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How to handle potentially gaslighting and very confusing PhD advisor?
I’m a new PhD student (3 months in) of a niche area, and I now feel like my supervisor (f, 56) has been constantly gaslighting me. English is not my first language and this is a really confusing situation so I will try to explain this as clearly as I can and go through all the events. Apologies in advance for the long post but I feel I must give a full account of her behaviour.
I study in a large and prominent university in my country but this particular department is relatively small which meant that my supervisor was assigned to me and I didn’t choose her. I’m currently her only graduate student and she is unfortunately head of the department.
So my original proposal which took around 6 months to plan and write was accepted some months ago as part of my application. My now-supervisor said that my proposal idea and plan was very strong and that the “whole department agreed” thought so. I was very happy about this. A few months later, after being accepted and just after registering, I received an email from my supervisor about setting up our first meeting and she asked me to send on any “other proposal” that I might have. I was confused about this as I assumed that I would be developing and expanding on the original accepted proposal. I asked her about this in email, and she ignored this part in her reply and only spoke about the time of the meeting which we arranged for the following week.
At the meeting, she asked me how I felt about the topic now and if I was still interested in it. I told her that I was still very interested in it and that I was looking forward to developing it and starting the research. She spoke positively about my topic and said that she didn’t know much about that area but that it had good potential and she gave me a couple of books and recommendations that were relevant to it. Between that meeting and the next (2 weeks later), she sent on a lot of articles about my topic (I’ll call it Topic A) which were really helpful and I formulated a report and discussion plan for our next meeting. A couple of days before the meeting she sent on a very lengthy article relating to a completely different topic (totem poles) and one which wasn’t even very relevant or related to our department’s discipline. She asked me to read it before our next meeting so that we could discuss it. I thought this was a bit strange as it was such a random subject but I read it.
At the next meeting she started talking excitedly and at length about this article and when I was able to get a word in, I said how it was an interesting article but I couldn’t really link it to my own chosen topic. Her face soured at this and looking askance said very sulkily: “I thought we’d moved on from that topic.” I was surprised as nobody had mentioned about changing my topic and I only had positive feedback about it from her so far. She then said in a sour tone: “I thought when I sent you that article that you would change your mind and do totem poles instead.” She never mentioned this beforehand. When i said I wanted to pursue my original proposal she screwed up her nose and said: “I just never saw any potential in it.” She also said that it’s “not a part of our discipline”. This is not true. I respectfully explained how it was accepted, how she previously said it was a strong topic and how it IS relevant to our discipline as it’s even mentioned in our discipline’s ‘manual’ which is the foundation book of our discipline. She then interrupted me and said to take no notice of the discipline manual, as it’s “wrong and prejudiced” and she again spoke over me dismissively and loudly told me to think of another topic and get back to her. I was very taken aback as only last week she spoke of Topic A’s very good potential and she had sent me numerous articles on it. I went away from the meeting dejected, confused and unsure of what to do next.
I later received an email from my supervisor where she said that if I was interested in doing a new topic based on the article she sent me then she could help me as that area (totem poles) was part of an “ongoing interest” for her. I couldn’t see how that topic was even a part of the department’s discipline but I replied and said that if she didn’t think my original topic had potential then I would be willing to compromise with coming up with something that we could both agree on. I came up with a different topic (Topic B, related to her interest as well) and she accepted this and said it was a good idea. So I spent the next number of weeks researching this new area. During this time she sent me on a number of articles including (very strangely) those that related to my ORIGINAL TOPIC (A), the one that she had dismissed so angrily at the last meeting.
At the next meeting, I was just about to start talking about what I had discovered so far about Topic B (that she had agreed to) and she immediately spoke over me before I got a chance to say anything and suggested a DIFFERENT TOPIC altogether. I politely told her that I would be happy to stick with Topic B and reminded her that she had agreed to it, but she spent the entire meeting dismissing it by talking over me loudly about other non-related topics that I could do and she then suggested that I make a “mind map” to come up with a different topic. She then mentioned if I knew the work of a random academic and I said that I had read one of their books once. She said: “Since you read their book you might as well do your thesis on that.” Again I left very confused.
She emailed me soon after and asked me if I would be willing to write a short paper on our discipline’s ‘manual’ as it was such an important part of our discipline (even though she had previously said the manual was “wrong and prejudiced”), while I figured out my thesis topic. She said it might not be relevant to my thesis (she acknowledged again now that B was my thesis) but that it would be a good exercise and that certain parts of it might come in useful in the future. I agreed, wrote up the paper and sent it to her. She replied a few days later, and gave very good feedback on my paper. She said that it was a good start to my thesis and that I can use that paper as the topic and beginning of my thesis. I said to her that she had previously said that this was just a side project and a useful exercise as it wasn’t related to the agreed topic (B).
She ignored this, and replied to my email talking in circles only about the manual and didn’t address what I had said. So at the next meeting the next day, she started off with again talking very positively about my review. I asked her (mainly to confirm) if it would be possible to continue work on Topic B, the thesis that we previously agreed on. She said “Of course! You can do whatever topic you want for your thesis.” We agreed that I would narrow down the topic question and come up with a plan.
So I spent the next while doing what she asked, and I told her that I would have it to her by a certain date. She said “No rush! Take more time.” So I took an extra few days to work on it and when I had it written out fully, I sent it to her. Even though this plan was based on Topic B that she had agreed to and acknowledged as my thesis theme, she replied and said that she was disappointed that I gone back to my original topic (Topic A, even though this topic was nothing like my original), and she gave a lengthy explanation as to why I should now concentrate on a thesis based on the discipline’s manual instead. She said that I should also do another review of the discipline manual but this time I should invert it and rearrange the entire book in terms of chapters and content, and that I should rewrite the entire discipline’s manual. She said that I should also incorporate totem poles into the work somehow. She also said that I am delaying my own research by not being able to decide on a topic (even though she is the one who keeps dismissing and changing topics and a few days before she had told me to take my time). She said that I may just be confused due to the still very early stage of my PhD.
I am at my wit’s end right now. When I try to speak or ask her to clarify something, she will either interrupt and talk over me or talk in circles about something that has nothing to do with what I asked or the topic that we agreed on. In emails, she will also avoid my questions and will reply with a lengthy explanation about a completely different subject. Some other potential red flags that also occurred:

One was that our first meeting (and all since) was more like a lecture: she interrupted and spoke over me and she got irritated and snappy when I asked questions.

At the first meeting I asked about the progress review and she said it would be at least 6 months away. About 3 weeks into the PhD, she emailed me to tell me that the university’s policy on progress reviews meant that it would unfortunately be 2 months after the start date. I asked her for more information about this and she ignored my question. At the next meeting I asked her again and she said dismissively: “We’ll worry about that when it comes around in 6 months.” She then spoke over me again and changed the subject loudly and avoided eye contact. It was clear she didn’t want to talk about it.

The second topic (B) that we agreed on is also slightly related to another discipline (which she suggested) so I asked her if I should start research work on literature in that discipline also. If the topic is also related to another discipline it’s only natural to read around that discipline too but I wanted confirmation as she’s been so confusing. She replied, irritated: “NO! NO! NO!”, and sarcastically said: “Why? Do you have a degree in that subject too??” Even though her totem poles article was also from another discipline. I later asked if it would be possible to incorporate a comparative element into the thesis, as she had previously mentioned that a comparative aspect would be very interesting. She replied angrily: “Why? What would be the point??”
The next day she very confusingly sent me articles relating to the
idea about the comparative study.

When I was accepted into the programme, I noticed there was a female co-supervisor named on the acceptance letter. When my main supervisor emailed me after I registered, she mentioned that her husband (also in the department) would be my new co-supervisor now but that he wouldn’t be taking an active role. So because of this, I’ve never met him.

She also recently asked me to set up a file share so that she could send me a large digital book. I did this and emailed her back to let her know it was set up. She replied (on the same day): “What is set up and why? I don’t understand ”. I reminded her of her earlier email and request and she replied: “I may look into this at some stage and send you something later but you have enough now for the moment.” Later that day, she sent me on the book through the file share.

She also added me to an undergraduate module on Moodle so that I could view some of the literature that she uploaded. She emailed me later that same day and told me that she would be removing me from the module as the literature is “private”. The literature consists only of old and public domain books. At our next meeting, she asked me if I had downloaded the literature because she would recommend that I read it.

