text:
I'm changing PhD programs, and I got a terrible recomendation letter form my advisor. I found out by accident. What do I do now? I'm shocked
I’ll try to not be too specific for the sake of anonymity. I’m a STEM PhD student at one of the top-15 universities in the US. My own advisor said that I did great academically and made good progress on a hard research project. I also passed my candidacy. But my project turned out to be pretty unrealistic, and on top of that, I had a lot of personal issues that were out of my control. Because of that, while my research progress was fine, my performance was chaotic in terms of making quality presentations for regular reports (for my advisor) and meeting deadlines. I was also kind of a lone wolf in terms of how I worked: I still talked to people and asked for advice from other lab members as well as helped them whenever they needed help, but I guess that’s not the impression my advisor got since he only saw a small part of of it all.
Anyway, I’m applying to other PhD programs now, and he already submitted his letter to like 75% of the schools I was gonna apply to. One professor from a school outside the US was so shocked by the letter, he actually reached out to me and warned me. Apparently, the letter says that my advisor kicked me out, briefly mentions that I’m “smart and hard-working”, and then, goes on to list all my flaws and ends up saying that “I might deserve a chance to try my luck at PhD at least somewhere” and that my advisor “has reservations”. That’s shocking because he told me he’d focus on the positives and that he never writes negative rec letters. It sounded like it would be mediocre or even mildly good, but this is downright horrible. The letter doesn’t even say he actually recommends me, so I guess technically, it’s not even a recommendation. That can’t be ethical, can it? I’m not from the US, so maybe, I’m mistaken.
The other letters are definitely supposed to be superb. What do I do now? Do I just ask someone else to write a rec letter? Is an absence of a letter from my advisor worse than a letter like this from him? Is there a way to fix those applications that already has his letter? Sorry for the typos - I’m kinda shaken right now.
P.S. If I exclude his recommendation after he submitted the letter, will it work (if the app portal allows it)? Is it a good idea?
P.P.S. I already got rejected from one program by the way despite me having multiple papers and stuff. It’s probably because of the letter.
Edit 1: I was kicked out from the group, not the program. I'm still technically working in his group unofficially (on a new research avenue that I had proposed an that he agreed was a good idea) to get at least one paper out of it. But I'm still officially a PhD student. But all the other labs at this university are either not working in my subfield, or they are full. That's why I'm leaving the program on my own terms (technically) and applying elsewhere. I should have specified it, sorry.
Edit 2: I asked "Will this be a bad, medium level or good rec letter", and he said "Well, I don't write negative rec letters. I'll focus on the positives because no one is arguing that you're smart and hard-working and all that, but I'll have to mention why you're leaving if they ask". To me, that sounded like it would be a mediocre letter at worst and a pretty good one at best. If I hadn't asked, I wouldn't have doubts about the ethics of it all. I just expected him to be a bit more upfront. Normally, people refuse to write rec letters if they cant write strong ones. This one isn't even mediocre...
Edit 3: He was super friendly to me, so I don't think I made an enemy. And if I did, I didn't even know that.

Not much help now, but for the future, always ask if a person if they will write a positive letter of recommendation.

@RichardErickson I did. I asked "Will this be a bad, medium level or good rec letter", and he said "Well, I don't write negative rec letters. I'll focus on the positives because no one is arguing that you're smart and hard-working and all that, but I'll have to mention why you're leaving if they ask". To me, that sounded like it would be a mediocre letter at worst, and a great one at best with negative comments only coming into play if someone asks him. But it turned out to be so horrible that it's not even a recommendation. Literally. Because he doesn't actually say he recommends me.

If what your saying is true, sounds like a backstab and that he lied to you. Sorry that occurred to you.

It's not clear to me what's happened to your position in this program: you say you are a PhD student, your advisor says you've been kicked out, you're applying for new positions, so, what's the actual state of things? It's not normal to leave a PhD just because your project turns out to be unrealistic (the scope and target of a research project often changes many times throughout).

@BryanKrause I was kicked out from the group, not the program. I'm still technically working in his group unofficially to get at least one paper out of it. But I'm still officially a PhD student. But all the other labs at this university are either not working in my subfield, or they are full. That's why I'm leaving the program on my own terms (technically) and applying elsewhere. I should have specified it, sorry.

I’m a bit confused why your advisor would say you were ‘great academically’ but also kicked you out. Can you clarify why they kicked you out as this seems important

@VroomVroom123 No worries, that clarification of your status is helpful, probably worth adding briefly to the post itself.

@BryanKrause I added it. Sorry, I keep missing details because I'm kinda stressed right now. Well, he kicked me out because of non-academic aspects of my performance. I was a little late with some reports, might have been a couple minutes late to a couple meetings (over the course of years), and my presentation skills weren't great. I've been suffering from depression due to a number of reasons, and that's what caused it. And some professors value these things more than others. Although, I think it still wouldn't have happened had my project gone better.

@BryanKrauseBut This project sucked by the way. Even my candidacy committee said it's not a realistic project. I was naive to pick this project.

The ethics of the external professor sharing the otherwise confidential letter with you is also somewhat murky here. A heads up might have been in order, but I'm a bit surprised you're quoting verbatim from a letter that you're not supposed to have seen in the first place.

At least you know not to use this person for a reference again and to seek an alternative.

@NuclearHoagie Yes. It's nice to know that some people at a high level have ethics which transcend the cloying formalities which pass for such in some cases. That i wht you meant by "murky", wasn't it?

@RussellMcMahon I might agree it'd be OK for someone to give the OP a heads up that they should not be using this letter of recommendation, but sharing the whole text seems like overstepping.

@NuclearHoagie A negative letter of recommendation out of multiple weak ones should probably not disclosed. But one out of several good ones is probably a signal that someone lied to the candidate. I probably would not have quoted verbatim, but still. Also, in many places, there is no guarantee that a candidate may not ultimately gain access to the recommendation (Freedom of Information, etc.). There is no reasonable expectation that the letter will remain confidential under all circumstances.

One thing to consider: this particular professor that received the negative letter might have gotten a different letter than others. Maybe your professor has a bad history with them and didn't want you ending up there.

@NuclearHoagie "confidential letter"? That depends on where this professor was. For example in Sweden every official piece of paper that comes across the desk of a professor is public. Anyone can call the university and ask for copies. There are no secrets for public servants. This is also the reason Sweden is one of the least corrupt countries in the world.

@CrisLuengo Nope. Pretty sure it's the same letter everywhere.

I think you've learned you cannot use this person as a reference. It's unfortunate you learned when you did; there is probably nothing you can do to retract these letters and I'm not sure it benefits you to try.
I'd expect some mixed response to a letter like this. Some people are going to feel it's a huge red flag about you and appreciate the "head's up" from your advisor. Others, like the person who warned you, may feel that a letter like this actually reflects poorly on the writer as much as the applicant, and may consider it in the context of all your other application materials.
If you do successfully reach the interview stage for any program, you can expect this letter to come up. I'd recommend addressing that situation as gracefully as you can, acknowledge that you've heard about the contents of the letter from other recipients, state that you were surprised by the contents, and then do your best to explain the situation you find yourself in from your own perspective. I think it will reflect best on you if you're able to take responsibility rather than give blame for your predicament (whether or not that's entirely fair), and be forward-thinking: focus on how your accomplishments and your struggles to this point have prepared to to be successful in this new PhD program.
Overall, though, I do think your prospects are a bit grim unless there are other professors you trust that can give very strong recommendations in your favor and possibly vouch for you through less official channels. Graduate admissions is quite a dice roll: admissions committees try to dig through the entrails of an application to find some hint that one candidate or another is likely to be successful in the program. Amidst all these unclear signs, yours unfortunately has one clear data point even without this letter: you've been in a program before, and it didn't work. Offering you a position isn't necessarily about making a decision about whether you're likely to succeed given another opportunity, it's about making a decision about whether it's better to admit you over another very promising applicant who hasn't had the chance yet.

+1 excellent response, including "clear data point". Unfortunately true.

Sorry you are going through this.
Life can be unfair at time.
You ask several parts and questions in your post:

The letter doesn’t even say he actually recommends me, so I guess technically, it’s not even a recommendation.

Nope, negative and positive are both recommendations.
It is a recommendation.

That can’t be ethical, can it? I’m not from the US, so maybe, I’m mistaken.

