitled first authorship. If you can't come to an agreement, you might ask that it be noted that 'the first two authors contributed equally'. That is somewhat common.

This doesn't adress the main question "what can OP do in this situation?". Tho I agree with sentiment #lessons #learned


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Is it a good strategy to reproduce figures from related articles in NSF proposal?
I am starting a tenure-track position soon and writing a NSF CAREER proposal for the first time. I have no preliminary data on this topic; therefore I am using a number of figures from related papers to illustrate my idea.
Without preliminary results, is it a good strategy to use others' figures at this stage (this is a bit philosophical question, but I am little worried about the impression I make with the reviewers)?

I haven't been on a CAREER review panel (I'm only a PhD student myself) so take my advice as the uninformed opinion that it is, but based on all the advice I've been given on writing CAREER proposals, using more than a few figures (at most) from other people seems like a bad idea in most cases. You want to show that you have the skills and resources to carry out your research plan.

I edited out the part about copyright because it's a duplicate of this question. P.S. for future reference: please ask one question per post.

I don't think it is a good things, especially since you're supposed to do it yourself. Anyway If you do it, don't forget to mention it is not yours, and why you did it.

Leaving this here for the benefit of future readers: applying for CAREER in the first year can sometimes work, but is often a waste of your first attempt opportunity. Spend your first 1-2 years gathering your own preliminary results, developing an educational program, and preparing to apply.

I would strongly advise against doing this. Instead, create your own original work that illustrates the main points.
Sometimes I see figures reproduced from a journal article in a grant application. Usually, the figure doesn't work well in that setting. When the grant writer copies the image into the proposal, they typically shrink the image to save space, which makes the image hard to read and understand. Journal article figures are often very complex, making points that are not necessarily relevant to the proposal. It's usually best to create your own figure that says what YOU want to say - to make a point about the science you want to do. Also, I worry that reviewers may regard this as plagiarism.

Hi and welcome to A.SE. Can you expand on your answer a bit, please?

Sure! Sometimes I see figures reproduced from a journal article in a grant application. Usually, the figure doesn't work well in that setting. When the grant writer copies the image into the proposal, they typically shrink the image to save space, which makes the image hard to read and understand. Journal article figures are often very complex, making points that are not necessarily relevant to the proposal. It's usually best to create your own figure that says what YOU want to say - to make a point about the science you want to do. Also, I worry that reviewers may regard this as plagiarism.

Thanks for the clarification! It it's OK with you, I added your comment to your answer.


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Is it a bad idea to mention informal PhD offers in a job application?
I am about to get my master's degree and have published a few papers in highly reputable computer science journals. I have gotten an "informal offer" for a PhD position from a world-class university. An informal offer here means that a well-funded professor has e-mailed me, strongly encouraging me to apply and to make sure to mention his/her name in the application so it gets routed to him/her.
For various reasons, I'm leaning towards not pursuing a PhD so I'm currently working on my resume. I'm wondering if it's a bad idea to mention anything about this informal offer in the personal letter. The professor making the offer will not be the one writing my letters of recommendation. Verifying the claim would not be hard, but it's not really a tangible accomplishment. On the other hand, why shouldn't I highlight the fact that I could get into the best graduate program in the world if I wanted to?

I'm voting to close this question as off-topic because it's for preparation for a non-academic career. This may or may not be considered on-topic at The Workplace, but you should read their FAQ and search for similar questions there first.

@BrianDHall I don't agree, because it can be answered from the perspective of "is this something you can claim as an achievement", not just "is this something that would be valued by non-academic employers." The latter is off topic, but the former seems fine to me. I guess we'll see how others vote :)

Why shouldn't I highlight the fact that I could get into the best graduate program in the world if I wanted to? Because people care about what you have done, not what you decided not to do.

