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Phase out postdoc position
I am a postdoc in cell biology and I'm considering to change my career path after having spent the last 1.5 years in a lab that has completely destroyed my passion for the academic life.
Background: I was working abroad for a few years and, due to personal reasons, I asked a PI with which I collaborated in the past the possibility to go back to the homeland. I knew this to be a suboptimal solution but I needed to go back. This PI accepted and, to smooth the transition, I wrote a EU grant proposal, which was funded (yay!) to move back to my homeland.
The new lab is mainly a clinically oriented lab run by MD, but it has contributed to the field with nice basic science discoveries, generally with the help of collaborating lab. My tasks were to basically to setup and run the cell biology section of the lab.
For the first year, I was forced to write grants for the two/three PIs in the lab and I (33 y.o.). We got in total 3 grants (~ 2 M€).
My project theoretically started last autumn, but I was "forced" by the PI to give priority to these new projects rather than to mine. Due to severe issues with our collaborators, I got the cell lines I wanted to work on in my project with 6 months of delay, and other issues did not allow me to physically start my project before 8 months of delay. Now, after 1 year into my project, the experiments have still to start, mainly due to:

the lack of a proper organisation in the lab: there are no lab meetings, there is no supervision on the experiments, the PIs work in a separate premise. There's also a shortage of workforce, as they pretend that 1 person (me) can run the whole cell culture facility AND perform functional experiments AND order reagents AND collect quotations from vendors AND do conference calls AND analyse results AND go to the ethic committee AND write grants.
a proper lab structure: all the 4 postdocs in the lab are treated as technicians and the PIs do not have skills to understand the basic science we do.  The two/three PIs do not understand that these are severe issues and they are constantly asking for results.
a decent mentoring: as I'm the most expert person in the lab concerning cell biology, I'm not receiving any helpful mentoring tips from my PI on my everyday work. Moreover, being the only one to understand a topic implies that the discussions on my topic are generally between me and myself.

Now, after 1.5 years in this lab I would really like to leave that toxic environment but this will mean to stop my EU-funded project (12 over 24 months left) and will clearly burn all the bridges for future academic position in my city and, probably, in the whole country.
I'm considering whether to switch to industry jobs, but this would mean to start again from scratch and acquire new skills. I've notice I've acquired skills and achievements (papers, h-index, citations, etc..) that are now completely useless in the current job market in my country. I'll do what necessary of course, but it will be a bad hit for both the spirit and the career. Start from scratch in another field in mid-30s isn't often a very successful strategy.
Do you have any tips or suggestion to escape from this toxic situation that is now also significantly affecting my health?
Thanks :)

First, congratulations on getting all these grants, it looks like you're very good at your job! It looks to me like the problem is not academia vs. industry, it's just that your particular work environment is terrible. Important question: are you the PI on any of these grants? it's sometimes possible for a postdoc to be PI, in which case it might be your responsibility to plan how the project is going to continue. Otherwise you can give your notice and walk out, it's their mess not yours.

I forgot to mention: there are certainly many companies interested in your skills, particularly your grant writing skills! so you certainly wouldn't have to "start from scratch", you may not realize but you do have valuable skills for industry.

Thanks Erwan for the reply. The grant I used to move back to my country is mine, while in the other three I'm not the PI even though all the grants rely on my cell biology skills, as at the moment I'm the only one in the lab able to perform those exps.
It is indeed interesting what you say about writing grant skills, and I will look actively forward to those positions. My fear is that, as cell biology is not very developed in my country, most of the industries would simply not be interested in those skills while they actively look for other profiles.

Sounds like a lot of work, but I have to ask - how did you expect less? Wasn't your PhD also juggling several responsibilities and dealing with myriad setbacks?

Yes, PhD was similar to that as well, but will less responsibilities (of course). Moreover, since PhD was an early step in my career, not many important decisions were made and I literally could have changed path without affecting much the later career. I was very calm and a bit more light-minded. Now that there seems to be only one career path, to recognise and understand that this single track is failing is really a terrible sensation.

I'm not familiar with finding mechanisms outside the USA, so I apologize for my ignorance. Are any of the grants transferrable? At least in the US, some of them are so if you switch institutions, that money goes with you. I would imagine most places would be happy to accept someone bringing them funding. If they are, try applying for positions at other institutions and make sure to mention that you already have funding and are bringing that funding to them.

You are working in a dysfunctional organization.  This can happen anywhere.  You can look for a job in a better organization.  Just keep in mind that industry organizations can also be dysfunctional.  When you make your next career move, investigate the reputation of your next employer to find out what their strengths and weaknesses are.
If any of your grants were in your own name, use those resources to control your situation.  Remember that your PI only has power over you while they have something you need.  If you do not want to keep working there, then that power is essentially gone and you can act in your own interests.  In reality, your PI needs you more than you need them.  Since you are apparently very good at grant writing, you bring in more money than you cost in salary.  This means you hold a great deal of power.


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Why would professors pay to publish in a good journal?
The journal that I think of specifically is Physical Review Letters.  I've heard that professors pay pretty high amounts to get published in this journal, which is considered a good, if not top-tier, journal.
When then would profs use their funding to pay for this?  If the work is good enough for a good journal, why not just submit it elsewhere, where there are no fees?

PRL is definitely a top-tier journal.

The publication charge for a PRL is $800. The American Physical Society, that publishes all the Physical Review journals, is a non-profit organization. They have to cover the costs associated with their publications. Some is through subscriptions, some through publication charges.

There is a implication in your question that funding (grants) should be used to pay for "scientific" purposes (experiments, equipment, personnel) but not "unscientific" purposes like publishing. How do you make such a distinction? What if $800 for promoting awareness of their research, e.g., through in a premier journal or putting up a clear and visually attractive website, might advance their research more than $800 of equipment or materials?

Note: as pointed out by Pieter Naaijkens, PRL indeed has a publication fee, making most of the original answer incorrect. I've rewritten the answer as a result.
When one pays a publication fee that isn't open access, one is effectively paying the publisher to distribute the paper. Most (subscription) publishers and journals are quite content to distribute the paper for free - a publication fee is bound to reduce submissions, which the journal needs to function. In this sense, Physical Review Letters is very unusual.
I have no knowledge of the internals of PRL, but I will guess that they have more expensive costs than normal because of the numerous full-time PhD scientists they have on their journal staff. They are presumably offsetting some of the costs by charging a publication fee. Cynically, they're able to get away with it because 1) APS is perceived positively by people (even though their open access APCs are on the high end of the market rate) and 2) they're such an important journal (note other APS journals don't have such a fee).
Why would professors pay the publication fee? I imagine the most important reason is because they really want the prestige that comes with publishing in PRL. Other lesser factors could be they like the review process, and because PRL as one of the premier journals in physics has a very wide distribution.

hmm, why might the professor retaining the copyright be important?

@Michelle I don't think it's "important" per se, but it can come up, e.g. https://academia.stackexchange.com/questions/49182/how-to-legally-re-use-images-in-paper-and-still-continue-to-use-and-distribute-t

PRL also charges a publication charge for non-open access papers, see https://journals.aps.org/prl/authors#pubcharges. The rates to publish open access are higher.

The TL;DR is that a PIs job security, promotion prospects and grant funding is unfortunately based not on the quality of the research they produce, but on the prestige of the journal they publish it in. To pass probation on my position I needed a publication with Impact factor > 10 within three years of starting. To keep my job I need a so called 4* paper once every 5 years.

There are two separate costs to publishing in many journals

Open access fees
Page charges/article processing charges

Open access
In general there are two sorts of journals - journals that are funded by the authors paying (open access) and journals that are funded by subscribers paying (closed access). Things are muddied by the fact that most closed access journals will allow authors to pay for Open Access for their paper, while most papers are closed (so called Hybrid journals or Gold open access)
Many of us page open access fees as a moral/ethical decisions - we believe it is wrong for research, that the public has presumably paid for, either through taxes to government agencies, or through donations to charity, it in accessible to the same public, as well as inaccessible to colleagues at less well funded universities.
However, moral issues aside, almost all funders in some fields, like medical research and life sciences, now mandate open access publishing.  In some cases the funder will provide a mechanism for funding open access publication.
In the UK, every 5 years there is the Research Excellence Framework assessment, where the government assess the research success of every university and gives funding on the basis of this. This can be quite a lot of money (its about 20% of my universities income i think). They make this judgement on the basis of open access papers only.
But this doesn't explain page charges.
Page charges/APC
These are a relic of the days when it cost journals for every page/colour figure you had in your paper. You'd generally get a certain number of pages or b&w figures for free and had to pay more if you wanted more or colour. This no longer applies, but journals still like to charge it as its a nice little earner. The last paper I published charged $2,500 in page charges on top of the $2,500 open access charge. Why would you publish in a journal that has such charges? All the top journals have them. For the reasons I stated at the top - as a scientists you are generally judged on where your papers are published because those judging either don't have the time, the skill or the motivation to judge you on the content of your papers - you need to publish in top journals.
Paying these fees can be a real problem - the total $5,000 for my last paper was 25% of the total none staff budget of my lab at the time. You are generally not allowed to pay this out of grant money (which begs the question, what money is there that isn't grant money?).

