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Submitting a paper as a nonacademic practitioner in a field
I am a professional with an undergraduate education.  Out of both curiosity and a commitment to continued education I read papers and research related to the field that I am interested in.
I recently came across a Master's Thesis directly related to my field of practice.  With my knowledge of the field I found the thesis deeply flawed.  The author was either ignorant of key information or excluded that information because they could not address it.
My desire is to publish something that presents the facts that were left out and shows how in light of that information and the arguments built on top of those different conclusions can be found. In order that 'the record' is correctly.
As a nonacademic practitioner how would I go around doing this?
If I am over reacting and a Master's Thesis is normally something that has the impact of students homework and is not built on top of by other academics explaining this to me is also a legitimate answer.

Just in case someone regards this a dupe of "How does one go about writing papers as a nobody?" the difference is I am a person with specific knowledge gained by working in the field and my own research who wishes to publish to add to the body of human knowledge.  Rather then someone concerned with bragging rights.

I agree that it isn't a duplicate of the "nobody" question, but I'd be surprised if it hasn't been asked before. The "related papers" in the sidebar don't seem to contain an obvious candidate. Someone with better search skills than I seem to have might find one or more.

Remember that master’s theses are graded in many systems. This thesis might be a “just passed the bar” thesis. After graduating, the thesis might be published by the university library automatically.

Given the input given by the people here I have come to the conclusion that a paper is most likely the wrong way to respond to this thesis.  I still wish to respond to the ideas put forth but I am thinking that I can do better in the form of a blog or video essay.

There's actually three questions here, so let's take a look at each:

The question you asked: How do I publish as a non-academic?
The question you implied: How do I publish a paper refuting another?
The question you should ask: Is it worth publishing a refutation of a master's thesis?

1. How do I publish as a non-academic?
Assuming you've got a paper you want to publish, the first step is to determine where to publish. Generally, your options are at a conference, or in a journal. Which direction to go depends a bit on your field.

Conferences are generally the place to publish (relatively) small, incremental works. Presenting your paper at a conference can generate valuable face-to-face discussion to inform your next steps. My field (computer science) skews towards conference publishing.
Journals are better for larger works with significant advances or particularly-reliable evidence. They're also better if you're not looking to travel to present your work. Older, more stable fields tend to do more journal-based publishing (e.g. I believe Physics tends to be journal-focused, though I'm not an expert).

Once you've determined your preferred medium, you'll need to pick out a specific conference/journal. This is entirely field-dependent, and your best bet is to find someone who has published in your area and ask advice. You can also generally get an idea of what a particular conference/journal is looking for by reading their call(s) for papers.
Once you've selected your venue, you'll need to read their publishing guidelines. Typically there will be a required style/format, usually accompanied by a template Word or LaTeX file. There will also be instructions on the actual submission process, typically run through a 3rd-party submission website. The actual submission is usually as simple as creating an account, uploading your files, and filling in your title, author list, and abstract.
(note when I say "usually," what I really mean is "in computer science")
2. How do I publish a paper refuting another?
This shouldn't change much about the publishing process, other than the fact you should strongly consider publishing in the same venue as the original paper.
The writing of the refutation paper is probably going to look a little different than a normal paper, but I can't speak with authority on the subject as I've not written such a paper before. I'd just point out that unless you believe the original author was behaving maliciously/unethically, you should look for a tone that redirects more than refutes.
e.g. instead of saying "Author OP said X, but that's wrong because Einstein et al. said Y," synthesize the two: "Author OP investigated question A, resulting in claim X. However, this is inconsistent with Einstein et al's finding, Y. Further work is needed, modifying OP's approach in the following ways, etc."
3. Is it worth publishing a refutation of a master's thesis?
This is the question most of the answers here address. And I agree with them, the answer is most probably a simple "no."
A couple sub-questions to find your answer:

Was the thesis published in a journal or conference proceedings?
Did the author of the thesis go on to publish other works based on the thesis (a Google Scholar search or similar would help answer this)?
Does your field, specifically, consider masters theses to be meaningful, significant contributions to its body of academic work?

If the answer to any of these is "yes," then it may be worth going ahead with your refutation. In particular, if the thesis was published in a reputable, widely-read/attended venue, then there's a very good chance the publishers would be interested in a paper that challenges or recontextualizes the original paper.
On the other hand, there's a very good chance that the answers to those questions are all "no." And in that case, there's very little chance any academic community will care enough to publish your refutation. Writing papers is a lot of work. Reviewing papers is a lot of work. Publishing papers is... well, still work, if a bit easier in the digital world. Instead of focusing effort on correcting a paper that was only seen by three professors at one institution for some master's student's final project, focus on ways to contribute your own expertise to the field directly.

Note that your points about conferences vs journals are very field-specific. As far as I know, only the "math world" (a silly catch-all phrase I am using here for fields that are math heavy;  mathematics, physics, computer science etc.) treats conferences as places to publish. In my field, biology, a conference is where you present results, often unfinished or ongoing projects, but papers are what counts.

Computer Science is notable by having some very important contributions published in certain very elite conferences. The acceptance rate at these is often in the low 2 digits.

The OP didn't mention a field, so I'll share what I know from math, since that's my area. In mathematics, there are a lot of master's theses online. We do not have a culture of building on the research findings within them or treating them as publications. We don't expect that they will make groundbreaking advances. If a master's thesis does prove something new and interesting, then the author should be encouraged to write it as a journal paper and get it published. When I referee papers that cite a master's thesis for a result that has not been proven elsewhere, I ask the author to include a proof, because I know just how easy it is for a master's thesis to be full of errors.
We also don't have a culture of "letters to the editor." And in this case, there is no editor because the thesis wasn't even published. I don't think you have to worry about "setting the record straight" or the idea that someone else might view that these assertions in an unpublished thesis went uncontested, as proof that they are correct.
Of course, you can write a paper sharing your insights. But if the point is to show that this master's thesis if full of errors, I'm not sure such a paper would be published easily, since most readers (professors) would probably assume that many master's theses are this way. I do think we view them more like assignments students do.
You might consider checking to see if the author continued on to a PhD program (which would make it more likely that they build on the wrong stuff in the thesis). And you might consider contacting the faculty member who supervised the thesis. Getting your insights into the literature would probably be a good thing, and if the master's thesis is part of the research coming from that professor's group, then it might make sense to collaborate with that group, so that they can benefit from your insights.

In many fields, an M.S. thesis is not that significant. When done from a university perspective, it is unfortunately quite frequent that important considerations obvious to a practitioner are left out. However, the existence of an MS thesis indicates that there is some interest in the academic and industrial community about this thesis, as the topic is usually chosen by the advisor and not by the student. My example tries to show that it is easy to misunderstand the drift of the thesis, and you do not want to be caught in such a misunderstanding.
If you have something to say about this topic, you should say it. You would start with a search on Google scholar (and maybe involving a research librarian at a near-by university. This might involve contacting faculty there.) Reading related articles starting with the references in the thesis will not only give you an idea what the state of the art is, but also how to write up your ideas.
Now, your idea of correcting the thesis is not a good one, whereas the idea of setting the record straight is a good one. MS theses are usually not considered sufficient quality for publication, (as a reviewed paper in a journal or presented at a conference in Computer Science / Engineering). It is even arguable whether they count as publications since their distribution is usually so limited (I think they should, but it is arguable). In Computer Science, Technical Reports used to be quite important but over the decades have lost relevance, and the same is true for M.S. theses. So, an article that wants to set the record straight by arguing against an M.S. thesis is usually not of interest to an editor or conference program committee. However, an article that treats the same topic as the thesis and is based on assumptions based in practice could be very interesting. Any good advice on the feasibility of such a project needs much more data.
Of course, you need to be careful if you criticize someone's work in a public forum. At the same time, the health of the field depends on robust interactions including challenges of assumptions. You do not want to be caught in mis-understanding something. For example, sometimes a project investigates the feasibility of a protocol under idealized assumptions. Practitioners reading such a thesis can be tempted to attack the assumptions, but the value of the thesis is not in making the assumptions, but in showing some theoretical result, which can lead the way to extending the research by asking how these assumptions can be made.

