text:
How do I reply to a professor's email who wants to chat with you?
I contacted a potential advisor for a PhD program. He replied to me that he was not in a position to accept any PhD students at this time. But he also wrote to me:

"I'd also be happy to chat about the program and my work generally if helpful, but would realistically have to be in mid-January. Let me know if of interest."

I am not sure what and how should I reply to him. I am interested in having a talk with him, but what should I ask?

He wants to know more about your background preparation and your research interests. He likely also wants to get a sense of how you would fit into his research program.
However, he may also just be interested in grad students generally and wants to think about whether some other prof would be good to work with you if he can't.
I expect that the chat will be entirely informal and give you a chance to look around the department and maybe meet a few people. I once asked a prof if he would be my advisor and he declined, but suggested another, who turned out to be a much better match. I don't think he actually introduced us (long time ago - poor memory) but think he just suggested I approach the other (more senior) prof.

Thank you for your reply. Would it be better to go to visit her or just have a chat through phone?

If at all possible, make it in person. You want to start to build a relationship there.

@Zhubenwuxin: I would only suggest going in person if you will be in the area anyway.  If he says he is not accepting PhD students, I think it's relatively unlikely that anything directly beneficial (admission offer, etc) will come of this conversation.  It would be worth having by phone, Skype, etc, but I don't think it would be worth the expense of traveling any significant distance.

If the professor is not interested in taking you now or in the future (if I get your post right), then what is the point? I had bad experience before with similar offer to just chat. It was an ideas phishing trap that affected me negatively. I would never do it again. I will always be careful.


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Is citation required when googling a short answer?
I was writing a research paper that required me to use quotes and cite the websites/databases those quotes came from. Later, I needed some quick stats, so I googled them. I only used the numbers and didn't quote the website; I put it into completely different words. Do I still need to cite it? If so, then what should I put in my annotated bibliography for that source?

Cite what you use. Be honest.

Anything other than citing the source is plagiarism and unethical.

Yes, you still need to cite properly

It sounds to me like you don't want to cite this source because you don't know how to format it in your bibliography. This is a terrible reason for not citing a source. If you can't figure out the appropriate format, make one up. I can assure you that the source would much rather be cited with an improper format than not be cited at all.
There may be good reasons for not citing a source (for example, if you're being helped by somebody whose company doesn't think he should be spending time on this kind of work), but I don't think you have any of them.

Even in a case such as the latter, one could cite the source in an anonymized way. Useless for verification, but one still wouldn't take credit for other peoples' stuff.

@Arno: One could, but I don't think there's that much point to it. It's not going to help anybody else who's trying to check the reference, and it might contribute to "outing" the person who wants to remain anonymous.

source: Stack Exchange

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

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Are there any issues with submitting conference papers in one language and publishing them in a journal in a different language?
I have some research I want to present at a conference in my native language but I would rather submit for publication in English after finalizing it. Are there any ethical issues with this I am missing?

Are you in CS/computer engineering? That would be relevant information because they treat conference publications differently than the rest of academia.

It's interdisciplinary. Expecting it will be similar to rest of the academia vs submitting on IEEE/ACM

How obscure is your native language?  (This is for practical issues, not ethical ones.)

By the standards of your discipline, would it be ethical if they were in the same language?  If yes, then you're fine.  If no, then the second publication needs to make clear that it's a translated and extended version of the first, you may need the permission of the conference publisher, and you shouldn't "count" them as two separate publications.

@NateEldredge this is the answer.

@NateEldredge Please don't write answers in comments.

I was hoping OP would answer the question about the standards of their discipline.  Then I or someone else could write a more focused answer.

As stated in the comments. It is totally irrelevant if they are in two languages. If it would be ethical to do this one language then it will be ethical in two. If it is unethical in one language then it will be unethical in two. In my field presenting at a conference and then submitting a paper to a journal is just fine, as long as the conference does not publish a proceedings or similar. In other fields, it is not acceptable. Again, the language matters not.

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


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Where to get second opinions on independent research?
Advisor mentorship, department peers, passing extended abstracts around at conferences etc. all come to mind for an affiliated researcher. None of those options except the last one apply to someone without an affiliation and the last one is cost prohibitive most of the time. What are the options for someone without access to traditional options like these?

Assuming the research is at an advanced enough stage, the best option is certainly to submit a paper to a peer-reviewed journal: free independent expert opinions, provided with advice on how to improve it!

[edit] If the research is at an early stage, there are often venues which welcome submissions of prospective ideas and "works in progress": it's often the case for small-scale specialized workshops, but there might also be journals which fit this profile as well (this probably depends on the field).
Of course it's always possible to contact academics to propose a collaboration with them. Some might be interested, but if you're asking them for guidance and mentoring then why not do a PhD with them? That's the standard way to get adequate research training.

Anything to expand on for earlier stages? Second opinions on research direction or methodology can be more critical than one would get from submission feedback for a full manuscript

@VictorS see edit.


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Is it possible to gain admission to an engineering master's program without an undergraduate engineering degree?
I tried to search for this and could not find it. This is my first stack exchange post so go easy please.
Here is my situation.
I have an undergraduate degree in economics from a top tier economics program, and a very top tier university in general, with a GPA above 3.5. After working in economics research at a highly respected institution for 2 years after graduating, I've realized I want to pursue a different career. The work I do is highly quantitative and involves some computer programming using C++. I'm also pretty good with mathematical and data analysis/statistical software, and have worked multiple RA jobs as an undergraduate.
Ideally I would do something related to software engineering or electrical engineering since I'm interested in computers. My question is, to what extent is this possible? Is it possible at all? Will universities see that I don't have an undergraduate engineering degree and reject me? Do I have any sort of shot here given my background?

The "roommate of mine" of mine who I mentioned here got an undergraduate degree in math, skipped a year from school (worked as an assistant car mechanic), then took some undergraduate engineering courses at another university part-time, then applied to and got accepted to MIT's graduate mechanical engineering program, where he got his Ph.D. in mechanical engineering a few years later. So yes, it is possible.


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Is it legal to discuss exercise problems and solutions for a textbook?
Is it legal for a website to create an entry for a particular book, and add all the  exercise problems (not the question completely but just the question number) and create a reddit kind of discussion channel for people to discuss different solutions ?

Duplicate or at least similar: https://academia.stackexchange.com/q/38175/72855

Could you add a country tag, please? Answers might differ fundamentally depending on the jurisdiction.

This question should probably be on the law stackexchange.

Does this answer your question? Solution manual and copyright?


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Elsevier Journal waiting time after review process
I have submitted a revised manuscript that has been "under review" again for the past 7 months. After a long wait, I have written a polite email to editor inquiring about a long delay in the revised review once I got positive reviews and minor corrections. It has been almost 3 weeks the Editor did not even replied to my email and still the status is the same. Any suggestions How long I should wait? or is it normal a practice by PHYSICA A journal of Elsevier?

I have no idea about  PHYSICA A (I am from another field).
You may try to write to Elsvier Support: https://service.elsevier.com/app/contact/supporthub/publishing/
Maybe they can somehow push the things.


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Pursue a German PhD with a Masters from the USA?
In December of this year (2020) I'll graduate with an MA in Applied Linguistics from a US university (via distance learning/online). I have been living and working as a full-time teacher at a bilingual school in Germany since 2012 and specialize in bilingual education (English/German) with a focus on the subjects of History and English. After graduating, I would like to pursue a PhD in a related field (linguistics) at a university in Germany with the career intention of conducting research and lecturing/instructing at a university. I have seen a lot of German universities host paid PhD research projects with very interesting topics, which seems like a direction to pursue, but I am not sure if the pay will be enough to support my family. I am the main provider for my wife and son (3 y.o.) and we won't be able to financially handle a huge cut to my current salary (about 4,000 Euro gross/brutto per month).
As to my questions, I am looking for some advice about the potential career-path. Does it make sense for an American to pursue a German PhD with a BA and MA degree from the US? Financially, would it be possible to continue to support my family while pursuing a PhD in Germany? Is it worth it at my age (35 y.o.) to pursue a PhD?
If the information helps, I plan on staying in Germany permanently as my wife is German, I do not want to continue teaching at the secondary school level, and I am fluent in German. Any advice or guidance would be greatly appreciated!

You know the statistics on what percentage of PhDs in your field actually find a job teaching at a university?  Temporarily?  Permanently?

Would your wife and son be okay with this ectreme movement?

@AlexanderWoo I unfortunately haven't been able to locate that information. I understand it's a relatively exclusive field to join, especially as a foreigner. Perhaps it is a safer bet to continue teaching at a secondary school.

@user111388 Thanks for your question! While my son is still very young (3 y.o.), I don't think the decision will effect him much. My wife, on the other hand, is very concerned with finances. My hope is to pursue a PhD that is financed about as well (based on circumstances (i.e. cost of living expenses)) as my current job pays.

You can compute your prospective salary yourself: http://oeffentlicher-dienst.info/c/t/rechner/tv-l/allg?id=tv-l-2020
Typically, TV-E13 but only 50% or 65% depending who funds your position. Whether that is enough is up to you and your wife. A career at the German university is a high risk gamble, and it take quite a while before you know whether you make it or not. If it does not work out, then you will have invested a lot of time in a career that did not work out.

