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Is it normal for a Ph.D. student to spend stipend money on research related items?
I am a TA and Ph.D. student. I find that I need to purchase some items, as my advisor suddenly told me that some one is coming for inspection. So far, I was working on devices to test my system. However presenting it to a donor with my setup doesn't look good. I have to purchase some equipment and, yes I know that my school has to pay for that, but in this situation my advisor is reluctant to spend money for I don't know what reasons.
Should I purchase these items from my own pocket and hope that it will be reimbursed, or should I mention to the donors that I don't get equipment in time? That will put my advisor in a bad position which I don't want either.
What would be the best approach in such a situation?

Which fraction of your stipend we're talking about?

While in principle everything that you use in your research should be paid for by those funding your research, in practice it's not unusual to buy oneself small supplies at the "minor office supply" level for sake of expedience, or because they're outside of the main line of one's research.
For example, a student might want a $10 piece of electronics today that would take several weeks to acquire through normal channels, and then might decide it's not worth it to them to get reimbursed.  You might also buy something for yourself if you want to be the owner: for example, I bought my own laptop late in graduate school, rather than using a school laptop, because I wanted it to be my own personal machine that I could take with me when I finished.
What you have written, however, sounds like a much more problematic situation: it appears that you're effectively being asked to lie to your professor's funder, by misrepresenting how their money is being spent.  If it's a significant amount of money, then you could be abetting in a felony-level crime.  As such, if it is a significant amount of money, I would strongly advise you to not buy the equipment yourself.  Instead, I think you should tell your advisor that you need the equipment, but if they don't get it, you'll just have to do your best without.
If your advisor doesn't buy the equipment, you shouldn't badmouth your advisor to the funder. Just do your best, and if they ask you why you don't have the equipment you need, you can tell them the honest truth: you've asked your advisor for it and are hoping you'll get it.


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What affiliation to put on a research paper as a college student?
I am an undergraduate, and I want to know what to put as an affiliation on a research paper.

Possible duplicate: Rules for affiliation for student doing unpaid research in his/her free time?

Normally, if you are a student, your affiliation will be the school / college / university that you attend (or if you have recently changed institutions, the one you attended when you did the work and wrote the paper).

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How to make improvements to an already-published paper?
I have written a paper for an IEEE Transactions journal. But now I have several improvements to the original paper. Can I publish the paper again with a slightly different approach? The introduction, etc., would be almost the same and hence I may retain and refer to the already published paper. But the implementation is different. How shall I proceed?

If the improvements are sufficient to constitute a new paper, then write that paper, referencing the already published paper (but not repeating it) and explaining the improvements.  If the improvements are not enough for a new paper, then I'd suggest preparing a new version of the published paper, incorporating the improvements, and posting it on the arxiv (or in some other highly visible place on the web).

If you prepare a new version, it's crucial to be very clear about its relationship with the published version.  (E.g., by adding a subtitle like "updated from the version published in blah blah blah", with a footnote explaining in detail what has changed.)  Otherwise, you are risking confusion and annoyance when readers don't realize there are multiple versions.

@AnonymousMathematician I agree.  The ideal situation would be if the original paper is already on the arxiv and the new one can be uploaded as a replacement for it.  But in all other situations, the fact that it's intended as a a replacement needs to made clear somehow.

I would recommend putting the new material in a tech report, and publishing it alongside your original paper on your website. This establishes prior art and makes the improvements available to other researchers, while also avoiding two ethically dubious alternatives: trying to publish the revision as a new paper, despite it being incremental over your original version; and substantially updating a peer-reviewed paper without the reviewers evaluating the changes.

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Adjunct position at Johns Hopkins Engineering
I was reading the Notices of the AMS, and saw an advertisement for a part-time adjunct position for the "Johns Hopkins Engineering for Professionals" (https://ep.jhu.edu/about/teachforus/) in the Applied and Computational Mathematics (ACM) masters program. A lot of their courses are taught online.
Has anyone taught for this program as an adjunct, and can you share your experience?
Edit: I am currently a postdoc in theoretical mathematics (in the US). I consider trying to gain more experience teaching applied mathematics or computing in the hope that these experiences will help me get a permanent position in applied mathematics/computing in the future.

Focus on a permanent position. This would, I think, be less valuable than another postdoc if you can't come up with something permanent.

If you already live in or near Baltimore (or another city with a large university) you might try to work up something collaborative with the applied math folk. No money involved, just a sharing of ideas and maybe a project you could attach to.

This answer is not specific to JHU and I have no experience there. But it might be useful background. An adjunct position is not a career and it is almost always poorly paid. Those people generally, who live off of such positions typically do "adjunct" for several institutions, have terrible overall teaching loads, and are still poorly paid.
The "ideal" adjunct for universities like JHU is someone who is already employed in industry (say), especially in research there, and who just wants a nighttime activity to keep them engaged a bit with academia and may love teaching. You would probably earn a small stipend per course, but, given that the salary of such a person is usually about double that of the full time faculty, it would probably not change your lifestyle. A retired person from industry who meets the qualifications and who wants to do something interesting, might find it worthwhile.
If you "sort of" fit that description it would be worth applying. If you are desperate for any (any) employment, then my might want to apply.
OTOH, some adjunct positions have union protections that the faculty doesn't have.
Whether it might lead to a permanent position depends on the institution and its rules. I think that at most you would get a small boost in a later application for a tenure-track position provided you fund a way to interact with other faculty. But it isn't really a path to such a position at that institution.

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Plagiarism - bachelor thesis
I recently turned in my bachelor thesis and just now realised that there is a missing citation in the text. it's kind of a grey area since i'm mentioning earlier formulas that are cited and based on that say that it will conclude in a specific mathematical expression. I'm unsure if this would be considered common knowledge. since it is a general mathematical expression. If not, would it be considered plagiarism?  The transition from the equation im talking about and the expression that im not citing is not 100% clear. What would you do?
Edit: I’m not explicitly deriving the expression. In this specific instance i have explained the nature of a specific model, which im citing. I then go on in a later part and say: ”because of the nature of the ”..”model, When we perform the transformation in equation ”a”and ”b”we can show that the expression will be ”x ”. In this case, ”x” is the amount of deegres of freedoms.

Is it true that you have no possibility to make a correction? Do they really expect perfection at such an early stage?

@Buffy Allowing corrections to a submitted thesis should surely be forbidden. Submitting an erratum is probably a better route.

The reason i’m asking is because the mathematical expression that im not citing is the deegres of freedom of a estimator from a model transformation that is studied in the thesis. Because of the nature of the transformation it follows that the amount of deegres of freedom will be a certain amount. Its not disputed and not someones idea. Rather a mathematical conclusion based on the way deegre of freedoms work. But im not sure. Would it still be best to email the person who will grade the thesis and explain the situation? Or Should i call him?

From my experience with Bachelor theses my impression is that this kind of thing happens all the time. If you are concerned it's probably not wrong to think about doing something about it, but regardless of this I'd not be very worried that this could be a big problem.

If I understand correctly, you state and cite formulas, then derive a further formula. Presumably, the derivation isn't new, and you are concerned that you didn't provide a source for the derivation. Given that you consider the further formula to be well-known, it perhaps doesn't matter so much. Nonetheless, to protect yourself, you could email your examiners and explain that you inadvertently forgot to mention that the derivation is not your own, it is a well-known result, perhaps providing a citation.

This is too weak and sounds like an excuse. Tell them that you omitted a citation. Definitely provide it.  Offer to provide a corrected copy. Apologize for the error. People make mistakes. Part of the genome. But for various reasons you want the copy corrected in any case.

@Buffy: You wouldn't cite a well-known formula. Of course, if it isn't well known, then it is too weak. Equally, if it follows trivially, it's obvious. Then again, a bachelor thesis typically gets nit-picked more than a research paper in such regard though.

The answer suggests erring on the side of "no problem". That is the wrong balance in such a situation. Others will judge the work. If they catch it and think it is plagiarism before you provide a correction then you are in trouble. Err, here, on the side of "abundance of caution".

@Buffy I found the OP's question rather hard to read. Their now-deleted answer, which seemingly adds further details, didn't help either. I'd likely amend my answer if I were able to better understand the question. As it stands, I'm making guesses, which I've highlighted.

If they catch it and think it is plagiarism before you provide a correction then you are in trouble: That's exactly why I advise emailing the examiners.

I have no issue with that. The issue is with the word "perhaps". There is no "perhaps", there is only "do". (Apologies to Yoda).

@Buffy There's really no need to cite a well-known equation. Especially as the author of such might not even be known. The OP writes, I'm unsure if this would be considered common knowledge. since it is a general mathematical expression. From that, I don't know whether a citation is required. I can only say perhaps, I don't know whether there is any need to do.

The reason i’m asking is because the mathematical expression that im not citing is the deegres of freedoms from an estimator that result of a model transformation that is studied in the thesis. Because of the nature of the transformation it follows that the amount of deegres of freedom will be a certain amount. Its not disputed and not someones idea. Rather a mathematical conclusion based on the way deegre of freedoms work. But im not sure.  Would it still be best to email the person who will grade? Or Should i call him?