Where are you not allowed to pay APCs out of grant money? That's very common in my fields.

Any UK grant funded by the UKRI (i.e. most government funding).

Well that sucks

Can I phrase this another way?  If your journal article could be listed on Bing for free, but Google for $1k, would you pay for Google?  I think a lot of people would.
In general, whether reputation for the journal (Nature is such a great journal!) or the journal is well known (yes, of course I've heard of Science!), readership is important.  People pay for perceived viewers, whether numbers only or quality of readers.
An author may prefer public fame of the general public (Science, Nature) over academic fame (e.g. JAMA), or they may prefer accolades amongst their highly educated peers instead of the public.  Whatever the reason is that they need money to publish, most PIs have money to pay for this expense.  I have to say -- I don't think I've ever heard of a PI "regretting" paying for a publishing fee.  This tends to be one of those easy questions--they tend to know the value of the journal requesting the fee.

interesting answer

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Reproducible, open, transparent, ethical Research when confronted to (patient) data anonymization : is it at all possible in practice?
A lot of Hype goes in reproducible, open and transparency for data analysis theses days in some fields mores that other. The code is to be share as well as the dataset.
How to achieve this in a context of patient data protection that all ethics' committees will require ? What are the best practice to overcome theses antagonistics goals ?
My team seems to think patient's data protection means the data (already anonymized) shouldn't leak and thus we have to work on the database's server without ever getting the anon db on our stations. This feels a tad too much / an overkill ?

I assume there are laws and that the laws vary by country.

I think "reproducible" doesn't really mean running exactly the same code on exactly the same data. You get much stronger evidence if an independent research design is developed for the same question and the results agree (or not).

@Buffy please see a previous answer about the difference between reproducible and replication https://academia.stackexchange.com/a/118511/33210

Yes I wasn't thinking about replication, more about transparency regarding the database : 1. there is a huge amount of data where the initial analysis answers only a few questions (for example by lack of power for the others) or 2. where the data would show the analysis done although(theoricaly sound by itself), isnt appropriate ...

Its totally normal practice for patient data to be allowed to be stored only on properly secured, regulated and monitored servers.
In my field (genomics), databases exist where researchers can deposit anonymized patient data, that is not "publically" available, but can be accessed by users that can demonstrate that they have good reason to use the data, that their use falls within the consent agreement and have the IT systems in place to keep the data safe (see for e.g. dbGaP and EGA) by making an application to a data-protection committee.
Code can be written in such a way that no patient data is in the code (loaded from secure locations, etc), so that the code can be shared.

Never said the practice to regulate access to sensitive data isn't sound, (actually it is of our ethical responsibility to do so and enforce it). But to me this practice seems to impeds real analysis transparency. And thus real openness regarding the justifications for some of the data manipulations or analysis done. (not showing the data, how can you really discuss those in any other form than vague ? I was desperate for (dreaming for?) a middle ground between ethics & reproducibility, guess it's a fool's errand if secure means closed. (what about reviewers be given same access than PIs?)

You said "This feels a tad too much / an overkill ?"
In the perfect reproducible world, you'd make decisions about data manipulations independently of the data. In face in the ideal world, you'd have written your analysis scripts before the data was even generates (yes, we all know that never happens). But you can still share you code, which shows what manipulates were done on the data, and provide some reasoning for why. You are still allowed to show summaries of the data (shapes of distributions etc) to justify things.

In my field, reviewers would generally be granted access if they asked for it and when through the appropriate vetting process, but to be honest, given that the processing steps generally take many years of CPU time in total, the chances of a reviewer rerunning them are pretty slim.

People have already though about the this. The American Statistical Association has guideline for reproducible results (here).

Reproducibility is enhanced by following best current practices, including:

a. Ideally, exclusive use of publicly available data. However if the research domain does not allow for publically available data for widely accepted reasons (e.g., medical data with high confidentiality concerns), the principles outlined in items (b) - (e) should still be followed;
b. Use of version control for all (collaborative or individual) code development;
c. Exclusive use of open-source software freely available to anyone in the world
d. End-to-end scripting of research, including data processing and cleaning, statistical analyses, visualizations, and report and/or manuscript generation, with the full workflow made available to others;
e. Use of container/virtual machine tools to capture software versions, dependencies, and platform specifics;
f. Publication of code in public repositories as with data; and
g. For projects that develop algorithms, implementing algorithms on standard computational platforms (e.g., R packages, Python packages, source code packages installable via standard methods, etc.).

Reproducibility shouldn't be thought of as a binary state: either reproducible or not-reproducible. It's more useful to think about it as continuum from hard to reproduce to easy to reproduce. The goal of any reproducibility effort should broadly be to move as many people as possible further towards easy-to-reproduce. This involves some technological (to make the right thing easier than the wrong thing) and some social (to give people the activation energy to learn a better process even though it's harder in the short-term) components.

It’s perhaps worth noting that in this era of “replication crisis”, reproducibility is the only thing that can be effectively guaranteed in a published study. Whether any claimed findings are indeed true or false can only be confirmed via additional studies, but reproducibility can be confirmed immediately.

Also, the medical literautre has discussed this. For example, Tucker et al. describe how to protect patient privacy when sharing data. Their two key recommendations were:

Data anonymisation/de-identification: Data holders are responsible for generating de-identified datasets which are intended to offer increased protection for patient privacy through masking or generalisation of direct and some indirect identifiers.

Controlled access to data, including use of a data sharing agreement: A legally binding data sharing agreement should be in place, including agreements not to download or further share data and not to attempt to seek to identify patients. Appropriate levels of security should be used for transferring data or providing access; one solution is use of a secure ‘locked box’ system which provides additional safeguards.

Searching through the medical and statistical literature will give you more ideas we well.

Thank you for the links. Best.

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Is referencing online solution acceptable when completing assignments
I'm not sure if I'm overthinking this.
Recently I had an assignment that is intended to be completed individually in which I cannot understand one of the questions at all. Lectures didn't help as the question assumed we have known some mathematical concepts before this class.
So I searched online for solutions because I realized that I would have learned nothing by keep looking at the question myself. And not surprisingly I found a solution.
I read through it, understood the solution, and wrote in my own words on the assignment paper. However since it is a simple proof my solution is essentially the same, so I cited the webpage and explained that I have written this proof after reading through the solution.
I know this does not constitute plagiarism. What could I have done better in this situation?

"I cannot understand one of the questions at all" Normally, this is when you contact the lecturer (by email or at office hours).

Perhaps check out and read up on the prerequistes for that course - sounds like you are missing one or two...

"Is referencing my neighbor acceptable when completing exams?"

This depends on the rules of the course and has no general answer. For some courses and for some assignments within them, this would be expected. In others, forbidden. Only the instructor can give you guidance.
But, you did the right thing in citing it. You were honest. Also, you learned something, which was the point of the assignment. But perhaps you didn't learn the right thing, which may have been the point: working through to a solution on your own.
The rules of a course should be clear. It is a problem when they aren't. But if challenged on this, just stress your honesty in citing your source. And follow the rules as you then understand them. But, sadly, instructors sometimes have unspoken expectations.
If I were your professor, and had neglected to make the ground rules clear, I'd accept your work, given the citation, but also caution you about future work if I'd rather you came to me instead of external sources. A professor can sometimes give a minimal hint to get a student over a block, but still allow for deeper learning to occur than can be done when searching out solutions. But I would also have to publish the ground rules.

But what would be your response as an instructor if a student did this?

I can't speak for other academics, but I would have no problem with this.  Unless there is an instruction in the assignment to the contrary, I do not think it is reasonable to expect the student to refrain from looking at outside materials.  (Indeed, one would usually regard it as desirable that the student would be proactive in searching for relevant materials.)  The fact that you cited your source, and wrote the proof in your own form, seems fine to me.

...what could I have done better in this situation?

There is nothing else you need to do in the assignment itself.  The only other thing you need to do here is to follow-up by getting some more help from your lecturer, to ensure that you have a broader understanding of the material.  There is a big difference between being able to read a proof and understand it (and then contemporaneously replicate it) and being able to understand the material well enough to prove something without first looking at another proof.  You can get away with the former when you are doing the assignment, but the final exam is where the rubber meets the road.
The only concern I would have if I were your course lecturer in this situation, is to make sure you are taking steps to achieve a level of proficiency that will allow you to take on questions in your exam, where you do not have access to worked answers to the question you are looking at.  I would recommend that you go and see your lecturer to get some help to get you up to this level of proficiency.