Thank you @Maarten Buis for your reply. You and the other respondents have given me a lot to contemplate. Your response has put a bit of doubt into me if it's worth it to pursue a career in academics. Teaching is a safe bet considering I already have a solid teaching position, but I have the drive and desire to do more and explore other aspects and levels of teaching. I imagine a PhD will help in that cause, but I am naturally worried about the financial investment.

There are many aspects of your question for which I also am curious about. I just want to point out that the numerical difference in your net salary might not mean that much depending on the city. I know for a fact that the old west German capital Bonn is way more cheaper than the current capital Berlin. Also, even though your net income might be lower, you might get a lot more benefits (cheaper healthcare, scholarships through DAAD, possible child payments or unemployement for your SO?). I believe the 300ish euro termly fee that every university student pays has perks such as public transport (and even maybe cheap dining hall benefits). I have seen in some phd program webpages that mention some benefits for students with kids.
What I am getting to is the living conditions for a student in Germany and for a student in US is very different (or possibly for any other country).
Update: I have obtained some figures.
DAAD offers long term scholarships. They usually pay around 850 euros + benefits. These benefits include:

Child benefit (about 200 euros per month)
Marital benefit (about 270 euros as long as your SO makes less than 450 euros)
rent subsidy (up to 250 euros*, conditions apply, roughly you are subsidized for anything reasonable above 25% of your income)
health insurance for you and your dependants
some amount of language course for you and your dependants

I also believe you can still work part time under conditions.
*this amount is actually for single scholarship holders. Conditions are different for scholarship holders with family but those don't include a designated maximum upper limit.

Thank you very much for your reply! This puts things into a bit more perspective for me regarding finances. That is my main concern with transferring from my full-time teaching job to working full-time towards my PhD. It's a bit reassuring that there are some additional benefits to being a student with children.

@speaslee I actually have some rough figures regarding one of your options. I am editing them in the answer now.

If I'm not mistaken, DAAD usually sends Germans abroad, not the other way around. PhD students are mostly financed as regular (part-time) jobs in Germany, so expect something like 1600-1800 Euros net for a 30h/week position.

@henning--reinstateMonica  It definitely supports froeigners for their studies in Germany. These include masters degrees, short term research projects etc. Ref:  daad.de/go/en/stipa50026200  ,  daad.de/go/en/stipa57140602 , daad.de/go/en/stipa57135739

@Bobby Mcboatface Good to know.

I would reach out to some professors in your field at nearby universities and discuss the local prospects with them. As mentioned in another answer, non-technical PhD positions are usually only half positions. However, if you currently have a full-time job, do look into reducing to part-time work. That can at least pay the rent (and health insurance) and see if you can get a half position (that will, of course, expect you to work full time as well). Getting a professorship will involve a lot of luck, so you need to ask yourself why you are doing this: To be a Herr Dr.? No. Because you have a passion for research? Yes. To get a permanent position? No.
It is also possible to submit a dissertation to a German university without having a position, that is, one that you wrote in your "free time", if your job leaves you enough. That way, if it is really a passion for research that is driving you, you can pursue that PhD without financial problems. Some universities now have coursework required, but that is even possible to obtain at a distance university such as the Fernuni Hagen and then have the credits accepted at another university. Ask around, it's a jungle of red tape!


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Which software converts academic publications from PDF to Word without mangling complex formatting?
I'm asking about this in StackExchange Academia rather than a software-recommendation site because I have conversion problems specific to the layout of academic publications. I'm helping a student who has problems with their eyesight. They find it hard to read academic papers and books on screen, when distributed as PDF. They prefer to have these converted to Word, then read that on screen. This helps them because they can change the font of any part that's hard to read, as well as highlighting section headings and other cues to help them navigate. There are many PDF-to-Word converters, but all the ones I've tried (see below) have defects. Can anyone recommend something better than those I've listed? The converter must not mangle tables, diagrams, footnotes, formulae, subscripts and superscripts, or other complicated content typical of academic publications.
The student does not like to read printed text, and only has an A4 printer, so blowing up the text and printing that isn't feasible. The pandemic introduces its own constraints, since they don't want to venture from their flat to use University computers. So they're restricted to what I think is a 22-inch screen, Windows 10, and their A4 printer. I only mention these because commenters suggested them. The student is comfortable reading Word files, and I want to help them do that, rather than force them to do something outside their preferences.
Getting back to PDF-to-Word converters, so far, we have tried:

Kofax Power PDF, but it's very erratic, though. For example, when I converted an archaeological report which I had to ask Power PDF to OCR, it "thought" it had found characters in the thin lines indicating boundaries in a diagram of the archaeological site. Power PDF also mangles structural chemical formulae, even when told not to OCR. Footnotes and tables cause even more problems, as do in-line chemical formulae, and subscripts and superscripts.

SmallPDF. This claims to be "the platform that makes it super easy to convert and edit all your PDF files". It is not. It converts some so they work better than those done by Power PDF, but crashes on others.

PDF24. This probably does a better job than either Power PDF or SmallPDF, when it works. But on some PDFs that need OCR'ing, it just emits the original page-images. This may well be a bug, and I've reported it, but I've not had any reply.

Does anyone have any recommendations?

To the close voters: please recall that, according to the outcome of this meta discussion, we accept questions about software recommendations related to academic tasks, and this is sufficiently specific to be considered on topic. See also this FAQ.

Comments are not for extended discussion; this conversation has been moved to chat. Please read this FAQ before posting another comment.

By the nature of how pdf works internally, it is unlikely that you will find something that will work with any pdf. You can try to find something that works well most of the time but if reading pdf's is really not possible then I think some combination of solutions will be needed.

Unfortunately, you're right. I do realise that this is a hard problem: I said that in a comment below. But I don't think it's insoluble, I just haven't had time or money to evaluate all the converters available.

Have you tried the obvious of either exporting the pdf from Adobe Acrobat importing the pdf into Word. I tried just now with two papers and the results are really good with regards to figures, tables, footnotes, references, layout, ...
original PDF
exported from Acrobat
imported into Word
Make sure to download the documents instead of viewing them in the Google drive. They will look closer to the original in Word itself than rendered by Google drive. The only major issue I can see is the title page in both cases--but the PDF export seems to do a slightly better job.

Doesn't work with scanned papers!  The OP has high standards!

@Mario Niepel Thanks for taking the time to show me that. I'll try that on some of the recent papers and see how the Word versions look. Unfortunately, user151413 is right about the scans. Some of our older archaeology papers have arrived as scans, and we do need to OCR them. There's not much we can do about that. But for the others, I'll try it. Question: has Word ever frozen on you when you've imported these PDFs?

Honestly, this is the first time I tried, so my experience is n=1. And of course any import/export feature is only as good as the OCR you use. If OCR is an issue, I would divorce this from the PDF question.

@Mario Niepel I've been considering OCR and conversion together because that's how the software companies package them. All three converters I mentioned do OCR, and I think all the others I've glanced at do too.

has Word ever frozen on you when you've imported these PDFs? This might be due to a lack of memory.

Converting scanned (OCR) PDF documents into Word documents with complete accuracy isn't possible.
When I teach my students about this, I tell them that when someone asks if they can get data out of a PDF document, the first answer should be "No."  The second answer, if pressed, should be "No.  Is there any other way to get it?"  And if still pressed, the final answer is "Fine, but it won't be very reliable."
This is especially true with OCR.  The software is using algorithms, often Google's Tesseract engine, to try and give its best guess what it's seeing.  There will nearly always be errors, especially if the scan may not be the highest quality.  You're going to see spacing messed up a lot, but also close values, like confusing a 1 and a 7, or a 0 and an O.  Tables are especially prone to being butchered.  If you upload any PDF to Google Docs, it gives you the option to convert it to text in the menu.  You can also download Tesseract hooks for Python, for example.
Honestly, even non-OCR PDF documents can be unreliable.  Have you ever copy-pasted text out of a PDF, and noticed that some of the spaces disappear?  Well, software converting it to text encounters problems as well.
The PDF specification isn't a plain text document the way Word files are.  For example, a trick not many people know is that you can unzip a .docx file into its component parts using regular unzip software, and one of those parts is a text file.  This is not at all true with a PDF document.
I feel like your student should focus on finding a platform and software that helps them read PDF documents.  Something with a magnifying lens, for example, or on a tablet.

I didn't know that .docx files were zip files! But thanks for the explanation. I have often noticed that spacing gets messed up when I copy-paste from PDFs. That is very annoying, and affects me as well as the student, just because sometimes I need to quote from a paper and only have it as a PDF. How do you get around that? And, out of curiosity, how is the PDF representing the text and the spaces in it?

@PhilvanKleur I'm not totally up-to-date on the PDF specification, but it's my understanding that it defines the position of each piece of text using x-y coordinates that represent its distance from the upper-left hand corner.  So there ARE no actual space characters; they're just white space left over in between the other pieces.  There's unfortunately no perfect solution to get around this, other than finding sources that aren't in PDF formats.