There is no requirement to be a member of academia to publish "academic" papers. If you write a valid paper that improves upon or corrects an earlier paper and do so in an "academic manner" (i.e. not making wild claims or insisting on viewpoints...) then it will be considered.
If an editor who receives it sees any merit, then it will be sent to reviewers. But the merit is in the paper, not the author.
Most academic papers are written by academics as they are more likely to have the required background. It isn't a requirement, however, as there are others, such as, perhaps, yourself, who can advance scholarship.
Writing style might matter somewhat. If you've read a bunch of papers you probably have an idea about how to present valid arguments. Just. Do. It.

"If you've read a bunch of papers you probably have an idea about how to present valid arguments." Which isn't to say you need to emulate the writing style for its own sake. A lot of people who try to write "in an academic style" tend to emulate the bad parts of the style (dense writing, convoluted phrasing) without the parts that sometimes make those bits necessary (wanting to be really really precise). Write for clarity and precision.


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PhD Reapplication
I had applied for a PhD last year but couldn't get in. The professor who I wanted to work under told me that he really liked my project and encouraged me to reapply this year. I do have plans to reapply to this university and to a few others, where I had reached out to professors whose areas of interest align with mine but since I did not have the desired level of language training, they insisted that I undergo the said training and then apply. I want to pursue a PhD in Asian studies where candidates are required to have at least college second year level training before joining a PhD course. Now I am through with the language training, but I was wondering if I should be reaching out to the same professors I reached out to last year (who were actually interested in my project but also asked me to first get up to the required language level) with the same project or should also modify my project a bit, and add further questions, etc.? Is it okay to reach out to them with the same set of questions that I reached out to them with earlier or am I expected to have worked further on my project along with working on the language?

East Asian Study programs are very competitive and often require two East Asian language (a primary and a secondary) at a very high level (my first Ph.D. was in Japanese Studies). If the professors liked your proposal I suggest reaching out to them, reminding them about the previous conversation and concentrating on letting them know how you progressed in your language studies (which is what they asked you to do).
I would not advise asking the exact same thing you asked before, instead you can remind them about what you asked and what they said and ask if there were any changes in that regard. It's how you phrase it.

What you suggest seems reasonable. Remind them of the previous contact and that your questions are the same if you think it necessary. They won't have remembered some or all of that, but it might be good to mention it.
Focus, of course, on your language studies since you last contacted them. But your approach seems sound. Good luck.

Hey, thanks for taking the time to answer. So is it okay to approach them with the same questions? Is that not going to reflect badly on my ability to conduct research since I had the same set of questions a year ago?

You have been focusing on the language.

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Thesis in use, potential employer wants to see source code
EDIT:
Let me clarify things and specify my concerns:

I wrote a program for my thesis that solved a problem for the target establishment.
The establishment now uses the program with my consent but nothing was signed and everything was verbal.
I applied for a job and that company now wants to see my program source code because it's relevant to the job I'm applying for.
My advisor is directly tied to the establishment using my program. I have notified him and we have scheduled to meet up and talk about it in a few days.

My concerns: ( just want to get more info before my talk with my advisor )

Is my program source code still my own? Have I accidentally given up my right to share it? Can my advisor and the establishment prevent me from sharing my source code to the company I'm applying for?
The source code is also included in the published thesis I submitted, doesn't that make it open source in a sense? Does that mean neither me or my advisor/establishment can claim ownership or anything of the code?
Are things different because my thesis is applied  to an actual situation as opposed to a theoretical situation? Like there is a period the thesis isn't made public (open source) like a grace period before it's open to the public?

Just to clarify- you're applying for a job with a different employer than the one for whom the code was written?  Have you asked your advisor whether there was any intellectual property agreement in place between the university and the establishment for which the code was written?

Now they use the program Please clarify who are they? Do they have permissions to use the program? If they did get the permission, who granted it?

Please make sure to tell your advisor that you gave the permission to that company to use the program if you have not told him about this yet.

Maybe you should offer to explain how you did it and possibly describe (not provide) a few relevant snippets. I would not give them the source code. But that's just an opinion.

This can be broken down into two issues:
(1) Can you show the new company your source code/can they ask to see it?
They have only asked to see it, not to use it. Maybe as a way to assess your skill, see if you fit their requirements etc. No problem in sharing this. You could even share a copy of your thesis. If they want to use the code, and say so, you can look into licensing options.
(2) Have you given away your right to share it?
No, because the absence of any written contract works both ways. It is part of your thesis, so it is still formally yours. Until and unless the target establishment tries to copyright it in some form, you have the right to share it.

An exception has been pointed out by David Z - there is a possibility that your advisor's 'tie-up' with the target establishment could constitute a work-for-hire agreement, and this may restrict your freedom to share. If such a case exists, either you or your advisor must be aware of the details and can find suitable redressal. If you were not made aware of this, ignore all concerns and share.

Do get your adviser's consent and guidance anyway, and also check your university policy on IP.

I'm not sure if we have sufficient information to conclude that the code wasn't made as a work-for-hire, or something equivalent in EWobble's jurisdiction if that's not the US. I don't think it's likely, it's just that I'm not sure the possibility can be ruled out based on the question alone.

The absence of a written contract should rule out the possibility of work-for-hire, unless the adviser had signed one such, and didn't inform OP. In such a case OP wouldn't be allowed to include it in his thesis. In theory yes, different jurisdictions might have different interpretations of contract, but I think having any agreement in writing is fairly universal for this sort of thing.

Based on what I read, work-for-hire status can be determined by the conditions under which the work was prepared, even without a written contract. Also, verbal contracts are recognized in some places (in the absence of a written one), so for all I know, it's possible that the code could have been a work-for-hire for the company but there was a verbal contract allowing the OP to include it in their thesis.

Why does the arrangement between the company and the advisor matter here? If the student wrote the code, the student owns the copyright (Berne Convention), unless the student had an agreement to produce work for hire. (In other words, I agree with Roland.)

@JeffE - What I (and I believe David Z) are delicately hinting at is an unethical scenario where the advisor informally 'sub-contracts' his contractual obligation to a student and possibly keeps the student in the dark. Indeed, Roland's advice is solid.

@user153812 Sure. But if the student is kept in the dark about their advisor's contractual obligations, the student can ethically ignore those obligations.  Hence my question.

@JeffE - very valid point.

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Why some papers are free while the other are not, even in the same journal/publication?
I am accessing this journal from university.
So, I assume the university subscribes to this publication/journal (Sciencedirect/Microelectronic Engineering).
But why some papers are free while the others are not?
example:

free
not free

I just want to make sure that my inability to access some papers is not caused by technical issues from my PC/access/internet/etc.

Why some papers are free, while others aren't, in the same publication
You can see that one of the papers was published under an open access Creative Commons license (hence freely available to everyone), and the other wasn't. So-called hybrid open-access journals have a system where some of the articles are published under open access conditions, usually in exchange for a publication fee. This appears to be the case for the journal in question. Probably the author paid to have it published as such, possibly mandated by their institution or funding agency, or possibly because they want to support open access.
How to tell if your university has access to a given subscription journal
Usually this is stated quite clearly on the university library website, when looking up specific journals. If the specific journal isn't listed, the university doesn't have access. Even when listed as having online access, there may be restrictions, e.g. online access may only be available for a certain time period, say 1983-2001. This is usually listed quite clearly.
One thing that usually isn't stated clearly, is that you might not have working automatic access, and may need to access the journal through the university website. If that website doesn't clarify things, or you still have problems, I would recommend asking a university librarian. Even if your university doesn't have access to the journal in question, they are often able to source a copy of the article through e.g. an inter-library loan.

So,does it mean that:

the university does not subscribe into Sciencedirect/Microelectronic Engineering ?

I can get access for the free papers because the authors want it to be open access?

I just want to make sure that my inability to access some papers is not caused by technical issues from my PC/access/internet/etc.

@Codelearner777 (In reverse order) 2. You (and everyone) have access to the open access papers - that's sort of the point. 1. Your university may or may not have a subscription to the journal in question. Sometimes I find that automatic online access doesn't work, but I can access papers through the university library website's listing of the journal. That site should usually also tell you whether your university has access or not, or what restrictions might exist. E.g. sometimes a university only has online access to papers published in a specific time period. If in doubt, ask a librarian.


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Does IEEE provide an ISSN or ISBN list for searching on a specific journal?
Does IEEE provide an ISSN or ISBN list for searching a specific journal?
There is this link from here but it is not active anymore.

I think IEEE has organised it here: IEEE Xplore Title Lists
This list now contains information of all periodicals, conference publications, books, and standards in the IEEE Xplore database.

yes, that's it! Thanks!