Sorry, but it is ethical. In hindsight, ask if the person will write a positive letter of recommendation.
Not necessarily kind, but ethical, sure.
If they truly think what they are writing is true and not doing to be vindictive.
No way you can prove the previous point one way or other nor is there anybody you can reasonably argue the point with for any outcome that would help you.
Also, some countries give more negative references than others.
Search this site for examples of this different cultures.
US tends to be positive only or omission of negative traits, but some people like your advisor give negative letters.
Edit: It is ethical to write negative letters. Saying one would write a positive letter and then writing a negative letter is not ethical.
But, there is likely nothing you can do about it.
So, your other questions:

The other letters are definitely supposed to be superb. What do I do now? Do I just ask someone else to write a rec letter? Is an absence of a letter from my advisor worse than a letter like this from him? Is there a way to fix those applications that already has his letter? Sorry for the typos - I’m kinda shaken right now.

First, breath and seek out some outside perspective.
It's not the end of the world.
Find someone you trust who can help you process this.
Ideally, someone who is not a another grad student and has perspective.
Perhaps a therapist at your current school or another committee member.
Perhaps a professor in your department you trust that you know from classes.
This is context specific and we cannot help you online with the specifics.
Second, yes, make sure you tell a coherent "story" about why you are changing programs in your letter.
Get references from people you trust.
Third, if you're leaving your program, people will know you're not a good fit.
It's up to you to tell them why and have references who support your story.
There are several other similar questions on this site that can help you with this.
Fourth, individual applications are school specific.
You would need to checkout those programs systems to see.

P.S. If I exclude his recommendation after he submitted the letter, will it work (if the app portal allows it)? Is it a good idea?

I would do this if you can.

P.P.S. I already got rejected from one program by the way despite me having multiple papers and stuff. It’s probably because of the letter.

I'm sorry to hear this happened to you.
Edit based upon additional comments from the OP:
You were kicked out the professor's group.
In hindsight, do not use them as a reference for anything.
And, you also need to tell a story of how the new programs would help you and you would fit in.
Ideally, you would have professional contacts in similar lab groups at other universities and one of those professors might be willing to take you on.
Or, you might need to consider a non-academic career.

I don't see how you cannot use them as a reference for anything. Anybody considering the OP will see they left a PhD program. They could find the multiple papers, and send an e-mail/phone call to the advisor. Or, they may automatically draw conclusions from the lack of letter and assume it's bad. The only thing the OP can do is present their side of the story first.

@user71659 That's another I wasn't sure about. I'm not sure how to present my side of the story. It's like whatever I say. it'll sound like I'm making excuses. I was told in cases like this, the only thing to do is to say it was a bad fit. But it sounds like I'm evading the topic alltogether.

@VroomVroom123 So why do you think you'll be successful in a different group? You said you missed deadlines, made poor reports, and didn't work with others. All of those are important in academia (and industry, for that matter). What has or will change? Answer that. If you can't, then maybe you shouldn't try again, at least for a while, because the same thing will happen.

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my background - industry for 20+ years.  Friends in tenured academia positions.
One of the first things you may want to do is use a site like checkmyreferences.com to see what's going on as an overall picture.
This also would allow you to check other references to verify that they are as solid as you think are.  People can be funny in that they will say one thing (IE avoid conflict) and do another (you asked for a recommendation and I don't really want to say them No).
You admit to being a lone wolf, if you don't work well with others, its not the end of the world, however most places don't want lone wolfs, they end up being a PITA and unless you can be a superstar doing your work, it won't be worth most peoples time to even interview you.
Did your advisor know about your personal issues and how/why they were impacting your work product?  While you don't necessarily have an obligation to share your personal details, when they impact work like they have for you, its helpful to have people understand why you are acting and performing the way you are, especially if its not your norm.  Otherwise people can only (and will) draw conclusions based on what they see you do and how you interact.
You have a major set back here since your advisor is basically providing a dis-recommendation for you and they are your immediate supervisor.
You may have to look at how you can get into their good graces and how could you rejoin the group.   IE What can YOU do to fix your advisors opinion so they write a recommendation that helps you move on.
You may need to approach your advisor and discuss some of the more obvous issues, ones that either they tried to address with you already  (hopefully they did?) or noted verbally to you.   IE whatever is in the discommendation that you theoretically would already know and wouldn't indicate that you now know the contents of his discommendation due to another professor sharing them with you.
Lastly you may need to take a year or two time hit, to put something in your subfield or similar between you and this advisor. IE distance yourself so that you can rebuild your professional reputation.
Ethics- i would be unethical to write a recommendation that was not honest and representative of how the advisor perceives you.  Its just poor form to say you will write a recommendation and then write (based on your info) a discommendation.  Generally in the US recommendations are understood to be "recommends" you for work.  It should be balanced and fair, however should generally be positive leaning.
I've had to say no to several people who were expecting a recommendation, and I told them I couldn't in good conscience write one given their overall performance.

Wow, I would absolutely not pay for a service to covertly contact your references and see what they say, and it wouldn't make any sense for grad school applications anyways: these recommendations are letters sent by the recommender, not phone calls where the prospective employer calls the references. Are you actually familiar with grad school applications or just answering from your experience outside academia? Within academia, at least within the US, recommendation letters are also typically treated as confidential as a letter not shown to the applicant is seen to be more honest.

Mainly with outside academia experience, other than going through grad school myself a few years back.  I conversations with friends in academia, recommendation letters are generally positive in nature, ergo recommendation.   In the OP case from what is stated they perception and the advisors are greatly differing.  Trust is fine, however verification is better.  IE trust but verify.   Here the OP blindly trusted and has had his career imperiled.

I wouldn't say OP "blindly trusted", that their trust was violated does not mean they were blind. But, I think your suggestion is dangerous, because for this particular circumstance, the assumption is that applicants do not verify and that is part of the establishment of trust in the recommendation process, and indeed, getting caught trying to "verify" could come with severe consequences that are not acknowledged/considered in this answer.


text:
Is my advisor asking me to commit fraud?
I am currently a postdoc, leaving my position in ~1 month. I am departing my contract a few months early after receiving an offer for a job in industry, about which my advisor is very upset. It is policy at my institution to pay departing postdocs for un-used vacation days.
My advisor has asked that I "use" my leftover vacation days, i.e. take them on paper, but actually use that "time off" to finish a few papers. His argument for this is that he "cannot afford" to pay me for them (this sounds bogus to me; how was he going to pay my salary, if he is so broke?). It seems to me he just doesn't want to participate in this policy.
Obviously, this would be shafting me first and foremost, since I would be losing out on this money, but I am not all that upset about that. I'm worried that the university, or our funding agency would object to this maneuver. Would it even be legal? Most importantly, could I be held responsible, for facilitating this?

If you willingly do it, then there's no way it would be fraud on your part -- people compulsively work on vacation all the time! Don't try to hide behind a rule. Just say you won't do it because you, personally, don't want to.

"His argument for this is that he "cannot afford" to pay me for them" What is "them": the vacation days or the papers?

@paperskilltrees the vacation days. My pay is not tied to papers in any way.

I agree with the previous answers. By the way, "cannot afford" sounds like utter bs: since you are leaving earlier, there will be money left in the budget, which would otherwise be spent on your salary. One argument you can make is that nobody knows how much time you will spend on finishing papers after leaving, which will be unpaid work; thus, it is even more unfair if your vacation money is taken away. But I warn you against this argument, as it leads you to making promises and gaining nothing in return. Perhaps, this is how your advisor wants to play it: wait and see him offering this deal.

Another Q&A that differs from your situation but has some overlapping issues about work in academia and how expectations and norms can differ with industry, leading to conflicts between people with more "industry-like" perspectives and those with more "academia-like" perspectives: https://academia.stackexchange.com/questions/148938/

@BryanKrause Thanks. As with that poster, I have had some prior problems with this advisor, and also feel that he bears the brunt of the responsibility for the delay in these papers being submitted. Perhaps that is factoring in to my thoughts on this subject.

Against whom are you imagining that the supposed fraud would be committed? And what law are you imagining would be broken by your agreeing to write papers during your vacation days?

A financially well-organized department will have some reserve funds to cover such cases. Either they didn't do their homework (bad for them then), or your advisor hasn't arranged these funds to be used (probably because he wants to squeeze more work out of you).

If you do work on your own time to write those papers you should be demanding to be first Author on them.(get it in writing) I would only be doing them for my own career advancement and passion. If it feels like work and you don't want to do it then don't.

The way to avoid this situation in future is do things in the correct order: (1) take all the unused vacation up to your planned leaving date, and (2) hand in your notice.