UPDATE: The question has gone through 10+ revisions since I wrote this answer. I haven't checked to see whether it is still relevant. I'll try to respond to comments.
I'll start by disclaiming: My initial solutions do not follow the prescribed pdf to doc conversion (whilst my last solution does, albeit, it's probably a bad solution), and I haven't tested them, which violates the OP's constraints. I disregard these constraints because I don't think they are particularly relevant.
It isn't clear whether on-screen, digital reading or printed, physical reading is preferred, nor how much adjustment in text size is desired, clarification may allow more focus.
The trivial, obvious solutions, which have surely been tried, are: Large screen plus zoom and printing to a larger paper size, e.g., A3 or A2 (the former being more commonly available), rather than A4. Annotations and highlighting can be applied to pdfs with numerous tools.
For various other enhancements, numerous tools exist on Linux, which can be scripted to suit needs. For instance, a page could be split into smaller parts and manipulated in various ways, e.g., split a portrait page into top- and bottom-parts, and blow up each part onto a horizontal page (optionally of larger size). All operations can be automated. This approach cannot fail particularly badly for academic papers. At worst, perhaps the split is applied in the wrong place, but, the two parts can be displayed simultaneously, aligned at the lower/upper edge, or by folding the top edge of a printed page.
Linux tools can also be used to convert to word processor format, for instance, pdf2ps and ps2txt can be combined to convert pdf to plaintext, which any word processor can open. (This is my worst solution. I doubt tables, footnotes, formulae, etc. will be handled particularly well.)
Converting to a word processor format seems like a misdirection. That's why my last solution probably won't work. Extracting another format from a pdf seemingly goes against the design goal of the pdf format, namely, to present documents in a [software independent] manner...encapsulat[ing, in each file,] a complete description of a fixed-layout flat document, including the text, fonts, vector graphics, raster images and other information needed to display it (source: Wikipedia).
My apologies if I'm way off mark here. I'm unsure of your precise requirements.

Thanks. I've updated my question to better state the constraints. A big printer isn't an option, sadly; nor is Linux; nor (during the pandemic), a bigger screen. I have actually tried an equivalent of what you suggest with PDF-to-PS-to-text, by running a PDF-to-text converter in the R programming language. R's good for scripting, and I could easily apply the converter to a list of files. But you're right, tables etc. were not handled well.

You're also right about the design goals of PDF. I realise that this is a hard problem, in the same sense that integration is harder than differentiation. On the other hand, it's not the 1960s any more, and AI has advanced beyond researchers believing that machine vision can be achieved in a summer ( https://news.ycombinator.com/item?id=12080565 ). The companies ought to be able to do better than they are. I bet the Department of Defense could ...

Many could, I guess there's not enough demand. Ordering a massive screen seems like an easy option, assuming there's a budget. Alternatively, asking someone willing to collect one from the department could work too. Equally, doing so out of hours could be a safe option.

"Many could, I guess there's not enough demand." Well, I can hope. Perhaps there already is such a program, and someone here will know it.

@PhilvanKleur Why isn't a bigger printer or screen possible? They can easily be delivered.

@Azor Ahai -him Errr... money?

@PhilvanKleur Well, you said "during the pandemic," and I wasn't sure what the pandemic-related restriction was.

@Azor Ahai -him That's part of the problem with updating a question so it explains to commenters why their solutions wouldn't help, I suppose. I think I added that to explain why we couldn't use bigger screens and printers within the University.

@PhilvanKleur That was in reply to your first comment on this post.

@ " Errr... money?" - So a software which costs 300$ would also not be a valid answer? You are narrowing your question down more and more.  In essence, you want a free software which can do what probably most journals' software can't do (at least, I have never seen a properly reformatted old paper, journals just scan and OCR them).


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No reviews after 7 months of paper submission
I have submitted a paper to IEEE transactions on knowledge and data engineering (TKDE).
Until now, it has been 7 months and the status of my paper is still "Under Review".
It has stayed in the same status from the first day of the submission.
I have sent an email to the admin of the journal, and she replied to me that the paper was being processed. I have waited more than 1 month without any update.
Has anyone experienced the same situation? What should I do?
Many thanks.

Plenty of people have experienced the same situation. See e.g.
Submission review is taking too long
I submitted a paper five months ago. Should I wait a little bit more for a response?
Elsevier Review Speed
14 months waiting for first review time to go elsewhere?
In general: ask the editor pointed questions about what's happening to your paper. They might not be able to tell you when the reviews will be available, but they should be able to say things like "we've invited 4 reviewers of which 2 have declined". Ask them for that information, and perhaps when the review due dates are as well. With this information you can make educated guesses about how much longer it'll take to review your paper. If there's no sign at all that the article is being reviewed, then consider withdrawing and submitting your manuscript elsewhere.

Probably it's the right thing to do, but I don't want to create any pressure. How long is typical for the review process, for IEEE trans in general and specific for TKDE?

@lenhhoxung it's not my field so I don't know what the typical review time is. I'd ask your advisor/colleagues/collaborators in the field. As for putting pressure on the journal: as long as you don't sound aggressive, the journal administrator is unlikely to mind. They receive lots of such enquiries from authors.

Now it has been 1 year and I sent an email to the editor.
He didn't reply. What should I do?


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Fine-tuning parameters for existing methods
I'm comparing my method against existing methods by doing some experiments on one dataset.
The existing methods do not provide results on the considered dataset.
My question is: Can I use default parameters from the existing methods? The fact is that there are plenty of existing methods and it will take a lot of time to fine-tune for each existing method.
Thank you.

Can I use default parameters from the existing methods?

Yes, but should you? Default parameters are unlikely to provide optimal performance, so you may like to try various parameters.

Do you mean we should fine-tune for all existing methods that we want to compare?

@lenhhoxung It depends what you want to achieve. You'll get misleading results by comparing your method with optimised parameters on your dataset to other methods with unoptimised parameters on a dataset they weren't necessarily design for. Perhaps you can find some other basis for comparison.

In my view this depends on a number of things:
a) Are the default parameters of the competing methods advertised as being widely applicable?
b) Have authors of competing methods provided appropriate guidance for how to tune?
c) Does what you are proposing require a lot of tuning, and did you tune yours in order to beat the others?
Answers a) yes b) no c) no point in the direction that you can use other methods with default tuning. If the resulting score is 3:0 or 0:3, my advice is clear. If it's 1:2 or 2:1, well, one needs to look at details, for example, is provided guidance by others so weak that chances are 95% of the users will use the default tuning anyway etc.?

Assuming that your goal is to publish a paper about your method, a way to answer your question is to ask yourself: given clear indications about how your method is evaluated and how the other methods are evaluated, would a reviewer consider this comparison inadequate, sufficient or convincing?


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Author biography information when submitting papers to IEEE Access
I'm about to submit a paper to IEE Access. Since the journal requires author bios at the end of the paper, I have added all the bio information of co-authors.
However, when I was preparing the submission, the submission system (manuscriptcentral) asked me to submit a separate file for the author bios (see attached figure).

It seems strange to me because the author bios are already added to the paper, and I think the system is going to combine submitted PDF files in a unique one, which will duplicate the author information.
Have you ever experienced that, and how do you solve it?
Thanks.

Why does this need to be solved?  Just provide the info. It does not hurt your submission.  A reviewer will not reject a paper just because they are two sets of authors info.

I think the same, but it seems a bit strange to me as the proof will have two sets of authors info

One way is to remove the biography information from the manuscript.

Hello, can you share your experience? What have you done in this regard?

I eventually added bio info to the paper and also had a separate file.
The paper was accepted already.

Is adding biographies required or optional? It seems optional to me.


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Gender, Independence, and Authorship
I have attended a few panels on applying to post-doctoral/junior faculty positions, and the topic of authorship and research direction always came up. All of the faculty on these panels noted that successful applicants needed to distinguish their research from their PI's by pursuing novel questions and publishing first-author papers.
But the women faculty also noted that regardless of the novelty of a question, a woman coauthoring a paper with her PI (even if she is a first author) is seen as less independent than a man coauthoring a paper with his PI. Consequently, the suggestion was that women should pursue sole-author publications or publications with colleagues at similar or earlier stages of their career.
These panels included faculty from physics, chemistry, and anthropology, but I want to focus on the natural sciences.
There are a few questions I have related to this advice.

Does it happen? Is what these women faculty describe true? For those of you who have served on faculty/post-doc selection committees, have you seen the evaluations of comparative candidates differ according to their gender?
Latino and Black applicants: There were no Latino or African-American faculty on these panels, but the reasons the women faculty gave for why women should go the extra mile in establishing independence seem to also apply to candidates from underrepresented groups. Have you seen evaluations differ according to whether candidates were from such groups?
Establishing Independence without Sole-Authorship: Supposing at least one of the answers to the previous questions is in the affirmative: It is not always possible for young scientists to develop sufficiently independent projects that lead to sole-authorships. How else might a candidate demonstrate sufficient independence from her PI? Recommendation letters can conceivably convey the quality and independence of a candidate, but are there things the candidate can do herself?

I recognize that the answers to these questions are likely opinion-based, but I am primarily looking for the opinions of stackexchange members in order to gauge whether the issue the women faculty cite is unique to my university.

