text:
Are there any fields that merges health and space science?
Currently, I am an undergraduate majoring in biophysics and minoring in astrophysics. I've always had a deep passion for learning about the universe (especially the field of astrobiology) and I also have strong interests in "applied" biophysics.
Initially, I wanted to pursue higher education to do research in either astrophysics or astrobiology. After spending time in both physics and biology research, however, I realized that research was not what I am most passionate to pursue and I could not find a calling in that career, although I enjoy the subjects very much.
However, through my experience in research, I was introduced to and developed an interest in the field of medicine because of many reasons, but especially because it provides me an opportunity to apply my biophysics passion to work on "practical" things such as creating new medical technology.
My problem is that pursuing further studies towards medicine by going to medical school would almost completely isolate my passion for space. So, currently I am at a crossroad and do not know where to pursue my higher education.
I can't find much information on how I could possibly continue to pursue both passions, which is why I am writing to ask if anyone has any ideas if there are any fields or directions that would still allow me merge my two interests (medicine and astrobiology)?

Neither of these fields is my area, so I'll mention an orthogonal path: you could become an expert in something else (e.g., statistics, game theory, programming -- right now the hot thing is machine learning / deep learning, but who know where we'll be in 10+ years), then you can apply that toolkit to both space programs and biomedical programs (whether through a university or through scientific consulting). Of course, it's an uncertain path, particularly if there is no "something else" that you are also passionate about.

Hmm, this is a really interesting idea! I'm learning a little bit of programming, but it's not my main focus. But I really like your idea of using skills from one field as a toolkit for the other. So, do you think I could just pursue medicine for now (which I would be fine with), and later if/when opportunities arise (due to a lot of advancements in space currently, like from SpaceX), I would be able to find a more space-related field? No problem if you aren't able to answer that; I'm young and inexperienced so I'm not very sure haha

I have no idea. I can't imagine (outside of some edge cases, like Buffy mentioned) how medical training would be useful in space research, or vice versa, hence my "orthogonal path" comment. But who knows, perhaps we will need doctors on Mars in 10+ years. Or perhaps you'll just be a regular doctor, which is not a bad fate.

Space Medicine is actually a thing, but I suspect that the opportunities are limited.
And I doubt that it is very connected to astrobiology.

I also read about that, but unfortunately you're completely right - it's very limited in opportunities. However, it doesn't need to be completely related to astrobiology - I'd just be happy if I could find something related to space!

Let me give another idea. This planet is currently being stressed and so the biological systems will be stressed. This implies that research in medicine will be required in the future as we try to adapt. It isn't exactly space, but it could be important. How do systems adapt to stress? Not exactly a new field, but new opportunities, perhaps.

That's also a good idea, and it sounds kind of similar to cag51's answer about using my skills from one field (like medicine) as a toolkit to apply to opportunities in another field in the future... I'll do some research on this and get back to you if I find anything significant. Thanks!


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How do you respectfully remove someone from your research group?
Recently, I began my work on an independent research project. A few months ago, while I was writing the research proposal for submission, I talked with a peer of mine who hadn't done independent research. As a good gesture, I told her that we could work together on it, since it would help her resume. In the meantime, I planned, wrote, and submitted the entire proposal myself.
When I offered her this "opportunity", I hadn't really thought things through. Now, I've realized that there really isn't much that she can contribute to the project besides stick around and do manual data entry - all of which I can do (she studies physics, while this is chemistry research).
I've already began the project and she hasn't done anything yet (because she doesn't really have the skills or experience, and it'd be too difficult and time-consuming for me to teach her). While I could definitely keep her around since she wouldn't bother me, I feel like it'd be unfair because I would be doing everything, but she would also receive the credit for it (and my "contribution" would therefore be viewed as less).
I'm not sure how to tell her that I don't want to work with her anymore in a way that she wouldn't be offended, but also in a way that doesn't make me look too bad for "going against my word". Any suggestions?

Pretty hard to do that without seeming to be, or even being, a jerk.

Don't go against your word.

It's your failure to plan. You knew that other person had no independent research, so it was your job to provide a route for her to become useful. But then, you seem inexperienced yourself, so take this as an opportunity to learn. She studied physics. That's an immensely useful topic to understand, is there no way to find a route for her to develop the relevant contributions? Propping up resumes is a dangerous reason to involve something for if there is nothing else, but it's done.

How do you respectfully remove someone from your research group?

To answer the question literally, although there is no nice way to do this, you can be respectful by sending a brief, straightforward email (and do it ASAP): "I am sorry but due to changing circumstances I don't think we can collaborate more on project X. I wish you the best in your future endeavors and I'm very sorry for the unexpected change."
However, your real problem is (as others pointed out) that you seem to be an awful mentor: although you have given no indication that there is actually any barrier to the student helping on the project, you (1) told them they could help, and then (2) mentally retracted that offer, apparently without them doing anything to make a bad impression. So retracting the offer here is highly unprofessional and unkind.

Now, I've realized that there really isn't much that she can contribute to the project besides stick around and do manual data entry

Can you really not think of anything she can contribute? You offered originally, so you should see this through and help her get up to speed. It will be a learning experience for her and an opportunity for you to become a better mentor.

I feel like it'd be unfair because I would be doing everything

You seem to just assume that you will do all the work; you do not seem to treat the student like a collaborator, i.e. with respect and thoughtfulness.

but she would also receive the credit for it (and my "contribution" would therefore be viewed as less).

Your focus on only your reputation here is telling. If she really doesn't help with the work, she should not be on any papers you submit at all, but instead you are worried about saving face and you would consider putting her name on a paper without her helping at all?

I'm not sure how to tell her that I don't want to work with her anymore in a way that she wouldn't be offended, but also in a way that doesn't make me look too bad for "going against my word". Any suggestions?

There is no way. She may be offended and you are going against your word. However, that doesn't mean there isn't a respectful way to do it, which I have suggested at the top of my answer.

Well... the trick in collaborating is in leveraging what others can do so you can contribute in ways they cannot.  Thus, if this person can enter data, this frees you from doing that task and - even if you could do that task - you can now do something else productively.  I can do all the work my students do, but if I spent my time doing their work I would have less time doing what I’m best at, which they cannot do.
So yes it’s frustrating but I would recommend you bite the bullet.
If you really must then simply tell this person in a private meeting that you do not think her contribution is sufficient to continue working on the project, and allow this person a chance to disprove or challenge your opinion, i.e. if the person insists she can contribute then agree on a useful milestone with a (fairly) strict timeframe.  If really this person is not up to the task, she may realize under time constraints that this is really not for her.

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I changed a word from a source, how do I cite it correctly?
I'm writing an analytical summary on Meditation II of Descartes from the compendium we have been given at school. We have been told to use this as our main source. Nevertheless, there is this specific part in section 12 of that meditation which I don't quite agree with:

[...] something extended, flexible and movable.

As per Marleen Rozemond in Descartes' Dualism [Source] in page 93, this is a poor translation.
The reason I looked this up was because the word didn't quite fit the context, and then I saw other people had translated it as mutable, which is also a correct translation for the french/latin word.
Complaining about the poor translation in the summary makes little sense to me, as it's not part of the context, and I have a limitation of 600 words to care about. Nevertheless, I am citing from the source of a document which uses the "movable" word instead of the "mutable" word.
How should I approach this? Should I make a postdata explaining why I have done what I did?
For reference, I am using the APA referencing style.

I'm giving you bonus points.

Write:

[...] something extended, flexible and [mutable].

You might like to elaborate in a footnote, e.g.,

The compendium poorly translates original word as movable, but mutable is more appropriate, as noted by Marleen Rozemond in "Descartes' Dualism," page 93.

(Depending on the style, you might like to replace in "Descartes' Dualism," page 93 with a citation.)

I ended up adding a footnote to the page, with a numeric mark. In this, I referenced the source which explained why it makes more sense to change the words.

A footnote is a good idea, you do need to explain.  You might also want to quote the text as "something extended, flexible and [mutable]" where the square brackets indicate an editorial change, i.e. something that was not in the original text.

@BenBolker The footnote in this case should also cite the original French/Latin text, rather than just the translation, so you can justify your re-translation of it.

An alternative would be to write (sic) movable and add the correct term with an explanation in the footnote. This keeps the text practically identical, only adding the sic warning that the original text contains an error while also providing the correct term.