@ff524 I read it primarily from the angle of "what would a non-academic employer like to see", which sounds to my ear more like job prep, but I don't feel especially strong about it, so indeed I'm open to how others view whether or not this is on topic here :)

tl;dr: No, you should not mention this "offer."
I wouldn't even call this an informal offer. An "informal offer" would be if you applied, and then were told by e.g. email or phone that you are admitted, and that the formal letter of admission will follow shortly. Encouragement to apply, no matter how strong, is not an offer of admission, and doesn't indicate that you would definitely get an offer of admission if you would have applied.
For example, you may sound great according to whatever information you sent to that professor, but your full application may reveal other things that lead the admissions committee to reject your application. Or maybe you really are that great and the professor has funding, but another, better, student applies that year and gets the offer instead of you.
Furthermore, individual professors have varying ability to actually influence the admissions process, depending on how graduate admissions actually works in that department.
Even for a "real" offer of admission, it wouldn't necessarily be a good idea to list it on a résumé. See for example this related question on listing fellowships that are offered, but which you decline. But being encouraged very strongly to apply to something is certainly not a CV-worthy accomplishment.

"I wouldn't even call this an informal offer..." I agree completely and strongly with this and the subsequent sentences in the paragraph.  An informal offer is a kind of offer, and the OP has not received any kind of offer.  Trying to "get credit" for something like this could really backfire.

I completely agree with you. I had such "offers" from at least 7-8 of the most prestigious universities in the U.S. and I applied for all of them but only 2 admitted me. Those "offers" mean nothing.


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Is arXiv strictly for new stuff?
If you have a very old paper pre-print, tech report or thesis lying around (one that you own the copyright to), and it hasn't been uploaded to arXiv, can you do it?
Or would this be seen as inappropriate?

Yes, you can definitely upload it. It's not just for new stuff.

To reinforce the point of @It'sMe : I know some people who posted older papers/work that is hard to access because of where it was published, v.g. defunct journal.

once I saw a translation of a paper written by Leonard Euler on ArXiv

Here's a very recent example, uploaded a couple weeks ago with the comment "23 pages. This paper has been published in 2004 but was never posted on the arXiv"

Assuming the content type and contents are appropriate, submissions that are of scholarly interest are welcomed even if old. Here's an example of a never-published preprint from 1981, that was only put on arXiv in 2016: 1612.00076.  However, I can also imagine some old documents no longer meeting the bar of scholarly interest, so do take that into consideration.

"lacks originality" from the Scholarly interest part -- Originality at the time it was originally written, or at the time it's uploaded? What if it's a preprint for an old, published but pay-walled paper?

@MWB Not sure precisely what policies the arXiv moderators follow, but I've seen enough preprints for old, published papers to think that is generally fine. Some might be available online under a paywall, some might only be published in print. In those cases, it is clear that the result is original to the author.

@MWB On the other hand, suppose you prepared a draft of an article 20 years ago, never circulated it, and never got it published. Then, ten years later someone else published analogous results. Can you then post a preprint now arguing that you had the results first? I'm not convinced that would be accepted even though the draft had original results at the time it was written.

A pity that the arXiv main page for a document doesn't have a date field for when the document (or submitter) claims it was authored.

@MWB If it's a published, pay-walled paper, there are likely to be copyright issues.  (Some publishers will care more than others)

@MWB: Rather important question: Is it your own old published but pay-walled paper, or are you in the possession of a preprint copy of someone else's paper?

It is OK to upload it, but in the Comments section you should say when it was written.

I've seen this a number of times, and it's perfectly fine most of the time. The exception would be if the result has already appeared in other people's work and you are claiming to have come up with it beforehand. Even if this is the true situation, I would recommend not putting it on the arxiv because of priority issues.
In the other extreme, I think people would greatly appreciate work done but never published back when a field was "hot". In my own experience there are a few things like that I would very much like to see, since I am always a little hesitant to use folklore results that I can't really verify myself.

Could you elaborate on what "because of priority issues" means exactly? Thanks!

If the result has already appeared somewhere else, there's no strong need to post it on the arxiv. Furthermore there's no way to prove you really came up with the result first, which can cause friction from others who might feel they are being cheated. So in this situation it might be best to not put the paper on the arxiv.

There are many older published papers that are hard to find, either because the relevant journals have become defunct or have no online facilities.  It is therefor highly useful to post old papers to arXiv if they meet the requirements of the platform (and subject to any relevant copyright restrictions).