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Is it possible take take part in a research project if I'm not a part of a university?
I graduated with a Masters of Engineering, concentrating in digital signal processing, in particular medical and audio, almost two years ago. I've always been interested in research, but due to personal circumstances I could never commit a lot of time to working on a research project with a professor, and obviously didn't get a chance to publish anything. Now that I'm more settled and have much more time on my hands, I started getting involved in some open source projects and reading some technical literature (engineering, mathematics) that I couldn't get to before. However, I'd still like to find someone to to collaborate with on a research project who is already established in the field and publishes papers. Part of the reason I want to do that is to be able to eventually apply for a Ph.D. program in a good school, and having publications would be a great thing on my resume.
What I'm trying to find out is how I can work on a research project similar to those graduate students work on as a part of their studies if I'm not a student anymore? Should I contact my old professors from the university? Is it possible to find some "open research" team that accepts collaborators from outside? Do I have to do it on my own (quite frankly I'm not sure I can give myself a good enough quick-start)? In short, I'm willing to volunteer my time in exchange for a possibility of publication in the future. Can I do it, and if yes then how?

+1 for a good question, which has generated a variety of responses!

How could we contact you? Your profile could fit our research lines

@flow andrey_krishkevich@ieee.org

It's certainly possible, though admittedly somewhat harder outside the framework of a university. Some potential avenues, answering generally - not all of them might apply to your particular circumstance.

Academic/Business partnerships. These are a new hot topic, and in some fields quite active. Universities love them because they're a revenue stream. Businesses like them because its harder to get closer to the cutting edge than at a major university. Look for companies that do this as potential employers? They're good for both dabbling in research, and also as a springboard into the research side of things - I've met several "private sector refugees" in my time.
Research-oriented companies. Quintiles, RTI, Westat, RAND, etc. all come to mind. There are tons of these companies, and many of them both pay quite well and actively publish. Are there any that serve your particular field?
Consulting. Research groups occasionally have funding for outside contractors of one sort or another - and if someone really wants to work with you, they may write such a position into a grant with you in mind. For example, I have some grant support for a freelance programmer. I've known other people hired for a particular expertise, or just "a warm body who isn't a student". This is probably the path you'd end up going down if you both contact your ex-professors and want to get paid.
Volunteering. Academics are cheap. It never hurts to ask if they've got some side project you might be suited for collecting dust in the back.

With regard to #4, you may find some resistance to volunteers (at least in the US). My group has a policy of not having anyone working in the lab who is not paid. The two big concerns seems to insurance and potential future liability for "exploiting" the volunteers. Anyone paid (which runs through the university) is covered by the university's insurance, and there have been court rulings that went against departments that made heavy use of "volunteers".

@dmckee---ex-moderatorkitten This resistance to volunteers working in the lab makes sense for the reasons you mention, but what's bewildering if that there is also reluctance to onboard volunteers that do theoretical work. I.e., folks who are passionate, don't need/want to get paid, and don't even require a desk as they could work from home would still get rejected when approaching researchers for potential side projects. The reason is: why, oh why!?
Do the same at the industry and they'd take you (almost) right away.

The short answer is yes, you can.
There is no need to be in a university, a research lab to work on a research project. There is also no need to have a PhD or any other specific degree/position.
This is however somehow unusual. But, there is a bunch of people in industry that publish on a regular basis some serious research work.
If you have no idea of the problem you want to address, or at least a broad domain, this will be even harder. I can only advice you to offer your manpower to people who are established researchers. For that purpose, you can go to seminars, you can maybe, if this is possible where you live, lurk into some graduate lectures, etc. After a while you will be able to talk with people and offer your services.
However, the simple way is to work with relatives. For instance, my brother is an entrepreneur, and he wrotes two papers with me (one is published, the other will be soon I hope). Of course, it was simple: I described one of my problem on a sunday lunch at the parents house, He had some ideas, we worked on it...

Yes - totally. Just think about this: a lot of professors even allow high school students to take part in research. Since you have some more experience, they won't have to spend as much time training you, so they are often totally willing to let you join in (after all, it's free labor).
You may have to be somewhat flexible (and to be prepared to accept unpaid work), but it can work if you're living with family/flexible friends [1]/relatives.
[1] Basically, some friends are willing to let you stay with them for free as long as you make their life more interesting (I'm willing to grant this favor to others since my life is rather bland at the moment), or if you can share in with the cooking/other chores.

"A lot of professors even allow high school students to take part in research" Really? Never seen that in computer science. What's the field/some examples?

Well, some students get high school research and are able to present it at science fairs like Intel ISEF. Though I think the research is probably more likely to be done with their postdoc/grad student. CS is a bit harder to make progress in with HS knowledge. It's more common in areas like biology and astronomy.

It is possible to take part in a research project, but your situation is not that common.
Many labs have paid positions for Research Assistants, where you will assist with managing all aspects of the research except for defining the problem to be solved. Details of the position will vary from lab to lab, but you will often be very involved in the research. Usually research assistants are not authors on publications, so you would need to discuss the details with the professor managing whatever lab you're interested in.
Also, many labs will take on undergraduate student volunteers to assist them with their research. Your having completed an undergraduate degree may make you eligible for these positions, on a case-by-case basis. You would want to speak with individual labs to see whether they would be amenable to this sort of arrangement. Note that position would almost certainly not be paid. Also, note additionally that there may be insurance issues which would preclude you from following this path... you'll have to look into this for yourself.

The best thing for you to do is almost certainly to just start emailing professors who do things you're interested in.
Especially if you mention that you're interested in eventually pursuing a PhD, they may be sympathetic.  Most researchers have a sizable number of problems on their personal back burner that they'd be willing to share, but in my experience, it's better to just go ahead and email a number of professors who do work that interests you.
Be prepared for a number of rejections, or even just to have your email ignored -- so you may want to email many different professors -- but it's not unlikely you'll find a professor interested in working with you.

there are 2 options

go to your nearest junior college and talk to a professor in the subject of your interest and see if they would be willing to let you sign up for an independent study course in their subject and be willing to guide you. You might have to take one of their formal course first to prove yourself and learn some modern techniques. In any case for this option you would need to have some idea of what research project you want to do. Junior colleges have much easier and faster admission and the professors are much friendlier, more dedicated to teaching, and much better scientists than at a university, so this could be a good option, many have their own research projects going with students that you might be able to join. The ego and bureaucracy at a junior college will be much less and the standards of learning, teaching and creativity much higher than a university.

you can do the same at a university. Almost all universities offer the opportunity to enroll in coursework without being formally admitted, they are usually called open courses, extension or some other name. In this case you are not a degree seeking student but can pay tuition to take a course. This is a good way to investigate their program, meet professors and decide if you would like to apply there as a degree seeker. It will be more expensive than a junior college and more paperwork because you are dealing with the huge bureaucracy and egos that are the university machine. You can also apply any coursework you take to a later degree if applicable

I have done both of the above and am now finishing up a doctorate, although I cant say that I recommend the doctoral program if you are pure and passionate about your subject and currently enjoy it.

It's not clear, based on your letter, what discipline you're working in, but I would assume that it's something somewhat "portable," since you don't make any mention of moving to the site of the collaborator's laboratory.
The main obstacle I would see would be how to credit your work. Technically, unless you're funded with or directly affiliated with a research group (for instance, with a university ID, etc.), there may be liability issues associated with your claiming their affiliation. Also, the collaborators in question may be leery of the same.
That said, there are still options. One possibility is that you create a startup-like business  that allows you to represent yourself as "Company X"; coupled with an academic or research affiliation or two, this should be enough to get you started.

Why do you need an affiliation at all?  I've seen several (math) papers that simply list the author's private mailing address.

@JeffE: In math that's probably OK, but in a field like the hard sciences which typically requires either laboratory work or access to "heavy" scientific computing, having a private address screams "mad scientist in basement," and is very much stigmatized. (I've never seen that for papers in chemistry, physics, materials science, or engineering.)

Hmmm.  I see plenty of "mad scientists" with academic credentials, too.  Is it really too much to expect scientists (of all people) to judge papers by their content?  (Also: A fair fraction of chemistry, physics, materials science, and engineering is really just math.)

@JeffE: I don't disagree with your assessments—at all. (The Andrulis affair lends credence to your claim.) However, that doesn't change the fact that journals in those fields severely frown on "unaffiliated" scientists.

Downvoted: You start by assuming the OP is not doing lab work (which makes lots of sense), then you discuss the importance of affiliations because it's important in sciences doing lab work. I think you could edit the answer to explain that in some disciplines affiliations count.