At some institutions, including mine, this could be essentially fraud.  If you work on projects with research from two or more different funding sources, and you perform unpaid work only on one of them, you are effectively overcharging the other one. (Research A gets more research hours per dollar than Research B).  This is an unlikely but very real consideration

You've earned the days as paid vacation, you don't have to work during them. The money it costs to pay you for those days is part of your compensation for the work you've already done and the stretches of time that you came to work instead of taking the day off.
If you do decide to take the time to work on finishing up some papers, that could be good for both your advisor and you. All your work is basically a waste of time if it never makes it into a paper. Maybe you're fine with that if you're all done with academia, but if you ever did want to return then any papers you can publish will be to your benefit. I think there's also a strong sense of personal accomplishment in publishing papers (why are you doing research if not to share it with the research community??), and as a post doc (or any other level of academia) your role is a bit different from a standard employee in that you're typically doing research not just as a job but as your personal work.
As far as "not being able to afford" to pay for those days, I think you can mostly ignore that statement, it's not connected to what you do next in any real way. However, it's probably not motivated by your advisor literally being that broke, but rather that they expected that the grant money they spent on your position would result in some output that they can use to get more money for future projects - that's how the academic funding cycle works. If they've paid you for a spot and you've failed to complete projects, that's in many ways wasted money for them. Maybe they can pick up your work where you left off but often there is a lot of cost of time and effort in starting from someone else's partial work.
I won't comment on legal issues according to any letter of the law, but it's extraordinarily unlikely that you would see any legal consequences for spending time off working to complete a project. It's also unlikely your advisor would see any consequences for making the request. It also doesn't seem that your advisor is seeking to cause you to lose out on any money but rather they're hoping that you see enough value in completing work to spend your earned vacation time working. Like I said in the start, you've already earned this time and don't need to work for it, but it's a bit different from trying to pull money out of your pockets.

@GoodDeeds in a comment pointed out that OP's advisor may be asking them to "quit early" and count the end of their work as vacation time. I was thinking more along the lines of OP determining their own end date but their advisor asking that they keep working to finish up projects. Also in a comment, OP indicates that they are willing to work to finish up the incomplete papers on their own time.
Based on those pieces of information, my advice would be to:
A) Assure the advisor that you are willing and intending to finish up these projects. I think that's their main concern, whatever conflicts there have been between you. Everything you've said in this post could be a completely honest, non-exploitative effort towards this goal. Maybe that's overly charitable towards them, but I think it's a good mindset to start from.
B) Come to agreement on an official end date, when your regular salary ends. You should be committed to work full time through this date, like you've been doing until now. This shouldn't have any relation to the vacation hours you are owed. Pretend they don't exist. After that date, you're committing to finishing the projects, but not to working any set hours. If your advisor wants this to be sooner, you can say that if you aren't an employee during those hours there are other things you'd like to do during that time.
C) If your advisor insists on involving the vacation hour pay, reiterate your commitment to finishing up the work. If it helps your advisor to think about it, those volunteer hours you plan to put in on these projects in your nights and weekends are effectively "working for those vacation hours", you're just not willing to have those be "full time" hours on a schedule, or to substitute for your normal work.
If they aren't okay with this arrangement, then they aren't being reasonable. You can hope they come around, but remember that you have some power here. Your advisor is going to want you to finish your projects. You have a new job and aren't compelled to work for them. So, if these papers are going to actually get out, the two of you have to work on mutually acceptable terms. Good luck!

Yes, this seems almost surely to be the correct appraisal of the situation. People do speak figuratively, and inexperienced people don't have the prior experience to be able to interpret exaggeration or figurative remarks...

If you do decide to take the time to work on finishing up some papers, that could be good for both your advisor and you.

I will certainly spend my remaining time in the group working the finish the papers, for exactly the reasons you mention. I will probably continue to work on the papers for a long time after departing. The only uncertainty is whether I pretend that I'm on vacation during this time, and basically sacrifice part of my employment benefits.

@early_departure Not sure I understand the distinction. You'll have some date that you are done officially working, but per policy will still get paid for X vacation days afterwards (whether you go on an actual vacation or sit on the couch or start a new job or volunteer for charity). If you plan to do some work wrapping up papers, does it matter whether it's during that period or afterwards? What is materially different for you in each case?

@BryanKrause I think the OP means that they have X vacation days that they can either use before their official end date, or get compensated for not using it. Their advisor is asking them to officially take vacation before the official end date, so that the days are counted as used, but actually spend that time working. In this scenario they will not get paid for unused vacation since officially there won't be any left.

@GoodDeeds That makes good sense, I'm not sure why I wasn't quite thinking of it that way.

I disagree with your assessment in part A - this strikes me very much as a dishonest, exploitative attempt to not pay out the accrued vacation time, which was part of the "mutually acceptable terms" under which the OP was hired. The OP didn't use their vacation time, and is contractually obligated to be paid for it. Not paying the vacation time changes nothing whatsoever about how many hours the OP works on the project, it just means they are not being paid what they are owed for the same amount of work. The PI is simply attempting to cut the OP's salary long after the contract was signed.

This answer is pretty confusing to me and I think a bit apologist for the toxic work culture than leads to this request.

As always, country matters a lot. In Europe, supervisors can personally get into trouble if staff working for them don't take their contractually mandated(!) vacation days. And (depending on some deep fiscal internals) money for paying out vacation days may not be accounted in the project budget and have to come from a separate pocket (not usually the PIs, but they will get the squeeze for that from the university). So this sounds to me like the advisor is trying to have their cake and eat it, too... (And they would have gotten away with it, if not for those meddling internet kids!)

The advisor is asking you to officially take the days off before the contract finishes, but to work during these days, so you get the work done and he/she does not have to pay these days off, as per the policy of your institution is "to pay departing postdocs for un-used vacation days".
So yes, he is asking you to do something unethical. With him/her you can confirm you will work toward the finishing the projects/reports/papers. But as long as you work, don't take your holidays. They were already in the budget, your advisor is trying to create money out of thin air, probably to be used to (under)pay another student/colleague to work "just a couple of weeks" on a thing that will last months.
If you accept your advisor's terms, you can be statistically sure you will contribute to underpaying someone for his/her work (yourself :) , and most likely someone else).

It's also likely that is is illegal.

It’s not really correct to say the advisor is “asking OP to do something unethical”. The advisor is behaving unethically by making the request, but OP would not be behaving unethically if they agreed to the request. OP has every right ethically to take vacation days, and every right to work on papers during their vacation days if that’s what OP wants to do. Nothing unethical about doing that voluntarily, even less if it’s done under some kind of pressure or coercion. But the adviser is certainly being a jerk and should absolutely not make such a request.

@DanRomik please think about the definition of illegal and unethical.
Is unpaid work unethical? yes. Is working during holidays unpaid work? yes. Is most of the work done in the academia unpaid? yes.
The conclusion is unfortunately straightforward.

Your logic reminds me of the old joke “nothing is better than eternal happiness. A ham sandwich is better than nothing. Therefore a ham sandwich is better than eternal happiness.”

@DanRomik unlucky you that you pick eternal happniess!

Your advisor's request is definitely unethical.  Don't do it.  There can be no benefit to your relationship because he has already burned the metaphorical bridges.

Legal advice is off topic and depends on your location.

Those vacation days have a monetary value.  It never makes sense to work through them.  If you have X days of labor to get to a good ending point with your work, then labor for those X days and then take a paid vacation, and terminate employment at the end of the vacation.  Alternatively, if you will be compensated for the days without "taking them", just terminate employment effective after X days and get the payout.
I do not see any circumstance where taking the vacation days and working through them makes sense for you.  Asking that you do so is unethical:  he is asking you to give up money which is owed to you.

Not fraud, simply a request he or she knows you’re adult enough to accept or decline. I’ve had colleagues who’d looked forward to vacation time in order to dig in and wrap up a project. I’ve had those times too.

Were your colleagues taking days off to dig in and wrap up a project? It sounds very strange.
Can you further a bit the concept of being "adult enough"?

This is most likely a budgeting issue. Unused vacation is something HR doesn't like, because it means they must accrue liabilities. Employees are for this reason expected to and usually reminded to consume vacation before employment ends. But now it's too late, so there's no point to argue.They can either pay you out or you take your vacation, of course without having to work.

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text:
On average what is the likelihood that a research fellow will eventually become a lecturer or an assistant professor?
I was trying to determine the probability that someone who is currently a research fellow will become a lecturer or assistant professor within the next five years and I was wondering if someone could approximate it here.
I suppose that it is dependent on many factors but is it possible to calculate a rough estimation without additional details or with stated assumptions?

Can you estimate it by taking the number of lecturers/assistant professors in your department and dividing by the number of research fellows?

Very discipline and university specific.  In my school, the probability is zero.

@Allure That won't quite get at it because professors are in their jobs longer. Probably a closer estimate would be # professors retiring/number of research fellows or equivalent, if we assume all professors are hired from people in research fellow positions or equivalent.