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/


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Is it OK to have a PhD thesis with shortcomings and inaccuracies?
I recently defended my PhD thesis and was awarded a pass with some minor corrections. I am due to submit the final version of my thesis very soon.
The examiners were both very happy with my thesis, which explains the final verdict. However, as the saying goes, no one understands a thesis better than its author, as the person was invested in it for years. When polishing the papers to send for publication, my supervisor and I found a major issue with the thesis, which although it does not invalidate the overall findings, it would change a significant portion of the methodology in my thesis. While I am currently addressing these issues for the publication of one of the chapters, as well as my job market paper, this issue has to led to severe depression and has made me feel inadequate as a researcher. I worked incredibly hard and had a particularly difficult PhD process; so it is difficult for me to find that at this stage (post defense) I am submitting a thesis that is predicated on a methodology that should have been approached entirely differently; and frankly while in my corrections, I have in essence remedied the problem so that it fits my analysis, changing it as I had intended it to would imply changing a substantial portion of the thesis. This in turn has caused a feeling of despair and inadequacy.
I spoke to a friend who is currently working as an associate professor and he comforted me by saying that irreproducibility, inaccuracies, and mistakes, be it major or minor are very common in vast majority of PhD theses and that I should not beat myself up for this and that the said PhD title is well deserved. However, I thought I ask for some second opinion.

Does this answer your question? "I've somehow convinced everyone that I'm actually good at this" - how to effectively deal with Imposter Syndrome

@AnonymousPhysicist I don't think that is the same question at all. It may be related to the answer though.

Shortcomings are normal in that vast majority of theses. - Inaccuracies: Depends. Quickly reading through your post it may cause future problems, but you may equally overthink it. - Your advisor of the university is possibly the better person to ask. Maybe you can add a note/an extension that details some of the problems if you have no means to correct them?

Thanks for asking this question. I keep worrying similarly about my published works too: "Oh, I could have approached it differently.", "I could have better that method.", "I should have done this, done that... etc". Don't worry. Congratulations, Dr. Henry :-)

You have a set of highly qualified folks happy with your work. Please feel free to not be less than completely satisfied with it  yourself - but don't let that slow down your moving on to better things. And honestly you really should move on to the next steps given the negative psychological effects.  While you prepare for your next career steps you might want to prioritize your own health and not a perfect corrected/updated version of the thesis.

Your PhD thesis is just your first academical work. You'll have plenty of time in your life for new, high quality research. Just get your PhD and move on! :)

Please Do Not Capitalize Every First Letter In The Title Next Time, If That's What You Did In Your Thesis, Then It's Not Okay ;-)

@JohnEye: Sorry, but it is standard practice in English writing to capitalize every word (except for articles &c) in titles: https://grammar.yourdictionary.com/capitalization/rules-for-capitalization-in-titles.html

Is It OK To Have A PhD Thesis With Shortcomings And Inaccuracies? — As opposed to what?

Perhaps an addendum noting what you've said here. "After further study this other approach would be more efficient(?) although it wouldn't change the end results."

There exist very few, if any, works of any kind (from theses to textbooks to articles to paintings and novels and symphonies) without shortcomings and inaccuracies. Obviously it depends on how short they come and how inaccurate they are, relative to the standards in the field.

One of the most cited senior researchers in my field once said: "I've never finished my PhD. Of course, I submitted the thesis someday, but I am still working on it." - in his 60's.

Well, a thesis is not actually peer-reviewed like a paper is.  So, yes, theses are introductions and proposals of some new ideas and, hence, they're expected to be imperfect.  Their knowledge can be refined by further contributions of following theses and research papers.

What is your country? My PhD thesis has lots of shortcomings ...

The thesis is a "good" one if you have passed and will be awarded your degree. Don't overthink it. You have learned something from producing it that you can leverage into future work. That is, in lots of ways, a big advantage. If your advisor is also happy and wants to work with you on any future extension, you have a positive outcome, if not a perfect one.
That the thesis "might have been better, if only..." is true pretty frequently.
My suggestion is to take the advice of the reviewers and get done. Then write a future paper extending and improving on the thesis. Don't make it harder than it needs to be. Your dissertation shouldn't be thought of as your life's best work, only its first.
Don't let the perfect be the enemy of the good. (apologies to Voltaire)

I think this is an amazing answer. Wow.