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Addressing the recepient on the cover letter for a PhD application
I am applying for a PhD position, and I am required to attach a cover letter with the application.
In the advertisement for the position, the main contact person is the "Head of the PhD program", so it feels natural to address the letter to him.
My question: As this person is also an Associate Professor of Mathematics, which title should I use when stating his address information?
My first intuition was to write:

Name Surname, Head of PhD program
(other address information)

but this might be a bit unfortunate as he is also an associate professor, which could be considered to be a title of greater value.
Alternatively I could just write:

Name Surname, Associate Professor of Mathematics
(other address information)

but then it sort of misses the point of why I am addressing the letter to him (though this might be obvious to someone working at their department).
I could also add both:

Name Surname
Associate Professor of Mathematics and Head of PhD program
(other address information)

Is there a standard way?
The university has their own online system for applying, so this might not be all too important. Nevertheless, I want to make sure everything is right.

In most places any of those would be fine. Some places are very formal about titles, though, such as Germany. But if his were the case here, I think you'd already know that. The important thing is that it get to the right person. It is relevant to the entire committee, of course, not just the "main contact".
But something simple is fine.

Even if the Head of the Department is listed as the contact it would be standard to address the admissions committee in the cover leter. E.g. "Dear admissions committee" or something along those lines.
(This assumes that you are applying to a graduate program with an admissions committee. If you are directly applying to be a PhD student in a professor's research group simply write "Dear Prof. X" even if Prof. X is head of the Dept)


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My article that was cited in a book does not appear on google scholar
The name of my article is Hominin interbreeding and the evolution of human variation and it is referenced in the book "Ingenious: The Unintended Cost of Human Innovation" But this does not appear on my google scholar citations page.
https://books.google.co.kr/books?id=CfyzDwAAQBAJ&pg=PA304&dq=Ingenious:+The+Unintended+Cost+of+Human+Innovation+hominin+interbreeding+and+the+evolution+of+human+variation&hl=en&sa=X&ved=0ahUKEwiBgNSLx9DlAhWYd94KHdhtAKUQ6AEIJzAA#v=onepage&q=Ingenious%3A%20The%20Unintended%20Cost%20of%20Human%20Innovation%20hominin%20interbreeding%20and%20the%20evolution%20of%20human%20variation&f=false
I am not familiar with how google scholar works, so I did send a message to them through the google scholar contact form.
Does it generally take a lot of time for google scholar to pick up citations from books? or is there another reason for this?

Welcome to academia.SE. Google scholar is generally not fast, so you should add some time information to the question.

They do not accept emails and there is no customer service. To get your article to appear, host it as a PDF on a university server, or if not available, at a repository like the Open Science Framework (osf.io). Google will scrape it within a few days, generally. You can also add articles manually to a Google Scholar profile. Also, see many similar posts in this forum: Why do papers sometimes appear unlinked in Google Scholar?


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What do you think of the reply and do you think he is interested in me and my application?
Recently i have been applying to various Ph.D. programs and i have approached many professors as my potential supervisors and among those, i applied to Harvard and this is what the Director of the Program in one of the Ph.d programs there replied:
" Thank you for your email and your interest in our lab.
To answer some of your questions, I do think that you would be a great fit both for ### and for our lab. Also, we will be taking new graduate students next year.
As you probably know, we do not admit students directly into any one lab, but there is an admissions committee that decides on the students.
 Once you are admitted to ###, then I would be happy to talk about a rotation in our lab, etc. "
So what do you think are my chances of getting accepted and how should i further proceed with the conversation.

It's a completely neutral reply. I write these emails to qualified candidates about once a week myself. It is, in essence saying: "You've contacted the wrong guy. I'm not making the decision about admission. We'll talk again if and once you've been accepted and here."
In other words, I don't think you can draw any kind of inference from the email -- neither positive nor negative.

Yep. It's the usual way in universities in the US and Canada.

I also thought of the same thing. can i ask you one thing is it like regular email professors send out to everyone who writes to them.

@khwajawisal -- as mentioned, I write such emails quite regularly, and I suspect many of my colleagues do the same (if they take the time to write back at all).

that's just what i wanted to know, thanks a lot and one last thing what is your definition of a qualified candidate.

Well, at the very least, you can draw the conclusion his interests weren't so out of line the professor decline to respond.

@khwajawisal -- like Azor Ahai says: when I write these emails, I've made a call that that person is at least of potential interest to the department. I can't say that I usually look at the file with substantial care to really say whether they have a chance to be admitted -- nor could I, because I don't usually have the letters of recommendation, transcript, GRE results, etc, that are used to make the admissions decision.


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Cite confidential source
i'm currently using several construction drawings to extract a note on how a certain design is usually done in the industry. I'm neither allowed to name the specific product nor the company. I guess I can't assume that the extracted information are common knowledge, so a source or a footnote would be required.
How do you typically handle this?

Do you mean drawings produced by some software product?

@Buffy Yes, CAD drawings. The used software is not stated though.

When you say “specific product” is that the software used to produce the drawings or the product which is represented in the drawings. This is an important distiction.

If your only sources are all proprietary-confidential type things, are you sure it's really all that usual?

@SolarMike The software itself is unimportant, it's just used to print the design the engineer made up.

@puppetsock  Good point, but by the amount of competitors in this area, I think I can safely assume that.

You can probably say something like: "A popular CAD* program treats the problem as follows...". Then use the footnote to explain that the program won't or can't be named for legal or other reasons.
In other words, give a generic description but say that it is a specific example meeting that description. Don't give the impression that all do, unless you have evidence of it.


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My article was not indexed by Web of Science (and possibly other paper databases) -- how to fix?
I recently published an article in a peer-reviewed journal. However, there was an issue with the assigned DOI at publication time which was not fixed until one month later (accessing the DOI led to 'Article Not Found' errors).
Now, two months later (with the DOI now fixed), the article is still not indexed in major databases such as Web of Science. I believe this may be due to the incorrect DOI at the time of publication. I am worried that researchers may miss my article if it is not listed in Web of Science.
Is there a mechanism to fix such issues? I was not able to find any way to 'submit' entries to Web of Science -- it seems everything is automatically indexed.
Other relevant details:

I am sure that the journal is indexed by Web of Science, and other articles published in the same issue of the journal can be found in a search
I only know that it is missing in Web of Science, but there may be other databases from which it is missing. Is there a list of other major databases I should also check?

Does this answer your question? Did scopus choose not to add my paper (from an accepted journal) or did something go wrong?

@Anyon Thank you for the link, it looks like my article was indexed by Scopus but not WoS. I have sent a data change request for a missing article in WoS using this web form

Do you find articles from the same issue of the journal you published in? Not sure how it is now, but WoS used to be notoriously slow with indexing new papers. You might just have to wait a little longer.

@Snijderfrey Yes, articles in the same issue (and even newer articles) are already indexed

I have faced a similar issue and have requested using form but I have not got any response in months.

@Hap  I have the same experience. My issue is still not fixed ~6 months after requesting a correction (I have not heard anything back)

UPDATE: after submitting this web form almost 4 months ago, they have finally notified me that my article has been indexed. So it just takes a long time

@Superbee I also received the email today telling me that my article is indexed.

In your situation, if it's bugging you out, request a data change on Clarivate WoS.
Personally though, I won't be too bothered as the DOI is now correct and indexed in Scopus.  Perhaps, check if it's Google Scholar 'indexed'.

Yes, I have requested this many months ago to no response. And while my paper has been picked up by most other databases, I would prefer WoS so I can set up citation notifications as I do for my other papers.

UPDATE: They have finally indexed my article after ~4 months (after submitting the web form)


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What are typical selection criteria for attendees at research summer schools?
In my field there are often summer schools for graduate students/postdocs to learn about a particular research topic in a short amount of time. Given that some of these summer schools are in exotic locations, or with expenses paid, I imagine that they receive a large number of applicants (probably far more than can be accommodated). In this case, how do the organizers typically select who attends? I can think of a few things they might consider:

selecting students from diverse institutions and countries, in order to maximize the impact of the school
selecting students of diverse academic backgrounds and skill levels, to facilitate mentoring and sharing of knowledge
selecting only the "best" students (e.g. by publication record), similar to scholarship/fellowship applications
selecting the students with the strongest demonstrated skills, so that the school can teach only the most advanced topics
selecting the first to apply that meet the minimum criteria (first come, first served)
something else?

Since summer schools primarily exist to teach, I feel they may be distinct from other competitive applications in academia e.g. fellowships or conferences. For those who have served on the organizing committee of such a school, any insights would be appreciated.

I suspect that each will be a bit different, but likely almost all of your criteria may be applied at any given summer school.