@Erik, yes. Offer a correction. Give the citation.

@Buffy Would i be better off calling the grader and speaking with him directly or send him an email?

Sorry, I can't say. Both?

Okay, thanks for your input. Hopefully he will appreciate my honesty and not fail the thesis. I’m feeling like shit to say the very least.

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Is physics (and engineering) at university more like high school physics or high school math?
I am in high school and I find myself enjoying math a lot more than physics, probably because of the more focused teaching approach found in physics, which looks at specific cases and experiments and then goes on to explain these mathematically, where as in maths it seems to me a broader stance is taken; only after a foundation is laid one goes into specific examples. Still I would rather like to study physics or engineering at university, as I am more interested in the subject of physics itself than that of theoretical mathematics.
So how does university teaching compare to that found in high school in physics and mathematics, and where do I place engineering in this comparison?
PS: I am from Austria and plan to go to uni in Germany, in case that helps with answering the question.
PPS: I know this question is open ended and opinion based so feel free to flag.
Edit: I`m thinking of this, this or that.

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

When studying physics at a German university, you will take three kinds of core modules:

Experimental Physics
Theoretical Physics
Math

Of these, experimental physics is somewhat similar to physics in school. You have a discussion of concrete phenomena, how you can measure them, probably quite a bit of lab time, too.
Theoretical physics is similar to math in school. You learn some more overarching theories about how to model things mathematically (like Newtonian gravity, electromagnetism, thermodynamics, and so on). A lot of what you do is calculations (compute an integral, solve a differential equation). If you want to learn how to do complex calculations with pen and paper, theoretical physics is where you do it.
Math at university level is a very different beast from anything most pupils encounter at school (at least in Germany). You'll encounter some familiar concepts (differentation, vectors), but in a far more rigorous way. You will not just be told that stuff is true, but you'll see the proofs (and be asked to prove simple statements yourself [at least if your math courses are shared with mathematicians, if you have dedicated "math for physicists" courses this might not be the case]).

I'm not sure about Germany and Austria, but in some places physics is not organized this way.

@AnonymousPhysicist I've clarified that I am talking about German universities here.

It should be added that the Math you learn as a physicists might be real university math, but it might also not - this really depends where you are studying. (If Math is taught jointly with the mathematicians - which I believe is getting less common - then it for sure is.)

To follow up on @user151413's comment: it makes sense to look at the website of physics departments where you might be interested in studying and see whether they do their own math courses, or send their students to the "math for math" courses.

I studied CS at a german university, and even though the math courses were 'math for computer scientists', they were very heavy on proofs. And at least for me as non-mathematician, the proofs we had to do also didn't seem all that simple ;) So I wouldn't just go by the name ('math' or 'math for X'), but see if there's anything available online about past courses.

@tim It is all relative, from a mathematicians perspective the hierarchy is somewhat like this: maths for mathematicians, then for CS/physics, then for econ and at the bottom math for dentints, veterinarians and similar things that somehow require a math course. So as a CS student you already get pretty heavy math.

@tim I would think that the physics math courses at the majority of German universities are much more rigorous than those for engineers or computer scientists. Either shared with or at least comparable to those taken by math majors. At least in my experience.

@tim For the "math for physicists", it really depends on the place, who teaches it, and possibly also how much the physicists push for one or the other way.

@Peter I have no prior knowledge of German education, but why would the math for physicists be more rigorous than the math for computer scientists? Consider that math and computer science were the same subject much more recently than math and physics were the same subject. Having done math and cs side-by-side in the US, in the upper level classes (proof-based) there was a whole lot of overlap of topics.

@user3067860 Just my experience from two German undergrad degrees. Maybe not the same everywhere (and grad school is obviously a free for all with regards to what courses you can take) but probably almost everywhere. Bachelors degrees are usually very strictly structured here and both early math and math for physics undergrad courses are significantly more rigorous than what is taught in the US or what the typical engineer needs to know (i.e. real analysis from the first semester).

@user3067860 I'm not sure “rigorous” is really the point. What's certainly true is that physicists' maths courses have a lot of difficult stuff from differential equations, functional analysis, topology, differential geometry etc. crammed into them that isn't considered necessary for CS, and the physicists' maths courses don't tend to spend much time on examples or otherwise explanations because the students are supposed to get those insight from their theoretical physics courses.

@Peter Real Analysis isn't the only rigorous math course... Your CS students are hopefully getting a good dose of rigor in their discrete math classes--or at least math courses masquerading as CS courses (Formal Methods, Analysis of Algorithms, etc.). Even "Relational Databases" turns out to be mostly set theory.

@leftaroundabout Yeah, but you're missing all the math that CS students need that the physicists don't. I don't think physicists need nearly as much graph theory, set theory... even proof theory and combinatorics.

@user3067860 sure – but for CS students, those are actually the advanced stuff that you learn during the studies alongside more practical courses that don't care about maths at all. Whereas in physics, you really need to get a firm grasp on the maths within the first two years before you can even start with more advanced physics courses.

Speaking as a physics PhD student here.
In physics you will apply and use math. You'll learn more math concepts along the way, but you will use math to solve problems. In that way, it is very similar to math in school. You'll learn physics in a much more profound way than they could ever teach in you in school, because you simply lack the math skills in school to do it.
Math is nothing alike anything in school though. You will rarely calculate stuff. You are more interested in showing relations and proof them. You will prove that a solution exists, but not necessarily, what this solution looks like. To me, this was always kind of boring. Sure, proving that a partial differential equation has a solution is a cool thing to do, but I'm much more interested in actually solving it (so thanks to the people who proved it's possible :p )
With that being said, I highly recommend choosing your field of study based on what is interesting for you, as a topic, not as a use of tools. What drove me into physics was to  to discover the mechanism of our universe. That you can do it by using math so solve problems is just a bonus.
I'd recommend math if you are interested in pure math itself, if you're interested in the reason why certain math operations are defined the way they are, what really lies behind vector spaces, group theory, analysis, linear algebra...

So that the other side also gets heard: I would advice the exact opposite. Choose the field based on the tools that it uses. That is what you will interact with every day and I think in the end for most academics actually more relevant to their motivation. I think you will find that if the tools are interesting there are interesting questions to answer in any field. (Or at least after working on problems in the field for a while you will think that all these questions are very interesting. Perhaps we simply become delusional ;))

To add: People that get motivated to do physics because they are so interested in the secrets of the universe often got discouraged by the difficult math and drop out. People that actually enjoy the math, which is the majority of the work, remain. It is much easier for them to keep up the motivation. Also nowadays the new "secrets of the universe" are hidden quite far away (very little low hanging fruit) so if finding those motivates you you will have to go for years without any pay-off.

It might be worth noting that there's a school in maths in which only existence proofs are taken seriously that also provide an algorithm to construct the solution. It's quite influential at the maths-CS interface; not so much at the maths-physics one.

Short: There is a progression in rigor and abstraction that goes like this: High school physics, high school math, university engineering, university physics, university math. There are large differences between different universities and between different schools.
Assuming that an Austrian Matura is similar to a German Abitur or Swiss Matur (I don't know for sure), then even courses for physicists and engineers are going to have more rigorous math than you are used to, but it's a natural progression and if you have a passion for the subject and liked math ok in high school, then you should be fine.
Courses for mathematicians (which you might be required to take if you study physics) are at a level of rigor and abstraction that is not comparable to the math required for a Matura. If you think about enrolling in a program that requires such courses, I suggest you look through some exercise materials for linear algebra I and analysis I or whatever your study program of interest requires - try to solve some and skim the solutions for the rest. You will get a much better idea of what it would be like to study those subjects for real than by reading abstract descriptions of what it was like for other people.
That being said, some schools offer much more preparation than others. There are Gymnasien which offer an optional math course which is actual math, statement, prove, example, repeat. Some offer more hands-on math that will make the transition to an engineering or physics program easier, but won't make much of a difference if you decide on math. Some might offer additional engineering courses, etc.
The universities in Germany are going to assume the least amount of previous knowledge that an Abiturient would have (which varies a lot among Bundeslaender), but starting university life can be a stressful transition and if you have some more than the minimum it's going to make the first weeks or even months a lot easier.


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Statement of Purpose conventions in Canada and Europe
I'm applying to universities in Canada and Europe (The Netherlands, Belgium and France) for admission to their computer science/mathematics master's programmes.
I showed my statement of purpose to a professor in a European university who I've worked with in the past - they said that while my statement of purpose would work well in the European context I may have to advertise myself more aggresively to the Canadian universities I am applying to. They did however clarify that they aren't familiar with the Canadian system and were speaking from the experience they had with the US system.

Is there a difference between the expectations that Canadian universities have of an applicant's statement of purpose compared to those of European universities?
Would I be at a disadvantage if I were to submit a statement of purpose written to the standards of a European university to a Canadian university?

If the answers to the above questions are in the affirmative, I would be grateful for an example highlighting this "aggresiveness". Here is what I understand it to mean presently:
European: My thesis in X has prepared me for Y research.
Canadian: I am the ideal candidate for Y research since my thesis was on X.
My objection to the above explanation is that the Canadian method seems redundant; naturally, applicants would only write good things in their statements of purpose.