For as liberal and as open as most universities claim to be, it is rather ironic that they often times also prop up some amount of bias and incongruence in their hiring and promotion practices.

The effect you describe almost certainly exists and is worse in some places than others, both for race/ethnicity and gender. But I think that the solution involves long-term, collective action on the one hand and personal action on the other. Advisors, can and, in my view, should, encourage their students to write sole-authorship papers even when joint might be appropriate. Some joint authorship can boost a student and others, as you note, can inhibit. But a lot of minds need to be changed. Working groups at conferences can be formed to address the issue within a given field, perhaps.

You might be able to get your questions answered if you separate them out and make them more objective.

"Establishing Independence without Sole-Authorship" is a good thing even independently of the bias concerns (which, I'm afraid, you'll never get a good answer for -- at least not from real-name poster --, because any admission of seeing these things happen will be piled on by "why didn't you do anything, enabler of sexism?" comments). But I'm afraid the answer will depend heavily on the field. In mathematics, it is fairly easy to get your own research projects started that have little to do with your supervisor; but in lab-based sciences? Suggest re-asking that question for specific fields.

Point 1 is persuasively documented in economics: https://www.aeaweb.org/articles?id=10.1257/aer.p20171126

@Dawn Though the author of that paper also noted that there is not a significant difference when there is a clear ordering of contributions (i.e. first-author-is-main-author style) or when the other collaborators are also female.

Close-voters, why do you see this as opinion-based? Aren't there any rigorous studies on the effect of race & gender on hiring or on perception of academic merit?

@henning There are plenty of studies, but the OP doesn't seem to have tried to find any of them. Instead this question is a solicitation of opinions from ASE.

Does it happen? Is what these women faculty describe true? For those
  of you who have served on faculty/post-doc selection committees, have
  you seen the evaluations of comparative candidates differ according to
  their gender?

Yes. This does happen. It is often hard to recognize - there's a degree of implicit bias at work all the time that's difficult to detect, because rare are applicants with genuinely comparative applications. It's easy to write off something one way or another - the prestige of the journals in question, the conclusions of the paper, etc. But I have, at times, seen it.

Latino and Black applicants: There were no Latino or African-American
  faculty on these panels, but the reasons the women faculty gave for
  why women should go the extra mile in establishing independence seem
  to also apply to candidates from underrepresented groups. Have you
  seen evaluations differ according to whether candidates were from such
  groups?

While I encounter this less commonly because of the wide underrepresentation of these (and other) minoritized groups generally, I have seen it happen.

How else might a candidate demonstrate sufficient independence from
  her PI? Recommendation letters can conceivably convey the quality and
  independence of a candidate, but are there things the candidate can do
  herself?

A couple things come to mind:

Being the PI on your own project. These may be small pilot grants or the like, no one expects you to land an R01 or the like. But it suggests some driving of your own research project.
Collaborations with not your PI. Your PI does not have to be on every paper you write, and it's possible to establish side projects etc. with other researchers. This occasionally has to be done with caution, due the the balancing of commitments, but it is possible.
If your job applications end up with a "Chalk Talk" where you outline your research agenda, nailing that. In my experience, this is where most candidates where I am, regardless of their gender, race or ethnicity, fail to establish their independence. You need to learn to tell the story of you the researcher, and how what you've done is, by and large, a logical arc into what you will do as an independent researcher.

These are good suggestions on ways to establish independence. In particular, using the "Chalk Talk" as an opportunity to tell your personal story as a researcher is something that I have never heard before.


text:
In which section of a paper/thesis to report tercile split and dummy coding of variable?
I'm writing my thesis in psychological research. On one variable I did a tercile split because in other empirical work it is often done so and literature says that most likely there will be effects on the extremer parts of the distribution. In analyses then, I will use a dummy-coded variable.
In which section I should report the tercile split? Directly in methods section when I describe the measure itself?
Or little bit later in analysis plan where I mention the statistical methods (e.g. regression) used?
Edit: I have to mention that the scale was a 10 point scale but in sample only values between 3 to 7 were observed, so this was also an argument for categorizing the variable.

Have you discussed this with your advisor?

Unfortunately, the adviser isn't available. Do you ask because splitting continuous vars may be an issue for itself? I have to mention that the scale was a 10 point scale but in sample only values between 3 to 7 were observed.

I’m voting to close this question because it's probably better asked on stats.stackexchange.com.

I agree that this may get better answers at CrossValidated, and have flagged and asked the moderators to migrate it.

Don't split your variable. This loses information for no reason. Instead, use a spline transform if you believe the response might be nonlinear. (If you believe you need to use splits because previous work did so, then consider running an analysis with a split and reporting it in an appendix. That other people ran bad analyses is not a reason to continue running bad analyses.)
In the "Methods" section, I would recommend you just explain the measure used, together with the relevant literature. Discuss any statistical transformations - whether splitting or spline transformation - in the "Statistical analysis" section.
This is at least what I would recommend. Alternatively, you could take a look at a couple of papers in the journal you plan on submitting to, and see how they dealt with similar transformations.

I agree with Stephen's answer and comment.  I think you may have added your edit after his answer, which is OK, but what I'm writing about is related to that.
Just adding that you say your variable is an integer from 1 to 10 but you only have 3 through 7 in your data. Then, splitting really is odd. You are going from a variable with 5 levels to one with 3. Also, you say that literature says the effects are in the more extreme parts of the variable -- in that literature, was the same scale used? Were the more extreme parts 1 and 2 and 8, 9 and 10?  Or was it a different variable?
Finally, that sounds like it could be a count variable, or perhaps a Likert-type variable; let us know which. And, is that variable the dependent variable or an independent variable?


text:
Professor stopped responding to emails suddenly. What should I do?
I am an MS student in France. It is commonplace here to seek out professors from other universities or scientists at research centres to do the MS thesis under them, which is usually during the final semester. So, I reached out to a professor at a US university to carry out my thesis under him. I attached a motivation letter, CV and transcript with the initial email. I also mentioned that I have a scholarship and will not require funding. I heard back on the same day from him and he thanked me for my interest in his research. He said he would like to know a bit more about what I am proposing and went on to ask me about the duration of my thesis, the thesis requirements from my university and what I planned to do following graduation. He ended the email saying he was looking forward to our discussion. I responded to the email within two hours but he never replied. I waited a week to send him another email but he did not respond to that as well. It has been one week since. I do not know what to make of the situation. Is it appropriate to send him another email after a week? I don't understand why he would lose interest all of a sudden when he already had a chance to not respond after looking at my CV?

Especially at the moment (early 2020, with coronavirus) he might be ill, or in isolation and unable to check his emails remotely. Perhaps his department closed before he could pick up a laptop to take home, or even set up an out-of-office on his email. You could try finding a departmental office contact through the university's website and email them asking if the professor is still contactable. Generic departmental emails are probably more likely to be picked up by staff working at home.

I hope that is the case. That's indeed a good idea! I'll try to establish contact with the departmental office to ask about him. Thank you.

You have options.
You could wait and hope. The person is probably pretty busy right now.
You could try again, but I'd recommend against flooding the person with too many mails or too much information at a given time.
You could cast a wider net and try a few other professors at other places.
You could give up.
You could use some combination of the above. But casting a wider net is likely your best option, even in combination with others.

Thanks for the help. Yes, I am planning to email other professors and I'm going through the research of a few that I've identified. I still hope I receive a response to this, even if its a negative one.


text:
What do you do if you are being 'ghosted' by the Chief Editor of a journal?
My situation/timeline is this:

Submit paper ~ 9 months ago
6 months in peer-review, at which point I
sent 2-3 unanswered emails after 4-6 months asking if any update
No acknowledgement of those emails, but major revision decision
eventually communicated with 4 weeks to do revisions
Request (and am approved) for an extension
Reach out to editor asking how best to resubmit revised version (since revision option has since expired through the official submission portal)
Check-in via email two more times (both the journal chiefeditor@journal.com email, and the personal academic email of the Chief Editor), and have now 4 weeks of waiting with fully revised version ready to submit just to receive advice on how to resubmit

I feel I have done all I can. I have been communicating with the Chief Editor, and the Associate Editor who handled the paper is seemingly anonymous so I cannot contact them.
The journal is a small-ish, but reputable journal in the field. Because of it's size, there is just the one Chief Editor, and there are no official admin staff (Assistant Editor I think it is called?) who I can contact at the journal.
I am at a career stage where first-author publications are so important. These delays suck. I'm trying to be respectful but also look out for myself here, but I actually don't know what else to do.
Do any Editors out there who have any experience of handling such a situation from the journal-side have any advice?

Keep in mind that while publication is a huge issue for you, the editor has loads of these things going on simultaneously.  From their point of view you're one noise in a thunderstorm and everyone wants what they want yesterday.

You have been sending a lot of emails to the editor. Way too many, IMHO. See this post and also the answers to questions linked there (there are a lot of questions on this site on the question "the status of my paper hasn't changed in the submission system for N months, what should I do?" and the answer is almost universally: wait and let the people involved do their work, sending emails is most likely both annoying and won't speed up anything.)
From those that you listed, the only valid reason to send an email I can see (apart from asking for an extension) is one asking how to resubmit. That's a valid question, but you shouldn't bother the (academic) editor with such an organisational / technical question, you should write to the editorial office (that is what you should be looking for, not assistant editor).
Why might the editor not respond? After so many emails, he or she might very well have gotten used to ignoring your emails.