@BryanKrause That assumes professors who retire are replaced.  In many places the positions end up simply eliminated, with the necessary teaching being covered with larger classes, higher teaching workloads for current staff, or poorly paid temporary staff.

@AlexanderWoo True, but it's still about as close as you can get. There are also fields that are growing where the math is more favorable, etc.

Is this a research question or are you just wondering about your own chances?

Does this answer your question? What ratio of PhD graduates in STEM fields ultimately end up as (tenured) professors?
Please clarify on which sector/country/gender you are interested: that would be fun!

As was alluded to in the comments, this really depends. I'm speaking from the perspective of computer science, which on average has a better job market than other disciplines. If you're talking about a research fellowship in very small fields (say, abstract math), you'll probably need to reconsider everything written below.
Successful research fellowships lead to the RF obtaining a number of impactful publications, an additional enthusiastic reference letter writer or two, and a broader research network. They may gain valuable experience writing grants and advising students, which further bolsters their prospects.
If these conditions are met, I'd say that in an average to good job market, such a research fellow is more than %50 likely to obtain a tenure-track faculty position in a reasonable university.
In a bad job market (e.g. the one we had in 2020), these chances decrease dramatically, but still - small, less reputable universities may still be willing to hire a good researcher as an opportunity hire (one that won't be available to them under normal circumstances).
Overall, the chances of a research fellow getting a permanent position are no better than those of a fresh PhD getting one, assuming all else is equal.

"Overall, the chances of a research fellow getting a permanent position are no better than those of a fresh PhD getting one, assuming all else is equal."  I find this claim hard to believe.

@AnonymousPhysicist Yes that seems unlikely. Can you give better probabilistic bounds?

Assuming all else is equal - yes. Lots of people do 6 or 7 years of PhD precisely to avoid needing to do a postdoc. Again, this is not data, just anecdotes.

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


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Is there a way to assign a fixed identifier (e.g. TOPIC-ID#) for a citation in bib files? Or a similar tool for accomplishing this?
I am using a refs.bib file for writing papers, as I'm sure everyone does.  However, the problem is that I don't have a quick way to refer to a particular paper when working on a different, non-latex document.  For example, let's say I'm handwriting a note or reminder to myself, and I want to refer to a specific paper without using the entire title (since the titles are usually unwieldy).  I want to refer to the paper using some shorthand notation like (TOPIC-ID#).
The problem is that refs.bib assigns a single reference to each bibtex entry, but those references change depending on where they are in the document, etc.  So, reference [1] today might be reference [7] tomorrow. I'm looking for a unique identifier that remains fixed long after the day it enters my bib file.
Is there a electronic citation tool (perhaps not latex/refs.bib) that allows me to fix a unique identifier for each paper that won't change?  E.g. (TOPIC-ID#) would be perfect.   Or, is there a way to force latex to organize my papers in the refs.bib file this way?

Why not use the unique citekey in the bibTeX database? You could standardize the format of those using whatever system you please.

I don't understand this question. The advantage of a bib file is the clear identifier for each source. Why do you not use this identifier? If you use a sensible naming system (e.g. I name all my entries with name of first author, EA for et al if applicable and year, e.g. SmithEA2010, plus an A, B, C if multiple papers fit that scheme) you can easily use tha same identifier in non-latex instances.

thanks @Anyon.  Can you please elaborate on what is a "citekey"?  Never heard of it.

@Sursula what do you mean by "name all my entries"?  bib determines the name for you, right?  Or am I misunderstanding?

There should be a unique identifier, a citation key, for each reference in your .bib file. That is how BibTeX figures out which reference to put in your bibliography when you write \cite{citekey}. If it isn't unique, you might end up citing a different document than you intended.
The .bib file is just a text file containing various entries, such as
@article{PhysRevE.85.046117,
  title = {Walking with coffee: Why does it spill?},
  author = {Mayer, H. C. and Krechetnikov, R.},
  journal = {Phys. Rev. E},
  volume = {85},
  issue = {4},
  pages = {046117},
  numpages = {7},
  year = {2012},
  month = {Apr},
  publisher = {American Physical Society},
  doi = {10.1103/PhysRevE.85.046117},
  url = {https://link.aps.org/doi/10.1103/PhysRevE.85.046117}
}

The anatomy is that they start with @, which is followed by the entry type (here article), and then the citation key. In this BibTeX entry downloaded directly from the publisher, the citation key is PhysRevE.85.046117, which you would cite as  \cite{PhysRevE.85.046117}, but you're free to change it to whatever you want. It's common to see author-year formats like Mayer2012, for example, which you'd cite as \cite{Mayer2012}. Just keep the unique identifier unique.
The proposal in the comments is that you can use the same citation key, perhaps written in some reasonably non-cryptic format, as a quick way to identify sources also in your notes in formats where you can't use reference management software. Reasonable BibTeX reference managers will be able to automatically generate citation keys according to customizable patterns. I don't know of one that will easily construct keys of the TOPIC-ID# form, but basing keys on fields in the actual BibTeX entries is typically possible.


text:
Independent researcher being solicited for an academic collaboration. What do I need to know?
I am an independent researcher and have recently been solicited from the director of a university research lab to see what potential there is for collaboration.  They found some of my papers and thought they were of sufficient interest to reach out. I just received an email from the director stating that my papers are being read by their team and the purpose of the email is to start a discussion about collaborative opportunities. Having never conducted research in academia, I don't know what I may be walking into.  I don't know the culture and what the upspoken expectations are.  What kinds of questions might I ask?  Is it acceptable to seek funding from them?  I am hoping someone can provide feedback on these limited facts.

Usually this is a rare constellation. Normally, independent researchers seek ways to publish and/or to connect with academia.
Basically, you need to consider authorship, IP, and funding (if applicable).

Authorship: the main currency of academia is authorship. If your contribution is the most important part of this work, in your negotiation you should find out how they intend work with you and how to publish the work. You could then ask about authorship.

IP: will there be any IP that is going beyond publication interests? Something that might become a patent or make money? Are you interested in that? If so, you probably need to be a bit more careful. NDAs might be relevant, but this also begins to move into legal territory, so off-limits to SE. If you do not see any commercial interest however, this is nothing to worry about (of course, you might find yourself unlucky that you let some highly profitable idea fly - but then, by far most ideas do not make money)

Funding: you have to distinguish if you wish payment as a contractor or as a (possibly temporary) university employee and covering expenses of the research (computers, travels, etc.). You have to find out if and in which form such money is available, if at all, and if it is not if you want to continue. If the project is very interesting, you may consider collaborating with the university in getting funding. Note that some institutions' bureaucracies heartily dislike working with individuals which means that you might have to set up a company for that purpose.

Finally: If you do not care about being paid, then you can ignore 3. Talk to people, find out whether you like what you hear, and have fun doing some research.

I suggest that you have a conversation with them, preferably face to face or, if that isn't feasible, using something like Zoom. Ask about how they envision a collaboration and what each might be willing and able to contribute. You might be able to arrange to have them fund a visit to their university if you are remote. That would be a good start and provide the opportunity for the discussions. It would also indicate good faith in their offer/interest.
If it is about a specific project of yours then talk a bit about authorship, probably making it clear that you are the principal. If it is more general, about an area of mutual interest then talk about the dimensions of that.
Only then should you talk about funding and it might not be them funding you, but mutually seeking funding from elsewhere.
Such things can have a future and be mutually beneficial. It is also possible, though less likely, that you wind up being exploited. Collaborations need to have active participants and a sharing of ideas.
I think it is worth exploring (usually), but don't make decisions until you know more and are comfortable.


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Deal with academic failure as an undergraduate
There are many students (subject being basic sciences) in my university (considered a good university in India) who simply do not care about the subject in a course but have stellar grades. They aren't interested in the subject per se, just the grades. These students never doubt anything that the professor says or whatever is written in lecture notes. They never ask questions. They would happily write in exams what they have memorised without understanding it 'deeply'. When I discuss anything with them about a particular topic which I don't understand, they simply don't care about it and tell me to not think about it 'deeply', and just memorise the stuff. But these students have stellar grades.
A lot of students, almost all that I know at my university, engage in malpractices during the exam, especially in the current online mode when there is no supervision. Some students sit in groups of 6-7 students during an online exam and discuss the questions before submitting, i.e. they solve the exam paper collectively. They often get exactly similar marks as well. Many instructors turn a blind eye towards this.
I sometimes feel jealous of the other students and get agitated at the university system as well. The 'other' students get good opportunities for research internships when they have explicitly mentioned to me that they don't care about research and are doing internships just for the sake of improving their resume.
I, on the other hand, have extremely poor grades. I've failed a 3 courses too. I spend a lot of time thinking about the stuff. I ask questions to the professors, which are received encouragingly. Some professors have explicitly mentioned that my questions are good and it shows that I have thought about the material well. I ask questions and answer questions on Stack Exchange as well, and they are received warmly as well. I am interested in pursuing research after my undergraduate studies but no good university is going to accept me as a grad student considering my poor grades.
I am not saying that my failure is entirely the fault of others. I recognise vices in myself too.
What should I do in order to improve my situation?