Does my objection highlight an invalidity in my present understanding of "aggresiveness" or does it simply stem from a poor understanding of Canadian expectations and culture?

The CV details "what you did" whether awesome or not. But the SoP is about the future, not the past. What are your goals and how do you intent to meet them? Mention the past only to support the future. Don't just recapitulate the CV.

@Buffy, I've been careful to do as you say here. However, what I'm concerned about is the general tone of my SoP. My SoP presently recounts my previous achievements (to support my goals, as you say) in a matter of factly manner. Would the Canadian universities take the lack of strong adjectives to mean that something is amiss? Would the lack of strong adjectives in my SoP make me appear weaker in comparison to a Canadian applicant who would (supposedly) use stronger adjectives than me?

@Buffy, what I'm asking here is: Would the Canadian admissions committees expect me to "blow my own trumpet"? I've updated the examples to highlight what I mean.

Praise should come from others, not yourself. And again, the purpose of the SOP is NOT to "recount previous achievements". It is about where you are going, not where you have been.


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What should I do if my advisor and committee members want me to do two different things?
My advisor said that when I write my thesis I should staple together my three papers.  One of my committee members says my thesis should have a unifying theme and a narrative that ties together all the papers.  My advisor thinks this is stupid and explicitly told me not to listen to my committee member.
Both of them have to sign off on my thesis.  What should I do?

Did you check whether your institute has some rules on how your thesis should look like?

I'm going to suggest a different perspective from those presented below: 1) Presumably your adviser is the one paying for you, so obviously their suggestions outweigh those of your committee members. 2) Once your adviser approves your manuscript it's hard for another member of your committee to reject it for several reasons of political nature. For example, simply because this would be a problem for both you AND your adviser. P.S. In the end this is YOUR thesis, so make whatever makes you happier.

Is it possible that your advisor and the committee member are from different areas of science? I heard that in some (sub)domains, "stapler thesis" are frown upon, while in other, it is quite standard.

Maybe it simply is a test. How mature and independent have you become and how do you judge the situation?

Is it really a contradiction?

The way you present it, it sounds like the two are mutually exclusive, but they are not really: a "stapler thesis" generally contains an introduction and a conclusion that are there to tie the papers together into a whole. This implies a unifying theme and a narrative. It's only a few pages, but it makes a big difference.
You should probably at least make some effort to introduce a narrative, despite your advisor's opinion. Of course you know them best, but in general it's less likely that someone would refuse to sign off on something because you put in more effort than they thought warranted, and more likely they would refuse because you didn't put in enough. Better to err on the side of doing more.

If you trust your advisor's ability to manage dissertations (does he have supervising experience at your institution?), follow his lead and forget about the rest.
The way I see it, it is your job to do 110% of the work that goes into the dissertation in accordance with your advisor's instructions. Your advisor's job is to manage the political aspects of the dissertation. Normally, he should not suggest anyone to be on your committee if he is not certain that he can work with them.
If your advisor can manage the committee, you should not worry about a thing. For the most part you should not even need to talk to your committee members beyond a simple formality. I only saw my committee members when I sought their advice explicitly. None of them told me to do things a certain way.
IF you have to justify your actions, go with a vague statement like "I appreciate your input, I tried to put it to work as much as I could. There were other factors I had to balance (vague hint to your advisor's role). All in all, I am pretty happy with how it turned out, thanks to your suggestions."


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Language of reference entries for sources in a foreign language
Must the entries in a list of sources match the language of their respective sources? For example, for a non-English text, may one include words and phrases such as "In", "volume", "edited by So-and-so and So-and-so", "translated by", pages xx-yy"?

Citations follow templates, e.g.,

A, B, & C (YYYY) Title. In BookTitle, volume X, pages xx-yy.

To cite a particular work, you fill-in the place holders, e.g., A, B, C, YYYY,  Title, BookTitle, X, xx, and yy. Hence, words such as "In", "volume", and "pages" can remain in English.
When a template does not specify how to include translations of titles/booktitles, I think it is reasonable to include bracketed translations, e.g., original title (translated title).


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Acknowledgments in google scholar citations
Is it acceptable to add articles under my profile in "google scholar citation" in which i was acknowledged for my real contribution rather than being a co-author?

Acceptable I'm not sure, but it really doesn't sound like a good idea.
The point of Google Scholar is to collect in one place the information on papers in which you are an author. If the paper in question was prominent enough in your profile to attract my attention, I would assume that something suspicious is going on, and there is no way for me to tell whose fault it is. Overall, it doesn't send the kind of signal you would probably want to send.

Being acknowledge doesn't count as authorship and claiming otherwise will make you seem clueless or fraudulent.
This being said, Google Scholar is a search engine not a scientific vetting service, it doesn't have standards as to what constitute a publication or a citation. Certainly listing articles you didn’t author wouldn’t be the sketchiest thing I’ve seen on this service.

@NajibIdrissi I made some edits based on your comment.

I was going to say that it's not acceptable, but now that I think about it a little more, the situation is a bit murkier.
If you are trying to do this to claim co-authorship on some high-impact papers in an attempt to boost your statistics and look like a more impressive candidate, this would be wrong. If the purpose is to draw attention to related work in which you participated, it's not nearly as problematic. I would still be unlikely to do it, just for the reason that there would be the question of "why am I listing a publication when I'm not an actual author.
Moreover, what level of contribution did you provide that was enough to merit an acknowledgment but not a co-authorship? (I had one or two of those, and I wouldn't bother to list it on a CV because it's just not worth it.)


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What does "revision is due by" mean?
I got a minor revision with the message "Your revision is due by 19 Oct 2022." I sent the comments in by Sept. 23.
Will I have to wait until Oct. 19 for an update, as the status still with the editor?  Does this message mean the revision will be reviewed in this period or after this period, as I need the acceptance before the end of October.

It means that if you don't send your revision by 19 October, they might start doing other things (such as assume you are no longer interested in revising your manuscript).
It does not mean that you will get a decision by 19 October, or that they will start working on your paper on 19 October if you send in a revision early.
If you need the paper accepted (more precisely, a final decision) by the end of October, you can send them a message asking if they can expedite the paper. It's possible they can, also possible they won't.

I would add that these dates are often negotiable, especially for major revisions and when new experiments or analysis need to be performed. My impression is that the date is mostly to ensure that a paper doesn't sit on the journal's books forever.

@Matt yeah from my experience working in academic publishing, your impression is spot on. If the authors ask for an extension we are generally happy to grant it, and the due date really only comes up when we do "spring cleaning" and remove all the inactive manuscripts.

@user1 it's not abnormal. You just say you need a decision quickly because of [insert reasons], just be warned that they might say it's not possible to expedite the paper that much, and there's no guarantee the decision will be "accept".

@Allure: are there really "inactive manuscripts"? That's surprising to me. It's hard imagining myself as taking all the effort to write a manuscript to later quit just before publication.

@GiuseppeNegro yeah, there are. I don't think the authors give up on publication entirely, but they might give up on publication in that journal - effectively withdrawing the manuscript by never submitting a revision.

@GiuseppeNegro I have one floating around because all the key players left the institution/academia and so whoever is the first author now might not have cared enough / had the time/resources to prioritize it.

@GiuseppeNegro There are also manuscripts where you intend to do some additional experiments, revise, and resubmit, but you have other papers and proposal deadlines...and then a year has passed and you still haven't done any revision.


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Would a paper on neuroscience make an impact for the Computer Science PhD application?
I'm pursuing a master's degree in Computer Science, and have no background in computational biology and bioinformatics. Although the paper I'm talking about does not propose any original, interesting computational model/method, it successfully combines two proposed approach -in a very trivial way-. I will be the co-first author of that paper, which is very likely to get published in a very impactful journal (IF>5k), since I dealt with all analytical and computational donkey work all by myself.
This paper is quite biology-oriented. I'm wondering about the impact of this paper if I apply for computational biology and bioinformatics PhD programs in US. It is obvious that my coursework does not focus on computational biology and/or bioinformatics.

Your description of the paper is confusing. You seem to dismiss it as trivial, but it will appear in a good journal. Your location might be helpful to know for any answer.

It is biologically very sophisticated, but in terms of computer science it is not original. I just combined two previously proposed models for a similar problem.

Location? Admission requirements vary greatly.

My experience is that, no, work outside the field of application will not significantly bolster your competitiveness. But hopefully my observations are incorrect. Good luck.

U.S. universities ranked between ~5 to ~20.

@transitionsynthesis Thank you!

Such a paper can't hurt and might help. CS is a pretty wide field with both theoretical and applied aspects. Your paper seems to describe applications. That would be more of a boost in some programs than in others.
But in the US, doctoral admissions is based on a wide variety of things, including letters of recommendation. Your co-author(s) may be able to help you there.
In any case, the paper is (about) done, and can't be a negative, so certainly include it in the CV and if applied CS is your goal, you might have something to add to your Statement of Purpose. Expect a lot of competition for slots in those schools, of course. You increase your chances if you widen the search a bit.