@GiacomoAlzetta: I think it would be more usual in English to write movable (sic). But I'm not sure that sic is appropriate in this case. A footnote is better all round.

To preserve a comment made by Ben Bolker as an answer, since comments should not be used as answers and can get deleted at any moment:
If you want to make an editorial change to a direct quote because you want to shorten something or fix a dodgy translation, the word(s) you change should be put between [square brackets]. This is to indicate that this is a deliberate change you made to the original text.

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Translated letter of recommendation from employer
I live and work full time in the United States. I will be applying to graduate school in France through CampusFrance. All documents, apparently including letters of recommendation, are to be translated into French (by a certified translator). This seems to preclude the possibility of my not having seen the letter of recommendation before it is sent, which I understand to be important for the documents. One possibility would be to send the documents to a translator without opening them, and blindly sending the translated version along to the institution, which seems risky. What is the best course of action in this case?

This seems to preclude the possibility of my not having seen the letter of recommendation before it is sent Was the double negative intentional?

One possibility would be to send the documents to a translator without opening them This assumes document authors will send them directly to you, which is unusual (for letters of recommendation).

Why is it risky to blindly send[] the translated version?

Yes, the double negative was intentional. To clarify, I should not see the letter myself, but it seems that I may have to see it.
My concern is that I wouldn't be able to verify the translator's work; is this a valid concern?

I don't think you should be concerned with the work product of a certified translator

Ask the professor to send the letter to the translator with instructions to return it back to the professor. Make separate arrangements to pay the translator. Then the prof can directly send the translation. And the prof can even verify it a bit if needed.
You don't need to be in the document loop at all.


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Applying to Teaching Position in the Same Department as My Advisor... Should I Mention Her?
I'm applying for tenure-track teaching positions right now and have, more or less, a single cover letter that I modify for each one of my applications.
It so happens that the department my advisor teaches in has such a position and I am intending to apply.  To give some context to this, my graduate program was at an institution that is associated to but very distinct from the institution my advisor is a faculty member of.  Though my PhD advisor is one of my biggest professional connections, I hardly have any other connections within this department, though most other people there know that I was her PhD student and would certainly recognize my name from my application.

My question is: Is it necessary/recommended that I modify my cover letter to reflect my relationship with my advisor in any way?  If so, what should be included?

I honestly think there is a slim chance I would be selected for an interview let alone hired, but I would like to get a sense of what's appropriate in this kind of situation.

I would mention her, certainly. You don't need to make a big deal of it, but just mention somewhere that you worked on your dissertation under the guidance of Prof M. It is probably a matter of public record in any case.
You should also probably give her a note that you are applying to her department. Under the circumstances you state there should be no issue about it, and she may be able to help you along if your relationship was good. Being at the same place gives you a way to carry on research trajectories already set in motion.
She probably won't do for a formal letter of recommendation, however.
And you can, of course, ask her before you apply about the advisability of it and also this very question.


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In Love With My Field...Luke Warm About Academia
I'm currently facing an existential crisis of sorts with my choice to pursue my academic passions while navigating the demands of an academic system that I don't feel ever catered to what I wanted and let me work at my pace.  I would appreciate community support and input on my possible choice and how to work through some difficult feelings around the options available to me.
My passion for the longest time has been to work in mathematical physics.  I pursued my undergrad in physics, and through some haphazard circumstances, ended up getting into a graduate mathematics program in a small consortium of liberal arts colleges.  In grad school I had the opportunity to pursue subjects I wanted to learn for many years and found a supportive adviser who mentored me in my research.
Midway through grad school, I was faced to make a choice about my research.  For my area of math, there was basically only my adviser I had to work with and no cohort of other grad students who were working on anything remotely similar to me.  My adviser, in her best of intentions, strongly encouraged me to put aside my interest in physics for the more practical/vocational goal of using my efforts for data science and landing a tech job after grad school.  Facing the pressure of not being able to land a job in math or physics, I acquiesced to her suggestions and dragged my feet to complete my PhD in an area of research that's only partially related to my true interests.
Now..., I'm in a position where I have no desire to join the tech industry, and I'm working several part-time adjuncting teaching jobs that together require me to drive great distances in the area I live.

To get to the point already: I would like to be able to have a tenure-track position at a school other than a community college
  (which I'm inclined to take if offered).  However, in order to
  reasonably do this I would need to dig my roots in an area
  of research that I could publish articles at a steady pace (other than my dissertation I only have one article that was approved and hasn't been published yet).  Is it worth it to
  continue my research in mathematical data science to any capacity to
  help ensure long-term employment at a reputable institution, or is it
  better to continue adjuncting and devote all my time to my true
  passion of mathematical physics, basically "going it alone", studying
  texts and articles myself and building an area of research that is
  satisfying to me on my own terms?

It's up to you to decide what's important to you.  But I would say adjunct teaching is never a good decision from a financial point of view.

Actually I don't think either of these are good options, considering your publication record.  Why not pursue a tech job?

@AnonymousPhysicist Two reasons: I'm not willing to give up my interest in physics and to force myself into a line of work that I have no interest.  Second, I do in fact have a lot friends at brand-name, well known companies.  I've asked them about my viability for employment and they've each told me to go after what I want now.  If in the future I decide I want a tech job, they're confident I could be employable several years after exiting grad school.  I see tech as a backup option, and if I pursue that now I lose my chance to actually pursue what I want.

So basically you are asking "should I take the low risk, low reward route or the high risk, high reward one?" That is a question that almost everyone asks themselves at some point in life, and it is one that only you yourself can answer. I would suggest to research both options, talk to people about chances and challenges, talk to people in your life that might be influenced by your choices, and then decide. Unfortunately, no one can make this choice for you.


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Why do some academic journals requires a separate "summary" paragraph in addition to an abstract?
At least in the field of biology, some academic journals have added a separate summary paragraph (for example: "Significance Statement" (in Journal of Neuroscience), or "Significance" (in PNAS), or "In Brief" (in Current Biology)) in recent years. Why do the publishers think an abstract is not enough?

There might be multiple reasons, I guess either they know or believe that it increases the readability of the content they published. Same goes with highlights.The aim of a scientific journal is published articles which are read.

They serve slightly different purposes.
Specifically, the abstract is what you'd tell your coworkers; the significance statement is more like something you'd tell your mom.
The abstract is meant to quickly summarize this particular paper. A good abstract will provide a little bit of context or background, lest readers wonder why you're studying gene X or brain area Y, but the bulk of the abstract is approach and results. "Here, we show...." The significance statement is meant to put your work in a broader context and explain/justify why your article is worth publishing. (I suspect these are also helpful in attracting media attention, if that is of interest).
For example, suppose your paper investigates an antibiotic resistance gene. The abstract might look somethng like this one from MacMahon et al. (2009):

The ardA gene, found in many prokaryotes including important
  pathogenic species, allows associated mobile genetic elements to evade
  the ubiquitous Type I DNA restriction systems and thereby assist the
  spread of resistance genes in bacterial populations. As such, ardA
  contributes to a major healthcare problem. We have solved the
  structure of the ArdA protein from the conjugative transposon Tn916
  and find that it has a novel extremely elongated curved cylindrical
  structure with defined helical grooves....

This briefly hits on the context, but doesn't really delve into it. A significance statement would talk more about this healthcare problem (e.g., X patients have multidrug resistant infections) and how this paper helps solve it (target for co-treatments or whatever?).
Edit: take a look at the PLoS Computational Biology guidelines and examples (linked therein) that @cheersmate found for some more direct comparisons.

"something you'd tell your mom" Exactly, see e.g. the guidelines for PLOS CB saying it should be a "non-technical summary" to "make your findings accessible to a wide audience that includes both scientists and non-scientists".

I think you are correct that journals require this so that the document can speak to two different audiences.  However, trying to speak to two different audiences is a bad idea.

@AnonymousPhysicist, I don't really see the problem here. Neither version is a "lie", but the sig. statement just has background material that's redundant for workers in that specific subfield, but not known to those outside it.