Summer schools where you pay a fee have relatively few criteria for selection. They will have some minimum standard that is usually published (they may phrase it as "summer school geared towards people with undergraduate degrees in x, y, z) but even those minimums are flexible. These schools are pure money makers for the universities and the universities accept as many people as possible until the max spaces are filled, usually on a rolling first come/first serve basis. I want to emphasise that these summer schools are not selective because they are not meant to be.
Summer schools which are free usually have posted criteria for selection and are selective. They may specifically serve a particular group (e.g. scholars from lower income countries; scholars working within a particular sector). Many of these require a letter of motivation and a CV (I know of two that even require recommendation letters) and applicants are selected based on how well the student's background and goals mesh with the content and goals of the summer school. They look for people who can really "use" the education from the summer school in interesting ways. They will also have minimum requirements that are less flexible but, too, have some flexibility if the student is otherwise intriguing.
(Note, I've taught on probably about ten different summer schools in about five different European countries)


text:
Can a PhD thesis consist of "exploratory research"?
I am a physics graduate student at the stage where I need to come up with a PhD thesis proposal.
I have an idea for a thesis project that I think is very interesting and has not been explored in the literature. Specifically, the idea is to take a powerful new numerical technique that was developed in a completely different field and try to apply it to problems in my own field. If it works, it could greatly impact the field by drastically reducing the computational cost of calculations, which is one of the biggest limitations of current research.
The problem I face is that this research would be exploratory in nature. By this I mean that I do not have a well-defined problem to solve beyond "attempt to adapt it to my field and establish how well it works on some basic problems". In contrast, every thesis I have read has consisted of applying known techniques to new problems. My approach would be to do the opposite: apply a new technique to known problems to establish whether it could be feasible as a new tool in my field.
So my question is: can exploratory studies such as this one constitute a PhD thesis? In my experience, I have never seen a thesis of this type, and I am worried that this is because it is a bad idea.

Well, those known techniques have to come from somewhere, don't they? Of course, if it doesn't work you don't have much of a thesis...

do you have an advisor? have you talked to you prospective committee members? have you talked to your institution physics department? what did they say? If you don't know who to talk to, ask your academic advisor for help, it's their job

"every thesis I have read has consisted of applying known techniques to new problems" Those aren't great theses.

"Drastically reducing the computational costs of calculations" by applying a new numerical technique to an old set of problems isn't "exploratory", it's just research (though if the outcomes are too obvious ahead of time then it may not be interesting research) - all good research has to have some element of uncertainty to be interesting. Yes, likely you should try some initial exploratory steps (effectively to see if your approach is feasible, but that's not what your thesis would be likely based on.

I had a student who managed to adapt known methods to improve state-of-the-art results by several orders of magnitude. He was worried that this would not be original enough. He didn't need to.

Yes.  A PhD thesis that introduces new methods to old problems can be an excellent thesis if:

The new methods are in some way better than old methods.
The new methods are widely adopted.

Some of the most successful physicists work in this way.


text:
Can I list my experience as independent researcher to my resume or CV?
I have graduated from my master's last year. I am very much interested in doing an additional technical master's program and/or a Ph.D. in my field. So, I started applying for both the technical master's program and for the PhD program. In the meantime, I thought of not letting my research interest decay, I started working as an independent researcher. And luckily I got a collaboration offer from a foreign university professor who was a great scholar in my field of study. I collaborated with him from my home and did nearly 8 research articles within a period of 11 months. But at the same time, I was rejected by all the M.sc. and Ph.D. programs I applied. However, my independent research works were accepted and published in reputed IF international journals. Now, I am applying for the winter semester programs, in that case, can I please know whether I can add my experience as an independent researcher to my resume or Cv which I submit to the educational institutions? Please kindly help me in this regard. Thank you in advance.

Unfortunately, "independent researcher" can mean a wide spectrum of things, anything from doing serious research published in good journals (as you've done) to sitting around thinking "deep" thoughts that never lead anywhere (and might not even make sense). The important thing for your CV is to emphasize the publications that show you're at the serious end of the spectrum. The phrase "independent researcher" can fill what would otherwise look like a gap in your history, but the publications (and, as Buffy pointed out, letters of recommendation) are the real information.

Thank you very much for your comments, sir, Buffy, and Blass, I will add it in my CV, I already have a recommendation letter from the professor and since my articles are accepted to Elsevier publication above a IF of 4, I think as per your suggestions, I will add it. Once again thanks for your comment.

Yes, absolutely add it, along with the publications that resulted. And, you should consider getting a letter of recommendation from the professor. Your lack of formal affiliation is of no consequence. It is the work that matters.
Don't hesitate here.


text:
Author affiliation regarding
I completed my master's three months back. Currently, I am writing scientific articles with collobrations in which I use the previous educational affiliation. Is this correct or should I use my current address as affiliation? Please do help me in this regard.

If you aren't still a student (or faculty) you can't use your previous university. But "Independent Researcher" is really enough. Affiliation is there for identification purposes primarily.
But you should probably not  use your current address. It is likely to change and become useless. But it might also attract spammy mails that never go away.
Some might list "none" or "unaffiliated", but "Independent Researcher" seems better to me. It isn't uncommon, actually.

Can anyone please tag me a research article where the author has given his affiliation as an independent researcher.

Thank you very much for your answers, I have just noticed research article mentioning independent researcher (eg. https://www.sciencedirect.com/science/article/abs/pii/S221169581830343X), I think also I can use this hereafter, and anyone this doubt in the mind can also use.


text:
Can I add code in the supplementary material of my thesis which builds up on an existing library?
I've written a thesis in the context of global illumination. The explorations are purely theoretical, but I've implemented the basic building blocks of the described approach and would like to add this implementation to the supplementary material of my thesis.
Since my work focuses on a particular aspect of the complex rendering pipeline, my code builds up on and extends an existing library (http://www.pbr-book.org/).
The code fragments I want to put in the supplementary material don't include anything of the code from that library, but it clearly references classes, functions, etc. from it.
My question is: Is there something I need to be aware of? Do I need some kind of permission from the library authors or add a particular disclaimer (apart from providing a reference to the original library, of course) to my thesis?

There may be restrictions imposed by the license the library is released under (which seems to be BSD 2-clause in this case. Perhaps https://opensource.stackexchange.com would be a better fit for this question.


text:
Does it matter whether I got a PhD in (applied) math or computer science?
I'm currently a third year PhD student in computer science. I got master degrees in both computer science and mathematics. My research is quite different from the other members of my group and is actually more about mathematics (stochastic PDEs, Markov processes, ...) with applications in computer science. For that reason, I was asked whether I want to pursue a doctoral in computer science or mathematics (but I guess it would be "applied mathematics").
I don't want to work in academia after my PhD, but in a R&D deparment in the industry. Does it actually matter wheter I choose computer science or (applied) mathematics for my PhD? I guess what's actually more important is the actual research I'm doing. However, the first impression of me would be the kind of PhD I got, I guess. So, I don't know what would be benefical for me.

There'd likely be less of a kneejerk reaction if you applied with a computer science degree. Frankly it depends where you apply. Ask folks in your network though.


text:
How should my name and affiliation appear in a scientific journal publication as a student?
I am an undergraduate student who is co-authoring a publication for a scientific journal for the first time. My advisor has asked what I want my name and affiliation to be but I need some guidance.
My full name is Elizabeth Grace Duncan, but I go by Lizzi. I go to Virginia Tech which has the full name Virginia Polytechnic Institute and State University although Virginia Tech is also an official name. I am majoring in statistics and minoring in math.
I'm thinking I should say my name is Elizabeth G. Duncan and affiliation is Virginia Tech Statistics Undergraduate. Is this appropriate detail? Any help is appreciated!

Hard to say about the middle name, that probably depends somewhat on the journal, but otherwise you want the full first name, full last name, full name of the university and department. The fact that you're an undergraduate doesn't really matter unless it's directed to an undergrad journal.

why not ask what other use for institutional affiliation?  Leave the undergrad part out.

It seems to be common to put the department before the university in the affiliation. Journals are likely to standardize such things, but I expect that they'll leave your name in whatever form you choose.

It's not common in most fields to list your actual position as part of an affiliation. Usually affiliation is just Department, University - no mention of your student role.

In terms of “standard” conventions, I would suggest:

Elizabeth G. Duncan, Department of Statistics, Virginia Polytechnic Institute and State University

If the research you’ll be publishing was conducted as part of a research group, however, you might list that affiliation instead, e.g., “Applied Statistics Lab, Virginia Polytechnic Institute and State University“

My suggestion for your name would be: whatever you come up with, do a couple of google searches first to find out if it is sort of unique.
If there are, for example, already a couple of Elizabeth Duncans active in some other area of science, it might be worth thinking about an alternative spelling of your name (or even Lizzy Duncan) just so that it is easier to figure out which research was done by you and which by similarly named people all over the world.
The go-to "default" (at least as far as I have seen) would be something like:

Elizabeth G. Duncan
  Virginia Polytechnic Institute and State University

You don't have to mention that you are currently in an undergraduate programm.

I would say: your name, your choice. Consider creating an ORCID which is unique. In case you feel like adapting your publication name, this ID remains the same.
As to the affiliation: usually there are guidelines by the instition. Ask your advisor and consider the affiliation they are using in publications.

If you use the full name Elizabeth, I would definitely suggest to keep the middle initial: it is useful to disambiguate you from other authors with the same name, and makes automatic citation tracking more effective.
You can also opt for Lizzi, which could make a warmer, more personal impression, but it could cause some minor trouble in future (example: you sign up for a conference in a far away country as "Lizzi", because that's the name you want to appear on your name tag; the organizers get you a visa to enter the country, and customs complain that the visa says "Lizzi" while your passport says "Elizabeth").


text:
Teaching stream faculty postion
I recently applied for a tenure track teaching stream position which requires to teach standard math courses but also math courses for non-science, non-math majors. It's been one month since I applied and have recieved no response. Do I just assume they went another way or should I try to follow up with an email? Also what would I ask in this email?