I am very surprised to feel as though I am being blamed in your comment. I would say that if truly, because of a few polite emails over the course of many months, they have indeed decided to ignore me, that is incredibly immature. We do not all the know the unspoken rules of academia - in any other profession this polite checking in would be more than reasonable.

There are no other email addresses available on the journal page (of an editorial office as you suggested), other than the production team  - who responded immediately to say they could not help. Hence the quandary.

But, thank you for the answer. It is very useful context to know that this is probably perceived as an overboard amount of emailing.

There are a lot of options for reasons of not getting a response: the editor is lazy, sick, overwhelmed, or you have somehow offended them in your communications, or your communications aren't getting through somehow.
As to how to resubmit it if the submission system isn't available, just send it to them directly with a (polite) note.
You can then be patient and wait for things to play out, though I understand your pressures.
Your other option is to withdraw the paper and submit it elsewhere, though that will just start the process over at a different journal, costing time. You don't need an acknowledgement if you choose that route. A note that you intend to withdraw the paper on (some definite future date) if you don't hear from them by then is sufficient.
For a truly reputable journal, patience is probably your best bet, though you need some assurance that your communications are being received.

Interesting, I did not know that potentially sending it directly to them might be an OK option here. Perhaps I will wait a while since I have emailed recently, then send it in if I do not hear back in the next month or so.


text:
Moving from business to academia
I've been working in commercial software development for quite a while for now, and I'm getting more and more disappointed in the way things are being done here as time passes.
So I was thinking to get back to academia, but the problem is that even though I hold master's degree, I have just a couple of publications (rather weak, I suppose), and there are no letters of recommendation in my disposal. Moreover, all colleagues I can possibly reference are engineers, not a scientists.
Basically, I'm quite used to applying to jobs I do not fit entirely (I mean not 100% of requirements met) judging by their requirements list in commercial sphere, but how mandatory publications and references are? My estimation is that I'm still capable of at least supporting research project as a engineer, while regaining lucking researcher skills.

What position are you hoping for?

Well, I guess "PhD student/junior researcher" should more or less precisely express my intents.

By junior researcher, what do you mean?

If you are disappointed by the way things are done in the commercial software environment, what do you expect to be different in the academic field? Attitude, procrastination, meetings and output....

Basically, I don't like software appliance. AI used to attach stickers to photo on the phone? Guess we can do better then that.

You can do it.  You don't really need publications.  You need to think through some things like income needs and status change (students are lower status in society than working professionals).  That said, it can be a very nice experience to be able to spend all of your time on some problem and know it best in the world.  You have a lot of time freedom also.  I  would not assume you will be having an impact on people/industry though (closer to that now).  But if you are of a theoretical bent, maybe it is good.

You question whether you satisfy the requirements for a position as a PhD student. The minimum requirement for such a position is a bachelor's degree, albeit, many positions will require a master's. You satisfy both of those requirements, so your move from software development to academia is entirely plausible.
You seem to believe that publications are required for a PhD student position. They are not, at least, not at many institutes. They are nonetheless useful, even "just a couple," even if "[they're] rather weak," since they demonstrate an ability to do research and an understanding of the research process.
You are concerned that your referees are engineers, rather than scientists. This isn't a problem, actually it is an asset, as is your software engineering background. Impact is a measure of success in academia and your real-world experience can guide you towards practical research problems that have more potential for impact.

You can go back as a PhD student and @user2768 has given a good answer to that. I just want to point out a different path.
Many research projects require software development. If you want to do research and not specifically computer science / engineering research, you could join a research group as their software developer. If you wanted to make a career out of it, you would probably need to get a PhD, but it may be that the research group would be able to help with that. In addition, it would allow you to see whether research is what you want to do while still being gainfully employed (albeit at a lower payscale than what you would get in commercial software development).


text:
Is my advisor being unreasonable by not approving classes in a different field than his?
I started my PhD in CS last fall in a lab doing one particular field (neurological-based deep learning) since that's what I was interested in when I was in undergrad applying and for about the first year of grad school. Since then, I stumbled into NLP and I find it fascinating I've been reading a lot of papers and  I think I'd like to pursue it for my academic career – I've even started attending lab meetings with another lab in my department doing NLP. I'd really like to take a formal course in NLP, especially one taught by the PI of this other lab, but my advisor needs to approve any course I take, and he won't sign off on any course that isn't in his field. He says there's no point in me taking a course that won't benefit my work in his lab. Is he being reasonable here, or should I be able to take courses in tangential fields?

I suggest you provide a few more details to get better answers. What country or part of the world are you in? Is your advisor funding you? Does he realize you plan to switch groups? Offhand: his position seems reasonable if he is paying for your studies and expects you to work for him; unreasonable if he realizes you plan to switch and is trying to keep you by force.

What country is this?  In many countries PhD students do not usually take classes, while in others they take classes in a range of topics.

What's NLP? Please, avoid acronyms when you write to a varied audience.

It all boils down to your advisor’s estimate of your capacity to complete your PhD in time. Perhaps your advisor sees your newfound love for NLP as a distraction from what should be your main focus: successfully defending your thesis within the span of X years. If you are well on the road to graduation and are exploring a side project then the restriction may be unfounded, though not unjustified (perhaps further establishing yourself in your field would improve your career prospects).
Of course, no one can stop you from independent study or taking a Coursera class, but your advisor’s reluctance likely stems from the concerns I mentioned above. This should also be something you shouldn’t take lightly: there’s often good reason to listen to one’s advisor.
Good luck!


text:
Why use 'advisor' or 'supervisor' instead of just 'collaborator'?
This bugs me a bit. I understand that technically the advisor or supervisor relationship may be a bit different from the more senior-level collaborations, but I can't help but think when I see people say "thanks to my supervisors/advisors for their help with this project" (i.e. on Twitter press-releases of research, at the beginning/end of presentations at conferences) that it is a bit infantilising... I am not suggesting it is a particularly important problem, but from many PhD students I know and from my own personal experience, the supervisor role can certainly be very much equivalent to normal collaboration between other academics. I think it makes a PhD student sound more independent and capable if they were to refer to their co-authors on papers published during their PhD as their collaborators - even if they are in fact their supervisor/advisor.
Keen to hear others thoughts!

Advisors typically provide a very different kind of help than other collaborators (both quantity and quality) and identifying them as an advisor serves to acknowledge that.

I like this question. And I would love the term supervisor to be abandoned. It has become a weapon to exploit students. But then many PhD students are too naive to be qualified as collaborators.

I always had the impression that the choice of words between "advisor" and "supervisor" was mainly cultural; "advisor" seems to be prevalent here in the US, while "supervisor" seems more common in Europe.  Maybe it's just terminology, or maybe it reflects an actual difference in how advising/supervision works; I don't know.  Perhaps a different question...

@NateEldredge I would say an advisor is a student relationship. As a post-bacc employee, I probably would have called her my "supervisor," not my "advisor." Good q tho

I agree with @NateEldredge, but at least "my supervisor" is better than "my PI".

You're overthinking this. "Advisor" is the easiest/least awkward way to refer to your advisor, and people are generally aware of the fact that advisees have largely varying levels of independence.

@kosmos : 'supervisor' is a weapon to exploit students? That's quite a claim?

-1, this isn't really a clear question. Either someone is a collaborator - because both parties appear as authors - or they aren't. Put it this way: You wouldn't add a "thanks to my collaborator" as a comment at the end of a presentation. If indeed it were a collaboration, the entire work will have been presented as a collaboration. If not then sometimes you still want to thank/acknowledge someone's help. I don't know what you are getting at really.

Certainly in the many experiemental sciences, supervisor is more accurate than advisor, because the "supervisor" has various administrative and legal responsibilities for the student - for example, the supervisor would be legally liable if the student is injured in the lab or engages in scientific misconduct, and the supervisor generally controls the purse strings.

Collaborating is not necessarily a 2-way street where both lanes to at the same speed: almost all students collaborate with their supervisors, but not all supervisors collaborate with their students.

This seems more like a statement of the OP's opinion than a question.

While advisors/supervisors are collaborators, not all collaborators are advisors/supervisors. So, be specific.

In pure math, advisors are typically not even collaborators, at least not on all of the student's work.

T_M - Surprised to hear that you think it is unusual to thank your collaborators at the start of end of a presentation? I see this all the time. Very few people in my field (biology/ecology) conduct an experiment without significant help (collaboration) from others. I struggle to see what is unclear in the question. I am surprised people are saying they haven't heard this before - clearly I have or else I wouldn't have asked the question. If you think its a non-issue then I would say your expertise isn't relevant to the question, rather than the question itself being unclear.