I wanted to answer just that, with an emphasis on writing a paper afterwards to solve issues in your thesis. Your thesis was accepted, with its shortcomings. Science moves ahead among others by fixing these shortcomings.

Top Answer! People forget that a PhD is a 'learning degree'. Too often, completion is treated as the end, when really it is only just the beginning. If you learned something and can express that you know how or why errors occurred and what they mean for your work, then you have proved you justify being awarded your PhD. A PhD is about the process, not the end result.

This Q + A was so good I shared it to my colleagues.

"might have been better, if only..." is true for most published research. The predicate can almost always be filled in with "if only...we had more time and funding".

Great answer, though the French saying "Le mieux est l'ennemi du bien" would be better translated by: "the better is the enemy of the good".

A thesis is a long document written by humans. It is therefore almost certain to contain at least one mistake. Everyone acknowledges this at some level; in many institutions "pass with no corrections" means "lazy examiners didn't read it closely enough". I found a typo in my printed one relatively recently – I'd missed an i in an exponential that really really needed it!

Even if it is hard to consider when you are doing/have just completed your PhD, the thesis is not your magnum opus, but rather less-than-perfect showcase of your skills that was assessed as good enough by your peers to consider you as an autonomous researcher.
In a way, I would say that it is closer to a swimming certificate that proves that you can now swim by yourself in the deep end.
It doesn't mean that your technique is perfect, nor that you are an Olympic athlete. It only means you can now be considered as an autonomous junior swimmer that knows the basics, but of course will still benefit from guidance from experienced swimmers to get better and perfect its technique.

Yes it's OK.  For example, the PhD thesis of Dedekind was actually rather average (not saying that yours is) and showed no signs of his future achievements in mathematics.  Everyone develops differently anyway.

Is it really possible to have a thesis without shortcomings and inaccuracies? In all, it is a human product. With your thesis, you put forward/test an hypothesis, a premise or statement, and that should be defendable given the work you have done. But it is never perfect and always open to interpretation and opinion.

In addition to @Titus and @Buffy answers, consider describing the known shortcoming(s) in Threats to the validity section of your thesis.
There is nothing wrong to have shortcomings or limitations. Explain the shortcomings and motivate why your results are still good enough.
By being upfront, you shield yourself from the potential critique that you have misled your reviewers and readers.

This is regarded as point of reference as most of the topic will be in detailed explanation of the fact. Some error and shortcoming of your own findings is almost normal for 95% of cases. It should not involve any misinterpretation of the facts. We can substantiate with new finding and negate almost all shortcoming in your future work will be the best attempt. All might not be in your hand or in your capacity to do, so justify it to you some other means whatever you feel satisfy you. Do not depress, world is not perfect.

If you kept correcting everything you found wrong in your thesis you would literally be revising it for the rest of your life.


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Is it appropriate to apply again for an internship you've previously turned down?
I am in the process of applying to summer PhD research internships in industry (I'm in CS). Last year I had two appealing offers, but of course could only take one. This year I am still interested at working at the company whose offer I declined last year. However, I am unsure if it's considered inappropriate to reach out to the lab director again to inquire (this is how I approached it last year). It's not as though I burnt any bridges previously, it just feels strange, kind of like saying "Hey, I didn't want to work with you before, but what about now?"
Is this appropriate? It is research and I am in a research program, so I don't want to ruin potential future collaborations, and I hope I have not already done so by declining a previous offer.
And more generally, if inappropriate, when making a decision between multiple offers, should it factor into your choice that you may declining for this, and all future, internship opportunities?

Yes of course you can, it's just a bit embarrassing is all.

It's not the same internship, but a new one. And do you really think they were so heartbroken when you turned them down last year they'd still hold a grudge? Really.

@Karl: Of course I don't think that, although your attitude is lovely. It is a bit of an awkward exchange though. I asked because, particularly in my case, I wasn't dealing with random HR folks or arbitrary interviewers, but the group director and a few of the staff researchers in a small group of roughly a dozen researchers. It's not as though I expect them to be "heartbroken," but, as I said above, it feels strange to come back to them a year later.