Did the advertisement include a closing date?  Has that date passed?

The date had a deadline for applying which as obviously passed, it's been one month.

It is in Canada. But probably very similar...

You can always send an email and inquire about the timeline of their decision making. Just be polite and professional.

One month is not very much time for faculty decisions - especially if they are on the tenure track. But don't assume anything. You will probably be told of any decision no matter how it falls.
They may be actively exploring another candidate, of course, and that takes some time.
But if you have other decisions to make, then ask by all means. If you write, express your continuing interest along with asking for an update.

I don't have any pressing plans at the moment, 5 months left on the current postdoc.  Would it be just wise to wait and see what happens?

Probably better to wait for now. But not forever. And keep your search going.


text:
An appropiate graph visualization?
I want to include a plot in my thesis to highlight regional differences in bicycle collision outcomes. Now there are several plot visualizations I could use, and I am not sure which one could be the most appropriate. Having a "scale free" y axis better highlights the differences between each region, but it may also confuse the reader.
I am aware that there might not be an optimal solution to this, but I would appreciate to hear your thoughts.(If you have a completely other suggestion for an appropriate plot than the ones below, I would also be happy to hear those).
These are the plots I have made:
Plot 1

Plot 2

Plot 3

Plot 4

This question would better fit the scope of https://datascience.stackexchange.com/. You could also try stacking bars by type of accident or type of area btw.

It might be good to consider a broken y-axis. See this example. In your case, you only apply it to bicycle-only and bicycle-car.

Many people dislike broken axis, including Hadley who created the software the OP is using to create their plots.


text:
Write my Literature Review
I started my dissertation and I want some advices in how to start the literature review. I know that it should be systematic and not a simple summary of each book or article. But my doubts relate to citations, i.e. not how to include them, but if I should start from the most recent work to the odelst. Second, if I should use Word for citations or  other softwares.

Universities often have dissertation guidelines or even templates for this sort of question. Ask locally.

The answer will likely be particular to your field, your topic, and your needs. At minimum, the literature review will establish that existing work in the field supports your work but does not duplicate it (i.e., it provides reasons why your dissertation is worthwhile.)


text:
Lack of indexing of article in google scholar
Our two articles have published in two journals
But they do not index in our profile
Titles:
The Design of Novel Kni-10729 Based Compound for Inhibition of
HTLV-1 Protease as Novel Insight for Development of Anti-HTLV Drugs
doi: 10.5812/ijhls.89840; Int J Health Life Sci
The PI3K-Akt/mTOR Signaling Pathway Roles
in Tuberculosis Pathogenesis - The First System
Biology Insight
JSM Clinical Cytology and Pathology
I am waiting for your response
Best regards
Dr. Karbalei

What exactly, do you expect us to do about it? Talk to the journal about whether it is indexed. Or use the manual entry process in google scholar.


text:
Is it appropriate to rewrite and republish another author's useful but very badly written paper?
I found an engineering-related academic paper from a number of years ago that was published in an obscure journal, likely not peer-reviewed. The English writing is very bad, like it went through three languages in google translate, and many key parts are nearly incomprehensible with awful grammar and incorrect word usage all over. Organizationally it's rather a mess too.  While it took me quite a long time to decipher it all, I recognized the value and importance in it, and I think should be more widely seen, as there is really nothing else published on this specific topic.
I was interested in potentially redoing the paper to better present and explain the ideas in it. I would want to add my own ideas of interpretation and application too.  I wrote to the original author and they responded, and I think they'd be ok with the project? I couldn't discern a clear answer from them yet.
In the sense of academic standards, what is appropriate in this situation? Is it acceptable in the first place to redo and republish someone else's full work? Do I become a new co-author, or simply an "editor", or new main author while at the start somehow noting it's a rewrite?  Or where is the threshold between plagiarism and a newly written paper if I redo it from scratch, but following and using all the original author's ideas and data, and then add my own thoughts?  I really can't maintain any of the original written content as-is, because it's just so badly done.

Freeman Dyson wrote up Feyman's proof of Maxwell's equations.  So you can probably take the same strategy.  https://signallake.com/innovation/DysonMaxwell041989.pdf

I think we need much more of this kind of expository writing. Many important papers aren't written very clearly.

As for you are already in contact with the authors of the badly written paper and continuing in this approach would rule out plagiarism except the self-plagiarism one. You can't simply rewrite that paper. It will be a duplicate at least. However, in practice, if the original is indeed that poorly composed and has appeared in an obscure journal, I think that you together with the original authors have plenty of way to bring a new look to that content.

It's certainly not unheard of to write papers that explain the key ideas in an important paper in a way that is more accessible, for whatever reason. The key is to not claim credit where credit is not due (an when in doubt I would strongly advise to claim too little rather than too much). Here is an example where a paper was rewritten for the benefit of a different audience (in this case, computer scientists as opposed to mathematicians).
https://theoryofcomputing.org/articles/gs006/gs006.pdf

There are lots of answers below, so I won't add to them, but I have done this sort of thing twice without issue. Once we added the original author as first author. Another time I reformulated an existing algorithm and described and implemented new variants. The reviewers debated how to weigh pedagogical improvements, and eventually they were deemed a contribution of the paper, raising it above the bar for acceptance.

I guess that if you clarify if 'rewrite' as of your title means 'linguistic editing' or 'elaborate on existing research' the dilemma will become much less dramatic at once.

There's a difference between plagiarism and copyright violation. If I just copy someone else's paper word for word, and clearly cite the paper I copied, that's not plagiarism, but it's likely a copyright violation.

Personally, I would be very happy to read an abstract along the lines of

ABC is an important problem because of XYZ. A solution to this problem was presented already by UWV et al., but is not widely known, partly because of the technical nature of their presentation. Here we give a readable presentation of UVW et al.'s ideas, showing that they can be interpreted in terms of PQR, and we give applications in the field of JKL.

If the paper is mostly a reinterpretation of existing work it might not get into a top journal, but if the problem is important and the solution is a good one, your paper will be a valuable contribution and is likely to be widely cited anyway, since most people implementing it will be working from your paper and will cite it along with the original.
There is no danger of it being seen as plagiarism if you are presenting their ideas in your own words, and state at the start that this is your goal. The other authors will likely be happy as well, because their work will become more widely known as a result of yours. There is no need to involve them directly at all, although of course this is possible as well.

Improving the exposition of good ideas in a poorly-written paper is valuable.
As long as you clearly give credit, you should be OK.
Plagiarism means presenting the contribution of someone else as your own. As long as you are clear that the ideas come from the previous paper and you are just giving an exposition, you are not plagiarizing.
However, you also need to be diplomatic because your implicit criticism of the original exposition could be taken the wrong way.

But most journals require some novelty in the research papers they publish. Wouldn't a copy-edited prior paper risk being rejected by high ranking journals due to lack of novelty?

I am reminded of a story in Quanta Magazine of a long-awaited proof found by a German retiree that was nearly lost to obscurity.  Basically, the proof was exactly what folks had been hoping for for decades, but because it was published in a weaker journal, written in the style/point-of-view of a Statistician, and generalized a step beyond what all were looking for, it was mostly overlooked - at least until a few others found the result and championed it in the terms of their wider fields.

@SomeRandomMastersGuy the proof was exactly what folks had been hoping for for decades - My impression is it was much more elementary than what people were expecting.

user000001 - It shouldn't be a copy-edited paper, but a new presentation of the ideas in the old paper, with proper attribution. You are still right that lack of novelty is an issue, but if the service to the community of clearly explaining the ideas is great enough, I think it's at least worthy of a middling journal. Better still, of course, would be to extend the results in some way.

I believe there are some journals which will take a large amount of well-written survey articles, but they generally have to be 'substantial' (so more than 50 pages?)  Just writing up an exposition of someone's else's article would end up with something which might be a bit hard to publish, which is a shame obviously, since more exposition is needed.

In general, with appropriate attribution and care in the writing process, you should be able to rewrite a paper without violating academic norms. This becomes even easier if the original author is involved in the process. That said, getting the rewritten manuscript published in a more visible and respected journal will be difficult, if not impossible. The key to me is:

While it took me quite a long time to decipher it all, I recognized the value and importance in it, and I think should be more widely seen, as there is really nothing else published on this specific topic.

If you see value and importance in the previous research, you should be able to build on that and do something that could not be done, or done as well or efficiently, without the previous work. Once you have built on the previous work, you should be able to publish the new work with an extended introduction that recreates the original work in a more accessible manner. Again proper attribution and care is needed to not violate academic norms, but this should not be a problem. The ratio of new to old will depend on the journal, how bad/inaccessible the old work is, and how important the work is (either the old work or the new extension).