A summary paragraph (without highlighting it by a section title) at the end of an article, especially letters without distincts sections, is very common if not necessary in most STEM journals.
Abstract and summary are different things. Abstract is an overview of content without references and limited, the summary often a conclusion of the results with outlook and references.
So one reason could be they want to stress the summary paragraph more again and therefore make a own section. It surely is of value. Especially for longer articles. Papers are not read in a linear fashion from beginning to end. Different readers with different background read papers in a very different way.
A significance statement is normally given in the cover letter or submission system of the journal, it doesn't belong into the summary, the significance of your research you should outline in the introduction, not at the end of the article.


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Contradiction on findings in existing literature
I'm currently writing my thesis where I have two underlying sources where one says that a variable (has the founder of a kickstarter project backed other projects?) has influence on the dependent variable, while another source says it doesn't. What do I do in such a situation?

Quote them both or figure out which is correct and why. Simple. (no, not really)

The conflict between the two sources is a good research topic by itself. Only one can be correct.

As Buffy notes, you cite both, and expound upon the apparent conflict.
If you are just reviewing literature, you would point out that the two studies came to different conclusions. If this is on-topic for your thesis, you would then dig a bit deeper and clarify what the studies have in common and how they differ, as it would lay out potential explanations for the apparent conflict.
This sort of thing is often the goal of reviewing literature to start with - identify a gap where there are no studies, or identify places where studies and/or theory seems to disagree.
Depending on what work you are doing, you may simply note this as a promising topic for future research, or you may want to try to address this conflict yourself with your own work to try to resolve the contradiction. The answer may be all kinds of things, from seeking out a mediating variable, to changing the analysis in a way that makes the conflict disappear, to ending up confirming that in fact "sometimes this variable matters, and sometimes it doesn't, and we don't know why."

Thank you for the broad answer, helps to understand the underlying logic behind each decision. In my case, the variable is only of secondary importance so I will simply note this as an interesting finding

A statistics caution: "not significant" does not mean "not different" or "not related."
If one study reports X and Y are significantly correlated, p=0.01, and another study reports X and Y are not significantly correlated, p=0.23 these results are not necessarily in conflict.
You likely don't need to go through a whole meta analysis procedure in your thesis' literature review if that isn't a major objective, but you should consider apparently conflicting information carefully to make sure it is actually in conflict, including both methodological differences and the effects of random sampling and sample size.

Yes, I was about to leave this answer myself. It's unusual to directly show that variables are unrelated, they instead show no evidence of association. One way to see if there's a conflict is to look at effect size and sample size. From the study that found significant association, you can find the effect size of the association. Using that and the sample size from the other study, you can calculate power. If the second study is underpowered, the fact that they find no association is unsurprising - they did not collect enough data. If they did have enough data, only then is there a conflict.

@NuclearWang Right. Even then they may not be in conflict, because effect size estimates from a single study can be very imprecise. But yes, you can use the power estimate approach to at least figure out how likely the second study would be to miss an effect similar in size to the one observed in the first study. Even if both studies are appropriately powered and assuming the effect is real i.e. null is false, according to some standard power threshold like 80% you'd by definition expect 20% of the studies to fail to reject the null hypothesis.

+1 very true, and this of course also comes up in regression models where many variables are dumped in and some aren't "significant", but may or may not improve the model depending on the comparison metric used, etc.


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How detailed should I describe my actions regarding code?
I am writing a thesis about a data analysis I'm implementing and am currently describing my data preparation where I talk about what needed to be done prior to the analysis (formatting the data, removing noisy data).
Now, I was wondering if I should also include steps that only helped me to work more comfortably like creating multiple different sets of data with different variables?
This has no direct impact on the analysis but I'm not sure if it still needs to be included.

In general it is good to be complete, if you can do so without being overly pedantic. But the example you give (multiple data sets) seems like an especially important one to include. This is especially true as a single data set is seldom definitive (if the analysis relies on statistical data - sampling). Multiple, similar data sets gives general confirmation.
If you say too little, you leave yourself open to questions about what you considered and didn't or whether your results are too sensitive to extraneous factors.
Give enough information so that someone else is able to independently confirm your conclusion.

I didn't frame that clear enough I think. The amount of rows per dataset is the same, I just include a different subset of variables per dataset. I could do it all with one dataset but it's just more bothersome workflow-wise as I'd have to specifically select the needed variables each time.
Therefore, I think in this case it'd be overly pedantic.

The answer depends on the expectations of your target community. Therefore, your best bet is to check similar papers from the same venue (journal or conference) and see how detailed the related instructions normally are.


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Who reads the NSF postdoc fellowship applications? (mathematics)
I am applying for the NSF Mathematical Sciences Postdoctoral Research Fellowships, and I noticed the guidelines say the following:

The Project Description should be written with both specialists and non-specialists in mind.

I am not sure what exactly "specialist" and "non-specialist" refer to. Suppose that in my application, my proposed research objective is to solve the Navier-Stokes equation. (This is just an example!) Will all the reviewers be experts in PDEs? Or at least in analysis? Or is the most I can assume that they are mathematicians (possibly working in areas like algebra or topology)?

If your application was only going to be looked at by specialists in your field then you wouldn't be asked to make sure that your project description was written to be read by non-specialists as well as specialists.

There is a 2014 blog post from an experienced (pure) mathematician which is more about the standard NSF Research Grants than the PDRFs, but which might nonetheless have some useful details https://www.galoisrepresentations.com/2014/09/26/applying-for-an-nsf-grant/

Some NSF programs are reviewed across sub-disciplines with reviewers that present a cross-section of mathematics. If memory serves me right, then that's true for CAREER proposals, for example, and I think also for the postdoc fellowships. In those cases, you'll have to expect that your audience consists of people in applied and pure mathematics, and you will have to find a level that keeps both of these groups interested in your proposal.

I suspect that the biggest communication gap is not best described as "pure versus applied", as though these were "two groups"... Further, not everyone self-describes as belonging to one of these two groups, after all.

@paulgarrett: But it is true that these two groups have rather different styles of communicating. Of course not everyone identifies with one group or the other, but largely, mathematics as a whole can still be divided into roughly these two camps.


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When citing a paper on arXiv, how important is the category?
The arXiv documentation says that we should reference arXiv documents using references of the form:
arXiv:YYMM.NNNNv# [category]

e.g.:
arXiv:0706.1234v1 [math.FA]

However, most papers that I am aware of do not bother to include the category.  i.e. they have references of the form:
arXiv:YYMM.NNNNv#

Furthermore, I can't find a BibTeX bibliography style which automatically includes the arXiv category (taken from the primaryClass in BibLaTeX).
Also, the arXiv documentation page "Preparing TeX/LaTeX Papers for Submission" suggests that arXiv documents should be referenced using just the arXiv ID, e.g. arXiv:0705.1234  (i.e. without the category).
My question is: is it OK to produce a list of references without any arXiv categories (i.e. just arXiv:0705.1234)?

The arXiv documentation page on "Understanding the arXiv identifier" contains the following sentence, which directly answers my question:
"Note that the identifier no longer contains any classification information and thus reclassification after an article is announced is possible."


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Re-applying to Math PhD programs while in first semester of current program. How viable?
I've looked at many of the answers on this site to questions similar to mine, and I've seen a huge variety of answers. My situation is a bit more specific, so I decided to finally make a post and ask about it.
I applied to Pure Math PhD programs this year (for Fall 2021). I was accepted into two, neither of which were my top choices (they were on the safer side). My partner applied to PhD programs in a different field (not math) but we were not accepted anywhere together. We want to reapply to eachothers institutions this fall in order to be closer. In particular there is one school (call it Y) who is strong in my research area and is close to my partner.
Furthermore, the university whose offer I accepted (call it X) is not strong in my research area - there is at most 1 person who I could maybe work with, but even they are not really super in line with my research interests.
To summarize, I have accepted an offer at University X, and am entering the Phd program there this fall. I really want to reapply to school Y both in order to be close to my partner and because the research there is more in line with what I want to study. I also want to apply to some other top programs in my field, since, if I don't get accepted to Y, I would want to at least be somewhere with strong research in my field. My application for this fall will be notably stronger than my application last cycle due to more research and graduate coursework at my undergrad institution. Is re-applying this fall acceptable, or will it be viewed poorly (although I believe I have solid reasons)?
I am seeking advice on how viable this is since there are mixed responses for other questions. Any input is appreciated, but especially if you've experience this yourself or are perhaps a professor somewhere. Thank you!
EDIT: It's worth also nothing that X is "strong enough" in my area and I love the location, so I could be happy there. Just not ideal, really. In particular I came more into my professional interests a bit later in my undergrad, so at the time of applying I wasn't firmly in one area of research (hence, I'm realizing a bit late that it's a little bit of an awkward fit at X).