Why would it feel strange? OK, if they spend quite some time/money on preparing your visit, and you only cancelled last minute. But i guess that was not the case, right?

On second thought, i think i know what you mean. Best be prepared to be the target of a few jokes when turn up for the internship. I'd certainly raze a rookie who thought my company only second best. ;-) But really I'd be glad to get your higher educated, one year older version.

I've been in this situation twice so far in just the last few years, and having to turn someone down who gave you an offer seems...well, downright unpleasant and awkward, doesn't it? I think this is because most of us do not like to receive rejection, and so we feel that saying no is itself unpleasant, and thus we can make the quick assumption that surely the person we said no to will dislike us or bear us ill-will, right?
Here's the funny thing: human behavior almost never actually works this way! It has taken me a long time for me to personally accept that people don't think the way I imagined they did, so I assure you this unpleasantness is completely natural - and something you'll need to get past right away, or it is going to hold you back.
It turns out that most decent people, when offering a job/position/opportunity, genuinely want you to take the best offer, even if they might be a bit disappointed that they couldn't offer you the most compelling option. Most people in positions to offer other people such opportunities have had to tell other people no themselves, and in fact regularly tell people no all the time now. They don't bear anyone ill will for this, and they themselves remember having multiple offers and having to take the subjectively best option at the time.
As a personal anecdote, the first time I recall experiencing this was for a summer internship at a company. I'd received a much higher offer to work somewhere else (nearly double), and I called the first company back and explained that I was very interested in their company, but received a very compelling offer and wondered if they had room to negotiate a bit. They checked, explained they could not for interns, but welcomed me to reapply once I graduate and they promised they'd be able to make a much more compelling offer. I thought they were being polite and would never seriously consider me again, but their corporate recruiter contacted me multiple times over the next few years to see if I might be interested in working with them. I had it happen again in a research position, where again the people I turned down seemed keen on trying to recruit me again!
It turns out that not only do reasonably people understand if you take a more compelling offer (especially if they consider the other offer impressive!), but the fact that you had the other offer - and how politely and sincerely you handled turning them down last time - reflects very well on you, and sometimes you'll find they end up liking you and wanting to recruit you even more! Not all the time, surely - but I've had it happen more times than I had the reverse occur. People who have a lot of options are desirable for lots of reasons, and the funny thing about being desirable is that a genuine expression of interest from you in them and their program is a far more valuable compliment than from someone who is deemed "less in-demand". They know you can afford to be picky, and that's often a desirable trait in any recruiting effort.
So by all means, it is absolutely appropriate to reapply - go for it! Be sincere, and if you feel like it you can even express how you hated to be unable to accept their offer last time, and would very much like to work with them. One caveat, though - this will only work so many times. If you decline them again and again, that's going to get old for just about anyone, so I'd suggest you be reasonably sure you actually want to work for them, or otherwise you're just stringing them along.

"It wasn't the best choice at the time, but now I think it's the best fit for me" is a phrase that has worked wonders for me. I wouldn't use this line twice with the same person though. Especially if it's a new program I wouldn't expect them to be upset or annoyed. They were once in your shoes, remember. They know what this process is like, and sometimes you have to turn down things you like.

This is perfectly fine.
You did not burn any bridges, which should always be avoided since there is nothing to gain from it. Since you still express interest in the same position it is obvious that you did have a reason not to pick up the offer the last time round. Obviously some reasons might be a red flag but I would not preemptively offer any sort of "explanation". Your updated CV will state what you have done last summer. This also shows that you did not just procrastinate, which is probably the biggest red flag.
I assume you chose the other offer because it was objectively the better choice and not just more convenient. In this case the people from the other side might very well be aware why they were not your first choice. Any sort of excuse would just insult their intelligence. They also know that everyone serious about getting an internship is looking at more then one position.
Since you are dealing with humans interactions can always have unforeseen consequences if one side is not reasonable at a professional level but this is certainly a rare exception for someone with responsibility towards staff. So yes it might be possible that you have already poisoned the atmosphere but if things are as described this would not be your fault. I would not expect the other side to hesitate to make you another offer for the sole reason that you turned the last one down. However, you will certainly be remembered if you turn down two in a row. Wether or not this will reflect on someone else in your group depends on the human factor as long as you did not make someone vouch for you.
If you do not facilitate a believe in the other party that you will definitely take their offer and thereby cause them to make arrangements you are not wasting their time and possibly resources to an extent greater than what they have to assume anyway.
Also, always remember that you are also offering something to them. You are hopefully not in such a desperate situation that you have to be grateful to get an internship. Which you did prove last year. One of the keys in job applications and interviews is a balance between showing that you are motivated and interested but not desperate. As well as that you are valuable and aware of it while not coming across as arrogant.