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Can I claim authorship on work I wasn't personally involved in, that uses a framework I developed for my research?
As a postdoc I joined an existing project of a PhD student. I made significant contributions to his code and developed an entire framework X in the code necessary for my research. Developing framework X took at least four months. After I finished the project and was put on a new project, he initiated collaborations with people from other labs using framework X (not including me). Without framework X this research would not have been possible (unless he would have implemented it himself).
Now I noticed that they are writing up an article about their collaboration. So far I have not been contacted as a co-author. My question is: should I claim co-authorship based on the fact that I developed framework X, which formed an important and necessary part of the code to obtain their results.

Presumably if the development of framework X is a meaningful intellectual contribution, you published a paper in which you describe it? So, he can just cite your paper.

Framework X itself is not a scientific contribution so I will not publish it. However, I do think it is a intellectual contribution, but I will need to look up the exact definiton.

It doesn't sound like you've earned authorship, then. Didn't you write a paper based on the research you yourself did with Framework X? Did you describe the framework in that paper?

What did the framework do? Did it supply an essential algorithm? Did it present the problem into a fundamentally new way (and did you come up with this new way of looking at the problem)? Or was it as essential as the "framework" of the building they were working in: essential, but not intellectually very relevant.

I provided an essential algorithm. It did not present the problem in a new way. It is more like a building block necessary to do the actual research. Based on comments I feel that I indeed do not deserve authorship, but this really left a bad taste as I feel taken advantage of.

Note that (at least in the case of computer science), many conferences have specialized tracks for work focusing on tools/implementation. Since submissions for these tracks are not expected to have a scientific contribution, they might be suitables places to present your framework.

@Optimist if you make Framework X open source, then it is a scientific contribution and can, indeed, be published.

If you compile your framework using GCC or if your framework is written in Python, do you include the people who developed GCC or Python as co-authors on any of your papers?

Authorship no, a citation or acknowledgment yes

@Optimist: In order that people know the value of your framework, you can of course give a list of publications that used your framework. Just like the authors of Python could list important projects using Python. Or a typewriter manufacturer could proudly list some bestsellers written with their typewriters.

@AnderBiguri Open- or closed-source is orthogonal to whether it is a scientific contribution. A scientific contribution is a knowledge advancement, such as a novel algorithm that solves a specific problem better than previous algorithms. A new open-source implementation of a known algorithm is not a scientific contribution.

@lighthousekeeper I guess I disagree. Tools to make scientific advancement easier for others fall, in my opinion, inside scientific advancement. If someone invented a new microscope, that would surely be considered an advancement. I think the same applies to software. Truth is there are tens (hundreds probably) of software packages that have been published in scientific journals, mine included.

@Ander Biguri In my view, if someone invented a new microscope, that would fall in the same category as describing a novel algorithm, which is a scientific advancement. In turn, making that microscope available to a larger community of scientists (like OS packages) is not an advancement in itself. I have also published articles on tools I built, but I would not claim them as scientific contributions - except for the ones that included some form of additional validation, which is a form of knowledge advancement.

@lighthousekeeper ahh I guess it comes down to the philosophical view. I sometimes think that its is even a bigger scientific contribution to the community to give them tools that they did not have before than inventing a new way and not giving software to do it. I understand your point, I just see it another way around. For the shake of this SE post: if the author would open source it and publish a paper about it, his/her problem would be solved, which was my point

@Ander Biguri I entirely agree that's an important form of contribution and it deserves much greater recognition than it often gets. I'm just not sure if labelling it as a scientific contribution is the best way to achieve that, but that's indeed philosophical. To the more concrete side, at least in my research area, open- or closed-source is not a main assessment criterion for tool-focused papers (although it maybe should be).

@lighthousekeeper well, you can not publish scientifically a closed source toolbox. But yes, it has to be more than just "open source"

"Can I claim authorship on work I wasn't personally involved in" No.

Do you think the company/author od the language your wrote the code in wants the same treatment as you?

Disclaimer: This is somewhat field-dependent. I'm answering based on what I believe to be the current situation in computer science / related fields.
1) Can you claim authorship given the way things have evolved? Probably not.
2) Would it have been a good idea for him to find a way to include you in the research collaboration so that you could get something out of your work? Yes.
The area of academia in which I work (*) is structured so as to value ideas over implementation. In practice, that means that it's not uncommon for people who write large amounts of code for a project to get little credit for it, which seems inherently unjust.
The way sensible people usually handle this is to make sure that people who do a lot of implementation work are given an opportunity to contribute scientifically over and above that - that allows them to justify their authorship in scientific terms, regardless of the fact that they also made significant non-scientific contributions to the overall project.
It's certainly possible to take advantage of implementers by not doing this, but people who do that tend to find themselves doing the implementation work themselves.
Bottom line: He should have had the common sense to include you in the scientific collaboration, and if he didn't have that common sense then his supervisor should have suggested it.
As an aside, I would view the situation somewhat differently if you already had a publication as a result of your work. In that case, you've already got the credit for working on the framework, and there's less of a moral obligation to include you in the new collaboration: instead, they can simply cite you. I'm certainly not of the view that writing a framework entitles you to be involved in every paper that is ever built on top of that framework - indeed, I've written frameworks that other people have continued to use for later research, and I wouldn't expect to be involved with the papers in question.
(*) As pointed out in the comments, this may not be the case in other fields.

I can see that this makes sense. I think I learned a good lesson here for future collaborations. I feel that he took advantage of me since he switched his research into my direction from the moment framework X allowed him too.

I think a usual way to handle the situation of "code written by X for project A reused by Y in project B" is to cite the paper of the person who wrote all that code. E.g., Y would write: "We use the Python implementation of the Fundamental Theorem of Basket Weaving written by X [1]." where [1] is the paper written by X for project A.

@ff524: Yes, assuming it resulted in an actual publication (sometimes it doesn't).

@Optimist: The bottom line is, there's an informal fairness code to be followed with things like this, and unfortunately not everyone follows it. My view is that you learn by experience which people don't follow it, and you avoid working with them.

It sounds like your answer is more about the case where X writes code for Project A, and then isn't given a chance to contribute more to Project A so as to earn authorship. Not necessarily the case where it's a different project, and X can still publish on A if he wants to get credit for his work. (The OP hasn't clarified whether he has a publication related to the original project or not.)

@ff524: My answer's more about the case where X writes code for no particular research project (i.e. to contribute to the overall framework of the group), and then projects are built on top of it without giving X any credit for that. But yes, if a publication came out of the original work, then it can just be cited.

Ah, I see. I had the impression that the OP developed it to advance his own research ("developed an entire framework X in code necessary for my research") not as a generic group contribution. It seems odd to assume the PhD student is responsible here and accuse him of lacking "common sense"; maybe the student believed (and had reason to believe) that the OP would have published his work by now, and that he could then cite it? (Maybe you could explore some of these subtleties in your answer.)

@StuartGolodetz your answer is exactly adresses my case. I have learned from this and will avoid working with this person in the future.

"Academia is structured so as to value ideas over implementation". While this is true, he should still at least be one of the authors of the paper, just not the first one. He did the work, so he should be an author. Simple as that.

@LouicVermeer: I didn't say it should be structured that way, I said it is. As it happens, I think there's a serious problem there that needs to be fixed. In the meantime, one way of mitigating it whilst remaining within the current rules is to make sure that implementers are given the opportunity to contribute to the science and not just the code.

@StuartGolodetz: In my field (biophysics), everyone who contributes will be an author of the paper. Even if they only spent the whole day pushing a button and changing a sample to do a measurement, simply because they invested their time they are an author of the paper. Maybe it is different in your field or country but you can certainly not generalise to all of "academia".

@LouicVermeer: Fair enough, I stand corrected - let me change my answer to make it clear.

@Optimist I don't see why you shouldn't be working with this person anymore. After all, he's a PhD and he likely wasn't aware of the ethics expectations. Second point: can you publish your framework so the collaborators could cite you?

By writing "the current situation in computer science / information engineering" it looks like these fields are similar or even the same, while science and engineering are actually very different fields.

@AndreaLazzarotto: Sorry, perhaps I'm not wording it as clearly as I might (the context is that I'm a computer science DPhil who's now working in a computer vision group in information engineering - the two fields overlap considerably, to the extent that people often submit to the same conferences, and the fields seem to me to work in quite similar ways). I'm not implying that science and engineering per se are the same thing; however, information engineering seems to me a lot like applied computer science. How could I word it that would make it sound clearer to you?