It really feels like she is gaslighting and being manipulative trying to get me to work on a topic that interests her the most, by being deliberately confusing and dismissing something that she will later praise if it suits her own idea (like the manual). She is extremely passive aggressive and contradicts herself constantly, talks in riddles and she will say things like: “It’s not important for you to narrow the topic but instead you should concentrate on narrowing the topic.” There is also another academic whose book she told me to use as a template for my previous plan. I did this and she then said that this academic’s book was “weak” and that I shouldn’t have followed it. I think she said this because there was no way I could include the totem poles idea into this format so again, manipulative I feel.
I’m also considering that she may have other issues going on as she seems like a somewhat unstable person, in general. In our meetings, she will talk very energetically about anything that comes into her head. For example, something will remind her of a cartoon she saw and she will then talk in length about it and all the characters and plot. She also talks about herself and her own work a lot even though it has nothing to do with the discussion and she gets excited if I mention a journal that she has published in, where she will then excitedly talk about her publication and then afterwards forget what she was previously talking about. She has also lied a couple of times about new theories related to our discipline that she supposedly came up with, and I discovered that this wasn’t true when reading older books related to our discipline that she recommended and which contained the ideas. Even though our meetings are supposed to be an hour in length, she will sometimes talk for 6 hours about trivial and unhelpful things like cartoons or her family and she will then say how she didn’t realize the time. She will also often email me drafts of articles or books that she’s working on (not related to my own work) and tell me how she’s the most innovative writer in our entire field.
As she is the head of the department and I’ve never had contact with any co-supervisor, I’m feeling really lost and confused about who to turn to about all this. I’m struggling to make any progress or plan right now because every topic idea (which is initially agreed on) is then later shot down in a manipulative and dishonest way before I have a chance to discuss my research and progress on it, and any questions are ignored, so knowing and expecting this, my motivation and inspiration are now really low. I’m just at such a loss as to what to do and I feel like I’m going crazy.
Any thoughts on what she’s actually doing, and any advice on what I should do next?

This question is nearly 3000 words long. I think you need to distil it down to something much more focussed if you want to get good answers here.

Better yet, please also give us TL;DR.

Having read the 3000 words: Unless you can find another supervisor (even if unofficially - are there any other PhD students who you could work with ?) I think you will have to cut your losses and leave. If people like her are allowed to rise to the top, there is something off in the department, so I wouldn't get my hopes up in being able to resolve this. For what it's worth, I don't think my (nominal) supervisor ever read my thesis and I graduated despite him, but I was in a very large & collaborative field, so it was easy to find other people who were interested in my work.

Could your supervisor be suffering from dementia? Constantly forgetting what she's spoken with you about, having difficulty concentrating on the intended subject and mood swings are all potential signs.

Is there a postgraduate programme coordinator that is further up the chain/more centralised that you can talk to? This is something you need to be talking to someone in a dedicated postgrad student support position about, outside the department. That there seems to be a system of a secondary supervisor to avoid the issues you are having, but that role has been completely neutralised, you should be talking to someone at the university level to ensure you have someone "on your side" if matters deteriorate.

Your supervisor sounds very like my own supervisor — I had exactly this sort of problem in the first year of my PhD and it cost me most of a year and ended up with us settling on a very mediocre topic. I stuck with it, but my advice is to get out of there.

This person seems entirely unhinged and won't do you any good. Their behavior will most likely get worse as time goes on.
Trying to decode intents or motivations from someone like this is entirely a waste of time. It may even damage your own mental health.
In my opinion, you should get out or transfer to another supervisor or program as soon as possible. (Disclosure: I have not been in a PhD program with a thesis component.)
As a minimal first step, you should contact either of the previously listed co-supervisor(s) and speak with them about the situation.

My (possibly biased) estimation is this:
Although your supervisor is not fully professional and maybe not even competent in effective academic research, the problem you have is lack of personal chemistry. The same behavior your supervisor exhibits could have been described positively by another person with a different personality or preferences from yours.
Basically, it seems she's improvising to find a thesis subject that would interest both of you, while you seem to prefer rigidity, accuracy and expect precise almost legally-bidding relationship with you supervisor.
For that reason you have two options:

Change supervisor or drop out.
Adapt and start to cooperate with the supervisor as much as you can to complete the thesis.

Here is an example of judgments about your supervisor that are based on subjective personal preferences, that helped me form my assessment of the situation:

"She also talks about herself and her own work a lot even though it
has nothing to do with the discussion and she gets excited if I
mention a journal that she has published in, where she will then
excitedly talk about her publication and then afterwards forget what
she was previously talking about."

I don't see what is objectively wrong with such behavior. You assume that a free discussion has a fixed "subject" from which she cannot diverge. And I don't see why that is so.

I might phrase this a bit differently, to say that it doesn't matter whether "your supervisor is not fully professional and maybe not even competent", and that a lack of personal chemistry/lack of agreement between mentorship style and desired mentorship style is sufficient reason to seek a different advisor. Probably best to set aside entirely the competence of the supervisor, because it could very well be that OP's own communication is lacking and their account here is misleading. It doesn't matter, though, because they do not need to indict and convict their supervisor of anything.

I think this would agree better with the sentiment in the rest of your answer, following the comma.

I'm sorry, but I didn't read the whole text. Nevertheless, I made some hypothesis which is as follows. Your supervisor just wants you to change the subject. She doesn't say it directly, but subliminally and uses various manipulative techniques towards you.
There are several ways to solve it, but we cannot declare here that it will work as it should. One solution is to change supervisors or the workplace.
The second solution is to submit to the trainer's will and change the topic. It is possible that you will then have peace for a certain period of time before another pressure comes that will be against your will. You will then have nothing else to do but submit and so on. In principle, it's about submitting to the trainer's will and telling yourself if what you have is enough for you, or if you want more. If you want more, you have to learn to operate two systems. So you will need to have two faces for her and for the academic community.
The third solution is to try assertive techniques. That is e.g. show that you understand the trainer, but at the same time stand up for yourself. Don't get dragged into an argument or a bad mood. If you do not know assertiveness, I recommend that you take a course. There are many assertive techniques. Assertiveness is built on accepting responsibility for oneself and the ability to understand the other party. Unfortunately, manipulators don't like people who can't be manipulated and are even more annoyed by people who control assertiveness. So this solution may either succeed or the trainer might get rid of you.
Of course, you may also try the combination of methods two and three.


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How to know whom I should trust to discuss my research as a bachelor's student and how to protect my findings if I'm concerned about "plagiarism"?
I made a post in this forum a few days ago because I may have developed a new math formula. I was asking about what I should do (I'm pursuing a bachelor's in CS, so I was somewhat lost), and I received really good and clarifying answers!
However, one of the most frequent pieces of advice was to talk to a professor whom I trust. The issue is that I don't know much about my professors, and I'm unsure if discussing a potential new discovery in the field with them might result in them taking the idea and publishing it themselves.
So, how can I determine whom I can trust, and is there a way to "protect" my work before openly discussing it with someone?
I'm asking this because I still don't fully understand how the research area deals with ideas that haven't been published yet. Thanks for any help!

I think your concern in misplaced.  A math professor is extremely unlikely to steal the ideas of an undergraduate student.  (That's a Hollywood movie plot, not real life.)

Can you upload your results to something like a private GitHub repo? I also really doubt you have anything to worry about, but just to give you peace of mind, if you're results are significant and credit gets stolen you'd have proof you at least discovered them before they got published.

@Gedgar, i see your point, i may be overthinking about it...but i still don't understand how the research area deals with ideas that haven't been published yet...i know it would be a rare case, but i don't know if i can talk to any professor of the math department or it has to be someone i trust....and how to avoid that very small chance of someone taking the idea.

@tarzh, that's a good idea, it could certainly help if something happens, thanks.

You should be more worried about being ignored (and for a reason).

If you are unwilling to share your ideas you will probably not get very far, sorry. The faculty at your university are, with rare exception, trustworthy. If you have taken courses with them you see how they interact with people and can judge. Most people in general aren't out to pirate the ideas of others. Exceptions? Yes? But not so common.
Not trusting others means that you have to do it all on your own, which ,in the case you described in the other question, probably isn't possible.
You may have a good idea or not. But don't act as if it is the only good idea you will ever have. Collaboration for novices is a good thing.
Technically it is possible to register a paper with the copyright/trademark office, but it costs money to do so and few bother to do it anymore.
I think, as I said in answer to the earlier question, the most important thing you need now is feedback, not safety.
Newton locked up his ideas about Calculus in a drawer and so Leibniz got credit for the idea(s) years later with independent development. The history is quite interesting, actually. It may be part of the reason we now use Leibniz's notations rather than Newton's since they were published first.

I got your point, you are right! The whole point, in the end, is to share ideas. Collaborating will be good for me to develop some research skills... I will try to find someone to help at my university. Thanks!

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What is 'journal rank'? How can I get this?
I am applying for a job and the HR is asking me to update my CV with a list of publication to include authorship role, journal rank and impact factor.
I am not sure what journal rank means in here. Is there a site to go with a complete list of journal rank?
Thanks

Any journal ranking is a low quality ranking.  They are likely thinking of https://www.scimagojr.com/journalrank.php.

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How to apply for a first ever physics research internship in the 2nd Year of Undergrad?
I am a 2nd year student studying physics in the UK. I am very interested in securing a research internship at the end of my 2nd year. However, I have not done any research internships in my 1st year, and I'm quite confused on how to write my academic CV(especially what to write in the experience section) for the first time, without prior experience in research. Also how do I email professors to ask whether they are willing to take on summer students? Any advice would be appreciated! Thank you!

Why can't you just go talk to one or two of your professors in person? Blind emails are probably going to be fruitless. That is especially true if you need funding.

