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I don't want to kill any more mice, but my advisor insists that I must in order to get my PhD
When my supervisor pitched the PhD to me, it was all about analyzing "big data". I had BSc/MSc experience in wet-lab biology (mainly culturing cells), however I wanted to branch out into Bioinformatics since I am, and always have been, fairly good at programming in C, and data analysis in general.
I chose this particular PhD because the idea was we take a particular tissue from a mouse, run all kinds of different assays on the same pool of cells, and then create an analysis that would essentially get more information out of the data than any 1 assay alone could tell us, by integrating the data together in clever ways. That was the plan anyway.
What actually happened was that the protocol to get this tissue out of the mouse had yet to be developed, and without the tissue there would be no sequencing, and without sequencing there would be no data. So for the first year I had to roll up my sleeves (figuratively), and learn how to kill a mouse quickly and painlessly, to cut out and purify that 1 tissue I needed for sequencing. Again, in reality, this wasn't so simple. Although you don't/didn't need a licence in Germany/Europe to just kill a healthy mouse and take out some tissue (only to kill it in stressful ways, or if it's a mouse with a special phenotype), I feel you should still ideally be taught. Unfortunately, although other PhDs/Postdocs in my lab work with mice, I couldn't get anyone to teach me at the time, so the whole experience was pretty traumatic. I started off by filling up cages with CO2 (completely) and then putting the mice in, rather than what I now know you should do, which is to slowly increase the CO2. This will forever haunt me. I later learned to do cervical dislocation, which is better for everyone.
However, after I was able to sacrifice and extract the tissue I needed, I started getting asked to do more and more frankly grotesque experiments. Draining all the blood from a semi-conscious mouse. Implantation of electrodes. Cold room experiments. I can think of several more, but it's not really suitable for here. Of course this was all legal and above board - and important science that needed to be done - however I just cannot personally continue doing this sort of work. It all makes me feel slightly sick, and more importantly, I hate myself for doing it. What started off as probably 20-40 mice for the data I needed, is probably now at 500-600. Maybe more. I stopped counting.
But the reality I face now is that there are still 2 more years to my PhD to go, and I really don't/can't continue this for another 24 months. I have explained the situation to my PI, but he tells me quite bluntly - "this is what you are required to do as part of your PhD". On one occasion he said if I didn't do it, that's OK, but "you won't have enough data for your PhD defense."
That is total nonsense of course. I've already published and the data analysis - which I am now spending most of my time doing - has gone great. I'll be publishing some of the tools pretty soon too. The problem is that if I stop killing mice, my boss is going to really make things miserable for me for the next two years - and the end result of that might even be I'm asked to stop working on the PhD. I don't know exactly how or through what mechanism I would get kicked off the PhD, but my boss/PI is obviously a lot more senior than me and he's paying me every month (which he reminds me of, every month), and we both know if I don't kill the mice, some one else is going to have to.
What should I do?
EDIT:
Out of respect for the German PhD system, I should point out that my supervisor isn't German - and I'm confident that another supervisor would have handled the issue very differently. Whilst I'm not confident it is an isolated case, I don't think in this scenario there was anything the Institute (or affiliated University) could have done better/differently.
Honestly, the take home message for me is that I wish I had asked this question sooner, had received all of the kind and encouraging words earlier, and then maybe I would have had the courage to do the right thing before it grew into something more difficult. Thank you all so much!

Can you talk to the department head? Or even better, a university ombudsperson (aka a neutral 3rd party who can discuss your options with you)?

I don't know - I'm studying in Germany and I can't speak German. More importantly, I absolutely cannot do anything that results in my PhD coming to an end. If my supervisor gets in trouble, it hurts both of us. If I cannot continue my PhD, then everything i've done until now - including the mouse work - will be for nothing. Having said that, I will definitely look into it, thank you

And yet if you continue killing mice, you're bound to hate your field so much that you'll eventually have a PhD in something you can't even stomach. Not to mention the damage you'll likely do to your psyche in that time. I don't have a good answer for you - though my heart hurts for you :( I will say this - the knowledge you've gained over this time, and the publications you've made cannot be taken away from you. So even if you leave and start again elsewhere, you won't have nothing. Remember that as you move forward.