A very simple, dumbed down definition of plagiarism is: claiming someone else's work as if you did it. So rewriting with yourself as sole author is just right out.
When considering "who should be (co-)author of a paper", there is no simple rule. The simplest you could get would be: anyone who contributed significantly gets to be listed as author. But that leaves a lot of possible situations:

The person who did the original research. Clearly the paper couldn't exist without this person.
Someone you had a discussion with who came up with a key idea that was used later in on the paper. Without them the paper wouldn't be like this, so this person has a claim to be an author.
Someone who did significant editing and writing on the paper, making it much better and possibly making the difference between success and failure (in publication/impact).
Someone who made a lab available, supplied key datasets, used their academic influence to secure funding - but maybe never actually did anything in the lab themselves? But without this person perhaps the research wouldn't have been possible in the first place. Some academic institutions reserve the last author listed spot for these people. In other institutions they might just get a spot in the acknowledgements. There's no one rule here that's used across the whole world.

So there's no simple rule that clearly says who should be author. When someone begins to make a big contribution to a publication, you should quickly have a discussion to agree on expectations. In any case, and also this particular case, the original researcher certainly should be one of the authors.
The ethical thing to do would be to have an open discussion, along the lines of "I think your ideas are good, I think I can contribute with my writing skill. Let's collaborate to together publish a more impactful paper."

An alternative would be to do original research of your own, inspired by the original author; and then cite the original author in your (better) publication. Science after all is about building on others' work (but giving due credit).

Note that co-authorship requires the permission of all participants.

Yes. When someone starts becoming involved in a project to the degree that they should be offered authorship, you need to also have a talk with the current authors: do we want another member? If not, we may need to tell this interested person to basically, cool off. What is altogether wrong is leading people on, taking their ideas but not being ready to take them on board.

I think this would be pretty hard to do ethically unless you can form a collaboration with the author. I wonder, though, if the paper also exists in an original language, in which case you could probably do a translation, but listing yourself only as translator, not author. But, again, getting authorization would be appropriate if possible.
So, keep after the author, and suggest a collaboration. Especially if you have ideas that extend the original. You can work on it, of course, but publishing without permission might raise issues.
If you are having trouble communicating with the author because of language difficulties, try to find a native (or fluent) speaker who also speaks English to act as an intermediary.

I would want to add my own ideas of interpretation and application too. I wrote to the original author and they responded, and I think they'd be ok with the project? I couldn't discern a clear answer from them yet.

To me this suggests that you plan to write an elaboration of a previous paper in collaboration with the authors of the previous paper.
As a reviewer I would have no objection to such a research plan: incremental research is perfectly fine, so please give the appropriate slant to your manuscript.
As a reviewer I would also feel obliged at a minimum to browse the literature you cite -- is it workable to add a link to the obscure source? I would then soon realize that your work is all the more valuable to the community.
The Vancouver recommendations, primarily intended for biomedical publications but easily to generalize to any field based on common sense, suggest that

authorship be based on the following 4 criteria:

Substantial contributions to the conception or de-sign of the work; or the acquisition, analysis, or interpretation of data for the work; AND
Drafting the work or revising it critically for important intellectual content; AND
Final approval of the version to be published; AND
Agreement to be accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved.

In addition to being accountable for the parts of the work he or she has done, an author should be able to identify which co-authors are responsible for specific other parts of the work. In addition, authors should have confidence in the integrity of the contributions of their co-authors.
All those designated as authors should meet all four criteria for authorship, and all who meet the four criteria should be identified as authors. Those who do not meet all four criteria should be acknowledged -- see Section II.A.3below. These authorship criteria are intended to reserve the status of authorship for those who deserve credit and can take responsibility for the work. The criteria are not in-tended for use as a means to disqualify colleagues from authorship who otherwise meet authorship criteria by denying them the opportunity to meet criterion #2 or 3.Therefore, all individuals who meet the first criterion should have the opportunity to participate in the review,drafting, and final approval of the manuscript.
...

So, if the potential coworkers are not clear-cut in the intention of co-authoring this work (that is, doing something), you may resort to simply citing their previous work.
A note of practical wisdom: if the obscurity in writing reflects obscurity in thinking rather than merely poor command of language, you should consider whether your effort will be mutually collaborative.
It would be unethical on their part doing nothing and exploit your good intentions.
In the perspective of an editor/reviewer I am interested that there are no ghost/ guest/gift authors -- please have a look at this decision chart of Publicationethics.org and its references.
Last but not least: ask for an opinion to the editor of a/the journal you intend to publish in. You may do it at two different times: before getting started, speculatively; when you approach the near-final state, for you might find other interesting corollaries along the ways. In the second case, I imagine, you will afford being more assertive about the cutting edge in your manuscript.
Good research hinges around merit and credit. From your words I feel you are doing well.

Other answers have focused on authorship, claiming and giving credit and further angles. So that's covered.
What about novelty?
In a comment to another answer, the question was posed, whether a journal would reject a re-written paper due to it being already published.
Well, some journals might do, however, if you are convinced that the scientific community will benefit from the re-written paper, then you might consider publishing in some open-access publication, arXiv comes to mind.


text:
Possible that one dissertation in Computational Archaeology could earn two degrees?
I'm planning on my PhD to be in CS, but it occurs to me that my research as it applies to archaeology/anthropology will be just as unique and valuable (hopefully) to that field in and of itself.
I haven't been able to find anything on this specifically as in most cases the two fields concerned are closely related and two separate degrees would be unnecessary. In this case, however, it seems fair to ask the question as the two fields are both widely different and at the same time this research in particular would be completely overlapping between the two disciplines.
If this isn't a thing I'd appreciate any insight on schools which have strong graduate programs in both of these fields; regardless of whether I can earn two degrees (which I'm not expecting) I want to tailor my research and my access to experts/labs/programs as much as possible.
TIA!

The last part of your question (recommending schools/programs) is what we call a "shopping" question and is off topic here; I've tried to answer the rest of your question without the shopping part.

This isn't exactly a duplicate, but the answer is here: https://academia.stackexchange.com/questions/17232/is-doing-two-phds-a-good-path

What exactly do you think you can use those two PhDs for?

@AnonymousPhysicist The point may not be to have two PhDs, but one PhD in either field. See my comment to BryanKrauses answer.

Does this answer your question? Double PhD: is it really worth it?

The possibility depends upon a specific school's policy, which makes your answer specific to a given school.

I don't really understand why you need two degrees, just to show that you are very smart? In the end only what you have produced during your PhD will count, not how many degrees you have. The "number of degrees" mentality is for undergraduate studies.

You will need to check with the university/universities where you plan to submit your PhD thesis. Before you ask anybody in person, I suggest to check the examination guidelines first. I found a couple of negative examples in a quick Google search:

"A  doctoral  thesis  that was  already  submitted  to  another  faculty  may  not  be  the  basis  of  the doctoral examination." Uni Bonn
"A student may not submit for assessment thesis material which has already been submitted for another degree at Sultan Qaboos University or any other academic institution." Sultan Qaboos University
"The application to become a doctoral candidate shall be rejected if the doctoral committee finds that
  ...
  the subject of the candidate's dissertation has already been submitted successfully in another subject." Uni Frankfurt

It's hard to say something is definitely not possible, but I think this is a case where it just really isn't worthwhile. A PhD says you can do research; from there, it's more your research output that matters rather than the title of your degree.
What I would strongly suggest, however, is that you pursue having a mixture of faculty on your thesis committee. The exact rules will depend on your program and graduate school policies, but even if there is a requirement that official committee members come from a particular department, at a minimum you should be able to add some "outside" people who can help advise you in your second research area.
You should also pursue publishing papers in both fields.
Of course, all of this will depend on support from your main advisor, so when you look for particular programs, make that part of your search and part of the early conversations you have about your fit.

A case where it's worthwhile to have a PhD in a given field is when you want to land a job in that field. A hiring committee in archaeology may definitely weigh a PhD in archaeology higher than a PhD in CS where the thesis has applications in archaeology.

It might also be worthwhile to ask if you’d be able to do a “double degree” PhD like some universities offer for undergraduates, so that you’ve got a PhD in Archaeology and Computer Science.

This is the best answer. I know people typically say the did a PhD in Computer Science, but I've seen equally as many people say they were PhD students in the CS Dpt. and did their PhD in . So it doesn't seem too far fetched to say that you did a PhD in Computational Archeology if your thesis committee consists of CS and Archeology faculty.