@StuartGolodetz if that is the meaning you want to convey, I honestly don't know. :) This is because I do not agree with your view. I have a MSc in computer science and a bunch of friends who study or have studied information engineering (some of them even switched from one to the other) and I cannot agree to the statement that computer science and information engineering are similar. At least in my country (Italy). :) They share programming, a little bit of signals-related stuff and that's it. I'm a computer scientist, not an engineer (and viceversa for my friends).

@AndreaLazzarotto: I guess maybe I'm just working in the overlapping bit and that's why I think they're similar :) What I do as an "information engineer" feels a whole lot like applied computer science to me. (Indeed, what I do is done in the applied half of computer science departments in some universities.) Perhaps I shouldn't generalise to information engineering as a whole.

For what it's worth, the way both fields are practised here, there's such an overlap that people keep mooting the idea of putting the information engineers and applied computer scientists in a single building. YMMV.

Approaching this question from a psychological rather than legalistic perspective, I would argue similarly to vadim123 that the question you should ask is not "should I claim co-authorship?" When you feel a need to "claim" anything, you are putting yourself in an adversarial position relative to the student and other collaborators. This is likely to antagonize them and put them on the defensive with the perception that you are coming to stake a claim to a piece of property they have ownership of. Given the marginal nature of your claim, this zero-sum type of logic would mean that your chances of success would be very slim and you would run a substantial risk of hurting your reputation and/or souring your working relationship with the paper's authors and other colleagues.
On the other hand, it's important to keep in mind that this is not in fact a zero-sum situation. While I don't think you should be talking about "claiming" authorship, there is nothing to stop you from suggesting that you may become an author to the work by participating in its writing and including the framework you wrote as one of the topics discussed in the paper. The key is to do this in a diplomatic, sensitive way that appeals to the authors' self-interest and points out various ways in which it might very well be to their benefit to add you as a coauthor. It's also important that your offer makes it clear that you don't intend to force the issue and consider a decision not to include you as a coauthor to be a reasonable and legitimate one. Above all, avoid any use of accusatory, entitled-sounding or negatively charged words (such as "claim" or "deserve").
Here's an example (perhaps slightly exaggerated for dramatic effect) of how an email to the student bringing up the issue might work:*
*credit to @ff524 for the fictional - I assume - basket weaving research theme ;-)

Dear Joe,
I heard that you and [insert name of group/collaborators] are working on a paper on your new results about basket weaving. Congratulations, I'm glad something came out of that project. I hope you manage to publish it somewhere good.
I thought I'd run something by you in connection with that. As you know, I spent several months working quite hard on the Basketweaving Framework that you used in that analysis. While I don't necessarily think that that should entitle me to coauthorship in your paper (and if you don't want to offer me coauthorship, I understand and think that's completely reasonable), it did occur to me that if you were to offer to let me take part in writing the paper and become a coauthor you could get several benefits that might not have occurred to you:
First, we could add a section about the basket weaving framework itself, which I created. I don't know if you wanted to mention it, but the new content could improve the paper and make it appeal to a wider audience, and possibly be accepted to a more prestigious conference, etc.
Second, another way that I could help is that I am a really good writer and put a lot of work into each paper I write - you can look at my existing papers and see how polished they are, with great figures etc. - and I can assure you that I am willing to work very hard to ensure that this paper has the same level of polish that would help the quality of the work shine through. Did I mention that my most recent paper was accepted to the International Congress Of Basketweavers? ;-)
Third, I've found in my career so far that while having coauthors does dilute a bit the credit you get for papers you write, it does so much less than you might think, and this effect is usually greatly outweighed by the fact that a coauthor is essentially a free spokesperson working for you, who goes around giving talks about your joint work at various places, and who can often say nice things about you in those talks that you couldn't easily get away with saying about yourself. Maybe it's cynical of me to be thinking in this way, but that's just one of the quirks of academia and how it operates and it's just as well to be aware of it.
As I said I'm happy with whatever decision you and the group end up making, just thought you might want to think about this.

+1 This is a great complement to the other answers, because it offers highly specific, practical advice for what the OP can do right now.

+1 It's pitched in just the right way to needle the recipient :)

Authorship is much like right-of-way on the roads, in that it can be given but not taken.  The answer to any question that begins with "Can I claim authorship" is no; instead one should ask "Should I receive authorship". Of course, both drivers and authors sometimes make mistakes (and can be criticized or punished for those mistakes), and sometimes people get hurt.
Such difficulties can be avoided by simply discussing, at the beginning of any research collaboration, what the possible authorship outcomes might be from the results.  With an agreement in place, a potential he-said-she-said situation disappears, and a withheld coauthorship becomes a clear offense.
As the other answers and comments indicate, the specifics of the OP's situation is highly contextually dependent.  OP should discuss how to proceed with senior members of his or her department, who will have more useful advice than strangers on the internet.

Isaac Newton is famous for saying:

If I have seen further it is by standing on the shoulders of giants.

and hopefully that's what the Ph.D. candidate has done.
The most important advice I would give you is talk to them, be forthright but not aggressive or accusative (certainly not to begin with). Use non-definitive language, i.e. explain how you see what has transpired, say that it seems to you that your contribution in writing the code may merit authorship - yes, don't be shy about that - and that you would like for them to let you know how the paper is going to look like for you to be able to understand whether or not that is the case. Don't claim they have done something wrong and don't talk about their motives. Make it seem like they would merely be putting your mind at ease.
About the actual question of whether you should be credited as an author or not:

If the paper doesn't claim (explicitly or implicitly) that they wrote the "framework", or the significant part of the code that you wrote; and if it doesn't present that code/framework as its novelty - then No, you can't and shouldn't claim authorship.
If those conditions are not met then Maybe, depends on the specifics. This is why my suggestion is to try to get more information; it might be the case that you can't expect more than a thank you note, it might be that you should be an author of that paper, and it might just be that they just refer to the framework as an interesting endeavor in itself which should be described perhaps in another paper than the one they're writing.

I completely agree with the accepted answer, assuming the contribution of the paper requires a reference to the output of the software.
In Computer Science (and in connected applied fields, such as Bioinformatics), the general tendency is to consider software as a "bona fide" scientific contribution, analogous in term of technicality and required rigor to a mathematical proof (the writer of which would certainly not be denied authorship in a Maths paper).  So I would say the sole contribution of an unpublished critical component of the research in itself qualifies the OP for co-authorship of that specific study. Field-specific conventions (first/last author, stars and daggers, dedicated section...) may be able to clarify the contribution of each author.
Moreover, in computational fields (as in "Using computers to analyze genomic/astronomic/ecological... data"), a reference/url to the software used for the experiments would typically be required by journals for the sake of reproducibility. Since you did not publish the implementation, then the reviewer may not be able to reproduce the claimed result. So, unless you plan to publish your implementation at a later time, the easiest option would be for the authors of the study to include you and mention this novel piece of software.

Even if he uses your framework, he wrote the code that uses it. So he is not required to let you claim authorship of it. However, you may be able to politely ask him to credit you (or similar).

Please read that the OP writes "I made significant contributions to his code".

@scaaahu The OP only asserts that on the basis of having written the framework, which is not what Dev seems to be discussing.

@Fomite I'll emphasize "I made significant contributions to his code and developed an entire framework X". Dev says "Even if he uses your framework, he wrote the code". It seems to me Dev thinks the PhD student(he) wrote the code without the OP's involvements.

@scaaahu I was more going off the second paragraph, where the OP seems to advance that the primary contribution was the framework itself. It's enough to be a little ambiguous.

@Fomite I agree the question is a little ambiguous. But, I think this answer is too ambiguous to be a good quality answer.

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


text:
Correct formatting of step-by-step equation demonstrations in papers
Working on some journal paper, it has pseudocode-ish/equation-ish demonstrations of the way some equations play out, along with actual reference values in the example proper; along the lines of:
i = i + 1
i = 2
Note: please assume the actual demonstrations are much more complex than this and actually require the reference values.
What is the correct formatting here? I have had it suggested to me the first line should be underlined, whereas I find putting the reference value in brackets more obvious - like so:
i = i + 1 (i = 2)
with the bracketed content right-aligned.
Suggestions?

@Roboticist In this context, the second line as noted.

Would it be a comment in the actual code?