That is true. I'm planning to talk to my personal tutor about it. But I'm still unsure on how to write an academic cv though. Do you have any advice on what to put in the experience section if I have no prior research experience?

Assuming you are just starting the second year of undergraduate, it would be unusual, almost everywhere, to have much of any research experience. Everyone needs to start somewhere, which is what you are trying to do. It might (might) be enough to just say "None yet", but I don't know the requirements of the systems you are applying to.
I would talk to someone local at your university. But it should be someone with some knowledge of what you are trying to do. Whether your tutor has that experience or not, or whether you need to talk to a more senior professor, depends on your university, but find that person. They might even have an opportunity for you.
There may also be summer internships available at some national labs, though I don't know specifics, especially for UK. Those should be advertised and professors may know as well.
But sending blind emails to professors is usually not fruitful, especially if you need funding. But this is another place where a local professor can serve as an intermediary for you, provided they know you and have a high opinion of your progress. They might, at least, suggest someone to contact, in which case you can say "Professor X suggested I contact you...".
Alternatively, you can look for announcements in various professional journals, such as those of professional organizations, of openings. Librarians can often help with such a search.
Your CV, of course, needs to be completely honest, not overstating your accomplishments. People will understand a lack of such for beginning students. But you need to avoid wasting people's time with blind requests having nothing to back them up.


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Verbal Postdoc Offer can be trusted?
How much a postdoctoral offer by email can be trusted? Did you face any issues for example bluffing or changing the mind of PI at the last moment ? Is it likely to happen ? Please share your experience.

I don't  think e-mail offer is only verbal. However, I am not a lawyer. Also, This question sounds like a polling question. Vote to close as off-topic.

If this is about India, what does the law there say about such things? Are they binding as they are some places? Do you have some level of distrust in the one making the offer? Or just general paranoia.

If it is a random email from somewhere you’ve never interviewed at, it isn’t real. If you’ve applied, been interviewed, visited, the usual job selection stuff, well, it is highly likely. As one weird HR thing, I’m supposed to make a verbal offer to candidates before HR will release the ‘real’ offer through their portal. I often do it by email because scheduling a call may be difficult and I want them to have the ‘real’ offer as soon as possible. And then their is my postdoc offer that was given verbally at a conference and some months later I flew across an ocean to start, no paperwork at all.

@Buffy It's just being anxious, skeptical about the delay, which is making me little bit frustrated at this moment.

https://academia.stackexchange.com/questions/191500/how-do-i-navigate-verbal-offers-for-postdoctoral-positions

A friend once told me that "the best contract is dealing with honest people." With this he meant that if you are dealing with an honest person who cares about their reputation, their word is the best contract you can have. With the opposite type of person, no amount of written documents will stop them from wiggling out of a commitment.
So,

How much a postdoctoral offer by email can be trusted?

It ranges from not at all to fully.
I did two postdocs, and both offers were verbal (not email, but verbal in the literal sense), and both came through.

I've had "unofficial" offers before. But that was a few days after the interview. The professor told me that the HRs take forever to process and wanted to know if I was interested. I told the professor that I wanted to read a formal contract before accepting. This was a university in the UK. The professor turned out to be nice and a trustworthy person - no problems there at all. That said, a communication from the HR on a letterhead is always a reliable offer.
It's unheard of, that a professor would bluff about a postdoctoral position. Finding a postdoc position itself is a difficult task, given the number of PhDs graduating every year, bluffing an offer would come across as sadistic at the best. Would the PI change their mind ? You said there are no funding issues. I don't know if you got the verbal offer after an interview. However, if you haven't applied yet then the professor should advert the job and conduct an "open" search. Some countries expect the University to advertise for atleast 30 days min (I think UK does that), in order to sponsor immigration - I don't know the country specific rules. If a person with a better set of skills do apply, then the professor has to make an offer to them. Universities do not like to give postdoc jobs without an ad, nepotism being one of the issues.
It's not uncommon for a professor to contact a potential candidate and ask them to apply or make a "verbal" offer. One of the reason could be that they read your paper somewhere and contacted you or your PhD advisor or sat through a conference talk you gave somewhere. All of these can happen. Professors look for talented people. That said, nothing is stopping you from applying elsewhere, incase things go south. Even if you accept a verbal offer, I don't think you are legally bound unless they type the contract and ask you to accept it (I'm not a lawyer).

Verbal or emailed job offers from a PI are not reliable contracts.  Normal university policy would forbid a PI from making job offers.  Job offers are usually signed by a dean or provost.
Bluffing and change of mind are not things you need to worry about.  Job offers run into trouble when the PI thinks there is money to pay you but actually there is not.
Examples:
The funding agency did not deliver the funding it awarded to the university.  Maybe the legislature did not pass the budget.  Maybe parliament was dissolved and the caretaker government will not deliver funding until there is a new government.  Maybe the university leadership suddenly announces a hiring freeze.  Maybe the university had a natural disaster and needs to reallocate money to emergency repairs.

I think that this is confusing two issues: one thing is the PI telling you "you've got the job", which means that you can stop looking for jobs and start looking for an apartment near the university. Another thing is the formal job offer from the university, which can only come from HR. Of course the verbal offer can fall through because of funding, etc., but the OP is asking about the PI changing its mind.

@Cheery That's addressed in the fourth sentence.  I do not agree that these are separate issues.

There is no funding issue, rest are all assured. I am only worried about the PI, nothing else.


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Going through mental stress in my phd coursework. Any piece of advice?
I am a phd student and I have 7 other class mates who along with me were inducted this fall (2023) to the department of chemistry. We have to take 6 courses together before we start doing research in our respective labs. The course work here is very rigorous and challenging. Group discussions and tutorials help you a lot but my classmates don't want to discuss with me I don't know why may be they hate me bcz I am on first merit position (merit is not solely based on grades here it depends on lot of things, GRE, communication skills, Co-curricular activities etc.) Or may be I am a hate-worthy person I don't why I am going through a lot these days. 5 of them have found niche in each other's company and when I try to socialise with them they give me a silent treatment and sometimes they age shame and weight shame me (as I am an overweight person who looks older than his age) All of of are in 25-27 age bracket but they think I am some older person impersonating as younger one. My grades this far are not good I am very week at some subjects which I need help for I have tried to reach out to senior students and students from Masters and other fields taking the same courses but no one here wants me on their groups or social circles. The reason behind my being a slow learner is ADHD which has seriously affected my academic performance but my research is still great. I am having hard time here as if I don't get certain grades I wont be allowed to continue. Can somebody give me some advice on what should I do in this scenario. Thank you in advance.

I'm really sorry to hear you're having a hard time. The first year of graduate school is particularly difficult – course material, the social aspect, everything. Many folks often have the same or similar challenges to those you described.
My suggestion is that, first, you contact your university's health center or counseling center. Many universities (most of US, Canada, UK, Europe) have easily accessible and free counseling resources. This can make a difference in helping find solutions or ways to reduce your stress, and make a plan on how you're going to approach the challenges you're having (including on how to maybe engage others in your cohort and start to form friendships inside and outside your program).
Second, I'd recommend contacting your university's office that works with students with disabilities or learning accommodations. The health center or health/mental health services could help direct you, and generally that information (email/phone number) is available on the university website. They can arrange accommodations for any challenges you might be having related to ADHD, which may further make a difference in your day to day.


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Master thesis report submitted for official record is different to the report graded by my supervisor
I am doing a master's study in a German university. I had some setbacks during my master thesis project's lab work. This delayed the time I had available to write  my report later on. The setbacks were not enough for an extension of my project by the examination office (My school has very strict rules for extension). So by the time the official deadline for submission came, I submitted a written report that was not very good quality (not so bad that I would fail, but not so good that I get a good grade either).
However, my supervisor knows the setbacks I had and the commitment and hard work I had shown to overcome them, so he agreed to give me an extra week to work on my thesis report and he will grade that instead (instead of the submitted report).
My questions are:

The extra time would allow me to do a much better work than the officially submitted report. What happens when somebody compares the quality of my officially submitted work and a grade that doesn't match with it (maybe better grade than the report deserves?)?

The official and more permanent record of my thesis would be a sub-standard report that does not reflect the time and effort I spent in the practical work. Is there possible way to fix this?

Is this considered an academic misconduct?

Thank you in advance for your insight.

It is certainly misconduct on the side of your supervisor, at least on a formal level.

While I realize that Germany is pretty strict about its rules, you haven't committed academic misconduct. I think the general view would be that if it is approved by your advisor it is fine. I assume they have the authority to grade you as they see best.
As to providing a better permanent record, if that is what you mean by "fixing it", I'd suggest that your advisor is the one to intervene. It might be possible, or not, depending on the rules.

I would say it is misconduct by the advisor to grade something which is not the official manuscript. On the same footing, you could give the grade just by knowing that the student did good work, without ever looking at the thesis, or despite the thesis being horribly written. All of this is very understandable, but on a formal level this is clearly misconduct: You have to grade based on the official thesis.