Have you secured references for the next cycle? Who did/will you ask?

@gnometorule, My plan is to obtain two new letters and have four total. One a letter from my new institution (I have not started there yet, I'm starting in the fall). I'm aware that this will be somewhat weak, but is important to mitigate adcom fears that I am just jumping ship and cutting ties. The other is a new professor who I have experience with at my undergrad institution (upcoming department head), and has connections at the key school Y. The other two letters are the same, but are notably my strongest (one is undergrad research advisor, other i took grad courses with)

There is really no answer to the "viability" question. The only thing to do is to apply and make your best effort to be accepted.
But, as you probably already know, getting accepted to a single institution, considering no others, has a pretty low probability of success generally, due to the competition.
But there is really no reason that you should't apply. If you are turned down you are no worse off than now. Most people will, I hope, understand your reasons.
But there may be another path open, if your partner is in a place with several universities in reasonable distance. You might apply to several universities within, say a 50 mile radius. In some places that is a pretty large set of universities. Not everywhere, obviously.
Your partner can take similar action. Maybe you'll get lucky.

Thanks so much for the answer, Buffy! Indeed, I plan on applying to multiple institutions, but am hoping for this one in particular. If worse comes to worse I am still excited about my current institution, but admittedly would be happier closer to my partner and possibly somewhere with more emphasis in my field. Your response is reassuring, and yeah, I guess I just have to try and see what happens. Thanks again!

If you (and your partner, for that matter) want to have options available, apply and shoot your shots at multiple institutions that you are both interested in as far as research goes.  If University X is the best fit of the ones where you accepted, no harm in starting there and exploring the field that that advisor researches in.  Maybe a few months in you'll have a better idea of whether that field is really a fit for you (and you may want to even stay there), or not.  This, ultimately, however, will boil down to whether you and your partner find it worth the time to try transferring to another PhD program (i.e., you NEED to know that where you are now is not a good fit both in the short-term and the long-term)
Another point worth mentioning, is even if you don't feel this field is the perfect fit for your PhD thesis, if it is still in line enough, is maybe master out of this program (if it is an option at institution X, of course) after exploring the field a little bit.  This way you don't burn so many bridges abruptly, and you get to explore multiple different fields right before committing to one. (A good amount of people do this, after a year or two in a PhD program they realize that devoting 5+ years into academia isn't the right fit for them)

Buffy's answer probably covers most of it, but what you are coming across is also known as the two body problem of academia. And I know there are some places that are starting to try to accommodate for this problem (though probably more at the post-doc/professor levels rather than the PhD level).
An alternative that you and your partner could look into is doing a PhD at both the universities (known as a dual PhD). This would make sense for you to also look since there are other universities that are better suited to your field (plus the two body problem). Though keep in mind that you'll probably have to jump through a lot of hoops (though you might be able to motivate your university since having these programs can look good, especially if someone else happens to sort it out for you). This may also be harder during the coursework component of your work but since COVID probably means your courses are already online so ironically you might have had perfect timing.


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how much benefit is there of working as a predoctoral research assistant
I would like to do a PhD in a machine learning related topic and want to enhance my resume. I am considering looking for roles as volunteer research assistant and was wondering whether the experience would be beneficial if I do manage to find one. From what I've read online a lot of what predoctoral research assistants do involve menial tasks (cleaning up data) and wasn't sure if this would strengthen my application.
I'd hope to look for a research role in an area directly related to my interest. But an alternative I was considering was to just work at a job which may not have a direct connection to my interests but is slightly more financially beneficial.
I was hoping to get some advice on what would be better

Is "volunteering" even possible? I think that most places it would be disallowed by normal employment rules.

That's a good point, as far as i'm aware, from what i've read online, volunteering is possible. Maybe at minimum wage? Ultimately, if it is possible, I would like to understand the pros and cons of participating in such a role in trying to better my application

@Buffy I think the correct wording was pre-doctoral research I was wrongly under the assumption you'd need to volunteer to get such experience

In many circumstances, yes, predoctoral research experience is an asset, in particular if you can get a strong letter of support for your graduate application, and can contribute to some publications.
Financial aspects are a consideration also, but it's hard to judge given the available information in the question.

I think thats fundamentally what I was wondering, Does a predoc researcher have the opportunity to contribute to publications or are they left up to clean up duty

In economics, having a high quality predoctoral position is one of the best ways to get admitted to top programs. I am not sure about ML but in my field it 1) exposes you to research process 2) helps you to understand research challenges and pitfalls 3) helps you define more interesting questions for admissions statements 4) involves networking. You are right that tasks can be menial but they are necessary to research.

@Dawn Thanks, that's very useful advice. are these roles referred to as predoctoral research assistant or is there another term for referring to these positions

Getting a publication probably depends on the field, the group and the student.   Suggest you inquire to the groups that interest you.  Also note that if there is a publication, it may not be immediate - could take a few months or even years.

definitely not publishing but being able to contribute to some of the research that results in publication. Ultimately some first hand experience for strengthening my resume

In my own field (neuroscience) there can be a lot of benefit to working as a "predoctoral research assistant" if you want to go to grad school, though it's rarely called that. These are jobs available to people with a BS in academic labs; often the people that take these jobs are former students at the same school (possibly they worked in the same lab for credit or as a student employee), though sometimes people get hired from other places. It's a way to gather the research experience and perhaps publication record that is necessary these days to be competitive for grad school, especially for people who haven't had a lot of research experience as an undergraduate.
You might have better luck looking for positions in an applied research area that is looking for someone with some ML experience (hopefully you have at least some experience from coursework; every single CS student and many people from other fields have several ML/AI courses these days, if not you are way behind).
A good position will have you doing more than just menial tasks/cleaning up data, though in practice pretty much everyone has to do those "menial tasks", whether they hold a PhD or not. The decisions made at that stage of analysis can be just as important and even more so than decisions made at later stages, it's not something to take lightly.

Thanks for your response, is there a more official name for such roles or is does it just depend where you apply? A lot of the positions in industry that involve ML research i've found tend to require publication/phd experience which I don't  have.
I completely agree with you about the importance of menial tasks, I meant it in the way that these tasks aren't exclusive to RA roles. I was just wondering about the opportunity of specifically helping out with the research

@questions The job title is going to vary place to place. "Junior scientist" seemed to be a common title given at my undergraduate institution, "research intern" where I work now. There may be variants depending on the specific job duties. There is also the concept of a "post-bac" which is more directly intended to prepare people for a graduate program. These are all academic positions; there may be roles in industry but it will typically be harder to gain the resume items you want to continue in academia there.

Thanks that's very useful information

Perhaps you have a misunderstanding. In the US, at least, there are two primary funding opportunities for doctoral students. A TA (Teaching Assistant) aids in the teaching process, often as a grader, but occasionally as an instructor. An RA (Research Assistant) aids in research in some way. Sometimes it is to assist in the running of experiments as required by the PI, but sometimes it is just funding for the candidates own research.
But both of those require that you are admitted to a degree program (usually a doctoral program). It isn't something that you do before you make an application.
Some research labs hire lab assistants but that is a different thing. They are just employees and are unlikely to see much of the conceptual background of what is happening in the lab. There might be some value in this, as you would get to see others with more responsibility doing their "thing".

"They are just employees and are unlikely to see much of the conceptual background of what is happening in the lab." - strongly disagree at least in my own field. Yeah, there might be some lab assistant jobs that are truly just "work" like cleaning floors but there are lots of positions to do actual academic work, too. Probably a better chance in smaller labs vs larger ones.

Maybe i've got the role title wrong again but I guess in that case i'm thinking of lab assistant roles that require prerequisite knowledge in the field. Would such positions not be that beneficial as experience for PhD roles?

If you can get a job with some "responsibility" and a connection to the research process it would help. @BryanKrause gives good advice here.