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Writing style when discussing other people's research in discussion/introduction
I was editing a friend's manuscript and I noticed that they do something similar to what I have been told not to do when referring to previous work done in the field of interest being discussed. I would often refer to the citation i.e. the study and then go on to say what they found in the study For example, I would sometimes say:

Smith et al. (2020) modeled how the life history of species x was affected by environmental pressure, they concluded that increased pressure would also lead to earlier maturation.

I have been told by different advisors that this is considered "bad writing", in that it is generally preferred to refer to the work at the end of a sentence as opposed to the beginning. However, no-one has explained why this is the case. I passed this information onto my friend as well, but I am curious as to why?
An example of how my advisors edited the above sentence:

Modelling of the life history of species x showed that increased environmental pressure would also lead to earlier maturation (Smith et al. 2020)

I understand that technically the edited version sounds better, my question is why specifically it is considered bad form to mention your citation/reference at the beginning of the sentence?

Might need a more concrete example; yes, the one you have here is a bit clunky and not great writing, but it's hard to know whether that's just because it's an abstract example without any real meaning.

@BryanKrause edited, hopefully this makes more sense now

What I find strange in the quoted sentence is the lack of a conjunction after the comma. That is, I'd write "Smith et al. (2020) modeled how the life history of species x was affected by environmental pressure, and [...]" or "Smith et al. (2020) modeled how the life history of species x was affected by environmental pressure. They concluded [...]"

"Smith et al. (2020) concluded that increased pressure would also lead to earlier maturation." conveys essentially the same information concisely. The "would also" is a bit clunky but maybe makes sense in context, otherwise "would also lead" could just be "leads".  "Modeled" is probably too vague to be useful in describing their approach; if their approach is important, it should be discussed more explicitly.

I guess in summary, I see some issues with this specific sentence, but I'm not sure I would put those issues in one bucket or if there's a general rule to gather here. I'm also not sure how you are spotting "bad writing" in someone else's work if you don't know what reasons your own was identified as needing improvement.

Have edited to clarify my question, it seems that in my attempt to be brief I completely messed up!

Neither alternative is good or bad.
I would put the citation first if the author or the history is important:

Darwin [On the Origin of Species, 1859] argued that natural selection ...

but the citation last if you just want to tell your reader where they can look to check your facts:

Darwin's finches continue to evolve [J. Wiener, The Beak of the Finch,
1995 (reprint)].

So it's a case by case choice. In this case I think your advisor is right.

I see nothing wrong with putting the reference at the beginning, and in fact I see some situations where that placement would be necessary. Putting the reference at the beginning or the end makes no difference provided you agree with the statement you're citing. But if you disagree (or even if you're undecided), then putting the reference at the end doesn't work. For example, it's OK to write "Smith (2020) wrote that the moon is made of green cheese, but the evidence doesn't justify that assertion." It's not OK (in my opinion) to write "The moon is made of green cheese (Smith 2020), but the evidence doesn't justify that assertion."


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PhD Recommendation Letter from Bachelor Supervisor
I am currently doing my Master in physics in the University X. Previously, I did my Bachelor in the University Y. I am applying for a PhD positions that requires two recommendation letters. The supervisor of my Master Thesis agreed to write for me a letter.
For the second one, I could ask a professor with which I did a course and a seminar in my current university X, or I could ask the supervisor of my Bachelor thesis when I was in Y. Who do you think is better? I add some information: I finished my Bachelor in physics three years ago (I hope he remembers me). I worked around six months for the Bachelor thesis and at the end it was awarded the highest grade. So in principle I would ask him, but I do not know if it is okay for PhD applications to have letters from the Bachelor.

"I hope he remembers me" - That is indeed the important question. If he remembers you as a strong student, his letter would definitely be helpful. If he doesn't remember you,, his letter might not be strong, which could be detrimental to your application. The bottom line is: when you ask him, make sure to ask if he can write a strong letter of recommendations.

Spend some effort to reconnect with the earlier professor. They will likely support you strongly, but might need a bit of a nudge to remember you. It is worth the effort to keep those old connections in any case.

Supervisor of BSc definitely would be a stronger option than some prof from the local university course. I don't see why wouldn't they remember you, really (it depends on the personality, of course, but most would) - on top of that, they would probably be delighted to hear from you and learn that you are on a good track towards PhD. Win/win!


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How should I split my code and data between an open repository and the article's supplementary files?
I am working on a paper that involves some data and a piece of code to analyse the data.
I want the results of the analysis to be reproducible and the code to be open. This concept of "reproducible research" is essentially non-existent in my field, and potential journals have no guidelines regarding code. Also, I have no requirements as to how to publish my data and code by an institution or a funding agency.
The question is, how should I split the data and code between an open repository and and the article's supplementary files? What I currently have in mind is this:

The R code itself (i.e. the functions) will be posted in an online repository, such as figshare or github.
The data and its analysis will be posted, possibly using knitr, as a supplementary to the article.

What are the pros and cons of this approach? Is there something I should modify?

Why not a full duplication? This way you and the publisher are independently responsible, to certain extent, that the archives survive for posterity.

Would this cause copyright issues, with the data and code published under difference licenses?

@Michael You wrote the code yourself, right? If so, couldn't you publish CC or Apache C from GitHub, then cite it fully in the article? That way, the code is open-source protected, and your article, through your express permission, is able to duplicate it in full.

FYI: you can publish the data and its analysis in GitHub as well, using GitHub pages.

A good way to think about the distinction is this:

Code and/or data in a supplementary is static, providing a snapshot that was guaranteed to work in a particular time and place.  Archival presentation is assured, but it cannot be maintained and thus is likely to eventually become obsolete.
Code and/or data in an open repository is maintainable, and thus can be a "live" project that is updated and continues to be executable.  For the same reason, however, it is also subject to possible destruction through a variety of means, including corrupting updates, deletion, and death of the repository.  It will likely be fine for at least a few years, but multi-decade preservation is much more questionable.

However, as @Davidmh points out in the comments, there is generally no reason that you can't put everything in both places.  Contrary to popular belief, there is nothing that prevents code from being distributed under more than one license.  This is particularly true if you first post it in the open repository, then place a snapshot ("fork") of that repository in the supplementary information.  Giving the journal control of a fork does not affect the original repository.
In many cases, however, the open license and the journal's copyright will not even interact with one another.  Many journals will not claim any copyright over the code or data as code or data.  Instead, the journal will claim only the right to distribute the bundle as a supplementary publication, which does not restrict the use of the information in that supplementary as data or code.
Bottom line: first put it in an open repository, then give the journal a snapshot as supplementary.  In the extremely unlikely case that the journal won't take it, the open repository is still a fine place for it to stay.

It is important to check any copyright transfer agreement to make sure that you retain copyright to material that gets submitted to the journal's "supplementary" web site.


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Any altmetrics statistics for physics papers?
I am interested in how many papers (especially in physics literature) have this certain altmetric score (see more on www.altmetric.com). I have looked in several journals e.g. Physical Review and have seen that many papers in physics have altmetrics score of 1 or 0. If it is 1 it relies upon a few tweeters only.
Is it really so that altmetrics score for physics Research papers is low? If yes, why it is mostly so low?
How many physics papers (estimated) have an altmetrics score of

Zero
1 to 9
10 to 30
more than 30?

Any answers would be greatly appreciated

Definitely not spam - altmetrics is a website, but also a movement. See the Declaration on Research Assessment for example. Altmetrics just does analysis on the different ways people "cite" research, including links on websites,  blogs, social media etc.

So, I don't have an answer, but part of the phenomenon may be how Altmetrics counts. Most physics papers appear  first in ArXiv and the ArXiv identifiers are used when people talk about them on the web. If Altmetrics doesn't count those, that may explain the low scores. However, it's certainly true that there is a lot of chatter on the web in the physics world, about current research, so the low altmetric scores are certainly biased measurements.


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Is it possible to do a research on both Computer Science and Law, without a Law Degree?
I'm currently a computer scientist, with work experience in both academia and industry. I'm starting to get very interested in the intersection of law and computer science. I do think we really need people that know law and computer science at the same time very well, to decide on the important issues currently we are dealing with.
What is the best way for me to deal with my decision? Do I need a law degree first, before I do research on this matter, If so I should start with an Bsc?; or should I apply for a junior research position in the law department?

Perhaps start looking for a collaborator in the law department of some university near you?

You most certainly can work in the intersection without a law degree, and a number of prominent people have done so.  A nice example is Edwina Rissland, who is a well-known expert on machine reasoning about the legal code, and who actually taught at Harvard law school for quite some time without ever having a law degree.  I heard one of her lectures on the subject once, and found it gave me a whole new understanding both about how our law really works and how we humans think about the world.
Do note, however, that without a law degree, you will likely need some collaborators who are lawyers, to help you with their expertise in the subject, just as if you were digging into computational chemistry without being a chemist yourself.  As for how to get into the area... just the same way as you would any other research area.

I got a 404 error on the link for Edwina, care to relink?