Omnia munda mundis
To the pure ones, all things are pure
In my experience, if you have a solid explanation (eg familiar or professional) it is totally appropriate for you to apply again (unless it was clearly spelled out in the original or current call that it is not allowed).
You might even make a reasonably credible case that now you are more experienced and skilled to better hoard your internship.


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Dealing with unsupervised research as novice researcher
I am currently working on a research project at a non-academic institution as part of a summer internship. They've brought me in to work on a topic that is somewhat within my area of study. However, there is nobody here who shares my field. There are other folks with related expertise, but it's not quite similar enough to be of help (at least not at this stage in the research). Furthermore, my work involves data that is quite different than what I'm used to working with. It's enough to say that the data requires different analysis techniques than what I'm used to--to the extent that the application of this research is whole sub-field in its own right.
I'm obviously reading papers to familiarize myself with this sub-field, and I've also reached out for direction from colleagues who have plenty of experience in this area. The real problem stems from the lack of an experienced adviser/supervisor who can help direct the project. As much as I'd love to be capable of doing this solo (and this will probably be a good trial-by-fire learning experience), I'm concerned that I'm still too novice of a researcher to go it alone.
I'm not throwing this project away, so what are some steps I can take to make progress despite this limited supervision?

If there are any open-source data analysis tools you can use, you could look up for their mailing lists. Such are usually active and allow asking questions. (At least in my field)

Also consider participating to related workshops, conferences, or seminars, if possible. Or try searching for some good books?

If this is at a corporation (and possibly other places), you should check with your supervisor about whether external contacts would need to sign an NDA (non-disclosure agreement), particularly if this is a 'strategic' research project.

Expanding from @mkennedy's comment: Even if your supervisor cannot help with technical issues, they should be able to help with questions about what sorts of resources you can access and how to access them.

Networking would be my run-to. I'm sure you can find someone that knows enough on the topic to help guide you.
I had a research paper that I had to do for my programming degree and I had to research programming for different platforms, in my case, web flash games in comparison to mobile game development.
I knew nothing about the software, code language, or how the 2 different platforms varied in the game industry so instead of just reading other papers, textbooks, and videos I went on to website where these games were found and left comments asking for the Devs to contact me, I contact the site owners themselves about getting into contact with one of their Devs, and I even posted an ad on Craigslist (I did actually find someone that taught courses in the subject though Craigslist and he was the best source I found).
You really just need to ask around and it's easier to find people than you may think as long as you put effort into it.


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Re-implementing one's own proprietary code as open-source
I wrote some software as part of an internship. It worked well for the task and we published a paper on it. However, because the internship was at a company, not my graduate institution, the code is technically property of the company and they do not want to release it. I've received several requests for the code, and I know that releasing the software will increase my paper's citations and impact. Is it okay to re-implement the code I wrote and release it as open source, or could that violate some laws or policies?
For the record, when I say re-implement, I mean start from scratch, not reuse most of the same code and change a few things.

Beyond copyright issues, you probably signed an NDA promising not to reveal any proprietary information or trade secrets (better go back and read it).  A re-implementation of your code could certainly reveal those secrets and the company might sue you. I agree with the advice to talk to a lawyer.

Note that this is essentially what @NateEldredge said already, but part of the title in your question is misleading: if the code is proprietary and held by a company you worked for, it is not your own code anymore. You can take some credit for writing it, and you can use its existence as evidence of your abilities, but you have no legal ownership of that code.

It might be possible to do what's known as clean room design as a way of getting around the NDA problem. But IANAL, so be very careful.