You're a good person, but don't let that get in the way. Understand the rules of the game. Maybe one day you can work to change the rules, but for now work on your grades. Understand what education/degrees are for: https://en.wikipedia.org/wiki/Signalling_(economics)

You already discovered a good strategy to get the grade that you need to pursue a career in academia: memorize everything! There's no contradiction to also thinking about it deeply - the two are not mutually exclusive. As a matter of fact, it seems that you actually need both to move ahead with your desired career.

Patting yourself on the back for being a deep thinker is not an excuse for bad grades Forget what others are doing nad get your grades up - unless you being graded on a curve. In that case talk to your professors. It looks like you have some rapport with your profs - keep talking to them and ask about undergrad research opportunities. Grad school admissions weigh prior research way more than grades.

Don't give up. I was like that too and I got a PhD. If you won't leave, they have to let you in eventually.

Allocate time specifically to prepare for your tests
This might seem like a waste of time, since you would rather spend it studying the course material more deeply. However, this is a trade-off you should be willing to make in pursuit of your long-term goal of entering into research. If 100% of your studying time is currently spent on learning the course material deeply, you may need to reduce that to 75–80%, and spend the rest of the time doing test preparation. I understand that test preparation can be extremely boring and feel completely pointless. But, as you've noticed yourself, you need to score a minimum amount of marks to stay afloat in the system. There is no need to judge yourself by your course marks, though; feel free to think of it as just an arbitrary number that you need to display in order to apply to graduate programs.
Furthermore, to the best of my knowledge, a few failing grades will not disqualify you from applying to the graduate programs of any university. I believe you have options to take the failed courses again, or at least their final exams, so make use of that. If you plan to apply to graduate programs in India, in particular, as long as your overall grades lie above the cutoff and you perform well in the interviews, you should be fine.
Finally, your attitude towards your education is commendable, but at some point the effort involved in going through the system may end up not being worth it. Several talented classmates of mine found this to be true for themselves, and chose to take other paths. You will need to choose your path, too, and possibly very soon. But try your best to fulfil at least the bare minimum requirements before deciding that this system is not for you.

+1 “think of it as just an arbitrary number that you need to display in order to apply to graduate programs.” The scores are not useful in themselves, but they can help you get to a place where you can surround yourself with likeminded individuals and thus learn more, which is the goal.

I deal with students with alternate needs and I know it is not uncommon for students to have similar experiences about  learning. Reflecting on the experiences of other students I have some observations about your story.
Firstly, other students will have a different way of learning to yourself and sometimes, just being different does not make their success a result of cheating. There may be some students who cheat perhaps, that is sure, but working in groups and discussing material can sometimes be a good way of cementing ones learning by the reflecting on the material in discussions. A student can get good feedback on what is good and what is weak this way.
Some students prefer to work alone and find that the material is difficult to understand until it has been explored in all its details and at full depth. At some point they reach  the "Aha" moment when it all falls into place and makes sense; then they can move on. They often reach this point through questions; "But Why" and then again "Why". Perhaps this is what you are experiencing.
The other students may not need to ask questions as their mode of learning does not need this deeper understanding, and they find it satisfactory to remember the facts or explanations provided by the teacher. When it comes to an assessment they use their memory to repeat back the explanation and facts from class. This repetition will satisfy the goals of the assessment that the student absorbed material from the class. Sometimes this is what is required, but sometimes it is not and a deeper understanding is required.
Knowing when the learning mode is memory and when it is deep understanding is sometimes difficult to discover. Some teachers can give guidance on this by indicating "you need to understand what is behind this..." as opposed to "remember and use this equation each time ...".
Eventually, the students who remember and those who look deeply will find their learning converge, because the layers of remembered information piece together through the years to build the complex picture of "how it works" and the students who did not ask questions get their own "Aha" moment. However it might have taken them longer to get there.
However, if one tries to understand everything before moving on, the pace of information gathering is slower. One can really only  focus on one piece of a subject at a time. This is how it can result in apparent failure as one has a great understanding of a small piece of the picture and a large void where perhaps some remembered information should be stored for later.
For example, I always found it hard to just rote remember mathematical formula, but I was excellent at deriving and proving them from first principles. When other students just "mindlessly" (in my perception) regurgitated the standard formula for solving quadratic equations in a school examination
 , I spent a lot of time re-deriving it. Even just now I had to Google it to save time! It made me appear slower and less able at maths, when perhaps the converse was true.
The same for physics, when often we have to suspend disbelief and accept things that we ourselves cannot prove. We may start with the theory of atoms and use the "ball and stick" explanation, but then this is just a simplification to satisfy simple minds. Later one might learn about electron clouds, and later the electron shells, later Schrodinger's Equation. Later still sub-atomic particles are used to explain things and we learn about the standard model. Even now physicists are learning that there are still things in the standard model that are beyond their learning and there is yet no answer to "Why".
Another example I use for students is driving. Do I need to understand every aspect of the operation of an internal combustion engine to be able to drive a car that uses one? It is good to know, but does not always improve driving.
My suggestion is that perhaps you should consult the learning support services of your university. In the UK most universities have a learning support service that assist students with improving their working practices and ways of study. Perhaps your does too.

The OP doesn't seem against students working together in general, but specifically students working together during exams (presumably traditional "own work only" type exams).

I would say it bluntly: one thing is what you do, the other is why you do.
No, Macchiavelli never said "End justifies the Means", but it does not matter.
So if you need good grades to get to whatever goals you have, optimize your strategy to prepare for exams having that goal. During your research career you will have to eviscerate again the very basic assumption of what you know, and that just to write introduction to your thesis, so whatever you "study" during your courses, you will need to study it again soon.
Usually, the exams will prepare you at the bare minimum level of a certain topic. If you have additional questions, doubts, thoughts on the topic, you can preserve them for after passing the exam.
If you do not manage to get excellent grades, it may simply be you were unlucky in the talents' drawings. Nature/God/the big Turtle were not kind, in the same way that not everyone of us is a Voltaire or a James LeBron or a Lionel Messi.

Your situation sounds similar to my own recent undergraduate experience, although I'm in the US. I enrolled in a top STEM school, failed three courses, and achieved poor grades in my first two years despite being a very motivated and hard working individual. However, I improved my academic performance and got into several good PhD programs.
Now you can't control if other people cheat. So if you want to get into a graduate program, the best thing you can do is focus on your work and show an improvement in your academic performance. You especially need to show improvement in course areas relevant to whatever field you want to go into.
This requires effort on your part to figure out how to academically succeed. Think about it this way: there (probably, hopefully) exists a set of (legal) academic actions that you can do to improve your academics. The problem is you don't know what they are, and you need to figure out what those things are. Here are some random things: find a supportive mentor/academic adviser who wants you to succeed (I strongly advise this), go to office hours more, plan and commit to concentrating with no distractions on a topic of study (easier said than done), find people to study and do homework with, ask friends about a professor's teaching style before you sign up for their course, etc.
Here's whats also important: Once you find what works for you, it will help to maintain a routine in which you balance all the things you need to do to academically succeed and also stay happy as an individual.
I myself simply knew none of these things, which are now obvious to me, when I arrived to college and so I performed very poorly. Perhaps they are not obvious to you too.
If you can improve your grades, then in your graduate applications, you can (briefly) explain why your grades were initially poor, but emphasize and draw attention to your improvement. It's important not to sound negative when you talk about your past grades or else you come off as an unreliable narrator, so be positive/objective.
Overall, I think if you are genuinely curious, motivated, and can successfully communicate these things to graduate programs, you will have a shot, especially if you can improve your academic performance. I think it's because people know that grades are not "everything." So don't give up.

I strongly think that though asking the right questions is highly important, what's more important is determining whom to ask the said questions to.
Not everyone (sadly sometimes even the professors) has the capacity to understand the intent behind the question, and it is possible that they could be taking it in a negative way.
As a resort, for now, I would recommend you to look for a mentor faculty with whom you share an academic interest (and who is receptive to your questions), to enhance your research capabilities.
And I definitely agree with what @The Amplitwist said you need to fulfill the bare minimum first.
Nonetheless, don't let such setbacks hamper your spirits.