@T.Verron No, just an on-the-fly display of actual variable values

I don't believe there is a correct way to do this, because you shouldn't put them together.
Writing i = i + 1 fully contains everything the reader should need to know about the statement.  If you really want to lay out both a theoretical pseudocode notation and walk through an iteration, I would do them separately.  One way might be something like:

for i in range(0, 10):
    i = i + 1
    print i

In this step we print to the screen the numbers 1 through 10.  For example, in the first iteration i takes on the value 0 from the first line, then has 1 added to itself.  The third line then prints 1 to the screen.

This way your pseudocode is treated like a mathematical equation in a paper, indented or otherwise separate from regular text, then examples as you go are just included in the text.  Depending on your audience and the complexity of the statements, you might also trust your audience to be able to parse your pseudocode without the need for filling in sample values.  Feeling like you need to walk through an example with numbers might be a sign that your pseudocode needs improving.
In short, trying to mash them together as you're suggesting just seems confusing to me.
The huge, important caveat to what I suggest: look through the literature specific to your field and see how this is done elsewhere.  If you can't find any examples of someone doing what you're asking about (which I assume to be the case since you're asking here rather than just emulating that), then don't do it.  Conversely, if you do find examples of it being done, copy that method.

Thank you for your answer (at least you made an attempt - which others haven't) but you're making an assumption about what is necessary based on a simplistic example I've given you, which is not as complex as the actual output.
I cannot find similar use-cases in the literature, which is why I've come here.
Also as mentioned these are pseudocode-ish equations, not pseudocode. So probably my question is better phrased as 'how to format equation steps with actual variable values' or something along those lines. Will update.

You're talking about display formulas (\[...\] in LaTeX), not about inlined formulas ($...$), right? In this case, I would use a two column table with a vertical line between the columns, i.e.,
  i = i + 1;   |  i = 2;
  j = k;       |  j = 3;
  k = k + i;   |  k = 5;

That looks cleaner to me than putting the second formula in parentheses.

Thanks for that - doesn't answer the question of whether there's a standard way to do this, but it's a useful suggestion, so upvoted :)


text:
Is there any reason not to crowdsource a subset of exam questions?
We're considering incentivising students to submit questions for the final exam in a large grad class (> 200 students) as we feel like the process of designing a problem and a grading rubric encourages students to study the material to more depth.
Is this commonly done? What are the pros/cons in the literature, or that you can think of with implementing an exam where a few questions are generated by the class? What precautions should we be taking? What should we incentivise?

It's an interesting idea, to be sure, but would risk striking the students as a lazy strategy on the part of the instructor(s), even if the questions ended up taking lot of work to compile and streamline. Another thing I'd worry about would be incomplete/inefficient coverage of the class material and/or types of questions. And I'm wondering about the possibility of the students sharing questions and answers among themselves well in advance of the exam. Any of the ones who exchange tips on their own questions in advance would have an advantage over the others.

Heck, I am running into situations where IT professors are using prefab exams found online for their quizzes/tests.  Granted this is Associates level at a community college, but the interesting thing is that the professors doing it are people who have gotten their masters in the past three years or so.   I can honestly state that the idea of striking students as lazy is accurate, at least to me.  I would assume that someone with a masters or higher would be able to write an exam on their own, and not need to outsource.

I'm not going to answer since I'm not familiar with the literature, but I don't think it's a bad idea provided you use it as an opportunity to explain what type of questions you'd like and what purpose those questions have (demonstrate practical vs theoretical, why better to have application of knowledge vs rote memorization, or if rote questions why, etc), and you are prepared to add/delete questions if you have too many/few on certain topics.

@trikeprof exactly, that's where the incentives come in. We would like to define "good" questions based on our evaluation of the question, the rubric and the class results, curving the grades... Students will always look for shortcuts, the question is how best can we discourage/use this to our benefit?

If you do this, the questions should not be used for this class, but for subsequent classes.

Is this commonly done?

I have no sources to answer this, but in my experience, no, it's not commonly done.

What are the pros/cons [...] that you can think of with implementing an exam where a few questions are generated by the class?

I can see two main issues:

It's not clear to me how you want to handle the communication of the questions and how you plan to use them, but some or, possibly, many students will know the questions in advance before the final exam.
As pointed out by @trikeprof in a comment, students might perceive this as a lazy strategy. Furthermore, they might not like the idea of being assessed on the basis of questions formulated by their peers.

I think that the idea of having students designing questions is good, but those questions shouldn't be directly used in the final exam.
An alternative proposal could be that of assigning the design of a question as homework, with the additional agreement that good questions will be collected in a booklet of questions/exercises, with recognition of the authors.

“some or, possibly, many students will know the questions in advance”  In particular, students who are well socially-connected within the class will be at a major advantage.  This does not seem fair.

There is the germ of a great idea in your question.  Let's take the basic idea and modify it a bit.
Have your students create an exam question, but not necessarily to include in an actual exam, but as a way of measuring mastery of the material.
You could, for example, offer several choices of specific topics that were studied in your course, and ask your students to choose one and design an exam question around that.
Since this is not something students are used to doing, it might be better to do this as a homework assignment than as part of an exam.
(If there are some real humdingers submitted, you could ask the individual students for permission to use their questions in future exams.)
I did not think this up by myself.  I heard it on an NPR special program about alternative education.


text:
Second PhD or postdoc and its effects on tenure track position
I am going to finish my PhD in the Netherlands within one year. Ideally I would like to get a postdoc here. However, due to competition or other factors I might not find a postdoc position. Then, there are two options:

Searching for a postdoc outside of the Netherlands, which is not the best option for me currently.

Doing a second PhD here.

What is the effect of doing a second PhD after I finished my first PhD, regardless if I extend it for some period of time or not. Will people see it as a failure? To me it does feel like failure!
One good point of working in the Netherlands is that PhD students are employed as research assistants. Thus, I think when I am able to search for postdocs in other countries it might not look as bad as I think.
Will doing a second PhD makes it harder to get a tenure track position later?

It is not possible to extend the PhD position for one year. However, my question is about after I finish my PhD.

See When does one go for a double doctorate?, and Is doing two PhD's a good path?

Why do you want to do second phd? Do you have visa issue, don’t like your current phd, or any other obligations to go for second phd? If not, can you just take research position (even if it pays low salary) until you find postdoc/position of your interest? I don’t see point of doing second phd without a very strong reason to spend another 3-4 years.

Nobody will care how many Ph.D. do you have when they consider you for a tenure track position. What will matter is number and quality of your papers/conference presentations after your PhD. If you want to change a field of your studies then it makes sense to do a second PhD. But if not, then it is a waste of time. It makes sense to delay your PhD defence rather than go for a second degree and use this time to focus on research.

I would expect papers published during a PhD to also factor into consideration, but otherwise this advice is sound. For a career, a PhD is just one of many stepping stones. Having two is unlikely to be useful, unless you're changing subjects.

Your question assumes that you would be able to find another PhD position in the Netherlands. I would be surprised if there would be another university hiring you as a PhD candidate if you already have a PhD, in particular if it is in a related field. There have been other questions on this site on the merits of doing a second PhD, and it appears that the general consensus is that it would not be worth it in general.
International mobility becomes an increasingly important factor, in particular in small countries such as the Netherlands. This somewhat depends on the field, but not being able or willing to do a postdoc or otherwise outside of the country could seriously impact your chances of obtaining a permanent position in many fields in the Netherlands.

I'm 100% sure that you could find a second PhD if you wanted to. A PhD is a considerably cheap source of labour, founded in the unspoken promise of a good job/life afterwards. If after seeing first-hand what a PhD truly is and doing it again, they are basically as desirable as possible to a PI looking or cheap skilled labour. I agree with everything else you say, but don't give the OP the idea that he/she would be very very lucky to get an offer for a second PhD! Truthfully, OP needs a holiday to reflect on their PhD process, then decide what to do next.

Well PhD students in the Netherlands are full-time employees, so although cheaper than a postdoc, it's still a non-trivial amount of money that has to be available. In the department where I did my PhD the number of available positions was certainly quite limited and also reasonable competitive.

It being a second PhD would give some serious warning flags. Given the serious money it is not something that only matters for the student.

I don't know how it is in your country, but typically in Germany (and I expect also in other countries) the following holds.
You cannot get a second PhD in the same field as you already have a PhD awarded.
Hence, you'd need to swap to another field, say to Mathematics from Computer Science, which might be hard to impossible.