@jakebeal The link you provided is broken. I fixed it. If my fix pointed to a different person, please correct it.

@scaaahu Alas: link rot happens. Thank you for fixing it.

Coincidentally, I started researching computational law around the time you originally posted the question. I've spent the last two years on fellowships at Harvard (Berkman Klein), Stanford (CodeX's CompK), and Ca'Foscari University of Venice (Venice is awesome).
Some of my preliminary findings are available at

https://github.com/legalese/legalese.github.io/blob/master/doc/intro-course.org
https://legalese.com/v1.0/page/past
http://legalese.github.io/doc/chapter-201707.html
https://drive.google.com/open?id=10n25p2uwoDP91V-JbyFdWBSAbXfoZOlM-F9YmHeJk5s

Based on this research I believe there's a big opportunity, as Marc Andreessen at A16Z might say, for software to eat law.
I'm working with a small research group to continue this line of research and ultimately produce some open-source software to illustrate the alignment between CS and law. If you'd like to get involved, please message me after you've skimmed the above materials, and maybe we'll discover some ways to collaborate!


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Is excluding my middle name on a graduate application acceptable?
I was born in Ukraine and when I immigrated to the United States at a young age my middle name was translated phonetically. In Eastern Slavic cultures, our middle names aren't quite the same as middle names in the United States. It's not simply an "alternative name" for me. Our middle names are patronymic. They are our father's names. I do not consider my middle name to be the same as the traditional middle name used in the United States.
I am currently applying to graduate programs and I have decided to leave my middle name out. The name is long and unpronounceable by most. On top of it being my father's name, it has a suffix ending "-evich" tacked on at the end. This makes it 11 characters long and it usually gets truncated to fewer characters when seen in my undergraduate university's system. This bothers me and I would just rather then not have the patronymic middle name in my records at all.
Are there specific reasons I should include my middle name on my graduate school applications?

I don't see a problem with that. The US are very liberal respecting such choices. If a school wants you, and you tell them you'd like to go by 'Rocky' now, it is unlikely to raise any eyebrows. To avoid confusion though, it is good to start to establish a naming convention that identifies you clearly from social security to passports; if not, you might later run into issues with some administrators.

Here is how I handle these things:

I publish papers with just my first and last name - no middle name or initial.
My vita and website use just my first and last name.
When I fill out "official" forms, like employment paperwork and tax forms, I use the full name that is on my passport and driver's license.  This helps to avoid any confusion when these forms are compared with each other.

For a school application, I would use the same name that is on your government ID. But this is just for the centralized records. Nobody in the academic department is likely to care (or even notice) if you just go by your first name and last name in public life.

thanks. what would you say about the name on the graduation diploma?

If you are in the United States, schools are likely to look at your transcripts to see if you graduated, not your diploma. I have never had to show a diploma to an employer in the U.S.  If you plan to move somewhere else, I suppose it has a nonzero chance of making a difference - but not a very large chance.

I sympathize with your problem: I have two middle names, and databases don't tend to believe in that.  Rather than fight the system or pick one, I typically omit my middle names except when explicitly required by the government (e.g., dealing with customs and immigration).
When you are applying for an academic position (grad school, postdoc, faculty, industrial research, etc), generally what the institution really cares about is simply that you are uniquely identifiable.  In other words, the exact name you use isn't all that important as long as it clearly connects to a real person and doesn't indicate any intention to deceive.

Your second paragraph contradicts itself: if the only reason they care about your name is as a unique identifier, shouldn't you be giving as many names as possible?

@DavidRicherby Please note that I did not say the name has to be the primary unique identifier.  One typically has to supply other things that are much better unique identifiers than names, such as various types of government-issues ID numbers...

I recommend that you do not include your middle name because it will be inconvenient to get people to spell it correctly.  In American academic culture, most people will respect whatever name you wish to go by (assuming they are able to pronounce it).
I routinely omit different parts of my legal name for different purposes and it has never caused me any problems.

For legal issues (application to school, work, passport, ...) you have to give your full name, and be consistent with it. Transliteration can be tricky here...
For informal contact, a nickname will do ;)
For publications, pick one and be consistent. There are people who publish under their middle name, or initial and middle name, others use full first and middle name, I use first name and middle initial. Whatever you pick, use it consistently. It is frustrating to see some J. Doe, John D. Doe, Jack Doe, J.D. Doe, John Demetrius Doe publishing in your field and not being able to tell if they are the same or different people.

what is your suggestion on the graduations diploma for someone who has not applied for the green card yet but plans to change the name for citizenship later on?

@Amir, I believe that is a different question. People change names for lots of reasons (e.g. by marrying).


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What does a seminar host typically do?
At the weekly seminars in my department, for any professor who's flying in to town this semester, there's typically a professor from our department that is the "host" for this seminar speaker.
And each week, there is a different host, for different seminar speakers coming to town.
What is the typical responsibilities of a host?
For instance, do they arrange for social activity (dinners?) for the seminar speaker, before and after their talk?
This is in reference to U.S. universities, math departments.

This varies a lot by institution. Ask locally if you have a need to know.

@Buffy I just clarified my question, hope that helps.

I meant "really" locally. One university in NYC might have completely different traditions than another in the same city. My basic guess is that the "host" is the one that invited the speaker. It might be nothing more than that.

This is so local I'm voting to close for 'depends on individual factors'.  This could be wildly different between the Harvard math dept and the MIT math dept, different between the MIT math dept and the MIT CS/EE dept, and even different between the MIT combinatorics seminar and the MIT representation theory seminar.

@AlexanderWoo, yep. really really local.

I disagree with the "too specific". I've given seminar talks at many different universities in several different countries, and there is a very clear standard pattern for how this works.

@Arno The question is not how giving seminars work, the question is what the role of the host is.

@user151413 I am very well aware of that, and "this" in my comment refers to the role of the host.


text:
labmate stealing ideas
I am a new postdoc at a lab and really worried/confused/upset.
As I am new to experimental work (I have a computational background) the principal investigator (PI) has grouped me into a weekly meeting with 2 PhD students (the lab, in the US, is large with over 20 members in total). One of the PhD students is a "star student". A star student without so far any ideas which worked out - so stealing my ideas seems to be currently her go to.
When I entered the lab the PI suggested I join these weekly meetings, because me and the 2 PhD students would be interested in similar topics. I, naively, presented the ideas I am interested in just to see that the star PhD student has taken them, implemented them (as she already has experimental experience she can do that quickly), presented them, while also presenting herself as benevolent (mentioning during her talk my name, saying that I must be surely interested in these ideas as well - um yeah, given that it these were my ideas..). She basically immediately abandoned her own ideas after she realized that the PI likes mine and is just copying 1:1 my ideas.
Worse than that, the prof, who really cares about the star student doing well and about her being happy with him, told her then how great it would be if "her" idea would work out, and then added an extension to her idea which was also mine (which he knows).
What do I do? I am new and can't get into a conflict, especially since this PhD student is the PI's favorite and well established. Ideally I would like to avoid these weekly meetings altogether, because if I go I naturally also have to share what I work on, which does not seem too good given that the star student does not mind stealing ideas and presenting them as their own. But I worry that leaving the meetings would already cause a conflict etc.
Also meetings should be a place where I can voice my ideas, safely, in particular when the PI is present, but given that he is helping to feed her my ideas I really don't know what to do. It sucks.

Have you tried talking to your PI, describing what happened, instead of automatically assuming what they think and feel?

Well the PI has been there during the entire process (me coming up with the ideas, her taking them over). So he knows what happens. Just does not care or does even support what she does. He is also very close to her and distanced to me, as if I am in a test stage - he really cares about his reputation and if I cause "trouble" he will cut me off and distance himself even more I am sure.

So he was present at the weekly meetings, at which the source of your grievance originates?

Yes exactly....

Then, if it really went down as you describe it here, I’d still consider discussing your role in this project first, and take it from there. Based on these few lines, you seem too focused on what other people think (or might think), with not enough emphasis on speaking up for yourself.

I think you're right. I will do so and try to do it as respectful/constructive as possible. Thanks

When you discuss this, make sure you state only publicly observable facts, avoid feelings, avoid attributing any mental states or intentions to anyone but yourself. Ask questions like, "I'm delighted to work in an environment where open collaboration is at the forefront, so I'm very glad you've organized these weekly meetings. But I did have questions about how authorship attributions are handled by the group." What you want to avoid is being accusatory, and be genuinely open to the possibility that you are presently misreading the situation.

Yes exactly! I see it the same way @transitionsynthesis First of all, I want to continue working with these people in a constructive manner. Secondly, I don't have a full insight yet, being new to the lab, and being accusative is not a good conflict solving approach anyway (people get defensive at best, or things become hostile at worst). So I want to be professional and friendly and find an optimal solution while also making it clear that I want my boundaries be respected too (between the lines, that will be the message)

The PhD student is giving you credit, even though the PhD student did all the actual work.  What exactly is your problem with this?