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PI wants to exclude me from collaboration despite having done significant work. What are my options?
I work in a multidisciplinary center, where a neighboring group started working on a topic I am an expert in. This group lacks relevant expertise, so the postdocs approached me to perform some work. I have documentation of my contribution through data and code shared via e-mail, meeting minutes, and detailed logs of my own hours spent working on the project.
The PI of the group leading the project was aware of my contributions for the past few months and has clearly being pushing his team to become self-sufficient to the point where they do not need me (they're nowhere close!). Although I have the support of the postdocs, the PI has announced publicly that I have not contributed anything. This is due to internal politics, and is a clear sign that he wants he off the project and will not credit me for any published work.
My question is as follows: Let's say I can document a significant contribution to the project, worthy of authorship, and have the support of the postdocs. If the PI decides to go ahead with publication without crediting me, what are my options? I assume what remains is the possibility of contacting the journal. I've seen some journals saying that they stay out of authorship disputes, but it's not clear what that means in this case.
I've seen other answers on similar topics, which while helpful, do not fully answer my question:

PI asked me to remove a student from author's list, but I disagree
My former advisor wants to publish a paper that relies on code that I worked on without giving me any credit. What should I do?
I was excluded from an article - what can I do?

What does your boss think? Does your boss agree with the time you're spending on the project? Who/what pays your salary?

"perform some work" can mean a whole bunch of different things, from washing glassware to designing experiments and more.  You give a cursory description of what you did, but nowhere nearly detailed enough to allow us to get a feel for your intellectual contribution, which would have impact on your authorship claim.

My boss is aware of the work, but is not involved directly. I have no worries about my current/future salary.
As for what I mean by "perform some work", I'm certain that the work I've done warrants authorship (and experienced enough to evaluate this). Thanks for the comment, although the question is not whether my contribution deserves authorship, but what options do I have in the scenario outlined above. I'd made edits to make this more clear.

I would start by suggesting having a meeting with the PI. Even if he really wants to push you away from the project, the meeting will be useful in order to understand his line of reasoning (or lack thereof). Don't beat around the corner, ask him directly questions like: "Why do you believe I don't deserve to be part of this project?"; "Given the considerable amount of work I put into it, how much is enough to deserve authorship?"; "Why do you try to train people in order to learn a procedure I am an expert at, instead of using my skills?". Just remember humans are very broken and inefficient machines in general, and sometimes the way someone answers a question (tone of voice, movements, eye contact) are more important than the answer itself, especially when we're dealing with very proud and dismissive people. Straightforward discussions are the best way to solve any problem in life, especially in science, but one has to learn what to look for during this type of interactions. It is likely that you will be able to infer that this PI simply doesn't like you (happens a lot), or thinks your work is of low quality, or maybe he/she will even be honest and give you a full answer. No matter what happens, this is the first thing to try IMHO.
Now, assuming that not much was gained from a direct approach and given that you have the support of other postdocs involved in the project, you can always invoke the fact that all authors in a paper have to agree about who should be listed as an author. In practice the final word either falls on the PI or on his boss (a director, a professor, etc), but it is rare to see a paper in which e.g. 3 out of 4 authors claimed X should be a coauthor, and in the end this person wasn't listed. There should be a consensus here. Unfortunately sometimes the other postdocs will agree that you should be an author but will not be willing to place themselves in the PI's line of fire by trying to insist on this. In this case you might try to talk to the PI's boss, especially if you now know the PI doesn't like you. There's a chance the PI will be reprehended and somehow forced to list you as an author, but what is certain is that from now on the PI won't simply dislike you... He/she will very likely hate your guts.
If talking to the PI directly, gathering public support or even talking to the PI's boss don't work, as you mentioned there is sometimes the possibility of contacting the journal directly. I would very much advocate that this is a very, very bad idea. You would be messing up the lives of all authors, not only the PI. You would also cause problems to the journal's editorial board, who have zero to gain in being involved in authorship disputes. This could lead the journal to include the authors (and you as well, and sometimes even your institute!) in some sort of "these people are trouble" list, and this is the last thing you want - especially in the beginning of your scientific career. Honestly, do not include the journal in this matter, unless you want to really start a war that has a huge probability of downing you in its end.

Thanks for your answer. I can add that the PI is a manipulative bully who doesn't like me, so direct contact will certainly be uncomfortable, and is unlikely to achieve much. The direct contact would have to be between the PI and my boss.

It might achieve something in the sense that everyone will know that you tried. Try to render your meeting very public, so that everyone can get a grasp of the situation. I had a boss once who treated me extremely well in front of other people, but once I was in his office with the door closed he called me an "idiot", "retard" (sic), "autistic", etc. He knew extremely well when and where to be himself after 50 years of bullying. Maybe your PI will let some of it out and someone will notice (hopefully his boss).


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A potential postdoc PI contacted my Ph.D. advisor without asking me for the contact info. Is this common?
I'm a recent Ph.D. graduate looking for a postdoc opportunity in the US. I recently interviewed with my potential PI, and at the end he said we will discuss later. A week or two after the interview, the PI contacted my Ph.D. advisor for a reference. My advisor said that the PI had asked him for a online meeting. This was great at first, because it meant that he was interested in hiring me. However, what made me feel a little uncomfortable was that he never asked me for my Ph.D. advisor's contact information. I think it's natural to ask me first, as far as my way of communication is concerned. I would've been happy to give him my Ph.D. advisor's contact information.  He and my advisor eventually had an online meeting in a positive atmosphere. My advisor says that he seems to be very interested in hiring me, and my advisor also said good things about me. Anyway I wonder if this is a red flag for the PI's communication style or personality. It the first time for me being at a academic job market in the US (and I'm not the one from english-speaking culture), so maybe I'm being too sensitive and reading too much into it.  What do you think about this?

Were is your PI located? At lease in continental western Europe I would consider this behavior the norm. All the reference letter writer in the US seems strange to me.

@usr1234567 and in the UK we list source of formal references, but the informal references as in the question are important too.

No, it's not a red flag at all, you are overthinking it.
While on the face of it the situation looks a bit like back-channel reference solicitation, which if frowned upon, I think this situation is different. It is universally assumed that while looking for your first postdoc job, your advisor will be your main reference. So functionally, all they did is cut some social dancing for the sake of efficiency. Consider that it's quite likely that they have met or corresponded before; this would make them asking you for contact details even more artificial.

People should not assume this. Some advisors behave badly and some people might have good reasons to not use their advisors as references. You can read this site to find all kinds of difficult situations that PhD students encounter through no fault of their own.

@toby544 My advisor is well aware that I am searching for a postdoc position and has also been informed that I visited the lab of a potential PI. I've shared these details with my advisor, so that shouldn't be a problem.

I find asking me for the contact info seems natural because I bet that my advisor and the potential PI have never met before. What seemed somewhat surreptitious to me was that he looked up my PhD advisor's contact information online, when he could have simply asked me for it. Anyway, I appreciate your perspective on this matter. Thank you for sharing it!

@oklu, but "simply" is a wrong word: it is a few clicks to look up a person online, contrasted to digging up your email address, writing you a polite email, waiting for a reply etc. So, the relevant question should be not about "contact info", but whether he should have asked if you mind him contacting your advisor. Maybe it would be polite to do so, but not practically necessary: if you did mind, you would have brought it up during the visit.

@toby544, if the advisor has nothing good to say about the candidate (whether or not for right reasons), there's no real way to conceal it: no recommendation equals poor recommendation (absent some explanation). One cannot realistically interview for a first postdoc job and assume that the opinion of the advisor will never enter the picture.

@oklu - if you are in alignment with the potential PIs group, why would you think your advisor has never met them? Certainly seems likely they would at least know of them, and may also be aware of various mutual collaborators. The academia world is pretty small, particularly for people who have been in it for a while.

Many years ago I got my postdoc with even less 'social dancing' - I ran into a lab director at a conference who said 'I hear from your advisor you are graduating soon - when can you start?' I had no issues with their back-channel communications.

@Kostya_l  I used the word 'simply' because we had already been communicating via email, and I had recently sent him a thank-you note for allowing me to visit his lab. There's no issue with him contacting my advisor; my advisor is well-informed about my situation, we have a good relationship, and he eventually strongly recommended me during his meeting with the prospective PI. I just find it somewhat awkward that he reached out to my advisor before responding to my email. The multiple responses here however, suggest that my concerns may have been an overreaction. :-)

@Kostya_I My advisor was never contacted for any of my postdoc offers. One of them a collaborator/committee member sent an e-mail, the other two groups knew a major collaborator (but didn't contact them AFAIK). The number and quality of publications I had showed that I was productive and worth an in-person interview. Results speak.

@oklu I wouldn't necessarily agree that you overreacted. Another way to interpret the votes is that a slightly inconsiderate behavior is seen as normal in academia.