From my experience with Germany, the only people who will really look into your thesis will be the people who grade it (your professor and the second grader). If they are both ok with this approach you will be fine.
Some universities will put the theses in their library afterwards, but I have never heard that they will also put the grades there, so even if someone were to loan your thesis out from the library, they will not know which grade you got.
If you apply to an academic or industry position afterwards, noone is expecting you to send your whole thesis with the application, but rather the topic and/or grade, or maybe a short summary.
So the chance of anyone really reading your thesis afterwards (unless you are actively forcing it) at low. As long as the prof and second grader are both ok, take the offer.

There are several thesis and dissertations which are not a final piece of work. Several students just do a reasonable work for thesis and submit to graduate. Professors are also okay with that. University/graduate school does not care as long as your committee approves it. So, if it is submitted and approved, you are done with your thesis. Move on.
Answering your first and second questions, I agree more time will help you to produce quality work. Instead of improving quality of thesis (if already approved by school), use extra time and effort to develop publishable manuscript to submit to a peer-reviewed journal. If you publish your work, people would not care about thesis. They will refer to your published peer reviewed paper instead of thesis. That is a big win and compensation for your lower quality work in thesis. People usually won’t compare your thesis and paper because everyone knows peer-reviewed works go through more rigorous review than thesis. Grades are not very important in graduate school and job market. For academic work, research is important and for non-academic job skills are important. So publishing your thesis helps to demonstrate your skills for academic and non-academic jobs.
Finally, it’s not academic misconduct. As long as you have done reasonable job and approved by committee and university, you should b good.
Alternatively, if you are not interested in publishing your work in peer reviewed journal but only want to refine your thesis, don’t even bother to correct it because if it is approved by committee and university, you are done with the process—just moving on is the best option. Resubmitting a revised thesis and replacing with new one is a big hassle and remains are permanent record saying “you replaced your thesis” which may be counterproductive as some people may assume you have done mistakes which force you to make corrections.


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How likely is it to get a second chance in this context?
I am currently pursuing a PhD degree and I do not yet have a lot of experience submitting journal articles. I recently submitted an article to an IEEE journal in my field. Around two months ago I got the publication decision "revise and resubmit".
The three reviewers were generally positive about the work and mostly asked questions related to the notation as well as further theory based questions which I think I all answered and added to the revision.
However, there is one comment which is a bit unclear to me. The reviewer there essentially asks a question of the type "why was the measurement X in experiment Y conducted in this manner, this needs to be clarified". Similarly, the associate editor asks a question related to the same experiment "in order to support claim Z of the paper, Z needs to be demonstrated". (Neither AE nor reviewers explicitly ask for additional experiments of a certain kind).
Basically, I believe the experiments I conducted already demonstrate Z, though I did probably not explain clearly enough as to why this is the case.
Right now in my answer to the reviewers and the AE, I essentially explain why I think my experiments support the claim in question and I also explain this more clearly in the revised manuscript.
In principle, I could think of additional experiments to gather further evidence for my claim, however, it is unlikely that these experiments would offer better support for my claim (since the associated measurements would be less accurate). I also mention this in my reply. Moreover, these experiments would be associated with a significant amount of work that I think would be outside the scope of the submission.
I wonder how risky it is to resubmit my revised manuscript without offering any additional experimental data and instead, explain why I think the work I did already supports my claim? If the AE does not agree, is it common to get a second chance at revision or is it more likely that the paper will be rejected?

What does your advisor think?

You should not listen to advice from anyone who has not read the manuscript.

You probably have to do something to satisfy the editor, but it might not involve additional experimentation. And a "rebuttal" to the editor probably isn't enough. Think about how you present things. If you believe that your current structure is sufficient to establish your claims then it seems likely that you haven't yet been convincing in saying that in the paper. Can you make it clearer to a reader?
If you have made jumps in your logic (leaps of imagination, in the worst case) then you need to explore that. Can those jumps be filled with explanations or do they, in fact, require more testing?
You have a (perhaps small) "chance" of publication doing nothing more, but you increase the chances if you specifically address the comments in some way.
Measuring your "chances" is harder. If the editor finds that reviewer especially trustworthy they might be low. If the editor thinks otherwise or trusts the other reviewers especially, then higher. But there is no way to know that. And, at a minimum, you need a revision as stated in the decision you already received.

This question's nearly impossible to answer conclusively without knowing the details. The AE's comment is "in order to support claim Z of the paper, Z needs to be demonstrated". Accordingly, you need to demonstrate Z. The more effort you put into it (e.g. by conducting new experiments), the more likely the AE is to be convinced, but this does not mean you can't convince the AE without conducting new experiments.
Similarly, how the AE might react is nearly impossible to predict. If they're of opinion you really need to put more effort into demonstrating Z, then they might conclude that you're not taking the review seriously and reject again. Or they might not.
The one thing you should be careful about (it doesn't seem emphasized in your question) is that the decision was "revise and resubmit". It wasn't "revise". That means the revisions required, in the AE's opinion, are probably very substantial.


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Does having no first author paper but multiple co-author papers hurt your profile for PhD application?
I have a good number of peer-reviewed publications but none as a first author. I am mostly 2nd author in these papers and sometimes 3rd-4th. I am a prospective PhD candidate, and I saw several professors' websites that they prefer students with at least 1 paper as first author.  Does having no paper as the first author but over 5 as co-authors damage my profile? Does it indicate sth like I can't do independent research or sth?

This depends on where you are applying and on who it is that makes the acceptance decisions. In the US it wouldn't be any issue at all. In Germany and some other places it might, depending on who you apply to and their own judgements.
I should think though that you are in a good position. You have some evidence of your ability to collaborate which is also valuable. Entering a PhD program doesn't (normally) require that you already have the skills that the PhD is supposed to give you.
Also note, that even for the professors you note here, that "prefer" and "would accept" aren't necessarily the same. It might be worth having a conversation with some of them if your work is aligned.

Thank you. That makes sense.


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CGPA Calculation for US institutions
A US university's application portal has provided this 4-point scale and told me to note the CGPA.
Where A=4, B=3, C=2, D=1, E/F=0
How do I convert my CGPA to this scale? MY undergrad CGPA scale has A+=4(80-100), A=3.75(75-79), A-=3.5(70-74), B+=3.25 and similar grades. The program page where the converted CGPA should be mentioned also leads to WES country resource page where 60-100 is A, 50-59 is B and so on. This is all a bit too confusing. Any help will be much appreciated.

The first an second system seems to be quasi identical, just with different resolution.

It is typical in the US to let the institution you apply to to do the calculation based on official numbers from your own institution and knowledge of the country.
If you are asked to do a conversion, it is fine to just say something like 3.8/4.0 if that would be the official GPA.
But note that in US institutions 70-74 might actually be a C or C+ grade, so it is very difficult to do a fair and honest computation. But institutions are good about knowing the vagaries of grading systems around the world. And the reason that 70 might be A- in one place and C in another is just the way that the educators in different places typically grade the student's work, including, perhaps, the difficult of the tasks graded. There is no universal standard. And not all institutions in the US even have A+ grades and when they do is probably more like 97/100 and above.
You are normally required, in the US, to provide transcripts as well, so that individual grades can be seen and the institution applied to has knowledge of where the grades were given and probably understand what is typical there.
So, don't overthink it. A simple statement that conforms to your degree granting institution is what  is expected. In particular, don't try to make it look better than it is.

Something that is harder to recognize is that if your own professors judge you on whatever basis to be an excellent student (A level) then that is very likely to be accepted elsewhere. That matters more, I think, than the numbers themselves. And, in the US you will be asked for letters of recommendation that are considered very important. More so than some other places. This reinforces the sense given by the numeric scores, however they translate.

Thank you very much


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Do recommendation letters need to be strictly from professors at universities?
I am pursuing a Masters degree in pure math, and will be applying to grad schools in the USA and Europe (and some other places) for a PhD. I have one letter confirmed from my thesis work, which I believe is my strongest and will be my primary letter. I hope to have another from a course that I'm taking right now, albeit not a very strong one in my opinion because we have started communication just a few months back and the letter needs to be submitted before the evaluation of his course.
More concerningly, a third letter is up in the air. I could approach a professor whose course I have done decent in (but not great), or a professor at my earlier college who I have done great under, but whose collaborations/connections are not very notable/have not spread far.
Another option that came to mind is this person who has been involved in my math journey for quite some time, but is now in an entrepreneurial position in a moderately-established startup organisation to train people in math (olympiad/advanced), not at any college/university. He himself completed his PhD (however in a pure math field different from mine) a few years back from a reputed university from the USA, is actively researching and has had his work featured in and himself invited as a speaker to quite a few conferences. He is someone I have discussed a lot of math with (including a bit of budding research in his area) and knows me well personally, hence could be able to write a much less generic and more comprehensively personal recommendation.
Given the choice, which ones should optimally be my submitted letters and in what order?

This applies to the US and possibly elsewhere. No, the letters don't need to be from professors at universities. However, the best letters, the ones that will matter, are the ones that both confidently predict your success in graduate study and can be relied on for the knowledge of the writer. That means someone who both knows you well and also knows about graduate study. This is more critical for doctoral study than at the masters level, but still applies.
I'd guess that your "optional" writer is an appropriate candidate for the above, and would be even for doctoral study.  It isn't about them, but about what they can say about you and be trusted in its accuracy. I don't see any problems here.