There are ways for a further education, however.

Some people still manage to get a second PhD in a different field.
A honorary title, "Dr. h.c.", might be viable, but it's more a political thing.
Germany and some further European countries have a notion of a Habilitation or a "higher Doctorate", it's basically the second, "wider" PhD in the same field, that qualifies you (in old German tradition) for a professorship. An Assistant Professor on a tenure-track is roughly the same.
A Habilitation for a Dr. med. is sometimes called a PhD to mimic the anglo-saxon manner.

Finally, is a second PhD really the thing that would advance your career? I'd think about it similar to a second MSc. It not really does.


text:
Should I apply for an Assistant Professor position if I only have one recommendation letter?
An assistant professor position asks for candidates to provide three recommendation letters. I had a strong and excellent relationship with my PhD Advisor. He will certainly provide me with one recommendation letter but I am quite sure this is the only one I will get, at least in time as my two other PhD supervisors do not respond to my emails as quickly as before.
As a young researcher in a post-doctoral position for one month, my Professor is the only researcher able to write a recommendation letter. In contrast, an Assistant Professor position that I'd like to apply for asks for three. Should I still apply or will my application be too weak?

Does your PhD supervisor have enough of a good relationship with the other two that the supervisor could pressure them to respond?

If the posting specifically asks for 3 letters and you only supply 1 it is likely that HR (or the support staff) will not let your application proceed. Get the other two letters.

Not only PhD supervisors qualify to write recommendation letters. Isn't there anyone else who knows your work to some extent? Do you have any teaching experience? A person who organised a programme in which you taught could write a letter. There are further options.

Seconding @JonCuster's comment: probably your application file will just be considered "incomplete, pending letters..." and won't be considered at all. At the same time, presumably it doesn't cost you too much to apply, anyway? Still, you'll likely not be competitive against people who do have 3 letters, and are otherwise comparable.

It is a waste of your time applying, and a waste of your letter writer’s time, if you cannot satisfy even the minimal requirements listed. Three letters means just that - not one, not two, but three letters are required.
Academia is very competitive. If you want to have a realistic hope of being successful, you should aim not just to satisfy the minimal listed requirements for academic jobs, but probably to exceed them significantly. (By this I mean not that you need to have 10 letters rather than 3, but that you need to have 3 very good letters rather than just 3 generic letters. And you need to similarly exceed the minimal requirements for other listed criteria like quality of publications, etc.)
Disclaimer: my experience is mainly in the US, but I also have some experience with French academia and think the above advice would apply there as well. However, ask a person with firsthand knowledge of the specific job market you are targeting (geographically and discipline-wise) for more authoritative advice.

Seems a bit (more than a bit) harsh. Also formulaic. No exceptions? Ever? So the OP just gives up?

@Buffy I try to give the most truthful advice. I didn’t say OP should give up, but as for the number of letters, yes, it seems virtually certain that there will be no exceptions (subject to the disclaimer explaining the limits of my knowledge).

While having fewer than the "requested" letters isn't optimal, you gain nothing by not applying. How you do will depend in part (as always) in what that letter says about you and your work. If the other parts of your application are strong you may be fine.
Perhaps the one writing your letter can press the others to hurry up and get it done.


text:
Computer Science PhD with BSc Econ and MSc Social Data Science
I am curious to know whether my background will be at all competitive for a PhD in computer science.
My research interests currently mainly lie in reinforcement learning from human feedback, both off and online versions and in relation to large language models. This is also what I will be writing my masters thesis on.
Most of my CS knowledge is acquired through my masters where I've taken some computer programming classes. I have also focused on reinforcement learning and deep learning and have completed coursework on multi-agent reinforcement learning in auctions where I leveraged my Econ knowledge of game theory. And I have coursework of building simple decoder only transformers for recipe generation. I do however not have any publications as of now (although I am keen to try to publish my masters thesis somehow).
I'm really passionate about these topics but have thus far felt that my econ/social science background put me at a major disadvantage. When looking at supervisors in various CS departments most of their previous students have come from CS/Physics or maths undergrad degrees. Is there anything I can do to show that I am capable of successfully completing a PhD in CS? And is there anyway I can turn my Econ background into more of a strength.
Thanks!

Where (countries) are you applying to?

Not an answer but a suggestion: use CS and Reinforcement Learning for a PhD in an Econ Department.

Look for universities with seminars that are dual Econ/CS or faculty with dual CS and Econ appointments.

@Buffy I'm currently mainly looking to apply in the UK and the US and am also looking at working as a research assistant of pre-doc for a year once I finish my master this year.

@user2705196 yes I have indeed been thinking about this. I think this could be a good pathway.

@Dawn thanks for your suggestions I will have a look into this I know some universities offer some sort of dual masters in CS and Econ so there might be somme suitable faculty teaching on those to supervise a PHd

Have you worked this out or do you need more advice? I could add some US perspective.

Many CS graduate programs are open to students from outside the field if they have sufficient preparation. If you want to switch fields, you might have to do a MS degree at a university that is likely to accept you into their Ph.D. program if you do well. In this case, most of your classes can be transferred. If you get an MS in CS from another university, the department might be reluctant to allow your classes to be transferred.
I would apply at a few graduate programs after talking to someone on their admissions committee. I would also advise you to not limit your research interests as much as you seem to be doing right now. If you have done implementations (i.e. if you have coded), make sure that this comes across.


text:
Why is it extremely difficult for me to concentrate, and why do I yawn repeatedly?
Whenever I'm attending a class or even watching an educational video on internet (mainly any educational activity where I'm required to focus), I keep yawning constantly and all the time (I didn't count it before but I think I might yawn once, or maybe even more, every minute), with my eyes getting teary; and I lose my focus constantly and overthinking starts to contain me, I many times not only think about an event, but even keep imagining events and stories within a particular idea; and then I suddenly pay attention to the fact that I missed what I'm there for and I'd been in a different world. I get things together and I try to focus again, but this keeps happening endlessly. Overthinking usually abuses my brain, but it gets worse whenever I'm trying to focus.

Take a break, get some sleep, go outside, do something fun and not related to work. Then try again. Repeat as necessary.

Talk to a professional. Maybe a medical doctor. It might anything. But you need to find out why. There is no appropriate help here.

Try doing the same thing at the same time plus 12 hours. Maybe you're a night owl, maybe you are an early bird. Focus and attention are much more affected by chronotypes than physical labor.

For your safety go see a doctor. Do it now. Covid-19 is a respiratory disease.

The comments and answers suggest numerous possible causes for your problem, and here's one more possibility: sleep apnea. It results in briefly waking up (so briefly that you don't remember it later) many times during the night, so you get far less sleep than you think and are extremely tired during the day. There are easy treatments for it.

Nothing psychological: is there sufficient fresh air where you learn? The recommendation here for schools is to keep CO2 levels below 1000 ppm - but hardly any school achieves this (they'd typically need to open all windows and doors for 5 min every 15 - 20 min): this corresponds to an exchange with fresh air of about 25 m³/(h⋅person). A second physical factor to consider is light (both brightness and color).

It could be many factors: lack of interest, screen time, poor sleep, inconsistent sleep, lack of hydration, too much sugar in your diet (causes crashes), eating before class, not eating enough before class, poor habit formation early in life, lack of physical exercise. There are many, many factors. However, to begin with, you should examine a few things in your lifestyle:
1) What is your diet like? when do you eat? do you eat consistently the same times each day? do you eat a carb heavy diet?
2) Do you get physical activity? Are you hydrated or always drinking diuretics?
3) Examine your sleep schedule. Inconsistent sleep can be worse for you than less sleep.
4) Do you care to be in class? Are you treating your classroom like a job? If not, you should be.
5) Journal your day so you have a record. After two weeks, identify poor patterns in your lifestyle.
6) After you take a deep look into your lifestyle, and the consistency of your lifestyle, consider speaking with a profesional about trying ADHD medication and integrating those medications holistically into your lifestyle.
Nobody here will know why you are the way you are, but those are some key areas of life that you can personally make changes to.

I am not a physician, or an expert on cognitive abilities, but if this happens persistently then I assume you may be simply a person who cannot concentrate or understand oral explanations and presentations. This is a common phenomenon. I think that about 20% of the population if not probably more cannot truly understand oral descriptions of academic subjects (this depends also on the quality of presentation).
This, if my assessment is true, does not mean you should quit academia. It simply means you need to strengthen other abilities and invest more effort and time in listening to oral presentations.
For instance:

Repeat the video many times until you get it.
Rely more on written material, and read it slowly and repetitively.
Be more active in your learning: instead of listening to others passively, try to actively ask yourself questions and answer them, while going back and forth with the presentations/written-material.