@lighthousekeeper What do you think is inconsiderate here?

@AzorAhai-him- See toby544's answer

In my experience this is not uncommon. (Although I guess the uncommon element is that you were not asked for a list of (potential) references when you applied, or did not give your advisor as a reference when asked.)
Asking colleagues about their opinions about on potential hires is fairly common practice. Usually this involves people the potential PI knows well, and whose judgement they trust, which could include the (former) supervisor.
Depending on the jurisdiction there may be some rules that need to be taken into account. For example, the fact that you applied somewhere, can be protected private information, that the potential employer isn't free to share. Similarly, there might information about the applicant that the supervisor isn't (legally) allowed to share. But, many of these can be skirted around by staying vague on the reasons why the exchange about the applicant is being held.
I wouldn't say that any if this is a red flag, per se. It tells you something about the potential employer. In particular, that they are probalby not the type to follow strict protocol, but that might not be a bad thing, depending on your own inclinations.

It is 50% of a red flag.
Some PhD students have advisors who behave badly or unreasonably. Others might have all kinds of other reasons for not wanting their advisors to be approached like this. For example they have told their advisor something about where they are looking for jobs, or they have not told them certain things.
The potential PI should have asked you first before contacting your advisor, and this incident suggests that the potential PI is somewhat inconsiderate.
I don't agree with Kostya_I who says "all they did is cut some social dancing for the sake of efficiency."

I appreciate your response!

I think it is unreasonable to expect that a potential postdoc supervisor wouldn't talk to your current advisor.  It is no secret who your advisor is and they would be the best source of information on how a researcher works.  Unfortunately, if you don't have a good relationship with your PhD advisor, you are going to have a hard time.

@NuclearFission Your last sentence is true, but that doesn't mean we should just shrug our shoulders. We should try to spread the idea that people like the potential PI should be considerate and ask the PhD student first.

For me it’s 50/50 red flag. If you have officially provided list of references, then your potential postdoc PI should be contacting them first. If you haven’t provided contact details of your major advisor, then contacting with your major advisor without letting you know may reflect your potential post-doc supervisor’s style of management. Some people may like it, but I personally don’t think that good. It could potentially be harmful if you don’t have good relationship with your major advisor—-common in PhD level. Your PI should have at-least asked you why you haven’t provided your major advisor’s contact details and if it is okay to contact your advisor.

Thank you. Now I feel like things are getting complicated, but at least I trust my gut. No matter how the behavior is fall into the 'normal' category, I am the one who will have to deal with this PI if I go to that lab. So it's a choice I need to make in light of all of this.

@oklu, I suggest defining what is your comfort level and trusting your feelings. Sometimes extra flexibility may be harmful while frequent micromanagement may be an good learning experience as well.

There are some things to take into consideration. If you applied to be my postdoc for example, then I need to secure about $115,000/year just to pay your salary (you probably only see 55-70k depending on location, but overhead, health insurance, everything else adds up on my end). That is a sizeable chunk of change from a grant - thus a big investment to just go in blind.
I will almost as a default assume your main reference will be your advisor. They know you and your research habits, and your ability to integrate and contribute to a group better than anyone else. If they are not, that is a MAJOR red flag. It will prompt me to investigate.
So, I will be inclined to reach out to your advisor, people I may know at your institution etc. Perhaps I may even know your advisor from some professional interactions.
Most faculty are well aware that advisor-advisee relationships do not always work out, especially at the interpersonal level. We take advice and comments with a grain of salt and we weigh them against your other references and your CV. For the most part, unless you have created serious issues in that group (delinquent, abrasive or confrontational, etc...) most people will find something positive to say about their former students... because ultimately you getting into a good postdoc reflects well on them in the long run. So unless you are trying to hide something serious, it's rarely an issue that would impact you (in my experience).

On the other side, most professors are fighting for tenure. Not all professors can do research or mentor students ethically. I've seen a large number of professors, if not the most, are guided by only their tenure needs. Some even impose their vested interest to advance someone else career by taking advantage of students. These are all reasons why students should be at least made aware of potential faculty contact and a reason why the major advisor was not included in the list of references. Sometimes, students want to change their career trajectory and their major advisor is irrelevant.

Only untenured professors are under consideration for tenure; most departments tend to have a balance of assistant/associate/full at most times until they become top heavy and have a string of retirements which leads to a string of hires. To impose the notion of unethical behavior on most pre-tenure faculty is about as fair as pushing racial or cultural stereotypes. Though I do sympathize that you may have had certain experiences which led to your current interpretation. Going from Ph.D. to postdoc is not a change in career trajectory, it is literally the most natural extension.

So unfortunately, a poor relationship with a doctoral advisor has lasting impacts which puts the onus on the advisee to explain, because the convention is that people in academia talk. So lead with why you do not wish to include their reference. It is uncomfortable. But unfortunately for you (and all of us in academia), a postdoc advisor is also another type of mentor, and they are likely going to want to speak to your prior mentor as they embark on a similar (but more advanced) relationship with you.

Also I am not sure why a downvote was necessary. It provided an experienced and honest answer based on current convention/realities. I.E. to help you understand why you encountered what you did, and why it is broadly not perceived as unethical among faculty. Sometimes hearing the other side of it is useful rather than simply an echo chamber.

Yup! Something I never understood in academia is why downvoting is necessary.

Not a red flag.  If I am looking to have someone join my group, get paid off my grant, etc., I have to do my due diligence and I am not going to ask permission to do it.  The PhD advisor is the first person I want to talk to.  Now, there may be certain circumstances wherein I wouldn't necessarily take everything they say at face value, but I'm sill going to hear what they have to say.  (I see others have written essentially the same thing).

Ok, how long does it take to ask the person that you are going to work with for the following years if it is ok to contact his references? You don’t have the time? I think you just care about yourself, and this is the reason you will never get genuine people, but workers that don’t care about your actual work, because you don’t respect them.


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Supervisor not giving helpful academic direction
I'm a second-year (almost third-year) PhD student having serious trouble due to lack of scientific direction. I initially worked well with my supervisor, but when COVID hit she essentially ghosted the research group for some months and has been irregularly present ever since. Lately, I've noticed that she seems checked out when I talk to her and so I started explicitly asking for clarification as to what exactly I should be working on whenever I see her. Unfortunately, this strategy has been foiled by my supervisor changing tacks about every 2-4 weeks. For example:
-Conversation 1: "You should focus on x, then do y. Do not include z until those first two are set."
-Conversation 2: "Actually doing q is a good idea, let's work on q together (for a month)!"
-Conversation 3: "What you should present at the conference (in 2 weeks)? Show the data on z, that is the most interesting aspect of the project."
-Conversation 4: "No, you should not work on q anymore, that needs to happen in parallel to z."
-Conversation 5 (after someone at a conference explicitly called attention to my lack of including y): "I understand you are asking to work on y but I think you should try to extend x. But I suppose you can include y."
-Conversation 6, only one(!) day after Conversation 5: "What do you mean about doing y, you should do your whole project without y. Also you should work on a paper with (random collaborator) on k! And actually you should also do/have done x completely differently!"
This is pretty frustrating since all the "x,y,z,q..."s I mentioned tend to be at least partially exclusive and take at least 2 months to complete, so I have sunk a lot of work into projects that are half-done. If I work on something that has lost my supervisor's interest, I don't get feedback, which makes it difficult to wrap up anything. My project is also related to two different collaborations, at least one of which seems a bit pissed off and is now proceeding to publish without our input. (The other one has shifted to emailing only me directly now, which is helpful, but I know my supervisor left the first set hanging at least once/tends to view answering emails as highly optional so I kinda get where they're coming from).
In terms of other people to talk to, our group only has one postdoc, who tends to take about a week to answer emails and is not very forthcoming in terms of mentoring PhD students. The other two PhD students in my group are close to graduation, and struggle with the same issue in the short-term (e.g. getting told to write an answer to referees disagreeing with the corrections on an article, then getting criticised for not having applied the corrections) but have already set the main academic direction of their project.
I'm not really sure how to handle this: should I confront my supervisor about the inconsistencies? Trying to set another meeting to talk long-term goals? Just do whatever I think is best and hope I don't mess up too badly without feedback? My supervisor doesn't always take criticism well, and I'm afraid that I'll just get blamed for being a bad student because I haven't produced anything publishable in a year.

Sounds like an opportunity for you, as an almost PhD, to sift through her various directions, pick one or meld a few, and take the plunge. Waiting for consistency: not always the right tactic.

Is this in the US or elsewhere? More important, were you assigned this supervisor or did you choose them?

@Aruralreader that is a fair approach, if a bit early (it's a 4 year program).