Sorry what? You can't just take someone else's project ideas and pretending they were all yours - telling me that "I must be interested in these ideas" as well does not seem sufficient at all

Not sure if this will work in your situation, but one option is to simply help supervise the star PhD student and get them to implement the ideas you keep coming up with. Then everybody wins: you get a good implementer as a collaborator plus supervision experience plus your papers out faster, and the PhD student gets some ideas since they don't have their own. Unless the PhD student is selfish for some reason, it might be worth a try.

TL;DR: As a postdoc, it's much more fun to supervise PhD students than compete with them.

She doesn't let me. One other cue indicating that she did this on purpose is that during the time that she implemented my idea she invited me out of her experiments under some excuse. Now that she has done it she asked me to join her again is I would like..

When I was a post-doc I considered giving good ideas to PhD students to be part of my job. If you become a professor are you going to keep all your ideas to yourself? There were always more ideas than time to pursue them all.

@JonCuster I have supervised students myself in the past. Given advice and sharing ideas is very different than her taking my project idea and running with it behind my back, sorry. Also not the same because as I am a new to experiments she is with that respect more senior than I am. Context matters.

Yes @Libor collaborating is a great thing and I love it and have always been open to collaborations. But collaborations also require trust. Stealing ideas and implementing them behind someones back and then presenting them as if they were yours is not it. But thanks for the very constructive and helpful comment implying that I am the problem. I hope you feel better now


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What is the typical cost of Summer Course education in the US?
I would like to pursue summer college courses - particularly a creative writing class and a computer science class - to help broaden my knowledge and improve upon myself as a person.
However, looking at some college courses in the local city, tuition alone for a single undergrad course is upward of $800 for a three-credit Summer class.
This seems a little excessive.  Is this a typical cost for college summer courses in most areas?  And is there a cheaper alternative if I'm seeking to expand my knowledge pool, and not necessarily seeking academic credit hours?

This sounds about right to me, you can get away a little cheaper by taking the classes at a local community college. I've seen as cheap as $60 a credit at some of those programs.

In same states, the cost per course decreases if you enroll in more courses for that semester. For example, the first two may cost you $800 each but additional courses may be less than $400 each.

@AustinHenley I'm aware of that much, though it doesn't help me very much when I'm looking for only 1-2 courses.

There's no reason for summer courses to be less expensive than fall/spring courses. Do the universities have continuing education programs? Those are non-degree and often inexpensive.

@mkennedy In my experience courses taken through non-degree or continuing education programs cost roughly the same as regular tuition.

@RogerFan I think he's referring to something else, because the college does offer such a program...they are largely 'training' courses for people already in a career and not really what I'm looking for.

The cost of summer courses in the United States is likely to be as staggeringly variable as the the cost of courses during the semester.  To the best of my knowledge, most universities generally do not change their tuition fees significantly during the summer.
As such, it will range across at least two orders of magnitude depending on the school you are dealing with, and can easily change by nearly an order of magnitude depending on the type of student that you are.  Consider, for example, this table of tuition rates published by the University of Iowa: you will find that summer course charges are almost identical to semester charges, and differ wildly for Iowa residents and students coming from out of state.

to help broaden my knowledge and improve upon myself as a person

If you don't need the credits toward a degree, then the solution is to audit the classes.  What might trip you up is that summer programs often do not allow auditing, whereas the fall and spring semesters do.
The audit fee is often on the order of 10% of the normal charge.
However, even that has a potential solution.  Send an email to the instructor, asking him/her to give you a call please.  (What you're going to say needs to be said in person or on the phone, not in an email.)
Explain that you would like to audit his class, but since auditing isn't permitted at this institution during the summer session, you'd like permission to do an informal audit.  If the instructor is a reasonable person, the answer will be yes.

On the other hand, if you need the credits, take a look at http://www.collegecalc.org/ to compare tuition rates.

Please note, you can get a very good creative writing course at some community colleges.  Sometimes that's the best place to get individualized attention.  Don't forget to check ratemyprofessor.com before you register for classes.

At some institutions allowing an informal audit will get the faculty member fired.  ratemyprofessor.com is not very reliable.

@AnonymousPhysicist, do you think the faculty member can say no to the request, if s/he does not wish to accept the proposal?  - - -  Agreed, ratemyprofessor has to be taken with a grain of salt -- but let me ask you, are you saying one shouldn't look at it at all?  Do you have a better alternative?


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Is there a concept of qualification examination in U.S. Ph.D. programs and how does it relate to credit counting?
So far as I understand, Ph.D. programs in the United States have entrance requirements and exams, but when you enroll in one, you start process of becoming a "Ph.D. candidate" first, which in the end will lead to defence of your thesis and becoming a Ph.D.
Before becoming a "Ph.D. candidate" you are usually in this system as a "Ph.D. student" until you defend your proposal.
Before defense of your proposal, "Ph.D. students" should prepare for a comprehensive examination, but basically this is depends on your advisor, who will set a rules of how this examination will look like. In my case, preparation of manuscript allows you to qualify for a Ph.D. and you become a "Ph.D. candidate", while some other professors give a test or an oral examination.
Why is this first period of a Ph.D. program not counted as credit for part of your thesis? Why does credit counting start from moment of your thesis proposal approval?

Well no, it really isn't understandable. I didn't vote on it, but what I seem to understand (and which seems a re-submission of an even less clear question) is so very different from any U.S. Ph.D. system I am familiar with that I'm scratching my head. 'Ph.D. student' or 'Ph.D. candidate' are interchangeable in fields I know; you take coursework (or not) for a year or two, and after have a qualifying exam (orally or in writing); and in some fields - yours it seems - defend a proposal, but the last is not even close to being universal (I never did).

yes, it is universal, I didnt know @gnometorule i thought this first part is going to be counted in credits, I didnt know it is not considered, PhD candidate is one that defended proposal

@gnometorule I dont study in USA!!!!!

becuase that is how my university represent themselves @gnometorule as US and AUS system based programs.

FYI, I cleaned up a lot of old comments discussing the previous iterations of the post.

@gnometorule my school —or at least department— termed us doctoral students during the coursework phase (~ two years) and, upon successful completion of the doctoral exams, called us PhD candidates for being in the dissertation phase. I think the official university terminology was "PhD, early phase" and "PhD, late phase" or something like that. But the distinction was purely bureaucratic. The terms were used interchangeably by everyone in speech and writing.

I think in most US PhD Programs, regardless of discipline, you have at least three major steps: coursework, exams, dissertation. What those things are called varies from school to school, and the names are not important, with the possible exception of the dissertation phase, where some grants in the social sciences require a "defended proposal" which is frequently a signal of being in the dissertation phase. With that basis, I don't understand why this is such a conflictual topic, or what the question is?

becuase standardisation is a common process everywhere @ThePompitousofLove except in your case

I'm voting to close this question as off-topic because it seems to basically be argumentative (why is the system the way it is).

Every United States institution is different and sets its own rules, so there is no single universal answer.  In the typical US system, however, there are three different requirements that are effectively orthogonal:

The student has to take some sufficient set of classes
The student has to pass one or more qualifying tests of some sort --- the details of these tests are radically different from institution to institution, but typically involve one or more elements of the following:

Being grilled on their knowledge by a panel of professors
Taking a difficult written test
Writing a formal research survey or proposal (sometimes of their proposed thesis work)
Presenting a piece of research (their own or others') and being interrogated on it
Doing very well in certain classes

Carrying out research and writing a thesis dissertation on that research.  This also often involves presenting this research and being interrogated on it in some sort of public defense.

The first is also generally sufficient to earn a Masters degree, so if the student fails in the second or third, then they are often given a Masters instead of a Ph.D.
In sequence, however, the order is often not strictly fixed, and there is no broadly adopted terminology to differentiate between people who have fulfilled different parts of their program.  I, for example, have known people who had to scramble to fulfill one of the first two requirements to prevent their graduation from being delayed because they'd been letting them slide while working on their thesis.

You have made some generalizations in your question that are not, necessarily, accurate.

Before defense of your proposal, "Ph.D. students" should prepare for a comprehensive examination, but basically this is depends on your advisor, who will set a rules of how this examination will look like.

This may or may not be the case at any given institution. For example, where I got my PhD, the doctoral comprehensive exams were highly standardized, and varied only by sub-specialty, not between advisors.

Why is this first period of a Ph.D. program not counted as credit for
  part of your thesis? Why does credit counting start from moment of
  your thesis proposal approval?

To be blunt - because it's a requirement to start your thesis.
In some ways that is counting it as credit. If you consider "Graduate with a PhD" as the end goal, then it is credit toward that process. But a thesis is a singular, somewhat indivisible unit of work - you either have, or have not, written your thesis. There's not really "credit" involved in the traditional academic sense of the word - you're not accruing hours, etc.
There are however, many ways where, if you mean more informally making progress toward your thesis, it's very likely your comprehensive examination may help. First, it may herald the end of classes - and this "credit" to begin working on your research as an exclusive focus. Second, in many cases, the subject of the comprehensive exam, and elements of it, may play directly to the questions of your thesis. For example, I have met people who, in studying for their comprehensive exam, essentially collected the literature review section of their thesis, and others who, in writing a "mock grant" as part of their comprehensive exam had made significant progress on the framework of their thesis.

thank you formite, damn, I am shocked, I didnt know that, chair of program assured me that only difference between master and phd is number of publications!

because it's a requirement to start your thesis. — ...in some PhD programs.  In my department, students are expected to have completed a significant fraction, if not a majority, of their thesis research before submitting their proposal.