Can anecdotally confirm from the student side:  By the time I applied for my PhD, I was 15 years into US industry and largely out of touch with my previous academic mentors-- enough so that it felt weird hitting them up for recommendations.  My letters were all from industry, one with a PhD, two without (but one responsible for managing PhD-level people.)  I got in.

Thank you very much.

As a general rule, it is perfectly acceptable to use letters of reference from successful people in research and industry positions outside academia.  Some of these people have equivalent academic stature to professors in a university and have similar backgrounds in their education and research records.  You should seek letters from people who can comment positively and credibly on your research work/potential.  This need not be restricted to university professors.

Thank you, I'll keep that in mind.


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Guidelines for labeling axes of inset plots
What are the recommended guidelines for labeling the axes of an inset displaying a magnified or reduced view of the primary plot? Should an inset include labels if the main plot is in linear scale while the inset is presented in log scale?
Based on my academic experience, individuals frequently add axis labels to insets. Is there a specific rationale behind this practice? I have reviewed several author guidelines but haven't come across any that specifically address this matter.
For an instance of an inset plot (axes are not labeled), please refer to the following example: Inset plots in Matplotlib.

Relevant question: https://academia.stackexchange.com/questions/18357/are-there-any-guidelines-for-labeling-axes-in-plots-graphs

I'm not sure there are any universally accepted guidelines. As long as the graph is clear and easy(ish) for someone in your field to interpret, you're good.

Indeed, take inspiration from figures in journal articles in your field. To me, not labeling axes is a bad practice.

In the liinked plot the inset axis labelling absolutely makes sense. People need to understand precisely what they see, and this helps.

If the inset and main plots have different scales (log and linear), then the inset plot is not just a magnified or reduced view. And in the linked example, the inset plot is not just a magnified view as it includes a red line that is not in the main plot.

Every time I peer review a manuscript with an inset plot, the inset is illegible.  I have never seen a well designed inset plot.
Change your inset plot to a separate figure.  It will be easier to design, easier to read, and the answer to your question will be obvious:  Yes, you must always label axes.

Especially if you're moving between linear and log scales...

I forgot to mention I came across an ACS Publications Author Guidelines, which discourages the use of insets. This is mentioned in the "Manuscript Submission Requirements Checklist" under "Artwork Tables/Schemes/ Graphics."

Could you please explain what the illegible point would be for Figure 6b in the following paper? https://doi.org/10.1103/PhysRevB.85.035135 It seems to me that the log-log plot in the inset is used to clearly show the appearance of minima.

@df7 That one is definitely better than most, but: 1. The small tics are marginally legible.  2.  y axis label kerning is wrong.  3. You can already see the appearance of minima in the big plot. 4. You could see the appearance of minima better if the big plot were not squished to make room for the inset.  5.  You gave a reason why the inset was clear; but you didn't have a reason for the big plot.  I would probably replace the big plot with the inset.  6.  If I read the rest of the paper, will it explain why there are no error bars (include systematic error)?

@AnonymousPhysicist I appreciate your thorough clarification of these points, especially the first one. Regarding point#4, it appears to me that the author has maintained consistent scaling for both Figures 6a and 6b. The purpose is most likely a straightforward comparison between two distinct scenarios (H∥b and H⟂b). It's worth noting that the y-axis scaling differs in the case of Figures 6c and 6d. Concerning point#6, the author has not presented any explicit reasoning.

If you mean the axis labels like T/K in the linked example, then actually I don't think they are necessary in the inset plot. It is obvious what variables are shown on the two axes.
If you mean the numbers next to the tick-marks, then yes those are usually necessary and valuable.
If the inset graph uses a different type of scale for one axis, e.g. log, then it would be better to show it completely separately. Showing it inside the main plot suggests that it at least has the same type of scale, linear or log.
The linked example is not very good in my opinion. It could be improved by making the lines that show the zooming (the little box in the bottom left, the straight lines showing the zooming, and the box around the inset plot) all be bold and in a different colour. And it is not clear why the plot doesn't show the Debye model outside that small range.


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Does a professor emeritus typically retain full health benefits?
Across four-year universities in the U.S., do professor emeriti tend to receive full health benefits?  Do professors ever retain health benefits in retirement?  If not, how do retired professors maintain health insurance coverage?

I'm sure this varies from place to place. I am retired from a state university and was able to keep my state insurance (premium deducted from my pension) as my medicare supplement.

This will vary a lot between institutions in the US, and depends more on the institutional policies on retiree health insurance then on the emeritus status of the professor.  For example, at my institution, all retired employees can keep paying their portion of the health insurance premium and stay on the insurance after retiring.

@EthanBolker But then you didn't actually keep your health insurance. You're paying for it yourself; you just managed to keep the same plan.

@WolfgangBangerth I paid for it when employed, too.

@EthanBolker Right. All I wanted to point out is that you didn't keep any benefits post employment. That you didn't have any benefits (in this particular regard) while employed is besides the point.

Generally, being a "professor emeritus" just means that you keep your academic privileges such as being able to advise students, to access the library, etc -- but not the benefits of employment such as a salary, health insurance, etc.
In that latter regard, they are retired just like everyone else, and that means that they need to have a way to support their life and their health insurance independent of any previous employer. In the US, that generally means getting Social Security, drawing from previously accumulated 401(k) moneys, being on Medicare, etc. Some (previous) employers allow to "buy into" their health care plans, but you will then generally have to pay the cost of insurance yourself.

This is a contractual matter and in some places a matter of state law, though I can't cite sources on the latter. "State policy" might be a better way to say it. So, it varies. My last employment was at a private university and I still have the same health insurance, paid by the university, that I did when employed, though it now coordinates with Medicare. They actually pay Medicare premiums. But not every place is so generous. Dental isn't covered and I have very modest co-pays on visiting doctors or hospitals. That was the same back before I retired. I never need to think about cost to go to a doctor. The plan includes pharmaceuticals as well, with some medicine free and some at low (co-pay) cost.
But there are a huge number of colleges and universities in the US and, while some fall into state systems with coordinated policies, most have institution specific policies. There are not laws, national or state level (AFAIK), requiring such things, so it is impossible to make general statements without a statistical study. My guess is that it happens "often" but not universally. Probably not "typically", but you'd have to do the study.


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Advice needed regarding whether or not to withdraw a DSA course
I am enrolled in a Data Structures and Algorithms course and am doing my B.Tech in India. Now, in this course I am currently below average and am expecting a 7/10 overall grade. However, if I withdraw the course and put in some effort next semester, I am sure I can get a 8 or 9. Since I might want to pursue a masters in computer science field, the grade in this course is relevant. I am confused as to whether a W along with a 9 grade in DSA would look worse on my transcript than a grade 7. Please give some advice regarding this.

How are you doing in comparison to other students? I know a few students who got into top universities (think Illinois, UCSD) despite a 7 in DSA (but in that class, 7 was still not worse than average).

7 is the average grade, and like I said, I am currently a few marks below average and will need to cover that up in the end-semester exams.

I'd advise you to discuss this with professors from your university (those who write LoRs).

This is hard to judge since graduate admissions seldom turn on a single data point, but some would question it. Your admission will depend on the judgement of individuals in some system, not the readers here.
But a more fundamental question is why you are doing mediocre in such a fundamental class. Dropping it might affect the option of taking more advanced courses next term and delaying your graduation, though I don't know your system. And if you are getting a poor (in your terms) grade for a correctable reason, I suggest you address that. Lack of time? Over extended? Lack of interest? Lazy? Unprepared? Cramming for exams? Inadequate notes? There are lots of possibilities, but it is just possible that a turn-around requires addressing the root cause.

I have gone over my courses for the next term and taking up this course again next semester will not delay my graduation. The source of my confusion right now is whether top universities would outright reject my application because of a W, even if I put in the work and do better next term. Also, if a 7 grade would harm my prospects at getting admission. I do realise I need to do some introspection and figure out the root cause before next term if I plan to redo this course.


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Establish communication with professors via email
I'm a second-year engineering master's student, doing my thesis research.
I've been exploring the work of professors from other institutes and would like to reach out. My goal is not only to seek help with my thesis but also to build a lasting connection and explore potential collaboration.
Any tips on how I should approach them via email?"

A lot of such email will be ignored. As a guess, the ones you most want to contact will be the most likely to ignore it - busy with other things.
A contact made by your advisor, recommending you, is a different story. If your advisor is willing to make the first contact with a short mail suggesting that you have things to contribute would be more likely to get a response. It is harder to just "trash" an email from a colleague or peer.
But, in some fields, those that depend a lot on conferences, a better way to contact people is in informal discussions at those conferences. If you or they are presenting it gives a place and time to meet them (just after a talk). Even coffee during breaks is usually filled with discussions.
But, for a blind email, I suggest making it short, with, perhaps, a link to a web page contains your work and qualifications. Mention one or two specific topics that you think you can contribute to. The goal of a first email isn't to convince them, but just to get their interest.