@tonysdg It's not possible for the person who wrote the original code to produce a clean-room reimplementation. The point about clean room is that you argue that there's no possible way you could have copied the original, because you never saw the original. The author of the original code simply cannot do that.

@DavidRicherby: Makes sense to me, but it might give the OP a way of helping others get around the problem.

I am not a lawyer, and if you are seriously considering going ahead with this project, I suggest consulting one.
The problem is that copyright infringement is not limited to direct copying. See, for example, the "My Sweet Lord" case. George Harrison is not believed to have consciously copied "He's So Fine", but he had heard it.
You have much deeper familiarity with the existing code. It is going to be very difficult for you to write anything similar without being inspired by what you wrote before.
If your former employer's reluctance to release is related to liability and support issues, they may be willing to permit re-implementation, so it is worth asking. If they are hoping to make money off the code, they will not agree.

It was internship-quality code. They're certainly not making any money off of it ;-). It's more likely that it'll be built on internally by others and incorporated into their massive code base. Nonetheless, this makes sense. The thing is that code is a strange beast. If someone else re-implemented it based on the published paper, it would be fine--this happens all the time (esp. for algorithms that are patented and published). Hence my uncertainty

@marcman Have you asked them for permission to re-implement, so that they would have no responsibility for the open source version?

That's definitely the place to start


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What types of administrative jobs can a faculty member get?
I am a professor of physics and just moved to the UK with my wife, who is British. I anticipate that it will take a year or so to find a faculty position matching my field of expertise. To avoid being idle during this period, I would like to apply for any possible job to be in academia.
As I checked, many administrative jobs are available in the UK universities, and the process seems quick (the interviews are normally scheduled for 2 weeks after the deadline).
Since I have worked as a department head for years with many industry collaborations, I thought I might have a chance at administrative jobs like director of small units such as enterprise, partnership, academic excellence, etc.
I understand that people with the same line of experience are rationally preferred, but I wonder if there are specific administrative jobs for which faculty experience is an advantage and the committee will be happy to consider such applications.

If this is not about the money, can’t you do some research as a visiting or sabbatical professor?

It's a slightly tangential point, but Professor of Physics is a slightly confusing job title in connection with Commonwealth countries. Are we correct in reading this as "permanent faculty with teaching experience"?

What @origimbo said - in the UK you don't apply for the job title of "professor", you get awarded the title eventually (maybe after 20 years in academia) on the basis of what you have done during that time. In other words, it's a very senior academic title, compared with some other countries.

@origimbo in some countries such as the US, academics who teach might be generally referred to as professor, but still, professor is not their job title (lecturer, assistant professor, adjunct professor, etc). I believe, the job title of professor has the same meaning, equivalent to full professor.

@herman -- what country were you a professor in?

I feel this is a question that's almost better suited for The Workplace. My fear in your case would be that you, having been a department head previously, are seen as vastly overqualified for almost every non-leadership administrative position (and leadership positions tend to not be filled as quickly as you mention). It may appear surprising to meritocracy-oriented academics, but people are generally not prone to hire overqualified staff - motivation and job satisfaction can become issues, and they are expected to not stay on long (as you yourself also don't intend to do).
That being said, I can't help but wonder whether you have any contacts in the UK that you can activate. Maybe there is some temporary administrative role that would suit your skill set, or a temporary teaching position in courses related to your experience. To me, that seems like a more promising shot than blindly applying to regular administrative posts, and hoping that the hiring team sees your very unconventional background as a positive.

As a sidenote, I also wonder why you are confident that you will find a faculty position in a year unless you already have one lined up. As I understand it, senior-level hires in the UK are a pretty rare and long-running processes, and hoping for one within a year, which you then also need to win, seems to be putting a lot of eggs into a very specific basket. If you already have one lined up, talk to the people there about some temporary contract in the meantime.

Regarding your sidenote: One department at my university is looking for a new department head for some years already now (exchanging the substitute head every now and then) and the process might well take a few more years. Thus, I totally agree that getting a faculty position, or even one as department head, might take far longer than a year if you just start looking now.

Re: The Workplace, see Why do companies not want to hire over qualified people?

I echo the sentiment in the final paragraph