Why is this first period of a Ph.D. program not counted as credit for
  part of your thesis? Why does credit counting start from moment of
  your thesis proposal approval?

Credits earned before the student advances to candidacy are typically counted towards credit hour requirements for the degree, but not counted towards credit hour requirements for the dissertation research itself.
For example, a 90 credit hour PhD program might consist of 60 credit hours of coursework and qualifying examinations followed by a 30 credit hour dissertation.
You might ask why a specific number of dissertation credit hours is required.  If a student can prepare and publish the research in a short period of time then why require them to register for more credit hours and spend more time as a PhD student?  One reason for this is that the university charges tuition for these credit hours (which might be paid by the student or might be paid by a grant or some external source.)  Another reason is that it provides the appearance of quality control.
It is also typical to require the student to go through some formal process of proposing the dissertation topic before starting to earn credit hours towards the dissertation.  Without it, students could simply register for dissertation credit hours without any specific approved topic in place and fiddle around on random projects that don't contribute to the actual dissertation.

I can contribute something regarding terminology that I hope will help clear up some confusion.
First, I'll outline how things work at at least some institutions in the US:

You take courses
You take some long, difficult, timed, paper and pencil exams
You look around for a topic.  When you've found one, and have been working on it for a while, and generally when you're at approximately the half-way point, you present your research proposal, live, to your committee, and answer questions the committee members throw at you, in a oral exam.
You work on your topic some more and start writing it up.  When you're done with the formal written thesis, you defend it in another oral exam.

You are a PhD student the whole way through, until you graduate.  But you get "admitted to candidacy," in other words, you become a "candidate," when you pass the first oral exam -- the one where you presented your proposal and answered oral questions.


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Publish a paper with a coauthor not affiliated to a university
I am supervising a last year high-school student (a very advanced one) who is doing some kind of a research project. He does some numerical simulations on problems that I suggest. If everything goes well the results of these simulations should be rather interesting and could be submitted to a reasonable journal.
I have an affiliation with a renowned university but the student obviously does not yet have any. Next year he plans to enter university X (and probably he can do that).
The question: can I submit a paper with him as a coauthor, stating that he is affiliated to the university X? May it create some problems for the student if he choses to enter another university Y later?

I think that the questions tagged with both, [independent-researcher] and [affiliation] will answer all your actual questions. Moreover, if the research in question was done during an internship or similar at your institution, you can give it as an affiliation (unless it has very strict rules about this). Alternatively, you can also give the high school as an affiliation.

Do not list a false affiliation.  If they are not, at the time of publication (or were not, during the time of the work undertaken), a student, staff, or faculty at University X then it is a falsification to say that he/she is affiliated with that University.

Listing an affiliation also means that explicitly or implicitly, the institution has given the author the right to represent the institution in the appropriate capacity.

Whether to list the university or the student's high school as their affiliation would be a question of academic affiliation, which does not require being formally a student or staff. In cases like this, it may be quite tricky to decide which to use.

I published a paper with two high school student co-authors.  I listed their high school as their affiliation.  They were not paid by the university.  It worked fine.

The question whether the student should be a co-author (of course, if he contributed a significant part of the work!) is separate from the question of what affiliation to list. For the latter, I think that in reality it does not actually matter -- the affiliation is simply a convenient form for readers to figure out how to reach the author in case they have a question, and a convenient form for authors to claim authorship in case their name is not unique by itself. In the case at hand, I see no reason why one shouldn't simply list the student's high school as affiliation. Or, if this was as part of some organized summer activity, the university at which that activity was done. From the perspective of the publisher, either should be fine, as would providing the student's home address.

"I think that in reality [the affiliation] does not actually matter" It certainly matters that you don't claim somebody has an affiliation they do not have!

Correct, of course. What I meant to say is that having no affiliation (and listing none) is not in itself a problem.

You don't need to include any affiliation. If you don't work at an academic institution then your affiliation is irrelevant private information that you should be able to keep private. It's none of the reader's business to know that the author works at some company X, or attends school Y in town Z.

You don't need to include any affiliation - but it's customary to do so, even if it is a high school, company, etc.  It's like meeting someone at a party and they ask what you do for a living.  You don't have to tell them, but it's customary to do so, and it will be a little awkward if you don't.

@NateEldredge  It may be customary, but then that's because it is usually useful. With more and more people from outside academia publishing in peer reviewed journals, it may be better for people who get into problems when asked for affiliations, to simply say that they want to keep that private, if that's in fact what they want. It's not really the same situation as in some social event, what should matter are the scientific results, it should be possible to contact one or more authors, but that's about it.

@NateEldredge, it makes sense to list your company or high school as an affiliation if the paper is about something you did at your company or your high school. But if it's work you did in your own time which is unrelated to what you do at work or at school then it's misleading to list an affiliation. Particularly in the case of companies, it could even cause conflict with HR if you list them without asking permission.

There’s no need to list an irrelevant affiliation, but it’s useful to list some kind of contact information. I wrote a joint paper with an undergraduate at another school who had taken my abstract algebra course when he was in high school, and he chose simply to give a mailing address.

I disagree to some extend. In terms of independent research it may be of very interest, if a researcher is working for a company known for lobbying in that field.

@Ariser Yes I agree, the point I'm making is that in case of independent research done, you'll more typically have the situation that affiliation is not relevant. Another issue to consider is that if it is indeed not relevant then mentioning the fact that you work for, say, Samsung should be considered inappropriate advertising for Samsung. If you got the results published without using any facilities of Samsung, then it's not too much to ask to give some private email address not connected to Samsung as the email address for correspondence.

I published during high school and my advisor listed me as being affiliated with his university.  I think it was fair because I did the work on their premises and was basically a volunteer/unpaid intern at the university.  I even went to their group meetings so I feel like I was part of the lab.

The problem with affiliating the coauthor with university X is that if he does not manage to enter X for some reason (maybe because he leeched, for lack of a better term, on their fame by a false claim of affiliation), either the paper will have wrong affiliation which may mislead people, or you will have to submit a correction to the paper. In addition, this might damage the academical career of the coauthor, even if it wasn't his decision.
In extreme cases, it might lead to rejection of the paper because if you're lying about something as trivial as the affiliation, what else might you be lying about? At the very least, if one of the reviewers knows that it's wrong, they could submit it as an error you should correct.
There is nothing wrong with listing the coauthor's high school as his affiliation. If the coauthor were to work for a company, you would also put down their company, right?


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What to do when publishing a paper about mistakes in previous literature?
Two years ago I read a paper in which the "Methods" section did not report enough information to reproduce the analysis presented by the authors.
I contacted the first author in order to have more information and he provided me the code he used to analyse the dataset presented in that paper.
I found out that in the code there was a conceptual mistake in the way some algorithms were used. However, I did not have a solution for the mistake. So, I just ignored the fact and started working on a different problem.
One year later, while working on the new problem, I found a solution that could permit to avoid the conceptual mistake that I found in the above-said paper. As in the meanwhile I stumbled across to another paper doing the same methodological mistake, I thought to write a letter to the journal in which the first paper was published to underline the problem in those two papers and propose a solution. The paper analyses a simple dataset in order to show the differences between the results obtained with the old method and with my new method. I also (of course) point to the fact that the data presented in the two papers should be re-analyzed, as a data analysis containing that mistake can produce misleading results.
The peer-review process went smooth, with constructive comments of the reviewers. At the end of this process the Editor informed me that they also requested a signed review by the first author of the paper published in his journal. So, the same person who originally provided me his code.
The recommendation that he gives on my paper is of major revision. His comments are (in principle) constructive but he requires me to cancel from the paper the reference to his paper because: i) the re-analysis of his dataset with my method (re-analysis that he did not share) does not show significant differences; and ii) the criticism of his results is not justified as the Methods section in his paper does not contain sufficient details to infer the error. Do you think that these request are justified?
During a private conversation with me he also made clear that it is his interest to make sure that his original paper "would not be destroyed" and that he does not consider to publish a re-analysis of his data. This is particularly nonsensical because the results affected by the error are just a rather small part of the results presented in his paper and could only be found out by inspecting the code.
Given this context, I think that his requests are quite unfair. It is clear that he is just trying to preserve his publication record. It also makes clear that all his positive comments in the review are just an attempt of bargaining a positive recommendation for the publication of my paper in exchange of erasing the reference to the error in his paper.
Therefore, my conundrum is if I should just give in to his requests for an easy publication (nice thing during a PhD) or do not bend, argument against his comments and get a rejection recommendation. What would you do?

Thanks for the suggestion. Fun fact: I opposed the reviewer since the beginning. In fact, from the conversations I had with him, I sensed which kind of person he was. However, in the case that a new paper points to an error in a paper previously published on that journal, it is the journal policy to ask for  a signed review from one the authors of the already published paper...