I've sent many emails to researchers about their work, starting when I was a student, and I've never been ignored. But I always opened with specific questions about a paper they wrote, not with "I'd like to explore potential collaboration".


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Master's supervisor said he didn't post projects because he's not taking in any students but said I should apply anyway for PhD in his group?
Basically the title. I have met my supervisor to ask for a LOR and he was genuinely surprised when I said I'm also applying to his group. He said he had already taken in 3 students and didn't want to take in more that's why he didn't post projects (when I asked that I didn't see any projects for him on the page). He said he generally does not like to post projects because he likes students figuring out their projects, but I should apply anyway and I shouldn't specify anything, and that he would love to take me in because I work well.
Now I am asking because my friend applied to his group and basically knew he was gonna get in because he was upfront with him, had a project and the process was very informal.
I understand from the last line that the takeaway is to apply anyway, but it didn't seem very encouraging and most of my friends who are PhD students are saying he's politely letting you down easy and I should ask again directly for a yes or no answer (because of funding and committees who review my application and how much he'll fight for me), which I am against and think it's going to be weird. Application requires 3 written statements and it would take time to write them that's why I am hesitant to commit that much effort just for a possible rejection from the get-go. But again it seems weird to be told to apply anyway and not apply?

"I'd love to take you in because you work well, but unfortunately I can't because I already have 3 students" would have been the obvious way of "politely letting you down easy". Encouraging you to apply with the intention of rejecting you would just make it harder for both of you down the road. So I wouldn't assume that to be the case.

@Stefan Thank you for your comment. That's a rational way of looking at it.

It looks like this is a question of communication between you and your master's supervisor: he encouraged you to apply, but you are concerned that he might not have been really enthusiastic about it. It's difficult for us to judge!
That said, I wouldn't read much into the "didn't post projects" part. I could definitely understand that as faculty you may not be actively looking for more students, but at the same time be interested if there is an opportunity someone you already know and whom you already think is a good match.
(Perhaps another thing to keep in mind, however, is the "already taken in 3 students" part. There is a risk that someone supervising too many students will not supervise them adequately. In my country (France), PhD advisors are typically not supposed to supervise more than 3 students simultaneously.)
Anyway, I don't see any way to dispel your doubts other than talking with your supervisor again, telling them essentially what you are telling us: applying is a complicated process to you, and you weren't sure of how enthusiastic he is because of the reasons you mentioned, so you wanted to check whether you understand correctly. There may be an explanation we're currently missing, e.g., your master's supervisor wrongly assumed you would not be interested or available in continuing on a PhD, and so was surprised when you asked. I understand you may be embarrassed but I don't think it's especially weird to discuss the topic again. Applying to a PhD is not a light commitment, I would understand that a prospective student needs to discuss the topic several times before making a decision.

Thank you for your answer. How do I ask without sounding like I am enquiring about the outcome of the application? I am worried I will sound: will you accept me or not?

I'm a bit unsure about the precise situation: is the "outcome of the application" decided by your prospective advisor or not? and are you "competing" with other students if you apply? but in any case I don't think it's so embarrassing to ask. Basically, does the prospective supervisor want to take you or not? and if it's not sure (e.g., it depends on getting outside funding; or you are in competition with other students, etc.), then you deserve to know, and to factor this in your decision to apply or not.

A good approach towards life is to take people at their word, rather than assume that they say X but mean Y (as you appear to do: He said something, and you are going through contortions to think about possibilities that he could really have been meaning something else).
So when he says "that he would love to take me in because I work well", take that as a compliment and assume that that is exactly what he meant: That he would love to take you into his research group.

Thank you. That is good advice.

Unless they're management ;)

He said I should apply anyway and I shouldn't specify anything, and that he would love to take me in because I work well.

If that's what he said, he obviously wants you in his group, there's no question about that.
So if you want to be in his group, you should definitely apply.
The rest of what he was trying to convey to you was that his attention and resources are divided across 3 students already, so you should be aware of that before going in, and factor that into your decision-making.
For example:

If you end up needing a lot of hands-on support (which is entirely normal), he might not be able to provide as much as both of you might be hoping for.

If you end up needing funding (which, again, is entirely normal—unless you have a fellowship), he might not have as much available, and may need your assistance with acquiring some (such as help with writing grant proposals, or flexibility in what projects you work on).

If you have particular existing projects in mind you want to work on, he might not be able to take you in for those particular projects, because he already has enough students on those.

Basically, his point wasn't that he wouldn't want to accept you, but that you might encounter sub-optimal conditions if you join.
tl;dr: He was trying to help you make an informed decision on your own side, not to have you filter yourself out of the pool.

Thank you so much for your answer. That's exactly what I needed to know and didn't know how to infer it according to the situation, for example: the supervision situtaion and funding.

To me this reads as I've got a few students, and I really don't want to take on another student that requires above average hand holding  so don't want random students. However I'm happy to take on more good / pre-screened students
I don't think this is unreasonable, taking on a weak graduate student is burdensome for someone in the group, and sadly too common.
Apply, particularly if your working relationship with this professor has been positive. he has explicitly invited you.

It sounds as if you are currently and actively applying to PhD programs anyway. Yes, it is a labor-intensive process, but the hard part is pulling all of your materials (LORs included) together. This particular professor encouraged you to apply, which is more than most (believe me!). Go ahead and complete the application, I am sure there are other schools/programs you are applying to anyway, so why not, right? Regardless, please continue to keep us abreast!

It seems to me you're very self-conscious, but I would think this pertains to your future and therefore like in many areas of life, it is very important to have honest and difficult conversations. If this professor ends up being someone who is difficult to communicate with and always gives vague answers, he's probably not someone you want to work with for 4 years anyway.

It's different in every country/school/department. If this happened in my department, it would mean that the professor doesn't have any more external funding left, but would be happy to take you on and fund you through the department (probably as a TA). There are pluses and minuses to being funded that way. If you are concerned, you can talk to him again and ask specifically what the implications would be for your workload (TA positions are often time consuming) and ask if he thinks there will be a future opportunity for you to switch to an externally funded project.


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How important it is to mention future research interests to a supervisor when asking for a LOR?
I saw this answer and thought I shot myself in the foot by messing up my meeting with my supervisor when asking for a letter of recommendation and not clearly mentioning what I am interested in. I did mention the universities and why I am interested in them, I mentioned key research topics but I noticed he didn't follow or maybe I did a bad job of explaining. So after I said "Key Topic1, Key Topic2..." we digressed and he gave me advice about research interests and emphasized I should know what I am going to do because I said I liked the idea of rotations in the department. I agreed and said I did come to a decision where I could separate what I can be idly curious about and professionally curious about, so again we digressed, and he focused on key topics I did show interest in and encouraged me to really find what I enjoy and like (same advice came up twice).
I genuinely enjoyed the conversation and learned from him as he shared past experiences but I got worried when I left thinking I should have presented a clear idea of my future plans. I trust him and I don't think it could affect it but I wondered if I gave a bad impression by not explaining clearly even though I think I did.
My questions:
Could his thinking I am not sure what to work on affect the quality of the LOR?
Should I salvage this by sending a statement of purpose draft that outlines specific research interests?

It sounds like your conversation went well and I wouldn't worry about it or take other steps. In general, though, it is a good idea to give some, fairly general, idea about your research interests.
It is probably counterproductive at this stage to be too detailed or, especially, too insistent on specifics. That is normally only explored (with flexibility) with a new advisor/PI once you get accepted (assuming it is for grad study). Likewise, in most cases for a tenure track position, though that is negotiated with the hiring group and its needs.
But, what you say sounds fine.


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How often are articles rejected after bona fide/non-accidental acceptance?
I recently submitted my first paper to a journal. It was recommended for minor revisions and ultimately accepted after they were done, but about a week after the acceptance, I received a new email that it was rejected. I'm disappointed by this, of course, but not blindsided by the general concept of it being rejected (it was a very long paper that I finally admit now needs to be split). What's more confusing is the post-acceptance rejection.
I've looked into questions about post-acceptance rejection here (Rejecting a paper after final acceptance notice, Is it ethical to reject an article after acceptance?, Can a paper get rejected in the copyediting phase (after peer review acceptance)?) and found very little evidence that this is a thing that...exists. The primary causes seem to be clerical error or extreme problems (e.g. plagiarism), neither of which seem to be the case here (I was sent an "accept pending minor revisions" with peer reviews, followed by an "accept", so clerical error doesn't seem likely, and the reason the editor gave for deciding to reject was the length -- there wasn't plagiarism or anything).
Is this -- the rejection of a non-plagiarised article post-intentional-acceptance -- a thing that happens at any meaningful prevalence? "Once in an average career", "I know a guy who knew a guy this happened to", "I saw it happen once in several thousand papers I handled as an assistant editor"? Or is it impossibly rare, and I got impossibly unlucky?

How did the second email explain the fact that the paper is being rejected after it was already accepted? Was it written by the same person who had earlier accepted your paper, or two different people? Did you try to argue or ask for an explanation? Consider the possibility that this is a genuine mistake (e.g., the editor clicking the wrong action in their editorial dashboard) with the original acceptance decision being the one they actually intended. If you alert the editor to this issue the decision may be corrected.