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What early career development questions to ask during a Postdoc Interview? Is is polite and acceptable?
I recently finished my PhD. I am going to have a Zoom interview for a postdoc position (in life sciences).
My postdoc goal is to get a better experience in Research and become independent in R&D -project management. Mostly, after postdoctoral training, I would move to the industry.
I love this lab research project, mostly similar to my PhD project. So I will easily get adapt to the methods and I am happy to learn new techniques.
However I want to know their lab culture, importantly how supportive this PI for career development.
During Ph.D. I had to be in a toxic environment, I felt almost trapped, where no support was given, mentally abused.
So, I don’t want my next move going to be in the same environment.
What kind of polite, professional questions I can ask this Professor during the interview?
My main concern is how much he supportive of career development and giving opportunities?
Also, what are other questions I should be ready to answer and ask him during the interview?

The questions you should ask are dependent on what you personally want to know about the position, professor, lab culture, university, city etc. We can't tell you what's important for you personally to find out.

If you want an industry job, you should get one now and not get a postdoc.  Postdoc pay is usually low.

"become independent in R&D -project management."  If that is what you want, start a company.  The postdoc's supervisor normally does the project management.

You can always ask to talk to another member in PIs group, such as a post-doc, and have a peer-to-peer conversation. Then you can ask this member questions more openly and get more honest answers... Also the post-doc member would know how much the PI is supporting them better than the PI themselves...

FYI, If you want an industry job, you should get one now and not get a postdoc. Postdoc pay is usually low, depending upon the field, sometimes industries do have postdoc position (e.g., Pfizer).

@RichardErickson I'd love to. The problem is it's hard to get an industrial position as an international student; VISA issues. At least I am thinking I'll get an opportunity to network with other folks during a postdoc. PhD was abs. slavey 24/7 4y.

@Dendrobium be careful, some post docs can be as toxic as your PhD situation. Also, you might just be putting off the visa problems, or, you could be buying yourself time for either visa situations to improve or network.

@RichardErickson Thank you very much. It seems to me you have a great experience in this system, Richard. I would love to have some insights from you if you don't mind. "How to survive in a toxic academic environment, especially when PI is not caring what happens in the ground as long as he gets the publications. How to focus on career goals in such enviroenments?" Strong leadership is vital for a healthy research group. However, today it's hard to see this supportive environment in many places. Mostly international students suffer. Let me know if I should ask this in a new post?

During my own post doc interviews (and PhD interviews), I asked what the situation would be like.
I've included examples for your questions:

What kind of polite, professional questions I can ask this Professor during the interview?
My main concern is how much he supportive of career development and giving opportunities?
Also, what are other questions I should be ready to answer and ask him during the interview?

Ask the Professor how they run their research group. Specific question might include:

How many people are in your group including post-docs, grad students, undergrads, and technical staff?
How do meet with your research group? One-on-one regular meetings? Weekly meetings?
What is your management style? Are you hands-off? Hands-on?

Ask how the professor has mentored previous post-docs.

What do they view the goal of a post-doc to be? Do they view it as mentorship role? Do you they view you as a labor source?
Where do their previous post-docs end up?
Do post-docs get the freedom to ask their own questions? Are you only limited to the PI's question?

Ask what the professor wants from you.

For example, do they expect X publications per year?
Ask what they expect from their post docs on weekly basis. Do people work 40-hr weeks? 80-hr weeks? Are they expected to be in the lab on weekends?

For more ideas, I suggest checking out the Ask the Headhunter newsletter.
He offers good tips for interviewing.
Last, reach out to current post-docs in the lab and ask them if they would be willing to have a call about what it is like to work for the professor.
Other answers on this page such as this one describe what you ask the previous and current lab members.

Thank you very much @Richard :)

The interview is not a time for the job applicant to directly gather information.  You can do that after you get a job offer.
When you get the opportunity to ask questions:

Do not ask questions that you could have found the answer to with Google.
Do ask questions that show you have researched the employer.  This shows you are motivated.
Ask easy questions.  You might have studied up before the interview, but the person interviewing you did not.  Do not embarrass them.
Ask questions that will give you an opportunity talk about why you should be hired (don't be too blatant).

After you get an offer, you can ask the supervisor the real, tough questions, whatever they might be.  Also ask people who have left the group; not all supervisors are honest.

I would disagree - the interview is a perfect time to ask what the outline of the first 1, 3, or 6 months will be. As somebody who hires postdocs I don't wait for them to ask usually, I tell them what the overall plan is and how we will position them for successful job interviews within 12-18 months based solely on their work with us. Interviews are two-way streets, and since the job of a postdoc is to find a job, how the place will enable that is obvious and fair game.

"The interview is not a time for the job applicant to directly gather information." I'm gonna disagree with that. The best way to show that you have done your homework is to ask good questions. "How will this postdoc support me in achieving my career goals, which are A and B?" is not a bad question to ask in my opinion.

That said, OP will receive better information by asking previous postdocs than the interviewer.

@xLeitix I'm not sure we disagree.  Your question could be an easy question and it could be a question that presents an opportunity to talk about why you should be hired.

I think that people believing this sort of answer is the right answer is behind a lot of the people who end up in bad situations here. When you interview, you need to interview the "job" just as much as the "job" interviews you. Don't wait for an offer to do that. If the PI/hiring manager can't take those kinds of questions you absolutely do not want to work for them. Yes, do your homework, but work culture isn't on the lab web page or list of publications.

@BryanKrause "Don't wait for an offer to do that." Why not?


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What are the available postdoctoral fellowships in Europe that non-European can apply for?
In life Science, What are the available postdoctoral fellowships in Europe that non-European can apply for?
Once joined an EU research center can a non-EU researcher apply for Marie-Curie postdoctoral fellowships?
during a PD interview, PI said, it's not possible once the applicant already joined an EU center?

Europe-wide, I believe that Marie Curie is the only significant option. There might be a greater variety of options at the country level, but these will obviously differ from country to country.

To answer your second question first, the Marie Curie fellowships require evidence of mobility - specifically, that you haven't worked in the proposed host country for more than 12 months total in the past three years. So if you join a lab in, say, France, after one year you will no longer be able to apply for a MSCA fellowship in France.
However, you'd still be eligible to apply for one hosted in any other EU country where you had not worked for more than 12 months in the past three years.
So, if you're happy and able to move labs, then you would still be eligible to apply for a MSCA fellowship. The full eligibility documents are on the call website if you want to read in more detail.
I don't think there's a short answer to your first question - the EU contains dozens of large scientific funders and probably hundreds of fellowship schemes, with differing requirements. There are likely search tools for specific countries/opportunities which would give a better answer.

Thank you very much Stephen. Helpful and sad answer. May I know where can I find Life science related funding opportunities for Sweden and Finland if possible. Thank you again.

Finland and Sweden are outside my experience, unfortunately - I'm not familiar with any sites with good coverage there. Someone with local knowledge (and who may speak the language) may be more helpful there. Best of luck in your search.

In Finland the Academy of Finland is probably the first place to look (though I'm not in your field so there might be better sources of funding). Last year's call was here: https://www.aka.fi/en/research-funding/apply-for-funding/calls-for-applications/apply-now2/funding-for-research-post-as-postdoctoral-researcher-2020-all-research-fields/


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Advisor's Postgraduate Career Machinations
I have been applying to postdoc positions, but I'm concerned about my advisor's recommendation letter.
I have been a productive researcher under his supervision and had a good, but stressful PhD experience and I believe I have been one of my advisors better students. He certainly seems quite pleased with my work.
I have a job offer that my advisor would strongly prefer I take, it involves working in a group indirectly controlled by him.
For personal geographical reasons (not related to my advisor or anyone I work with) I would prefer to work elsewhere.
What troubles me is that I'm not certain my advisor will write me a recommendation letter that accurately reflects my abilities as a researcher in order to force me to accept the position more closely associated with him. He's certainly been pushing me to accept this position by refusing to expend any effort to find more funding for me until I finish my PhD. I'm graduating next month and I've been without fellowship for the past few months). The people in charge of this postdoc position are happy to start paying me as soon as I agree to work with them.
I realize this sounds somewhat paranoid, however my advisor has done something similar to one of his previous students in very similar position. This student had been extended a tentative offer for a position at very prestigious institution, which was then revoked when our advisor sent a private email to this students prospective employer implying that the student had already agreed to work with him after his graduation. This student only found out why the deal fell through later when he met personally with some people working with the prospective employer and they were sorry that he wasn't available to work with them at that time.
I don't doubt this. My advisor is certainly the kind of person who would conspire in this way. He's sort of roguishly brilliant and I'm sure he justified it to himself by thinking it was in this student's best interest. He's one of the big names in our field as well.
What do I do? I understand that omitting my advisor from the letter writers can raise some eyebrows. Is there anyway to inform prospective employers of this situation without sounding insane?