@LeonMeier Major

To begin with, I find it highly problematic that this journal has a policy of inviting authors to review any paper that criticizes their work. That seems to me to be highly inhibitory of criticism and likely to produce situations exactly like the one that you are facing.
I find it doubly problematic that this author has chosen to communicate with you outside of the review process in order to persuade you to change your writing. His communications can easily be interpreted as an unethical quid pro quo request: you drop your criticism of his paper, and he'll drop his criticism of yours.
What is not clear from what you have written, however, is just what the journal intends to do with the review that they have received. Surely the journal must understand the potential conflict of interest here.  So is the review mainly to allow an author to point out errors in the critique that those less familiar might overlook, or are they going to treat it just like one of the other reviews?
I would thus recommend taking the following approach:

Write to the editor and let them know that the author has approached you separately with what you are concerned may be an unethical proposal --- the editor needs to know about this and should be able to make their approach clear to you. Ask the editor how they would like to proceed.
In parallel, use all of the constructive parts of the criticism to improve your manuscript.
Consider slightly softening the language in your criticism in the manuscript. I do not know how you have written it, but it's often possible to use slightly less definitive language to make the same point, e.g., changing "Papers [1] and [2] should be re-analyzed to see if their results are affected." into "As it is possible that results might be affected, we would recommend considering re-analysis of papers [1] and [2]."  Same substance, but less confrontational and allowing you to write that you have adjusted the paper in response to the review.

Hopefully, the editor can provide you some clarity as to how to navigate the difficult situation that their journal has created for you, and judicious adjustment can allow you to pass peer review without compromising your ethics. If not, there are other good journals out there that will not have this unusual conflict-generating policy.

No, the substance of your rewrite is not the same (if it were, it would not be "softer"). The new version implies that consideration of re-analysis might lead to no re-analysis. Otherwise, good answer.

In case of a corrigendum there is a standard practice to ask the author(s) of the original paper (OA, original authors). However, ignoring the "opposed" request is highly problematic assuming the journal offers such a list. Take a different journal, write the new editor that you will put OA into the opposed list, and ask (do not request) the editor whether such a list would be observed. State that if it won't, you'll withdraw the paper, and that you'll wait for a clear yes/no before submitting. Yes, and all your e-mails should be utmost polite, but still clear.
Your re-submission should be improved in any case. Use the comments of the OA.
Cite OA, scold his technical results, but acknowledge himself a lof for his source code and reviews.
If everything fails, consider a journal of negative results. There are some of them around in the meantime.

I think that it is a very bad idea to just withdraw the paper without talking to the editor.

I mean the editor of the current journal: as I wrote, we do not know how the editor intends to deal with the conflict of interest in the situation. If they ignore the problem, the paper might need to be withdrawn --- but even with the COI, the paper may well be published with an appropriate response. If they appropriately mitigate, there is no need to withdraw.

I agree, and this appears to have been bundled in with a number of other constructive criticisms from both the COI reviewer and the other reviewers. There is no indication in any of that about how much weight the editor gives to the particular request that the OP finds problematic.


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Allowing flexibility in term paper topic
I could use some advice from more experienced instructors.
My social science course culminates in a term paper based on independent research.
However, in some cases students end up changing the topic of their term paper because they hit a bottleneck.
In the past, I encouraged them to make the most of it, even report null results. But now I wonder if I can be more inclusive if I allow them to abandon a topic, but report on why and then elaborate how they will course-correct and even begin that new line of research, albeit in a preliminary way (because of time constraints).
What do you think of this approach? It is essentially allowing them to combine two papers into one. Anyone tried something similar? Other ideas?

Are they changing topics because they're only finding null results, or some other reason, like lack of any research at all?

Do they choose their topic originally or you? Do they change with permission or on their own?

And, are you the designated instructor of the course or a TA?

They sometimes change topics because they lose interest — this term paper may converge with their thesis if  they plan wisely

They choose their item topic, I sign off on it

I’m the instructor

How far through the term do they generally want to change topic? Letting them change topic too close to the submission deadline might mean that they are only demonstrating that they can "start" independent research but not see it through when it gets tougher.

When you say "more inclusive", what do you mean?

You're starting at the wrong end if you ask "Should X be allowed?". Rather, start with "What do I want me students to (i) learn and (ii) demonstrate?" For example, I assume that you want your students to learn research design, the evaluation of data, drawing conclusions from the data, and then putting these conclusions into the context of the literature. For all of this, it is not necessary to have positive results: One can write a cogent term paper about a research design and the evaluation of data so obtained even if the data only supports the null hypothesis.
In other words, if a student can demonstrate what they learned, then the actual form of their paper should not actually matter all that much.
To sum this up: Focus on the "what" questions, rather than the "how" questions. That's because if you know the "what", you often know which "hows" are useful and which are not.

Quite right, but writing a paper that says "we don't have enough data to support any of the alternate hypotheses" is not really possible, because you cannot do the intended evaluation. Can still be a good exercise in error estimation, or in designing a study that would give sufficient data, but thats again a change of topic.

If you don't have enough data, you get that the likely range of your parameter is  3+/-12. From a learning perspective, being able to derive this is just as useful as someone coming up with 4.22+/-0.03. It also teaches that whether a hypothesis is supported or not depends on your error bars and, consequently, the amount of data. That's why testing of COVID vaccines could be done so quickly: Because it was easy to get huge numbers of cases together in such a short time during a pandemic, as opposed to testing vaccines for rare diseases.

even report null results

Null results are incredibly important in science. There may be institutional and individual biases against null results, but students should not be encouraged to change course merely because their results are "uninteresting". To the contrary, they should be encouraged to understand the importance of null results and learn how to properly interpret these results, which is often much more challenging than interpreting results that clearly favor a particular hypothesis.

changing the topic of their term paper because they hit a bottleneck

Bottlenecks are the hard part of research; if the term paper is meant to give students exposure to what it means to do research, then they should learn to confront and work with these bottlenecks. Hitting a bottleneck should not, in itself, be sufficient reason to change topic. Bottlenecks are distinct from other obstruction in that there is in fact a path through, even if it is narrow or uncomfortable.

allow them to abandon a topic, but report on why and then elaborate how they will course-correct and even begin that new line of research, albeit in a preliminary way

This has been the standard approach in biology courses I've been involved with that have a research or pseudo-research component: when things go wrong, students explain how they've gone wrong, how the things that went wrong impacted their results, what they've learned, and, since usually there is limited time to take the next steps of redoing things incorporating what they've learned, at least outline a plan for what they would do next if they were able to spend more time.
You should choose the approach that best fits the learning goals of your course, however. There may be certain barriers that prevent a student from achieving those goals, and that may require a change in topic, hopefully as early as possible (and you should try to identify and prevent these issues if at all possible at the initial topic selection phase). For example, if your course has a quantitative component, obstacles to collecting any data would preclude a student from doing the quantitative component, so you may consider alternatives such as simulated data. It is certainly true that these types of projects are often very difficult for students, though, and they likely need a lot of guidance in navigating through their projects. Some balance should be reached between letting them flounder a bit and giving recommendations. Definitely avoid letting their evaluation be based on things they could not foresee.

This is from experience with a doctoral dissertation in mathematics, so it may not apply exactly, but sometimes it is necessary to change topics. But it should be done with permission so that you get a chance to advise them.
In my doctoral studies I worked on three problems. The first turned out to be too easy and I was able to develop one or more theorems with proofs every day. It was a bit fun, but also trivial. Hence boring.
The second problem was like a perfect diamond and there were no tools that I could find to "crack" it. I worked a few weeks totally unsuccessfully. Nada. Nothing but frustration.
The third problem (are you getting "Three Bears" here?) was just right. It was significant but approachable. The thesis turned out to be a complete theory, not just some minor results. Some of the parts were easy, some hard, but it was possible to attack both with existing and with new tools.
My advisor was involved through all of this, agreeing when it was time to move on and also making suggestions.
I realize that a term paper is much less consequential, but, perhaps the same constraints should apply. Seek permission to change focus. An give advice when permission is sought.
An orthogonal idea is that, depending on the field, a single university term/semester may not be sufficient to tackle some topics and so you may just be forced to make some accommodation in fairness. It is impossible to schedule results when true research in many fields is undertaken, since it is a look into the unknown. In such cases, an explanation of what was done and how and why it may have failed can be as valuable for learning as something more "tidy".


text:
What is the name for "section topics" printed in the margins
In older publications of many languages, there are frequently printed text in the margins that detail the topic of a section of the text (see below on the left and right):
Excerpt from Magnum Oecumenicum Constantiense Concilium:

What is the name for these? I considered marginalia, but they are not handwritten.

Why can't marginalia be typed?

Although many marginal notes are made by hand, the term marginalia is also often used for printed ones. There is even a book about "printed marginalia". A definition of marginalia given here states

The term "marginalia" generally refers to handwritten or printed text situated at the borders of the page.

Depending on the textual content, words like gloss, annotation or side note can also apply (although the latter also has a more metaphorical meaning).