The exact quote in the rejection was that "your article has been revalued following revisions", and that they had decided to reject it due to length (for what it's worth, it's an online-only journal, so while there are logistical copyediting concerns for a long article there aren't print cost ones). I'm taking this at face value, i.e. that they were genuinely rejecting it rather than misclicking.

One data point: In the 54 years since my Ph.D., I've seen just one instance of such a rejection.

I've never seen this, and I've been around for some time. It may depend on the field though.

@vaticidalprophet Have you considered revising it according to the word count allowed? I've seen editors reject pieces due to word count before, so this isn't unheard of.

@Parrever I've split it into two papers, which was the only viable route (it covered a couple different subjects that we felt were better handled in one paper, but the word count just ruled that out in the end, and the two papers are themselves long and in-depth).

Anecdata from someone who's worked in academic publishing for many years and seen several hundred papers:
Of the papers I handled personally (here meaning I have firsthand knowledge of the process from submission to acceptance, including who made the decisions and the reviews received) I remember only one paper which was rejected after acceptance out of maybe a couple hundred accepted. The handling editor decided on accept, triggering the decision letter, and then the editor-in-chief overruled the decision.
Of the papers I've heard about (from acquaintances in academic publishing), there was at least two which were rejected out of ~a hundred.* Apparently the papers were accepted by mistake, but since the decision letter was already sent it couldn't be retracted easily. There was however a careful plagiarism check that led to some of these papers being rejected (I don't know why this wasn't done automatically before the papers went into consideration).
Of the papers I've read about (from/by people who I don't know) it certainly happens, but I have no way to tell what the denominator is. Example, example:

In 2012, Sage was named the Independent Publishers Guild Academic and Professional Publisher of the Year. The Sage publication that accepted my bogus paper is the Journal of International Medical Research. Without asking for any changes to the paper's scientific content, the journal sent an acceptance letter and an invoice for $3100. "I take full responsibility for the fact that this spoof paper slipped through the editing process," writes Editor-in-Chief Malcolm Lader, a professor of psychopharmacology at King's College London and a fellow of the Royal Society of Psychiatrists, in an e-mail. He notes, however, that acceptance would not have guaranteed publication: "The publishers requested payment because the second phase, the technical editing, is detailed and expensive. … Papers can still be rejected at this stage if inconsistencies are not clarified to the satisfaction of the journal." Lader argues that this sting has a broader, detrimental effect as well. "An element of trust must necessarily exist in research including that carried out in disadvantaged countries," he writes. "Your activities here detract from that trust."

*This is an educated guess of the number of papers accepted by this person. It does not mean that I've only heard of a hundred papers from all the people I know in academic publishing.

It (almost) happened to me. I am a mathematician. Once upon a time, me and my collaborator wrote a long (70 pages) paper. The refereeing process took 3 years, eventually the paper was accepted and went through the galley proofs. Then, when we did not expect this, we received a letter from the editors stating that the paper is rejected since the journal "no longer publishes papers in this particular research subarea." We complained to the editor-in-chief who reversed the rejection decision (without much of an explanation) and the paper was published. The whole process (from submission to publication) took 4 years. I think, our paper was indeed the last paper published by this journal in that particular research subarea.

I am not sure if this example counts but here it is. There was (still is) an open problem in my field of geometry and for over 10 years there was a preprint in circulation claiming a solution. The mistake in the proof was not particularly subtle and spotted by various people who informed the author. Pretty much everybody aware of the problem knew about the mistake in the proof. However, the author decided to send the paper (without changes) to a journal. Editors chose a "wrong referee" who did not know about the issue (most of the "proof" was analytical while the mistake was topological and the referee was not a topologist) and recommended the paper for acceptance. The paper appeared in an online version of the journal. I saw this and wrote to the editors explaining the situation. The editor-in-chief apologized and the paper simply disappeared: It disappeared from the online version and was never published in the printed version.

I have published (peer-reviewed papers) in the triple digits in my career, and have never had this issue. I've been rejected once early into my independent career after receiving an "accept with minor revisions" as one of the referees had a change of heart even after we addressed everything. This case in particular was handled by a less experienced editor, and my guess is the referee was someone well-established which they did not want to second-guess. It was frustrating for me, the work got published anyway, it is now well cited, but I actually killed that project anyway, and am not overly proud of it (it was derivative and although well done, it was not that interesting), so in hindsight I could see why a referee just didn't think much of the work.
I think such circumstances are so rare they aren't even worth worrying about.


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Referencing for an unknown source
I copied a work from an uploaded copy and the references were incorrect. how do I get the correct reference for the work?

You've asked a vague question. The vague answer is that you search for the proper references and document as much as you can find. If necessary you say "the references in the copy of xxx I uploaded from xxx are incorrect and I have not been able to find correct ones".
If you are at a university your librarian is your friend.
I trust the uploaded copy you are working from is not pirated.


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How do I chase down this old PubMed article?
I found this interesting article and would like to read it: https://pubmed.ncbi.nlm.nih.gov/3551058/. I have a title and author and PubMed ID, but no DOI and not much else to go off. Also the author died in 1997.
How can I hunt down and read this article?

Dear OP, please see our canonical question for such requests.

What do you mean by "not much else to go off"? The full citation is on the PubMed page you link... You'll probably just have to ask your library if they can help obtain papers from Schweizerische Medizinische Wochenschrift.


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Listing something recommended for publication on publication section
This is my first post, so please let me know if I made any mistakes.
I am applying to math phd programs this year, and one of the things I encountered is that for multiple schools, they ask me to list publications if I have any. I have a paper currently recommended for publication by a peer-reviewed journal(it's on arxiv and thus accessible to public), but it's not strictly speaking accepted. Since usually I get an entire text box to fill in my answer, what I did was that I list my paper, the arxiv link, as well as it's status that it's recommended for publication in that textbox. The status I listed in answer to the question should make it clear that this is not yet published or accepted in this peer-reviewed journal, only that it's "highly probable", and that it's available on arxiv.
I was wondering if my approach here is ok. I am an honest student, but I also really want to emphasize that I have this paper which has been recommended somewhere along with the application other than just on my CV. One of my recommenders have also suggested that this should work.

What exactly do you mean by “recommended for publication”? Usual you would only get to see the referee reports together with the editor decision.

Sorry for the confusion. What I mean is that I've gotten referee reports back which suggested that they recommend my paper for publication after I fix a minor issue and resend the paper back to them, which I've done. Since the process takes usually months at least, I haven't heard back since then.

What I have done (in a different field) is use such phrases as "In revision (minor revision)" or "Accepted pending minor revisions" depending on which fits the Reviewers' and Editor's feedback.

Let me suggest that you be conservative in such things as some might judge you as padding your record which would be to your disadvantage.
If a form is flexible enough you could list it as long as you add the note that it is submitted and likely to be published based on the recommendations of reviewers. It certainly is not yet a publication and won't be until acceptance, at which time is is still "to appear".
But it is also sufficient, I think, to just list it in the CV as Work In Progress in such a section and mark it submitted, awaiting editor decision.
This is both honest and, IMO, an advantage. I think that having a valid Work in Progress section is always a plus in such things.

Thank you so much for you reply! I already had it in my CV under Papers/Preprints section where I listed the paper's status as recommended for publication (revision under review) The reason I wanted to  list it outside of my CV whenever possible is because this is my first serious academic paper and I really wanted it pointed out somewhere in addition to my CV.

If it is in the CV then it will be seen.

I see I see. Thanks! Sorry for the trouble but one last question: what about schools for which I've already done this? Do you think that maybe I should email them and tell them what's actually going on? Or do you think I should just let it be? Given that my CV has already indicated this.

Decide whether what you wrote is completely honest or might appear to be padding. It could go either way depending on what you wrote. It might be clear to readers or not.


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How to politely ask for credits in a shared project?
I am a PhD candidate working on a component of a larger, transnational project that my professor got funded by an external donor. In this project, I am to work with two other PhD candidates and a Master's student, each taking care of a different study area. While we focus on different countries, the scopes of everyone's research share key elements (i.e. assessment framework and social survey) that we were supposed to individually develop, specifically for our own research interest. However, as others received setbacks of various kinds in their progress, I was told that they will all use the framework and survey that I developed for my own study area, and slightly edit them to add to their own theses.
I developed this framework and created the survey questions from scratch, with months of literature review, and discussions with colleagues and experts. I intend to publish both as a stand alone manuscript, hopefully in a respectable journal. Therefore, I would like to make sure that the others in the team credit me in their manuscripts, either as a source or a co-author.
Here comes my issue with this arrangement. My professor has made no mention of me being credited in the other people's work and I have received no reassurance from others that they will credit me. To add on another layer of difficulty, we all have different committees and presumably, their publications (and all related decisions on me being credited) will need to be approved by all members of their committees.
As my professor has not touched on this point in any of our team meetings, how do I politely raise my voice and make sure that my work is justly credited in this case?

my colleague had similar experience. It turned out the professor just forgot that. You can just remind him/her politely -- something like I have done XXX, if the contribution is not enough to be an co-author, may I be acknowledged? something like that

It is possible that this is simply an oversight at this point and people aren't yet thinking about specific authorship and attribution. That isn't ideal, of course, but it happens.
Have a talk with your supervisor and raise the concern that you do here. It isn't impolite. You have put in considerable effort and it contributes positively to all the work. You would like to be able to validly claim some credit for your CV but that others need to agree to this. Ask the supervisor to raise the issue with the group and try to get some consensus.
Once the issue is raised, preferably through your supervisor, it is harder to put off. I don't see any misconduct here, though there is potential for it to occur. A conversation can, possibly, avoid problems in the future. But, don't think of it as impolite. You are an actor here, not a spectator unduly claiming credit.