I think you're correct that the supervisor role can be equivalent to normal collaboration in that the student will bring their own unique ideas, knowledge, and experience to build on a mutual project collaboratively. However, where I think there is an unavoidable difference (at least, in every student I have met including myself) is the conception of viable projects. In my field I've never heard of a student (masters or PhD) conceiving from the ground-up their entire project. They're always built from a project advertised to prospective students, or developed with the supervisor (often from previous work) where a research relationship already exists.
As a student, you're learning to become an independent researcher. This means learning what is and isn't scientifically interesting and viable, how to search the literature and theory for relevant information, etc.. This is what a supervisor is teaching, and this is a very specific relationship that isn't properly conveyed with "collaborator".
This distinction is most important when there are multiple co-authors on a paper, including co-authors that are not the supervisor. The non-supervisor co-authors fit the description of collaborators and still should be described as such, no matter their academic "rank".

Indeed. The point of a PhD is to learn to be an independent researcher. Thus, by necessity, the PhD student isn't and independent researcher when they start. It is the job of the supervisor to guide the student on the journey from dependent to independent. Some students will be need more guidance than others.

Thanks for your input. I agree with what you have said. I have come across some people that have very much had a ground-up approach and I suppose that is where one contradiction appeared for me.
I suppose another element that spurred this is for a project I am doing I worked with what would be a 'collaborator' for much of a chapter of my thesis with my 'supervisors' doing far less actual supervising than the collaborator. Again, just seemed a contradiction that made me question the terminology.

I don't think I have ever seen anybody ever "thank their advisor/supervisor(s)" (in a presentation or press statement) without explicitly name them.  One of the purposes of such a statement is to communicate the existence of a particular student-advisor relationship. There is a number of reason someone might want to do so:

The relationship will immediately provide some additional context to the scientific work being presented for people in the community familiar with the advisor/supervisor.
Acknowledging the relation provides appropriate credit to the advisor. This is particularly important when the advisor is a junior faculty, since the successful supervision of students is one of the criteria they are judged upon. Seeing students of a researcher appear at conferences plays a role in reshaping how the community views a junior researcher as a viable more senior candidate.
The reputation of the advisor can be used as leverage to help people take a student more serious, especially when presenting research that is a bit "out there".
The reputation of the advisor my help shield against some members of the audience being particularly nasty.

+1, The last point is actually two, a good advisor and his group will additionally already have roasted you with nasty questions before the conference, so you wouldn´t actually need him in the audience as a sentinel, but could defend yourself. ;)

Thanks a lot, very interesting points - I agree that inheriting the reputation and using them as a human-shield is something unique to a 'supervisor' versus 'collaborator'!


text:
Are nonfiction writers, that avoid the use of footnotes/endnotes, respected by the academic community?
I've seen books of Jared Diamond (biogeographer) and other fine nonfiction writers, that don't use any references or footnotes/endnotes - not even bibliography. Instead, they put a "for further readings" section at the end, where they "talk" about related books, papers and articles, and they don't seem to express directly that they used any of those books for their writing.

Is that enough to be "respected" (or recommended to friends or family) by the academic community?
Doesn't he incur in plagiarism in any way?
What method would you use if you were writing for the popular?

There is a difference between 'popular' (meant for a wide audience) and 'scholarly' (meant for other academics). Which are you writing?

Popular, 100%, but I would also like to be "accepted" (not read) by scholars and academics.

I voted to close because this question is about the opinion of the writing community (not the academic community) on the writing of nonacademic books.

Academic books need those in-text citations.

You are right. I'm actually asking for the opinion of the academic community on Diamond's (and alikes) way of "adding references". I've restructured the whole question to be clear. Thank you for the observation.

Question 1 is unclear. What does "validity" mean here? Academics have a notion of validity of research articles, but that obviously doesn't apply here.

With validity I mean if you would recommend it to friends and family. I've edited the question one last time. It seems to be a topic that no one gives attention to. I haven't found an answer online. A lot of nonfiction writers with academic backgrounds are avoiding notes and references with the "further readings" option, which I believe incurs in plagiarism and ethical harm (according to standards). They even have won Pulitzer Prices... So, if both the popular and academics don´t care about it, maybe it's just an old ethical practice that today is no longer needed.

@RichardF. This is not really your question, but from what I can tell, Diamond isn't all that respected by the academic community. See, e.g. here: https://www.reddit.com/r/AskHistorians/comments/2mkcc3/how_do_modern_historians_and_history/

Your question does not address an attribute of a person (in this case: J. Diamond), but of a publication - or to be more precise, of the social system (e.g. system of scientific publications, system of popular books).
If X writes a paper for a scholarly journal, X needs to use footnotes or in-text citations because the scientific system requires the ability to trace the origins behind a statement. Otherwise, the system will reject the paper (through peer-reviewers and editors).
But if X writes for a popular press, such references are not required; editors may even reject book proposals if they seem 'too scientific'.
Thus, Jared Diamond uses footnotes or in-text references when he writes for an academic journal (such as this paper for the journal Biological Conservation). And Google Scholar tells us that this peer-reviewed paper has been cited more than 2.000 times in scholarly works. There therefore seems to be no lack of respect for Diamond's scientific outputs within the scientific system.

I don't see an issue in many (most?) cases. Especially if they are writing for a popular rather than academic audience. The question is the tradeoff between readability and the need for specificity in such works. Let me give an example.
While I'm a mathematician who taught CS until retirement, I read quite a lot of books on anthropology and archaeology. I don't read scientific papers, but try to follow advances as reported in the press as they occur.
There are two kinds of books. One in which an author will give a narrative covering what is known about a topic (say early humans in what became North America) without inline citations. These can be very readable, I find. There is no danger of assuming plagiarism since the author(s) give the further reading section which lists the source. Most of the ideas presented are "in their own words" rather than copied from sources, and most represent a scientific consensus along with some information about where the consensus breaks down.
Other authors, writing on the same topic use a large number of inline citations, with footnotes or (usually) endnotes. I find these to be much harder to follow and it is often necessary to go to the endnote as more is presented there than just the source, such as a few additional ideas. They may be a bit more precise, but for the audience, not essentially so.
So, in some sense, your question is, whether popularizers of science are respected or not. Some are, others not, of course. Great story tellers are valued, I guess. But it is a choice that an author makes. The ones I read are careful not to plagiarize, but are a bit less specific about which ideas come from which source. However, once a scientific consensus is achieved, even with some dissent, it seems less vital for these types of work. The "further reading" gives you a sense about how the consensus arose.
But if you are writing at the edge of the known world, the rules about citation are much more vital, since a consensus has not yet emerged.


text:
How to prepare for the job market during a (pure math) PhD
First of all, I apologise if a similar question has been asked before, I did some research but couldn't find a satisfying answer.
I'm a second-year pure math PhD-student (in EU, if that matters) in a field with relatively few real-world applications (low-dimensional topology). I am already determined that I won't pursue an academic career after the PhD, so I will have to transition into the job market at some point. However, this frightens me because my field has no real-world applications, and I think that it might be a good idea to start expanding my knowledge to a different field (say, computer science or economy). This brings up the following question: How do you do this during a PhD?
To be more precise, let's say I am interested in financial markets and would like to steer towards a job in quantitative finance. What is the best way to prepare for this during my PhD studies? The following options come to my mind:

Reading books and self-study. However, do employers value knowledge purely gained from self-studying (without any degree behind it)?
Participating in relevant courses at my university. However, does that make sense if I'm not a registered student and therefore won't get grades?
Participating in online courses (such as Coursera, for example). However, do employers value the participation in such courses?
Not doing anything, focus on my PhD and start looking for internships afterwards (to get knowledge).

I am aware that in almost any case mentioned above, I will still lack any sort of actual work experience (which is probably going to be the biggest problem in finding a job). However, I believe that I still might be in a better position if I already have some theoretical knowledge about a job's broader field rather than no knowledge. Of course, if there are any other options that I didn't mention above please let me know.
I would highly appreciate any advice, guidance or personal experience on this topic. Thanks!

Could you say why you are interested in financial markets? Have you read book or even done anything so far in this direction?

The interest in financial markets comes from my high-school education which was economy-focused and because I recently had my nose in books about financial mathematics and financial markets theory. I also figured that this might be a good place to both apply and benefit from my mathematical education. However, I am not fully determined yet in what direction I would like to go, another option would be computer science in which I'm genuinely interested and have a minor in.

@user331406 Different employers value different things. Some hedge funds would rather hire you with zero knowledge of finance, because at least you have no bad habits. Others would only hire you after you have done your time in an investment bank and have been properly indoctrinated. Your research in topology is almost certainly useless in finance and it merely signals that you likely have an IQ high enough to be worth investing resources in. The signal is there already — regardless of whether you finish the PhD. If you lost that loving feeling, dropping out can be wise. Learn how to program.

Try reading some of the AMS's advice, at least some of which should be applicable in Europe: https://www.ams.org/profession/career-info/career-index

Also, here's a closely related question on this site: https://academia.stackexchange.com/q/128318/19607

Take a look at this and this.

Thank you very much for your comments! I will take a look at the links you provided. @Kimball I totally missed the question you linked during my research and I'm sorry for that. It seems to me that my question is a bit more specific on what to do exactly during the PhD studies, but maybe it's worth to close/delete my question nonetheless.