Before I answer, I'll say this. As someone with a PhD in archaeology...certainly get your PhD in CS. If for some reason later on you found yourself wanting to apply for a job in an archaeology department, a PhD in CS focused on archaeology is perfectly acceptable, depending on the position.
To answer your question in a round about way, I wonder if your idea of a PhD is just a little bit inaccurate. The PhD is a bar you pass, a bit of proof that you are able to do a certain level of analysis that leads to a (very small) development in one or more academic fields. A single PhD can contribute to one field or it could contribute to several fields, but you don't get a separate PhD for every field you make a contribution to. A lot of research is multidisciplinary, but that doesn't warrant a PhD in every discipline that you're working in. You get a PhD from the (almost always) one field that the bulk of your method+theory rests in, in the department who agrees to accept and examine your work. Further, this is the department that you or some funder has been paying for the years of your PhD.
Take me for example. I got a PhD in Archaeology. Aside from a terrifying viva comment that was basically "We think this is a PhD, just maybe not an Archaeology PhD", all was fine. However my research was more in Criminology and Politics, with a bit of Law, and since then I've had a strong academic career...though I've never been in an archaeology department again. I do, however, know how to lay down a tight 1x1m square and always know where my trowel is.
Here's something you may not have considered: would an archaeology department accept you? If you don't have a background or previous degrees in archaeology, and don't know the full background of archaeological method and theory, it doesn't matter if your project helps archaeology, you likely aren't going to make it past the admission hurdle. Now perhaps you were some sort of double major, okay, but take a good look at your project. Is it a CS project that just uses some aspect of archaeology as an example, test case, or data set? If so, there isn't an archaeology PhD in that.
Another thought: does your project actually require archaeology supervision? Will your CS department be able to advise you on the archaeological aspects of your project. At my Uni, if this really was a crossover project, we would suggest you have an archaeologist on your supervisory team. You'd still only get the one PhD of course, but you'd have someone who was there to make sure what you were doing wouldn't be considered insane in archaeological circles.
Lastly, some advice. It looks like you're thinking that it can't hurt to ask about getting two PhDs for one project. It might not hurt if you don't plan on having ties with archaeology but, really, they are going to think you're a bit mad for asking. At best, it sounds naive about, again, what a PhD is. Better would be to introduce yourself and your project and ask about collaboration or supervision arrangements.


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Is it possible to recover a career from a bad PhD outcome?
I am an Indian, who defended his PhD recently in materials science in the US. However, I did not do well in my PhD, as I faced lot of difficulties throughout my PhD. I was doing research in a field different from my supervisors expertise. This did make me independent, but reduced my outcome drastically. I underperformed when compared to my colleagues and research field peers.
I have just two first author publications and two co-authored publications in 5 years of my PhD. I believe that I had worked hard to get the job done. However, I am not sure about my future prospects.
During my PhD, I have taken two undergraduate TA's and found it an interesting experience. Academia has always been my goal. But now, it seems that the career is elusive to me.
I am searching for postdoctoral fellow positions, but not feeling confident about my future academic career.
I realize that my PhD has been mediocre and I don't deserve a career in academia. But, is there no way to recover from a bad PhD outcome? To make the matter worse, I am 30 years old.
I have been offered a postdoc position by my PhD supervisor and that's what I going to do next year.

You might be underestimating yourself. You might want to read this question, which deals with a surprisingly similar case.

I suggest that you don't give up. You are probably suffering from a bit of letdown after the end of an intense and difficult experience. This is normal and common. But the way forward is to work at it and take advantage of opportunities, as you seem to be doing.
Nothing you say suggests failure. Age is just a number. Two papers is just a start. But I would suggest building a circle of collaborators who can share ideas and work together. Your advisor can introduce you to some people.
But, don't waste time or the post doc opportunity. You have a bit of breathing space. Use it to develop some ideas, perhaps jointly, but also to explore more permanent employment.


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Is it “legal” for a Senior Vice President and Provost of a College to be Intimate with a PHD Candidate in their editing?
Is it “legal” for a Senior Vice President and Provost of a College to be Intimate with a PHD Candidate While working on their dissertation of the same School?

The legal answer depends upon the specific policies and laws applicable to the student's institution. The ethical answer depends upon the culture of your university and the nature of the professional relationship (e.g., how much power does the person in a higher position have over the person in the lower position?).

Do you mean ‘intimate’ as sexual relations, or ‘intimate’ as in closely involved in the work?

So, if a senior academic accepts a position as Provost here, and moves to this city to take the job, then it is illegal for his wife to enroll in courses at this university?  I doubt it. In fact, we may have policies that family members of faculty (including the Provost) get reduced tuition here.

https://xkcd.com/314/

The law varies widely, but I doubt that there are many places that would have laws against this. But university regulations are a different matter. More, but not all, would have rules, usually to forbid it. It would be, in most of those cases, a violation of the VP, not the student, I think.
But the situation can be fine, provided that the VP has no influence whatever over he grading/ranking/prospects of the student. This might be the case or not. It would probably be unethical if the student's future depends in any way on actions of the VP, rules or not.
Whether it is wise is another matter. Reputation is important.

This depends on the rules of the university in question (and maybe also on the laws of the country). I've seen universities where relationsships between professors and students are fine and some where they create huge problems.
At the very least, one should consider that - like in every company - relations between a "high" and a "low" person (in terms of their position) will probably create problems with collegues who might fear that this student will be treated better/believe the student is incompetent and gets only forward because of sleeping with the higher person etc.


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Professor wants to submit paper, but no real results
I am an undergraduate student who is working on some research projects applying machine learning to medical problems at a small, primarily-undergraduate college.
In one of these projects, a Master’s student suggested a feature extraction approach and wrote some code based on it. Unfortunately,  I couldn't reproduce the results. I tried to talk to him about it, but we couldn’t reach an agreement. I showed the professor leading the project that the results were not trustworthy, but she wants me to write a paper based on the method, where the other student and I would be listed jointly as first author.
In the meantime, I do not have any alternative results in hand. The problem we are working on is very difficult and has never been attempted before, and I am still developing the codebase for my own approach.
This conversation has been going on for a while, and my professor is getting impatient and wants to publish quickly. She says that some people within the department are pushing for her resignation (for reasons not pertinent to this question), and I think that may be the reason.
I am unsure of how to handle this situation because

I do not want to get the professor in deeper trouble
I want to remain a good member of our team
I want to do good work

I do not really have anyone who I can go to for advice without getting this professor in trouble, and I have no idea how to navigate this situation.
Why I couldn’t reproduce the results:
The model only performed well when trained and tested on all data, but under those circumstances, almost any model could, and many silly ideas can even outperform it. The technique didn’t really make sense within the domain, either, and I am not sure the student understands what it does.
Similar Questions
I have looked online for similar situations, like these ones, but I am still not sure what to do.
professor pushing me to get result when nothing is right!
Paper on project without any result - how to conclude
What to do with a result too small to be publishable, but interesting nonetheless?
How to proceed when the baseline (state-of-the-art) published results claim much better performance than I can reproduce?
Problem with undergraduate research supervisor, how to proceed?
Informing my supervisor of discrepancy in the results
My Professor is pushing me in a problem that isn't solvable for the deadline
Is it good to publish a research paper with many partially answered questions with sub-optimal results?
Is it morally correct to submit a paper to a conference with wrong results?

Be careful you do not taint your reputation with sloppy research. Let them sort out the authorship amongst themselves, training and testing on the same data is a severe breach of protocol unless you correct for the overfitting and they do not seem to do it. Avoid co-authoring that paper.

@CaptainEmacs So should I avoid being involved with it at all? I am the only native English speaker on the team and they may need e.g. proofreading and paraphrasing. They were counting on me to write up the results

You can do that as a favour and decline being on the author list. Acknowledgements is ok for that. You have to know if you want to be co-responsible for the content (i.e. a co-author).

Just beware that some professors know a lot. If not of their field, of what to do. It is a real possibility not to be ruled out.

To the OP and to @CaptainEmacs, note that you aren't responsible for the reputation or future of the professor. Only she is. If you don't believe in the outcomes of your explorations, back away.

@Buffy That's precisely what I implied. Authorship means endorsement.

@CaptainEmacs, yes. Agreed.

You have two options. First option: decline to be the author of the paper, second option: write and submit the paper as first author. In the second case, the paper will go under review and the reviewers and the editors will decide if it is a good publishable result. Personally I would choose the second option in a high-medium ranking journal. In this way, if the paper will be rejected, it will not be your fault and you will not enter in contrast with your professor.

It unfortunately sometimes happens that a professor or other PI may see a result from a student that they want to be true, but then a more junior student fails to reproduce the result, and the professor trusts the more senior student.
If you have time and it is not too stressful for you, writing the paper can be good practice, and may help you communicate more effectively with your coauthors. It is always possible that you are the one who is confused, and you will learn from the writing process. It may also be that once your coauthors see it in writing, they will understand better what you are trying to say.
I agree with @Gab that the reviewers can and must ultimately decide whether the work is publishable, assuming:

there is blind review (they won't know the authors) and/or your coauthors or institution are not particularly famous. Note that more fame is more power and entails more responsibility. Reviewers may give some people the benefit of the doubt. You can say the world shouldn't be like this but a) reviewers are human, and b) actually, you get more certainty from knowledge from multiple sources. So there is a matter of professional responsibility too.
you don't allow anything with your name on it that you do not believe to be true, or that you believe to be deliberately deceptive.

As long as everything in the paper is factual, the significance of the work might be better judged by other authorities.
If you do think someone is trying to deceive someone else, then you may have an obligation to talk to the supervisor of whoever the lying party is.