If your supervisor is manipulating you to take a job that benefits them, and not you, then you should end the supervisory relationship swiftly, probably by graduating and obtaining a job outside their control.

Is there anyway to inform prospective employers of this situation without sounding insane?

I'd suggest that if you are clear with your supervisor you are leaving and are not open to changing your mind, they will probably write you a good letter because writing you a bad letter makes your supervisor look bad.
I can think of no explanation a recent PhD graduate can give for omitting their PhD supervisor's letter that looks good.  Your other letter writers could give an explanation for you.

I like this a lot. I think in many cases this is the correct answer. Unfortunately, in my case the position my advisor offers is quite good, and I would accept it and deal with the consequences to my personal situation should nothing better be available. On the other hand, by doing this I may be kicking the can down the road and remain under my advisor's thumb...

You don't need a recommendation from your professor.
Some professors are magnanimous. Others are not.
Talk to the key people involved in your desired postdoc and inform them that your advisor may not be enthusiastic about your leaving, and they will understand.

This is one of the rare moment where it is worthwhile to apply for the position without attaching reference letters, only providing the reference contacts, and after a week or so having a call directly with the PI or the responsible person for the new position.
What you describe here is best discussed "in person", so you have time to clarify all the details and your goals (i.e., exactly what you wrote here, but in writing they sound heavier and, counterintuitively, in writing it is less clear and there is a lot of space to misinterpret).
Maybe you do not realize it, but you are looking for a way out of an oppressive and manipulative advisor. Yes, he has been a good one[1], but better to cut your working relationship with him before discovering his bad sides. You have your PhD, you are and you must be independent from such a person (from any person, actually).
[1] when you say stressful, think about someone undergoing that stress with some personal/family/health issues. Do you think he/she would have dropped out?

He's not uncompassionate, only manipulative. If there was a situation as described in your footnote I'm sure he would give me the slack to handle it. You point out a really critical thing with what you say about communicating in person. Thank you very much for your answer. Unfortunately, I've discovered some of the positions/fellowships I'm applying to require a reference letter from an advisor.

"The people in charge of this postdoc position are happy to start paying me as soon as I agree to work with them." Then you can honestly win some time. Tell them that absolutely, you are happy to work with them as soon as possible, then tell them you can provide three reference letters immediately (but not from your advisor), but the reference letter from the advisor can be delivered at the earliest in 3/4 weeks only (give no reasons). Do not mention it will be late because you will ask it in 2-3 weeks ;) , if they express the need.
Be smart, you have to outsmart a manipulative person.


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Supervisor using my dataset without my consent to submit papers with his other students
During my PhD (field of machine learning) I've been working in collecting a very large dataset. The whole work took more or less 1 year. I had the idea, collected most of the data and wrote all the software for data collection and data annotation. I acknowledge I had help from other people setting up sensors and collecting data, but mostly technical work.
Recently I've found out that my supervisor is giving this dataset to his other students without my consent and even submitted 2 papers (even before the submission of my own paper, so I don't even get a citation).
In those other papers, they wrote my name in the acknowledgements. I didn't find it fair and I've claimed at least co-authorship from the other papers. But my supervisor claims that he purchased the equipment, and the funding came from his project, so he owns the dataset and he decides what to do with it.
I took 1 year doing everything, and other students spent 0 hours, and I just get an acknowledgement? I really didn't find it fair.
I'm trying to solve it internally with my supervisor, but it's not working. Since the papers were already submitted, I'm not sure I will be able to change authorship. I have many proofs that this dataset was mainly developed by me.
What's the best way to try to solve this problem? Report it to the department? Address it to the conference chairs (the papers are still under review)? Or just forget about it and finish my PhD without complain?

Is there a possibility of making the data public? If yes, write a paper on just the "Data" and publish it with your supervisor. Then all papers can cite that data paper. There is no fun fighting with your sup during PhD.

Possibly a duplicate or at least relevant: https://academia.stackexchange.com/q/116307/72855

@Coder Half of my paper has a description about the dataset, and I'm trying to release the dataset. We need approval from our sponsor,  before I release. My paper is under review at the moment and hopefully it will get accepted and the other papers can at least cite my paper before they are actually published.

@Roland I'd say the supervisor is probably legally correct, but not probably breach professional standards around authorship. So an appeal to the courts would probably fail, but an appeal to the person responsible for professional integrity at the Uni might succeed. Of course doing so, you'd probably be making a life-long enemy of your supervisor. Do you have some sort of independent advisor or thesis committee in your department?

@IanSudbery I contacted once an independent advisor to complain about my supervisor about some other issue. During the time, he suggested that I could challenge him, and show evidences about the issue, but he said I would lose my funding if I had to change supervisor. The independent advisor in the end suggested not to take any action since it could get even worse. But now I'm nearly completing my PhD, so probably I can say something after I finish, so maybe he can at least face some internal punishment.

I kind of disagree with all the answers so far. If a student put a year of work into something and then there is a publication based on that work, then obviously the student should be an author on that paper. There just aren't any ifs or buts about it. To submit a paper without them is clearly unethical.

Fighting with your supervisor is probably going to negatively affect your own career. Don't let your future hang on this one thing whether it is fair or not. Forcing punishment on the advisor will not get you the letters and recommendations you need to get out and on your own.
Get your own paper published. "Make nice" enough that you get good recommendations. Get away. Build your career.
If you focus just on the "justice" of it you could easily be the one to suffer blowback. Let the past be the past and optimize for your own future. This paper and this dataset isn't going to define your future, nor, hopefully, be the best work of your career.
And, no, I don't make this recommendation happily nor lightly.

... to negatively affect your own career It depends on the career. It will certainly make their life miserable/complicated/stressful until they can hang the PhD diploma on the wall. If after that they plan to leave academia nobody cares (including recommendations).

I don't see anything problematic here, unless the papers that your advisor wrote with the other students take credit for developing the dataset (which would be a clear ethical violation).
Many papers in computer science use one or several datasets developed by other authors, and it's not a standard practice that the dataset developers are invited to contribute as authors. In fact, doing so may lead to vastly inflated author lists for papers that use many datasets.

Agreed, but they probably should cite his paper about the dataset, even if this is only to explain how the data was obtained.

@Louic Agreed. Of course, for this, the paper first has to exist in a citable form. OP should push the sponsor for the OK to release the dataset (which seems to be needed), and then publish the paper on arXiv, so that it becomes citable.

It is normal to use many other datasets without the developer as author, agreed. But this happens when the dataset is publicly available, no? My dataset is not publicly available and I didn't even get a citation. In their paper they say that they applied the method in their "own dataset", but they give acknowledgments to me for the data collection. At least I would expect that my supervisor would ask me if I agree that other people would be using it.

@user1998012 There's also cases where the dataset is not publicly available, like, when working with an industry partner. I would agree that your supervisor's behavior lacks courtesy, but it's not unfair, since the creation of a dataset usually does not lead to authorship (unless the dataset is a contribution of the paper).

I am not in computer science (so comment and no vote), but in my field, the OP would have deserved authorship for at least the first paper (or set of papers). An FYI for future readers.

@lighthousekeeper What does citable form mean? Is there some reason they couldn't cite the OP's forthcoming paper as "Blah, blah, blah, in preparation"?

@RichardD.James That would be a citable form, but it sounds like it's not even clear if the paper will eventually be published in the first place (OK from sponsor pending).

It should be considered positively if the dataset is used by completely somebody else. I remember that number of acknowledgments can be used as a metric in some grant application or other types of report.
If you prefer citation or authorship, then I'd recommend to make your dataset citable as soon as possible, e.g. as your own publication, article or as pure dataset. Public dataset can be uploaded and cited by services like Zenodo, which generates citable DOI.
Your career won't be affected by on less co-authorship. More important is your attitude to work. Personally, I'd be very happy if some of my datasets are used by my colleagues, anyway I do not know exactly your circumstances and lab relationships.