Here are a few things that might benefit both your PhD and your preparation for the job search:

Communicate with your advisor. Setting goals and making plans with your advisor will help align how you measure the success of your graduate experience. You can also report to your advisor about your progress towards these goals; accountability goes a long way. Finally, your advisor can help you prepare for and find a job in industry, but only if they know that's what you want to do!
Code and compute. If you don't know how to code, take some courses and learn how. If you do know how to code, keep improving your abilities. Computing is a valuable skill for research, since examples will help you make sense of new ideas and constructions. In industry, computing will be invaluable. As a mathematician, employers will want to hire you for your analytical skills. These skills will be much more useful to them if you are comfortable gathering, producing, analyzing, and communicating data that they care about.
Connect. If you have the opportunity, do an internship in industry. You may find things that you like or dislike about working outside academia, and you may gain new insights into your academic work. You should also try networking. For better or worse, who you know makes a big difference in finding jobs. Your advisor might have some contacts in industry, or your university might have an employment center that can help you with this.

As an aside, even low-dimensional topology might not be as far removed from applications as you might think. Differential geometry and algebraic topology both have applications to data analytics and machine learning. Depending on your exact specialty, topological data analysis could be an opportunity for you to apply ideas from your PhD to finance or whatever industry you decide to join.

Thank you very much for your answer! You mentioned some very good points. I did quite a lot of programming in different languages during my bachelor's CS minor, and it might be a good idea to freshen things up.


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How to fill "department" for the author actually without department?
I found many journals require the department information for all authors during submitting manuscript. However, some authors indeed don't have department information. How can I fill this form in this condition?

I don't see anything wrong with "N/A". Don't overthink this --- odds are that no one with a say on the acceptance of your paper (editor, reviewers, editor in chief) will ever look at this field. They are only there for the convenience of the journal staff, as far as I understand.

Which is not to say you won't have a minor inconvenience later dealing with this, as the staff might not initially accept the idea that an author has no affiliation and request it be provided, or try to guess what it "should" be based on an e-mail address or another author, or recycle an old affiliation they had the last time they published with the journal, etc.  I've had all of these happen to me in recent memory, sometimes more than one (or the same one multiple times during the process) on the same submission. So you still have to pay attention, but none of this would disqualify the paper.


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How to seek advice/collaboration from other profs in the dept
I am a postdoc who changed the topic quite drastically entering the postdoc phase.
The big issue is that my advisor does not provide any guidance or advice at all regarding my project.
It has been quite difficult for me to come up with a good research topic in a whole new field on my own and I would like to seek advice from another professor.
Would this be rather unusual? Thinking from other professor's perspective, I don't think they will be too willing to spend time on someone else's postdoc.
Ideally, I want a situation where I can continue to discuss my work with another prof and get advice from regularly, but I am also trying to look a for a topic that will allow collaboration with other groups.
I can put in the time and our lab has good funding so I feel like I just need a little bit of insight from more experienced resear.
I would appreciate any advice! Thank you.

Does your advisor provide your funding? Was the current project his/hers?

He provides funding but that's pretty much it. To give an example, if we hypothesize that this funding is for cancer research, he is happy as long as I do something cancer and that's about it. The difficulty is that cancer is an extremely broad term and every member in the group does something vastly diff from me (e.g. plant biology).

Funding is good though and he is supportive of new ideas

If he is funding you, don't you sort of have to figure out with him something that you can work on together?

Can you get a collaboration mentor? Someone that you know have great collaboration networks or work well with others that can help guide and provide hints?

You are a post doc now. You can and should network with other researchers like an independent researcher that you are... For most post docs, most of their time is spent trying to land another job and role. It is quite well expected in most fields that networking and collaboration is expected for ongoing jobs and survival.


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Submitting code from my R package to a conference
I'm submitting a paper to a conference. The conference encourages also submitting code for reproducibility. My paper builds upon a previous paper, which had a corresponding R package. Therefore, for this paper I've been updating this R package with the various modifications that the new paper presents (but I haven't made these changes public). When submitting my code, should I say something like 'This code has been adapted from the XXX package'? Or could this be seen as breaching anonymity - even though I don't state it's my package?

The answer depends on the conference. Conferences often have more detailed instructions than "anonymous", did you check what they say? If they are not clear enough, ask the chair, it is their job.

The version reviewed and the version published don't need to be identical in most cases. For the reviewed version say "adapted from XXX with permission". Take advice from the program/committee chair about changing those last two words.

If you don't include such a statement, then you're not adequately showing the provenance of your code, just as surely as if you left out important citations.  In addition to the obvious academic concerns this would cause, it could certainly cause licensing issues down the line.

I don't think "This code has been adapted from the XXX package" breaks anonymity, but you should probably mention this issue to the conference people when you submit the paper.
Also you should check the license conditions for the package. Pretend you are not the package author and see if other people would be allowed to adapt it like this.


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How can I focus my research without being overwhelmed?
I'm a first-year statistics PhD student. I have a general problem that I'm trying to solve and as part of that I read a lot of papers on various ideas/approaches. I often find a very nice approach that I like the look of, so I try to understand it and read the paper thoroughly, and also implement it if I can.
However, in reading the paper, I will often then click on the sources and find another idea, which I find just as interesting. I then often end up with a long list of papers I think I need to read and find myself stuck on which approach I should pursue further. In an ideal world I would read as many papers as possible and then pick the 'best' approach for my problem, but my time is limited. As only a first-year, I'm worried that if I don't read enough of these papers, I will miss a key part of the problem and not be able to solve it using the best approach, because my understanding of my research field is still far from comprehensive.
How can I remain focus on my research problem? How do I know which papers I should actually read and which I should discard? I would appreciate some general framework or tips from those who have gone through this.

You mention a "research problem" that you would like to focus on. How specific is this problem? Do you have defined hypotheses already or are you in the process of finding them?

I made it through the same thing as you. Now I am a third-year Ph.D., close to my defense. So the best tip I can give you is to look at which authors are mentioned the most in the introduction.
While you are looking for papers online you use specific keywords. Stay close to "up2date" papers, which are not older than 2 years. Look who is the corresponding author, and who is cited the most. So if you read the 5-7 popular papers in your field you will get a good feeling for who is important and in front of the novel project in your field.
Also, there are small tools for help to use, i.e. VOSviewer. This is a program you can use with a web of science and visualize the main authors and journals of the field you are interested in. After that, you should make a small PowerPoint presentation for yourself with the information on what is already done and where you see a chance to fill some missing papers in this field. While working on your presentation you will see, if you need more papers or not.
I hope this helps you to begin!
And then write a short abstract about what your project should be and talk with your supervisor about it. And try to start to work on it as soon as possible and don't read too much :)

Two years? Your field is moving fast.

@henning for sure you can look for older papers, but sounds like he has already a lot of papers. so don't stick to too much at the beginning. you can always rearrange the time

@Andrea I'd go by how often survey studies are typically getting published, and start with those as well. Find the most recent and decent one and go through the newer studies after. Two years between major survey studies is a fast moving field.


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Choose a referee who knows me better or one who is better known?
I'm currently choosing my second referee for a masters application. I did an academic internship and I worked closely with two people while there. One of the people was the Director of the institute and is more experienced than the other. However, I know the other person better and believe she would write a better reference. Should I go for the person who may be better known in the world of academia, or the person who will write a better letter?

Can't you have both? Both attributes are obviously potentially helpful.

On any sort of application, for school or a job you want to build a portfolio that highlights your suitability for the desired position. Neither of your referrers will be there with you if you get the position. All they can do is speak to your suitability as they see it.
So, choose the one who can best speak to your abilities and general characteristics that suggest success. This would seem to suggest the "other" person.
However, you know something about each of them and are a better judge. But it isn't the capabilities of those giving references that will be judged. It is what they say about yours.
Later in your career it might be different, if you have a powerful sponsor who will continue a collaborative association with you going forward.


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Using Google Scholar for meta-analysis
I'm working on a meta-analysis proposal/protocol, and one of the databases I would like to use is Google Scholar because of an anticipated scarcity in papers on the topic of my meta-analysis, and I'm thinking using Google Scholar would increase my yield.  Of course, it applies that I vet the papers I select, and thoroughly assess for bias.
If one is thinking of publishing their meta-analysis, would editors take using Google Scholar badly?

Can you add more context?

Using Google Scholar is usually discouraged as your primary database in systematic reviews because the searches are not reproducible (recommended are databases that provide reproducible searches such as Web Of Knowledge, if you have access, or CrossRef). Using it as one of the secondary strategies, is not necessarily problematic but the issue of reproducibility still applies.
The reproducibility of your search strategy is important because it is your method for the systematic review (in your case a meta-analysis) and determines which effects are included.
Also note that if you already consider your literature to be scarce, Google Scholar might make it more difficult to find sources, because of the low specificity of searches (Google Scholar tends to have way more results than are relevant to the search on the later pages).

"Reproducibility is unattainable, but you can prove...results were derived by [systematic review]" -- https://academia.stackexchange.com/a/120064/22768


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Can I get an admission for a mathematics masters program with only an acceptable GRE subject score and an unrelated bachelors degree?
I have a degree in Civil Engineering and I want to continue my studies in the field of mathematics. I think the only option that I have to enhance my application is to take the GRE mathematics subject test. If I can get a good score, will I have a chance to get an admission in a top university?
Thanks.