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Want to change my career to Physics from Software Development
I have always been fascinated by Physics But due to the CS hype in India took a miscalculated step to get my bachelor's in CS, After 4 years dedicated to a job in Software Development I want to change my career to physics I always used my weekends to brush up Maths and Physics topics during my job I now wish to pursue my dream of doing Ph.D. in physics from a foreign university ( MIT, ETH Zurich, etc ) meeting new people getting their perspective about a topic from a different angle, research and push the boundaries of science. I am 26 now and planning to get myself into a master's program in physics from India itself from IIT or HCRI (Harish Chandra Research Institute). It will take 2 years to complete my MSc I will be 28 by then. Is it still possible to get my Ph.D. abroad ???

Frankly, I don't know why you would think age 28 would be a problem. Would you please clarify the question?

@Nobody Thank you for replying . I meant that will I be accepted to a foreign Phd program after doing a masters in India Starting my masters in theoritical physics next year. The concern is that will my past CS career will hinder my chances to get a elite Phd program ( dreaming about the programs in MIT Columbia Tu Berlin etc ).

Your past choices won't hinder it per se, but you obviously would need to work harder than someone who was on that path from the start. Good luck.

@Lodinn Thank you .


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How to deal with a reference that doesn't make sense?
I am currently reading the following Ethnic and Racial Studies article from 2018:

Marino (2018): Ethnic identity and race: the “double absence” and its legacy across generations among Australians of Southern Italian origin. Operationalizing institutional positionality., Ethnic and Racial Studies, DOI: 10.1080/01419870.2018.1451649

In it Marino states the following:

Southern Italians were treated differently
from Northern Italians, and considered not-yet-white-ethnic. Such ambivalence was concomitant with the legacy left by the White Australia Policy
that passed in 1901 and intentionally favoured immigrants from certain European countries, mainly northern Europeans. This was in order to build a “white Australia” (Nelson et al. 2013)

Wanting to understand the claim further I looked into the Nelson et al. 2013 reference. The only 'Nelson et al.' for the year 2013 in the references was the following (DOI 10.1177/0956797612447798):

Nelson, S. K., K. Kushlev, T. English, E. W. Dunn, and S. Lyubomirsky. 2013. “In Defence of
Parenthood: Children Are Associated with More Joy than Misery.” Psychological
Science 24 (1): 3–10.

However that article is from Psychological Science and doesn't even mention anything about Italians or Australia.
Did Marino accidently reference the wrong article or am I doing something wrong? If the former would I now have to contact Marino somehow to get a correction?

In the absence of finding an answer such as the one provided by CrimsonDark, contacting the author for clarification is indeed typically the way to go. You might still want to reach out and let them know about the issue.

Someone has made a mistake; quite possibly a copy editor! The reference you want is (almost certainly):

Nelson, J., & Dunn, K. M. (2013). Racism and anti-racism. In A. Jakubowicz & C. Ho (Eds.), 'For Those Who’ve Come Across the Seas..' : Australian Multicultural Theory, Policy and Practice (pp. 259-276).

Just so that it doesn't appear magical, I located this by doing the following:

Noting that Marino refers to a specific page of the Nelson article ,
namely p. 260.
Noting that the reference in the bibliography not only
seemed weird, it also did not include an appropriate page number.
Using Google Scholar with the search terms "author:nelson white
australia" (without the quotes)

The first result on the search list was the one I have repeated. It includes the appropriate page number, and when you visit the page that includes an abstract of the Nelson et al. article, you'll see that it all makes sense.
There is one glitch that remains. The in-text citation of the Nelson article is to "Nelson et al.", implying more than two authors, whereas the article I mention has only two authors. I suspect that this is entirely attributable to an error-prone editorial process and a failure on the part of the author to check everything before publication.

Perhaps the author put Nelson2013 into their citation manager and picked up the wrong one. An easy mistake to make.

It's even Nelson and Dunn twice

"The in-text citation of the Nelson article is to "Nelson et al.", implying more than two authors" - I suspect the in-text citation was automatically generated; if the article is written in some software such as Microsoft Word, you can insert citations from a menu. Having the wrong article in a bibliography file would explain both errors.


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What does "File BauProf" mean?
I am doing some research on Nigeria during its colonial period and as a result I have found the following thesis by Uyilawa Usuanlele called "Poverty and welfare in colonial nigeria, 1900-1954" very interesting.
One of the quotes the author uses is then referenced by the following (Page 129):

365 Quoted from File BauProf 1356 in Abubakar, “Health under Colonialism: A Study of British Colonialism and its Health Policies in Bauchi Province, 1900-1960” Thesis, 264.

Thanks to other Journals referencing the same thesis I was able to track it down to Ahmadu Bello University Library where its listed in its library catalog: Health under colonialism: a study of the impact of British colonialism and its health policies in Bauchi province 1900-1960
While I try and track down an electronic version of that thesis does anyone know what "File BauProf 1356" means? Could it maybe be an internal university system?

I found a document K. Brunk" Zum Landnutzungswandel in der südlichen Sudanzone am Beispiel des Bauchi State (Nordost-Nigeria), Berichte des Sonderforschungbereichs 268, Bd. 5, Frankfurt a.M. 1995: 51-67 here. The relevance is that the document has a bibliography with named categories. There are several "Bau Prof" references listed under the heading "Unveröffentlichte Archivunterlagen des National Archive Kaduna (NAK)", which loosely translates to "Unpublished archival records from the National Archive Kaduna (NAK)". Based on this website for said national archive, I would guess that "BauProf" / "Bau Prof" may refer to their "BAUCHI PROVINCE RECORD GROUP" and that 1356 is a record number within that group. Either way, I suggest you consider contacting the NAK.


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Education and knowledge preservation
I have gone through several academic perils to be educated to be what I am today, throughout my 63years old life on the Earth. But with ageing, whatever I learnt also gets forgotten, though the ashes of the fire of knowledge do remain at my useful access. I always wonder how much information to be retained and what to be deleted from my memory! Looking back, I find no stage where I could say it is enough for the rest of my life on the Earth. Is there any global common consensus on this issue available with the planners of future educational institutions and organisations?

Knowledge gets outdated very quickly. So, the role of knowledge in academic education is primarily to provide context for future knowledge rather than something that will be useful on its own. What tends to remain useful longer is skills to acquire or generate new knowledge.

I disagree with your statement: "So, the role of knowledge in academic education is primarily to provide context for future knowledge rather than something that will be useful on its own. " Education is useless if it doesn't help in judging deciding and activities on a CURRENT situation. Both past and future knowledge are, and their accessibility, variables.

Education is not applied immediately, but at some point in the future. However, at that time it will be obsolete.


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Back Date publication
I finished a research paper 2 years ago, and it was related to the covid pandemic. I didn't try to publish it because my father passed away and I stopped research work for a long time. Is it possible to do backdate publication for that paper?

Why do you want to do that?

Seems likely to be an XY problem question - what's the problem you're trying to solve with this solution? (echoing Azor Ahai)

No, you submit now and see how it goes.

No
The journal provides the date received, the date revised, and the date published. Since your paper was not received two years ago, the journal cannot say it was.


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Independent research
I'm considering taking up freelance journalism full-time, while also hoping to publish research on cultural studies in established journals. I have been published on a research website before, and have also presented papers, but this was all about 5 years ago.
Wanted to know what the hurdles are while publishing academic papers as an independent researcher?
PS: I have done two postgraduate degrees in the field and I'm trying to build up a research portfolio before I apply to PhD programmes.

Does any of your research require ethics oversight (usually because it involves collecting data on human subjects or experiments on animals)?

also related: https://academia.stackexchange.com/questions/83309/publishing-as-an-independent-researcher

A PhD program is ultimately intended to train you to perform and publish research in your field of interest.
Most PhD students find this process very difficult, especially in the beginning, even with help. Most people with successfully completed PhD training still find this process very difficult, especially as they take their first steps independently of their mentor (though that doesn't mean mentorship ends at the end of a PhD; post-doctoral positions ordinarily have an explicit mentorship component, and tenure-track faculty still rely on mentors for advice).
The most immediate barriers you will encounter are not issues of "independent research" but rather issues of not having research training. If you've completed two postgraduate degrees, it sounds like you're ready for the full-time research training that comes with a PhD degree, and you should start applying now.