If you can’t reproduce the results at all, I’d back off. Don’t put your name on something you don’t trust.
But feature extraction techniques, SEM, CFA etc are well known to be tenuous and very sensitive to the data. Any informed reader will (should?) already appreciate that.


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Journal Editor does not respond about status of paper ~1 year
I submitted a paper with my co-author to a Springer Journal in the area of computational Mathematics.  It has been nearly a year now and we have not heard from the editor. There was no response for inquiries made every 3 months.  I  requested status from managing editor few weeks ago but still with no response. Given the length of the wait and the fact that the journal is the right avenue for our work, I was not sure what are the right steps ( wait more, withdraw and submit elsewhere?...)

Getting no response to status inquiries at all is not normal. Make sure you're contacting the right editor. Unless the journal is dead (i.e. no new papers accepted and published), someone out there is organizing peer review. That someone should be able to answer your question. However if you're writing to the wrong email address which might not even work anymore, then your email might not even be getting read.

See if you can reach the journal office (i.e. Springer's employees). I don't know what journal you're referring to, but e.g., for AIDS Research and Therapy they say at the bottom "General enquiries: info@biomedcentral.com". Try writing there.
See if you can reach the editor-in-chief.
If you've already tried and the editor-in-chief isn't responding: search for him/her via Google, see if their email address has changed.
If you've confirmed that the email address is correct: try sending from a different email address, in case your current email address is blacklisted for whatever reason.
Failing all of the above, try contacting a different member of the editorial board.

thank you for the suggestions, will try contacting a different member of the editorial board. The journal is Foundations of Computational Mathematics. I have also already contacted the editor-in-chief.

Withdraw. That is far too long especially given lack of any communication as well as fact that journal isn’t even quite the right fit.
But you need to get it withdrawn. Have you contacted the general editor?  Time to escalate.

thank you for the suggestion. After repeated attempts, I contacted the editor-in-chief, but no response. The general is up and running, and paper was not rejected, so I have been confused. I guess I have to send a note of withdrawal email and just proceed

Hail Mary approach - email EVERY editor on the board at the same time.


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Use of bolded variables in conference paper
I'm currently writing my first conference paper and am trying to determine a variable naming convention. I like the approach used by Di Carlo in Dynamic  Locomotion  in  the  MIT  Cheetah  3  Through  Convex  Model-Predictive  Control:

[skipped irrelevant convention] Vectors are bold, upright, and lowercase (a,ω),  matrices  are  bold,  upright,  and  uppercase  (A,Ω),and  scalars  are  lowercase  and  italicized  (a,ω).

The conference recommends following the IEEE guidelines outlined here, which does not comment on the topic. I assume it is thus up to me as the author to decide. Is bolding variables frowned upon? Is there a alternative, preferred method?
Thank you!

Some papers will look fine with this notational convention; others will have so much bold stuff that they look terrible.

For textbooks and self-published material, it is very good practice to follow a convention such as that proposed by Di Carlo, which is widely accepted as the general convention in mathematics.
However, it sounds like are talking about a submission to a conference to be collated and published as conference proceedings. This would typically have a review and editing process like submissions to any peer-reviewed journal would.  In this case, especially since they don't stipulate any conventions, it matters less because they will likely edit your notation where applicable so that all the submissions to the conference proceedings are consistent in notation and formatting.

Publisher Editing for conference proceedings? Almost not done at all - IEEE does not do this. Springer does this to a very limited degree (formatting of the title/author list and reference list), but certainly excluding the mathematical notation.

Then I guess it doesn’t matter either way, does it?

This is not a general convention in mathematics. Maybe in applied math, but certainly not in pure math.

@Earlien-reinstateMonica thank you, that makes perfect sense. I didn't even consider the conference would likely modify the notation to be consistent with the other submissions.


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Failed in PhD candidacy and applying to a new graduate school
I failed in PhD candidacy and planning to apply in a new graduate school. Should I mention or hide the failure in my SOP as it is a negative in my profile. Please help

Others that may be relevant or even possibly better: https://academia.stackexchange.com/questions/107351/what-would-be-the-possible-consequence-of-concealing-an-incomplete-degree https://academia.stackexchange.com/questions/14971/academic-dismissal-from-phd-program-what-next/14983


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Typical research on experience for physics graduate school applicants
I am applying to US PhD programs in physics. I do not have much research experience because I am an international student transferring from a completely different field. When checking the profiles of people applying to physics PhD programs, a random profile looks like this: 4 REUs in astrophysics and computational fluid Dynamics resulting in 2 first author publications, 10 graduate courses in such and such. If this is a typical profile, then I feel I have no chance getting an admission to a single graduate school.
My question is: To what extent is this representative of physics PhD applications in the United States?

Try looking at profiles on physicsgre.com or gradCafe. I don't feel that the profile you described is representative of the average applicant. Also I think there is a difference between 'representative of an applicant admitted to a top-5 program' and 'representative of an average physics PhD applicant'.


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How to leave PhD program without causing problems
I am a second year fully-funded PhD student in a stem field at a large American public university. In my department, most students spend the first two years (and sometimes three years) only doing coursework and working on the qualifying exams. This is unusual in other programs, but here it is normal. Consequently, I do not have a research advisor and have done no research since I came here. Since I've passed my qualifying exams, I am now at the point where I am expected to find an advisor.
Here's the problem... I never liked research as an undergraduate. I absolutely hated it, and I even had multiple "prestigious" experiences at different institutions with different research mentors and groups. The only common denominator is me and I don't think I can blame my former research mentors for why I was miserable. I applied to PhD programs after my undergraduate career because it was suggested to me and I didn't know what I wanted to do with my life. I was also advised to apply to PhD programs and leave with a master's degree if I decided I don't like it (since masters programs are unfunded).
I want to leave with a master's degree and move on with my life. I don't know how to explain this to my department. I fear they will try and force me to leave without a master's degree even though I have met the requirements. I also fear how they will react in general... I'd rather not burn bridges or experience intense pressure to stay. I have never heard of someone quitting after passing the qualifying exams, so I imagine the department will find this to be very bizarre.
Any suggestions on how to navigate this situation are appreciated.

Why do you think they won’t grant the masters degree? If you want to leave does it matter that much anyway?

"because it was suggested to me and I didn't know what I wanted to do with my life."  I'm sorry you got terrible advice.

I want to leave with a master's degree and move on with my life.
  I don't know how to explain this to my department.

Directly, as though the department chair were an actual reasonable human being and not a soul-sucking tentacled horror from the nether dimensions.

I fear they will try and force me to leave without a master's degree even though I have met the requirements.

I would suggest starting by finding out the mechanics of getting the master's degree.  Perhaps if you do nothing, the degree will magically appear in your academic record, but more likely there is some paperwork that you have to fill out.  Find out what that paperwork is.  Fill it out.  Collect the necessary signatures, and submit the completed paperwork to the relevant campus office.
You don't have to tell them why you want the master's degree. In my experience, it's quite common for PhD students to pick up a master's degree along the way to their PhD, either as a backup if the PhD falls through, or as a boost on their resume when they look for summer internships / employment.  Once the master's degree paperwork is done, inform the department that you will not be returning next term.  Finish your classes, look for jobs, and move on.
But at a more fundamental level, you really don't have to defend your decision to leave.  You did not promise to complete the degree program.  You did not sign a contract.  You are not an indentured servant.  You do not "owe" the department.  Your departure will do  the department no permanent damage.  Yes, a few people may be disappointed by your departure, but they'll get over it.

I have never heard of someone quitting after passing the qualifying exams

For what it's worth, I left my first PhD program with a master's degree after passing my qualifying exams.  (Admittedly the circumstances were different — I left to join a different PhD program — but I was far from the only person in that department to leave after passing quals.)

Passing the quals her usually involve getting a lot of extra help from profs. I just feel bad that one of my professors helped me so much to pass that exam and don't want him to feel like I intentionally wasted his time. (I was naive and thought that passing the exam would make me want to stay and it actually had the opposite effect.)

But you didn't waste their time!  One of our jobs as professors is to help students pass quals.  You've asked your profs to do nothing more than their jobs.

Or, to quibble slightly with @JeffE's portrayal of our jobs as profs: it's to help grad students learn_basic,important_things (and, incidentally, thereby, pass qualifying exams).

Since you have funding, find a job first, then leave.
It is not rare for PhD students to leave with a master's degree.  Most departments will not be surprised.  They may prefer you complete your PhD, but there is no reason for them to make a big deal about it.  Since you are not doing research, they may be pleased to take your funding and use it to recruit a student who will do research.
If you want, you may be able to get your master's degree first, and then announce your departure.  If they ask why, say it is so you have the option of gaining teaching experience at a community college.

Unfortunately, I don't feel like I can obtain the master's before announcing my departure. To get it, I have to fill out the candidacy form which involves listing who my research advisor and committee is. It feels wrong to lead on an advisor and then be like "uh no thanks". But I am going to talk to the coordinator and see if I maybe we can explain it to a faculty member and have them sign it, with the understanding I am leaving and don't expect to research with them.

That is an odd situation.  You really should have been required to identify an advisor earlier.