Unpopular opinion: be happy that your dataset was used for, not one, but two publications!
You'll get your paper out, then at some point you may write

"This dataset was used in the following publications \cite{otherstudent1, otherstudent2}."

So that people will know that your contribution was important. That's kind of counterintuitive because you are citing them. But people reading your paper will understand the usefulness of your work. And that's more important than bibliometrics.
I understand that having two more papers in your CV will positively impact your career. But the gain of two more publications is greatly outweighed by the loss of a bad recommendation letter.
My advice is to get the paper out, focus on the fact that your research was useful (that's our goal at the end of the day), and move on.


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Which authors to cite for open source software
While I have worked on open source software myself I'm, strangely, uncertain about how to cite it in a paper. I do know how to cite software itself, I'm just uncertain which author(s) to attribute it to.
I've got two programs to cite, one of which is a fork, with different copyrights over different files, not to mention the many unmentioned contributors to that work.
Do I just cop out and go "main contributor et. al"? And in the case of the fork, do I take the original author of the original software or the author of the fork?

Much open source software provides guidance on how to cite it, e.g. https://www.scipy.org/citing.html and some style guides, e.g. APA, also offer advice. https://blog.apastyle.org/apastyle/2015/01/how-to-cite-software-in-apa-style.html

Unfortunately the software I'm working with does not come with its own guidance, as it's not software normally used for research but rather related to file management (in this case,  files containing research data).
The APA Guideline gives me some confidence I'm heading in the right direction, by citing the main programmers. I guess I'll keep it at that for the draft and see if someone corrects me on it later.

@StuartF Can you please change your comment into an answer?

@MadeOfMagicAndWires,
I have worked with open-source software and even using it (Linux).
So citing an open-source software in your journal will require you to check out the main source (repository owner as in GitHub) and cite according to using APA format or the format of citing you are required to use.

This is what I've done as well, but I was a bit uncertain about who would count as an author in these cases.
Is it just the owner of the repository, or everyone that has contributed to the software? In case of forks, or when an app makes use other open-source software where different files will often have different copyright holders, do you cite those?
It's funny that, as someone who has contributed to open-source, I am quite sure on the licenses and copyright holders of this type of software themselves, but not quite sure on how that translates to academic contribution.

@MadeOfMagicAndWires, Please check this out: https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cad=rja&uact=8&ved=2ahUKEwiJ5IPc-ZPlAhXOTsAKHcGJDfIQFjAAegQIARAB&url=https%3A%2F%2Fgithub.com%2FAASJournals%2FTutorials%2Fblob%2Fmaster%2FRepositories%2FCitingRepositories.md&usg=AOvVaw1w6ZePH_l4VEqNXi3uAffy

Thanks, this is helpful, but it doesn't really go into who to cite, which is the big clincher for me. The example they give for example, only cites one author, when it has three contributors.


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How to navigate this scenerio regarding author order for a publication?
Let me start off by saying that I am really a nobody in my field of research.  Several months ago I reached out to a very well-known researcher, one of the big names, with a draft paper I was working on.  I was very surprised to get an answer back from them.  I originally wanted their input on a paper I was preparing for publication and thought having them add their two-cents into what I had written would really improve the paper.  In exchange I offered them to be a co-author.
The researcher was hesitant to agree to my offer citing that they believed what I had was a really nice piece of work and they were concerned that by adding their name to the paper, people would end up attributing the work to them.  Instead, given that my paper was theory heavy, they wanted to do a follow-up paper together that was focused on experimental verification of my theory and also bring in their PhD student to help. I can understand that they saw this as an opportunity for the PhD student to get in on a paper (who does not have any publications yet) and at the same time give me an opportunity to collaborate with them (the big name researcher).  Everyone would benefit.  Anyways, the researcher in question suggested the possibility of the PhD student taking the lead as first author and that we should rank authorship based on who contributed the most.
I am not sure if the PhD student was too busy, or just didn't understand the topic but for whatever reason they showed very little interest in actually doing the work to get the paper done.  They did put their name as first author on the paper at the very beginning of the research effort but then did very little after that.  I ended up writing at least 80% of the paper, and my collegue did all the data processing, with the PhD student capturing the data and writing an abstract and a paragraph in the introduction. I could see when they made edits to the paper and it was always last minute (the night before our meetings).
Now, I would not necessarily care too much about the author order here; however, because I don't think the PhD student understands the topic well at all, I don't want correspondence for the paper being sent to them.  I wrote almost the entire paper and also all the details of the algorithm/theory used to produce the results.  I know the material very well and am able to actually answer questions and discuss the work with those who may be interested.
This is an awkward situation for me.  I don't know how to discuss/propose the authorship order change and also don't want to cause a fuss because I want to work with this researcher more in future projects.  I saw this project as starting a relationship with this researcher and don't want to rock the boat too much. I have more ideas that I want to work with them on. Can anyone please help me navigate what to do?

*Instead, given that my paper was theory heavy, they wanted to do a follow-up paper together *
What paper are we discussing here? if the PhD student collected the data for the follow-up paper, I can see why they feel they deserve first author spot in the follow-up paper. However, what you are worried about is the corresponding author, which is not the same thing as first author ...

It's not clear to me whether your original, theory-heavy paper was published. Was it?

@BryanKrause The original paper has been submitted for publication and is in peer review.

@EarlGrey Yes, the PhD student collected the data for the follow-up paper but essentially did nothing else. My coworker and I did all the processing, analysis, and writing the paper (minus an abstract. Between him and I we wrote 95% of the paper. Maybe the answer is just to ask for the corresponding author position.

It's often a problem that burden of effort shifts during a project, and that initial authorship expectations should therefore be modified. However, it's far better to make these modifications along the way rather than at the end.

I ended up writing at least 80% of the paper, and my collegue did all the data processing, with the PhD student capturing the data and writing an abstract and a paragraph in the introduction.

Really, before you took on writing most of the paper, you should have renegotiated the authorship arrangement, or at least had a conversation about it. Some things you may need to consider are:

Writing can be either a relatively minor contribution or the major feature of a paper. I would not necessarily consider the person who wrote the most words to be the person most deserving of first authorship.

Likewise, data collection is sometimes a very undervalued part of a project, depending on the type of data; for other projects, data wrangling tasks can be just as important and time-consuming. In some cases, you really need to do an entire separate hidden research project that's nonetheless completely unpublishable and uncredited just to start data collection. I don't know whether that's the case here, and you may not either, but it's something to consider.

It's not really fair to 'steal' a paper by doing someone else's work. If you start a collaboration with someone, you should expect that your project with them is not their only time commitment. If you separate the tasks, it's good to communicate about expectations of when those tasks are to be done, but if you'd like things to move more quickly and therefore start taking tasks that weren't yours, well, it's not really fair to then say the other person didn't do the work: you didn't give them a chance to.

With that out of the way, your next step really is to just have a conversation about it. Maybe everyone is in agreement on a new authorship order, and there's no real problem to solve. If there are disagreements, then you can start weighing the alternatives. Try to have a good sense of what things you value going into that conversation, rather than fixating on a solution. If your field recognizes "senior"/last authorship, maybe that's an acceptable position in the author list for you and your role. It may be useful to have a neutral/semi-neutral party help mediate. As in any negotiation, you shouldn't expect to get everything you want, but hopefully you can settle on something that everyone feels is a reasonable compromise.
I do not get the sense that the "very well-known researcher" you initially contacted will be a barrier - they already proposed a very reasonable solution when you initially reached out. If they were the sort of person who abuses authorship they'd likely have had no problem being an author on the first paper. They may also feel a duty towards their PhD student, however, but I think you really need to have the conversation first and see how things shake out before you worry too much that you're rocking the boat or burning bridges with them.

You make a lot of good points.  I will say the data collection portion of this paper was not significant...it was the processing/analysis/writing that took the majority of the effort.  When things started to shift I should have brought up authorship earlier.  That is a lesson I will remember next time.  At the same time, my conscience is in the background telling me I took over the project and maybe should have given the PhD student more of a chance. (+1) for the helpful answer.

Worth considering how much real time would having to do the data collection (and any associated work) have taken from the OP if they did it themselves ?  It may seem a minor contribution but it can often be a real necessity to have someone who does this often thankless grind work.