Forget about credentials - how prepared are you for a Masters in mathematics?  Have you learned how to read and write mathematical proofs and learned the material in standard upper level mathematics courses such as real analysis and abstract algebra?  If I asked you to prove that every subgroup of index 2 is normal or that the integral of the limit of a uniformly convergent sequence of functions is the limit of the sequence of integrals, could you do it (with some review)?

I’m not sure how much of a difference it makes - but would this apply to both pure math and applied math studies?

@GrayLiterature: I wrote that with pure math in mind.  "Applied math" has a wide variation in methodology, from research that looks like pure math research but is on topics with more obvious applications, to what is really theoretical biology that isn't in a biology department because biologists aren't comfortable with colleagues who don't have physical labs.

@AlexanderWoo, you are pointing out very valid concerns, but since I intend to apply for Applied Math I thought these might not be important issues. Would you say that it is plausible (in an acceptable degree) to get into such program?

@K.Ara - It depends on what you mean by a "top" program.  For historical reasons, applied math of the theorem proving kind has higher prestige than applied math of the modelling kind, so "top" programs tend to be biased toward theorem proving (and frequently are part of the same department and degree programs as pure mathematics).  At such a university, you will be completely lost in a graduate class in applied mathematics without the necessary analysis background, though you might not need the algebra.

@K.Ara - Two more comments.  First, in the US, most top programs no longer admit students only for a Masters - they admit students (with only a Bachelors degree) straight to their PhD program, though some of these students will end up with a Masters if they do enough before dropping out of the PhD.  Second, if you are willing to pay tuition, there are some (even quite well-regarded) schools that will be happy to admit you, take your money, let you attend classes, and give you a Masters degree they know no one respects even if you learn nothing.

I'm going to guess that it will be difficult, depending on what you mean by a "top university". Your CE background has some math, it is true, but you are probably missing quite a few of the courses that math graduates will have had.
The math subject test itself is very difficult and tries to cover many topics. Even a math graduate will have had no courses at all that cover many of those topics and even they won't be able to answer them. I did quite well on the test (with a very strong math major) but still felt terrible on finishing the exam.
The only way to be certain, of course, is to make application to a few places. But I think you might need more math background than would be typical in any engineering degree. An applied math program might be within reach, though.
There is a lot of competition and most of it coming from people with a full math curriculum behind them.
I'd suggest, however, that you find a way to talk to (or even visit) a potential institution and discuss it with an admissions person. They might have specific advice about what you need and how you could get it. A pretty steep climb overall, I'd think, unless your background is unusual.


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What should I do if I was wrongly accused of cheating?
I used to think that online exams allow me to perform better in exams in a more relaxed setting, but today after an examination I changed my opinions, because the tutor proctor probably thought I was cheating and he reported the incident to the professor.
Just 20 minutes into the exam somebody was knocking my door (I did not dare to respond at first but the knocks kept getting stronger), so I opened the chatbox in Zoom and asked the tutor to let me leave my seat. Sadly, I may have forgot to close the chatbox, and because I used my mobile phone for Zoom (because my macbook encounters the errors "There is no connected camera" constantly), during the period of my leaving my camera was not opened. When I got back to the seat I hurriedly close the chatbox and continue with the examination. What I did not see is the mesage by the tutor "Why did you close the camera?". So during the period of my leaving my tutor did not see me. But this is not the end of my misfortune (or the consequences of my carelessness)
At the end of the exams, when students were supposed to upload the scripts, I realised I forgot to write down my student ID on the first page of the script, and I hurriedly write down the ID, all while the tutor saw me writing it down. He immediately messaged me in the chatbox telling me he would report it to the professor. What followed was my nervous pleading in the chatbox that I did not cheat and all I was writing down was my student ID.
I feel very dejected after this exam. I am an extremely honest kind of a person when it comes to academic affairs, and I take research and thinking very seriously. The examination was an exam on network models and the difficulty lies in the proof, so there is no way I can cheat in such a short period of time. The exam is even open-book so I am allowed to check the facts I forgot, and I need not memorise any algorithm so there is no need for a computer. But I think my nervous impression and the subtle anger of the tutor already sounded a death knell. I cannot write down in words how catastrophic this feels for me, because I suffered from extreme anxiety in the past and this significantly impacted my grades already. But after recovering from this I chose mathematics as my minor anyway despite its difficulty instead of choosing an easy path to improve my grades. I was improving my grades a lot last semester, but here comes this unexpected incident. I am now thrown into the mode of reminiscence and remorse, as I feel like despite my honesty to my own feelings and thinking, for example in pursuing my dream as a neuroscientist instead of taking the more respected career of medicine, or in choosing a harder minor as opposed to easier junior electives to inflate my grades, these are all just living in my own head, and they carry no value when an incident like this arises. I do not know if I can still stand this impermanence.
But I know very clearly I have to do something to minimise the damage done. What rational actions should I do?
=============Updates 2:54 pm 19 May 2020=============
After settling my mind down I feel much better, and I received the email reply from my professor saying that "There is nothing serious. So don't worry!". So it seems that he does believe in me or he is a professor very tolerant of students' dilemma. On my anxiety-induced Google search of similar incidents, I found due to Covid-19 and the shift to online exams and learning, many more students are facing such difficulties. For future readers who will have similar concerns as mine, please in addition to all the panicking and worrying realise somebody has been through similar problems and be them lucky or unlucky they definitely understand your psychological tension, a fact that should be solacing you too. Also, please think and write a logical defence for yourself, and if needed please collect similar cases and present a stronger case.

Don't worry! If you did not cheat you should be able to just explain as much what happened. There are a few previous questions about this. Search for "wrongly accused of cheating" or "falsely accused of cheating" and something should come up that answers you.

Given what you describe - if you were the proctor watching students what would you think of the situation...
So, when they contact you, you will have to present your side of the story, then a decision will be made.
Why did you not just shout at the door “I am in an exam, go away” - at least the proctor could not construe those words for trying to cheat.
Also consider putting a note with times on your door saying you are in an exam and will not reply.

Thank you for your advice, your thinking shifts my focus from myself to others and I am feeling much better. I realise your advice is very logical and easy to adopt too.

@Hephaes glad it helps you, best of luck I hope it gets sorted.

This answer is a good advice for those online  exam takers. I am wondering where those downvotes came from. Upvotes for the answer and the question.

@scaaahu Thank you for the vote and compliment.

I wasn't a down vote, but the "Why did you not" paragraph and following might have generated one or more. It would only have been useful for the OP to have seen this prior to the exam.

@Buffy sometimes answers have a future component for others not only the op...

Yes, I know and usually write for the future, but a different phrasing might have been better here. (I read your Meta, BTW, and this post came to mind).


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Is an informal postdoc offer in an email by a top UK university relatively secure?
A few days after two rigorous interviews for a postdoctoral position at a highly reputable UK university, I received an email from HR, along the lines of:

Could you please send us your passport details, so we can confirm you for the role?

I wasn't quite sure what the email implied. While I was cautiously optimistic, I was not certain whether it is just bureaucracy, or if it indeed suggests that I have secured the role. After immediately sending the requested documents and not hearing anything else from the HR person, I contacted the interviewer, who mentioned that the email implies that I will be receiving a formal offer soon. I started celebrating for securing said position and sent an email in response to the interviewers, to thank them, and to express looking forward to work with them. A few days have now passed (4 to be specific), and I have yet to receive a formal offer; although, one of the interviewers who was CC'ed in the email that I had sent days earlier, just congratulated me in response this morning, and also expressed looking forward to work with me.
I wrote the HR person this morning, asking whether they could confirm that they have received the passport details that I had sent them days earlier, and if they need any other documents - I have yet to receive a response (albeit the email was sent this morning). I have started to get somewhat nervous and wondered if this delay by the HR is normal?
Additional info: I am a UK national, so while I could have appreciated delays due to visa requirements etc, this does not apply to me.

Did you send your UK passport details, or are you a foreign national?

@AzorAhai-him- I am a British citizen and sent UK passport details. I could have understood delays if I was a forgeign national, but I am not.

Re. delays: A lot of university admin is short-staffed at the moment, as people need to use up their leave entitlement by the end of the year.

Hiring in universities can be very slow at times, and I had about a month between my informal postdoc offer and my formal offer.
In general, if the professor/interview panel has decided you are the candidate they want to hire, that can only really change if HR finds something wrong with the application (e.g. you don't obviously meet the requirements and the panel didn't explain why you are still their choice), if you won't be able to obtain legal permission to work, or if the funding for the position falls through.
The best thing to do is to keep in touch with the PI who is hiring you. They can advise you on where in the process things are (e.g. if it is with department chairs for review/approval, forwarded to finance for approval, forwarded to HR for action, etc.), and if it becomes a long time after the informal offer they can also try to chase HR to get them to make the offer.

Relatively, yes. Absolutely, no. Don't turn down other opportunities until it is formalized. The formal offer might not be possible until they confirm some details such as they have requested.
Action within a day or so might not be possible. Relax.