In summary:
I cannot asses you personally, but in many cases this is simply a constant property of ones' cognitive abilities. Not something that can change (unless one is willing to take amphetamines etc.). Therefore, you need to find good strategies to overcome this.


text:
Graduating from a terrible department in an ok University vs. a fantastic department in an obscure university
I'm a PhD student in a terrible department in my field, in an overall ok university, and have just applied to another program (also PhD) in a very new but fantastic department (research-wise at least -- they just had a load of new world-class hires most of whom know me and my work; expected ranking in the field is top 5 in the world, by the next year) but in a very obscure university. I'm wondering if I should go if I get admitted, at least considering the future job market prospects. Would the obscurity of the university make so much difference even if the department is going to be highly valued?
Any help would be appreciated!

I suggest that instead of worrying about rankings you think about the quality of your own work and whether your advisor is helpful and has enough clout to get you on your way. The rest of the department means little.

The answers here may be relevant.

Also, you may want to separate the two questions -- we can't say anything meaningful about the situation at your current department based on what you wrote here, so I would remove the second paragraph and create a second post about that if necessary.

Generally speaking, for your future academic career, prestige of University as a whole is less important than prestige of department, and that is less important than prestige of advisor. And all of that is tempered by the strenth of reference letters you will obtain, and by the directly observable quality of your work. (By the latter, I mean how good your dissertation / publications are, the specifics of this highly dependent on your field).
Also worth saying, however, is that if you leave academia, the rank order of those factors for getting a good nonacademic job is generally reversed. (Ph.D. students generally don't like seriously thinking about nonacademic career prospects since their goal is an academic career, but in many disciplines the proportion who will go on to nonacademic careers is shockingly high, so you should at least contemplate this.)
In your instance, I would add 2 factors to consideration.

It's clear you aren't happy where you are now, and feel you would be happy somewhere else. Life is too short to deliberately choose an unhappy road to a (good) Ph.D. if a happier one is or becomes available to you.

"The grass is always greener on the other side of the fence." Don't overindex on the negatives of what you are experiencing now, and compare that with only expected positives of what your potential alternative is. In particular, look hard in the mirror: what have you learnt to do differently if you go to a new place, and do you have a tendency in life to frequently hit the restart button -- especially multiple times in a row? (Bluntness alert!) Everyone in academia develops pattern recognition for smart people who somehow serially fail to deploy, and are always restarting, but the restart only leads to another restart later on. We don't know you, so don't treat this as an implied accusation that this applies to you  -- but do look in the mirror to consider whether this is the case, and if so, what you need to do differently to not have to restart again.

With all that, best wishes, and do what (with self-reflection) feels right!

Thanks, this is helpful! I will contemplate the situation more thoroughly.


text:
How can I use my mathematical background when applying to physics PhD program?
I am a senior undergraduate and I am in the process of applying to physics graduate programs in the US.
Through my course of study, I've been excited about the interplay between physics and mathematics and studied mathematics up to graduate-level algebra, geometry, topology, functional analysis, etc. while pursuing a double major in mathematics.
I recently finished my first draft of SOP (Statement of Purpose). I stated that my experience in mathematics helped me grasp modern physics' mathematical formalism.
When I asked my colleagues to review my SOP, most of them said my mathematical background is "irrelevant and unimpressive," and they advised me to elaborate on my physics research experience.
I do have some research experience in physics, but it is rather weak. All I can say is that I attended the undergraduate research programs in both the physics and mathematics departments, and I wrote my theses there.
Admittedly, I didn't specialize in a specific research area in physics while pouring a lot of effort into completing a double major and exploring various subjects. Will this critically reduce my opportunities for being accepted to physics graduate school? What can I do to look appealing to admissions committees without exaggerating my experience?

Who are your "colleagues"? Other students, or professors? Professors of what?

Have you considered looking into mathematical physics programs?

Does this answer your question? How does the admissions process work for Ph.D. programs in the US, particularly for weak or borderline students?

The graduate math courses that you listed certainly don't look "irrelevant [for physics] and unimpressive" to me.

I think I should have asked a more specific question on my SOP. Nearly half of my SOP is about what math subjects I studied, how I expanded my understanding of physics through them, and the undergraduate research I conducted in the math department. The grad students' opinion is that it is unclear what is good about my mathematical background for physics research and many physics professors in the US will not appreciate it.

Writing my SOP, I assumed that my mathematical prowess would be appealing since I'm used to the language of topology, fiber bundle theory, etc. that are important in theoretical physics. For instance, the holographic methods (motivated by string theory) in strongly coupled systems seem to require such knowledge. Is it a naive idea?

Dr. @Buffy, they are physics graduate and undergraduate students. I haven't shown my SOP to any professor, but some professors I talked to said I had wasted my time indulging in pure mathematics. One of them was even a formal theorist working in Quantum Gravity, which arguably requires the highest level of mathematics among theoretical physics branches. This led me to believe that my mathematical background will not be appreciated by most physics researchers.

I actually think the problem isn't that your math classes are off-topic. I know lots of Physics PhDs who double majored or minored in math.
The problem is that you're focusing an awful lot on your coursework in your SOP. Your classes really shouldn't be the focus: anyone reviewing your application gets that information from skimming your transcript. Most professors in physics departments are familiar with the classes you took by their titles and already know how they would relate to physics research, so making it a centerpiece of your SOP is a waste of space. You can give the double major at most one paragraph to tie it into your goals.
You should talk about your research more. It doesn't necessarily have to be impressive, but your ability to function as a researcher is more important to your promise as a PhD student than how many upper div math classes you took.
A double major will not totally make up for a lack of research experience in a grad school application. Succeeding in classes is a different skill set than succeeding in research.


text:
My previous PI used my data in an article that was published in a high profile journal. My name is nowhere to be found in authors list
Last year I worked in a research lab in the US. My PI was very abusive so I eventually left for another lab. This individual was always extremely vindictive but I didn't expect that he would use all my work (graphs, tables almost verbatim) without even mentioning my name in the authors list or acknowledgments. One month before I left the lab we had submitted this work in a conference, and I was listed as a SECOND author in the submitted article. I have multiple emails between me and the rest of the lab members where I regularly sent them my data for discussion, reviewing etc. Also I have an email from a former colleague in which she explicitly asks me for my data after I left the lab. I never sent the data to that person at that time because I didn't trust her and I was struggling with my health at that time. They could retrieve them however anyway from my abovementioned emails, common dropbox etc. A new researcher who came to the lab after me, just one month prior to the submission of the article to the journal, ( and had zero involvement in the project before) is listed in the authors list.
I am young and new to the whole word of research and academia. Also, I would like to mention that I worked for free in that lab. That professor had promised to help me with my career instead of paying me (I know, what a fool)and instead he used all my work without giving me credit.
I don't know how to go about it and if I actually have any chance of getting something out of it.
I would appreciate your advice.

Have you tried searching this forum? I believe your question has been asked and answered already.

Welcome! I'm sorry you are in such a dire and unpleasant situation. You may want to have a look at https://academia.stackexchange.com/q/13700/19627 and the linked  questions, that are probably a good place to start. Please, edit your question if you believe your situation is wildly different, or as some other specificity, from what's described in those posts.

Thank you for your replies. Does publishing graphs and tables verbatim from my unpublished work constitute plagiarism?

Creating the graphs and tables for a paper does not necessarily entitle you to authorship (https://publicationethics.org/files/Authorship_DiscussionDocument.pdf).  But creating those graphs and tables nearly always requires some other activity that does entitle you to authorship.  Your work should be acknowledged at a minimum.
If you are entitled to authorship based on the standards of your field, you may:

Request that the professor ask the journal for a correction of the author list.
If that fails, request that the journal retract the paper for plagiarism.

Thank you for you reply. Two months earlier, when we submitted the article to the conference, I was apparently entitled to be second author. I ran the whole statistical analysis-based on which I created the graphs- and collected data as well. I know he is doing this as retaliation for leaving the lab , some of the people listed as authors did absolutely nothing.

What is the chance of a high profile journal retracting an article for authorship dispute?

@estranged If the journal thinks the author list is wrong and the authors do not agree to correct it, the journal will retract.