If the PhD student collected the data for the follow-up paper, I can see why they feel they deserve first author spot.
However, what you are worried about is the corresponding author, which is not the same thing as first author.
Keep the PhD students as first author (isn't it what you agreed with their advisor? did they do the bulk of the work for the paper, i.e. data collection?) and then  at submission  put your name as corresponding author (I guess you are dealing with the submission, so you have a certain responsibility and you deserve that role).

I don't think it makes much sense for OP to be the corresponding author (he could be journal contact author during submission - but that role is thankless slavery). I believe professor is by far the best for corresponding author position for few reasons: 1) he will keep that mail (PhD student and OP are more likely to move on) 2) he knows both the theoretical and practical side of the paper to some degree 3) he is the bridge between PhD student and OP so he can easily forward questions he can't answer himself. OP would need to go through professor to send experimental question to the student.

@ZizyArcher You make some reasonable points, but I think it is all in the interest of OP to be corresponding author, if he feels he dominate the subject, (up to being the first author on an experimental paper) let him be a peer on par with the professor. More in detail:

there are many ways to contact a researcher;
nothing prevents the corresponding authors to reach back to the coauthors;
you do not need a bridge to get in touch with the PhD. You get directly in touch with the PhD, if he/she does not react, you get in touch with the professor.

There seem to be several issues here, most prominently, a collaboration gone bad.
IMHO the authorship question may now be considered fallout of this issue.
Albeit this is easy to say in hindsight, but if you have had the feeling the PhD student didn't contribute sufficiently, the proper way would have been to discuss that with the student and if afterwards your impression persists, potentially escalate that with the professor.
Anyway, regarding your question. Corresponding authors and first authors are a different concept. As you seemingly are from a field which aligns authorship roles with contribution, the first author is understood as the person contributing the most. Totally separate from that, a corresponding author may be indicated. However, neither you nor the PhD student are a good choice for this position as people may contact you in five years from now. The professor is the best bet as a person who can be reliably contacted after that time. Furthermore, since you write about experimental data, usually the professor can always provide access to that whereas you might not necessarily be able/allowed to.
Finally, to provide a suggestion: Have you discussed either changing the author order with the PhD student or the option of sharing first authorship? IMHO this is the most sensible way to proceed here with the latter providing the highest likelihood of success. This way you may indicate that you are the person most involved in the conceptualization/execution. However, this should be discussed with the PhD student before involving the professor.
If you select to go with this, this can even be done in a way that saves the PhD student's face if let's say the mutual first-authorship is brought up towards the professor by the PhD student, much rather than you. This way, the student may say he thinks so highly of you, you should be elevated to co-firsthauthorship.

"Finally, to provide a suggestion: Have you discussed either changing the author order with the PhD student or the option of sharing first authorship?"  I haven't discussed it with him yet.  I guess I felt bad about bringing this up in the eleventh hour as the paper is essentially done now.  How does one share first author?  Could you explain that more please?

If you consider A, B, and C a normal author list, one with shared authors would look as follows: A*, B*, and C. with an indication directly below the authors list in the manuscript (not whatever platform is used to upload the manuscript) that these authors share this position in the authorship list, e.g. "*these authors contributed equally".

However, if you approach the PhD student, it might be good to have a small table, on the one side stuff he/she contributed and on the other stuff you contributed, and why you feel they weigh equal. Be aware that the PhD student may not immediately (or at all) agree with you, in any case, it would be good to give him/her some time to think about your position before escalating, if necessary.


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Can I avoid having bad grades and a dismissal show on my record if I transfer colleges?
I'm considering transferring to a school with a worse CS program to avoid 3 semesters of W's (withdrawal grades) and a dismissal on my record come graduation time. (Or would I just have more explaining to do?) Should I stick with my school?

If you completed the classes in previous semesters those should still show up on transcripts. Being dismissed does not (at places I'm aware of) wipe out your prior academic record.

I suggest prioritizing your recovery over restarting your studies.

Not what you asked, but having some horrible semesters followed by some excellent semesters is actually a really good "story" -- much better than someone who did mediocre work all the way through. The catch is that "excellent semesters" are not so easy to achieve, especially if you are still recovering.

If you don't inform of your prior college you can probably fresh start for your graduate school app. You will lose out on prior courses though. If you transfer you might be able to hide it, it depends if they ask where you transferred from.

Graduate schools generally ask for all of your undergraduate transcripts, not just transcripts from schools you got a degree from.
Transferring is a decision you'll have to make on your own, but it is probably not a mechanism to clear your record of Ws if that's your intent.
In the meantime, probably best to focus most of your attention on your mental health, followed by graduating itself, regardless of future plans past then.

"probably not a mechanism to clear your record"  That should say "certainly not".  Hiding your pre-transfer record in an admissions application or job application would be misconduct, and could well be a reason to get dismissed.  https://academia.stackexchange.com/a/104674/13240

@AnonymousPhysicist Kept that uncertainty in because I don't know whether there are any systems where this wouldn't be true, but certainly for the US aka the system I know then yes, agreed with you 100% that this is certainly not the way to go.

I would have no problem lying about it myself, you're in a competition not a purity contest. Obviously the OPs success hinges on if he can get past or not. I know a ton of people who have very successful careers who lied about a lot of shit starting out

@FourierFlux Not everyone shares your ethics, and I think perhaps your cynicism leads you to leave a lot of bad advice for people in the comments on this site.

The fact that people like @FourierFlux lie does not make it any less wrong.


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Prizes on Academic CVs
I rarely see academic prizes mentioned on academic CVs. I suppose many students who are completeting a PhD also have a few of such prizes. I am thinking, amongst others, about

best MSc dissertation,
top of year,
top mark in a certain module,

but also about

scholarships,
reduction of tuition fees, etc.

Often, these prizes (or medals/certificates) have some fancy names and are awarded in combination with some money. Yet CVs of academics rarely mention such prizes.
Is simply no one interested, do just too many people in academia have such prizes? Are they regarded as meaningless (compared to papers/reference letters/attended summer schools/teaching experience)?

I don't know about UK specifically, but note that in some (many?) countries or fields there's no tradition of awarding prizes at any level, and scholarships or reduction of fees are not considered particularly noticeable and are not considered as figure of merits in selections.

A department will only issue one best MSc dissertation and top of year award per year. Perhaps even to the same student. So, the number of such awards are scarce and shouldn't be expected of every student. Of course, lesser awards, such as top mark in a certain module, are more common, but they're less prestigious and may be omitted. Scholarships or fee reductions are only relevant if awarded on the basis of academic merit (and perhaps some cases I've neglected). So, to answer:

do just too many people in academia have such prizes?

I think the converse is true: (Significant) Prizes are rare, so don't appear on the majority of CVs.

From comments:

Would you say...prizes are even rare amongst PhD students? ...surely, graduating as top of the year is not that special?

PhD students that finished top of their year are still special: Such students are a minority in each PhD intake, since Number of departments worldwide (making top of year awards) < total PhD intake (per year).

Thank you for your answer! Would you say there prizes are even rare amongst PhD students? After all, only the best students from the universities and top international students come to complete their PhD. So surely, graduating as top of the year is not that special? I see that it may be different for an application for a masters or if you go into industry but not in academia?

@Alex Students that finish top of their year and pursue a PhD are still special, since they are still a minority in each PhD intake: Number of departments worldwide (making top of year awards) < total PhD intake (per year).

As for all CVs, they get less important in time. If you're applying for graduate study straight after undergraduate, they're good to list. Your acheivements at this point are likely to be from academic performance, rather than from independent work. When you've completed the graduate programme, no one will care that you came top in Module X in your second year of undergraduate. If the scholarships and fee reductions were based on academic merit, then list them, bearing the same in mind.

Your observation is contradicted by virtually every researcher's CV I get when assessing grant proposals (natural sciences). People list their prizes as appropriate for their level (a professor will not list anything that happened during undergraduate studies, for example). The CV of Ulrich Schubert is quite representative here. As he is one of the most cited chemists in the world, it is out of question that he is an outstanding researcher. Still, he lists the prizes most important to him.
Also at conferences, when speakers are introduced, the chair quite regularly mentions some important prizes the speaker was awarded. So prizes are considered important.

This isn't true.
Awards such as top of the class ("Bronze Tablets") are often listed by the GPA under the "education" heading.
Undergraduates, especially in engineering, will often include "relevant" or "selected" course work that will highlight interesting projects.