@Buffy This is in Europe. I chose my supervisor when entering the program- there is no assignment system at my university, at as far as I'm aware of.

I sympathise. Are these conversations verbal or in writing? Try and get as many of these instructions in writing so that you have some evidence to show a week/month down the line when she asks you why you're working on topic x. Then you can say, "look, you told me to in this email".

As a phd student your job is to ultimately create your own track of successful research. An ideal advisor would suggest reasonable lines of research, help you develop your ideas, and give guidance and advice if you ever get stuck. In practice, advisors tend to fall in one of two camps. In the first camp, advisors treat their students as employees who produce results for the advisor's group. In the second camp are 'hands off' advisors who don't do much at all. It sounds to me like your advisor is the hands off type. Take initiative, decide what makes the most sense to work on, and do that. Unless your advisor has explicitly told you, "I expect you to work on X and your graduation depends on finishing X", they probably just want you to do something publishable and don't care much past that. Take the opportunity to work on whatever you feel is most interesting or most beneficial to you in the long term.

Verbal conversations are an inefficient means to set directions for a successful PhD project. Random verbal conversations even less so, let alone after a few months of absence for whatever reasons.
Define what you want to achieve for your PhD. Formulate hypotheses to validate or problems to solve. Establish the steps needed to get from where you are to where you need to be. Put the work in context to the current state of the art. State the technological or scientific relevance of the projected outcomes.
Put your plan in writing. Set a meeting and present your written plan to your advisor. Ask for directed feedback. Ask for an opportunity to present your plan to a committee of faculty who you know should have an interest in the success of your work.
In the US, this step is called drafting a dissertation proposal. Some PhD programs require that candidates pass an oral defense of their PhD proposal as the first step to be admitted (given official permission) to do the PhD research.
A dissertation proposal is not a guarantee to be given a PhD. A dissertation proposal is not an administrative recipe for all steps in the research. A dissertation proposal is a roadmap that says I am here, I want to go in this direction, I want to visit these stops along the way, I hope to get at least this far, I plan to use these modes of transportation, I expect the trip should take this long, this is why the trip is important, and these are the pictures that I should be able to show once the trip is done. A dissertation proposal is a plan to help both the dissertation advisor and the PhD candidate frame future discussions about changing plans when something in the research suddenly goes dreadfully wrong, when something only tangentially related to the research plan becomes exceptionally exciting in its own right, or when either party steps aside from the research activities for a few months (for whatever reasons).
Finally, you do not need to ask your advisor for permission to make such a plan. You are far enough along that, in my observation, you should consider taking the initiative. To this end however, you should inform your advisor of your decision. A reasonable approach in your situation is to tell your advisor that you see many directions that you might be able to go in doing your research, that you see possibilities for roadblocks or distractions along the way, and that, with all of this, you feel a strong need to focus at this point on creating a research plan for the best path forward. Use this opening as the way to establish that you will draft a dissertation proposal/plan for joint discussion and approval (with the draft to be completed in perhaps a month or so if I be so bold).


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how to decide on first coauthorship for a paper
I know this topic is kind of depending on which school each researcher is from, so i would like to gain more information regarding the topic.
I am a phd researcher and I have a specific task to do, a colleague of mine have similar task but using different agents. this colleague came up with an idea to compare both agents and write a paper about it, s\he performed his\her experiments and started writing the paper, s\he then approached me with the idea to compare, so I agreed, performed and analyzed my data, which took me weeks to finish, and shared it with this colleague. As I was working on another manuscript and s\he wanted to write this new manuscript by him\herself, I only contributed to read and correct writing-wise (plus of course my data and results) but the most recent version was never shared with me, last one shared was around Nov-Dec 2020, and till this moment I dont know how my contribution was written in the author statement. I got to have a fast look at paper after submission and saw that the graphs always had one part regarding my data, yet i am only a co-author and this colleague is the first author. My question here, was I supposed to have an equal contribution and supposed to be a first co-author? my other colleagues pointed this out and that s\he should have put me as a first coauthor with him\her, and I am not sure if its true or not, i dont have much experience writing manuscripts, and my (our) SV never pointed this out to me. Now its anyhow late to ask for a coauthorship, but I would like to avoid such situation in the future, so would really appreciate if someone has an experience on how to handle such situation.
Sorry for the long message and thanks in advance!

@Roland, while I agree in principle, roles can change over the life of the project.

Both of you could be corresponding authors. It does convey a kind of equal weight /role of authors.

Speaking as somebody who reads a lot of papers, my only desire is that it should be clear who did what on a paper, because if want to contact the authors I want to know who to contact.
In general, whoever WRITES the majority of the paper should be the first author. If some person did some critical task that was more important than writing the paper, then to my mind the way to handle that is to make them the second author but put a note in the paper describing their contribution ("Dr. Smith spent five years hand nursing over 50 ferrets to make these experiments possible... etc"). That way the reader knows who did what.

I agree that you'd want to know who to contact, but it's not always as clear cut. In my past collaboration, a colleague and I set out to explore two directions (one each). "His" worked, while I never managed to obtain the results using "mine". He set up the experiments and got the core results. We discussed frequently. At this point, I was adamantly refusing first authorship. And then other responsibilities crept in and he had no more time to work on this - I double checked the current experiments, ran some more, and wrote the bulk of the text. Which of us would you prefer to talk to?


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May not be able to finish minor that I noted on my PhD applications
I applied to graduate schools and have a couple of interviews lined up in February. I listed my statistics minor on my application (which is declared on my transcript and everything) but I may not be able to finish it because I am on the waitlist for the final two classes I need. I am doing everything in my control to try to get into them (emailing/petitioning professors, talking with an academic advisor), but there is no guarantee that I will be able to enroll if I don't get off of the waitlist.
This will not affect my ability to graduate with my neuroscience major. Additionally, the classes that I need to take are not very relevant. In the event that I am unable to finish the minor, how do I inform the admissions committees where I have interviews, and will it substantially affect my application?

No need to bring it up unasked. No one will look at your transcript when you enrolled to double-check your major and then boot you if you didn't finish. If someone asks ... don't lie

My department has an unofficial policy of helping students in your situation. I highly recommend talking to the instructors of the classes you need and also to the director of undergrad studies of the department that offers the classes you want to take.

I can tell you, as a longtime member of an admissions committee for a prestigious PhD program, the committee is looking at the depth and breadth of your preparation. Your major and minor are less important. What courses and experiences have you had, and how did you do?
Another commenter said that disruptions at the end of one’s studies are not uncommon. I agree with this.
Lesser programs might be overly rigid about majors and prerequisites. The better programs engage in holistic review to see the full spectrum of an applicant’s preparation, experience, and non cognitive attributes.
Good luck!

I doubt that it would be an issue unless it is specifically required for entry into your desired program, but to be completely honest, make sure that at some point you inform people of the situation. This might come in an interview: "Oh, by the way, I might not... due to waiting lists".
As long as completion is still a possibility and you haven't been closed out, I don't think you need to update applications, but you don't want to leave the impression that you have padded your CV.
I'll note that final year disruptions, during the doctoral application process aren't especially rare. And I doubt that extensive statistics is required for application to a neuroscience degree, though some specifics might be needed for certain sorts of research. But that is also true of many fields that depend on statistical methods.

Depending on your university, it might be worth a visit with the department head in statistics, especially if one or more of those courses is actually required. There might be a way to expedite your attendance. I don't guess this is especially likely, but it might be worth the trip.

The classes aren't required for the programs and they honestly aren't very relevant. As you mentioned, I just don't want to be perceived as padding my CV. Thanks for the advice!

Each situation is unique. But if I was recruiting a PhD students in Neuroscience, I would be more interested in seeing how much knowledge students has in my fiend of research rather than a statistic minor. PhD is itself a long journey and you will have plenty of chances to take courses if you like. So as long as you have fulfilled other requirements and have good research interest match with your advisor it should be okay. If you can take stat minor that would be great if not it should be okay.
On a side note, you may get chance to do stat minor as a PhD student. You could transfer courses to fulfill requirements for stat minor from your current (assuming you are completing masters degree with several stat courses) school towards your PhD. So, if you could do it, else don’t worry too much.

Where are you that minors in doctoral programs are even a thing? I've never heard of such a thing.

@Buffy I hadn't either, but at least the Indiana University School of Medicine requires a minor.

In my materials science PhD we were required to do a concentration outside of the department. For me that was 3 courses in quantum optics (useful in various laser experiments).

@buffy There are plenty of minors at PHD levels. Stat minor is one of the very common field. Some university requires someone from the department to be in the dissertation committee and some just require to fulfill course hours.

@Dr.Baje Mine requires both