As a biologist, I'm amazed by this story and I have a hard time believing something. To use animals in experiments, you need a kind of approbation by an animal care board (maybe called something else in Germany). It's doubtful you can publish without saying you have this approbation. It's more doubtful you can get an approbation without a careful and respectful plan of how you're going to euthanized animals. How did you publish without this?

@Emilie: my wife worked as a biologist postdoc at a top ranked university. She had huge moral (and professional) issues with the fact that a tech in the group was constantly breaking even the most basic of protocols. From what she described, I would estimate that the mouse count for experiments doubled due to this tech's disregard for protocols. She had no such issues at her previous lab. So while it may not be wide spread, not everyone follows the rules.

What do the other students in your lab say about this? As you don't speak German I am wondering if your supervisor is abusing your isolation.

Forgot to mention this in my earlier comment, but - if you are feeling depressed/mentally exhausted/emotionally distressed, do not hesitate to go see a mental health counselor/psychologist. They are trained to help you in these scenarios.

I believe that your institution is also at fault. Under FELASA (european animal science association) guidelines, you are supposed to receive training in both the relevant legislation in your country as well as practical training (on post mortem animals) before doing anything on live ones -- here is a german example. In the UK, your supervisor (and you) would potentially have committed crimes, and your institution could lose its animal research licence. I would report this incident and seek advice. Good luck.

AFAIK, every PhD project has a responsible Professor (the "Doktorvater" in German). Is the supervisor who insists you keep killing mice your Professor or one of the Professor's employed scientists, post-docs, etc.?

Comments are not for extended discussion; ongoing conversation about... how to kill mice painlessly... has been moved to chat.

Sorry to hear you have been put in this situation. I am surprised to hear that can happen in Germany, anyone asked to kill an animal for scientific or any other purpose should be trained to ensure they can do it in the most humane matter possible. What you have described is illegal in uk, rodents are not included in animal welfare rules in some countries but I am very surprised to hear this in germany. If someone supervising you made you kill animals with no training in a civilised western society they should probably go to jail.

what you described is illegal in Germany and any EU country.

... it didn't go well :( It got to the point where I don't want a PhD anymore. Originally due to the mice situation, although that did get better, but later due to purely scientific disagreements in possible analysis outcomes. I have some very specific concerns about some very sketchy math in a number of published analyses, including my own, and frankly no one cared. But I cared. I only did that awful mouse work to get this data, you know. I really cared that the outcome might be bogus. My supervisor and I had nothing to talk about. He isn't a Bioinformatician. We stopped talking.

tonysdg asked in a comment

Can you talk to the department head? Or even better, a university ombudsperson (aka a neutral 3rd party who can discuss your options with you)?

and you replied

I don't know - I'm studying in Germany and I can't speak German.

While it might be a good idea to learn German, you most probably don't have to know German to contact your university's ombudsperson.
Universities tend to be very international environments, and English being the predominant language in middle and western European international research, the ombudsperson is likely to know English and maybe even some other foreign languages. If they don't (or if they don't know English well enough), they can probably get hold of a trustworthy interpreter/translator.

More importantly, I absolutely cannot do anything that results in my PhD coming to an end. If my supervisor gets in trouble, it hurts both of us.

Similar to medical practitioners, priests and attorneys an organization's official ombudspersons are usually required to grant confidentiality to all who come to them for seeking advice or for filing complaints. They might be trained in de-escalating hairy situations of power abuse by superiors in scenarios of dependency like yours. Usually, they will not take any action that you didn't agree to, unless they are required by law to do so (which isn't the case often) or when the situation requires escalation to stop severe harm (e.g., if others are in danger by someone's action).
The exact rules might differ from organization to organization, but it is neither rude nor is there any shame in asking the ombudsperson what rules apply to their role before even deciding whether to confide in them. So if you don't make public that you're going to see the ombudsperson, doing so should pose near-zero threat to you and your PhD project.

Having said that, I will definitely look into it

Please do. Even if your university does not have an official ombudsman or ombudswoman, there might be unofficially assigned persons of trust in the institutes fulfilling a similar role and playing by similar rules. (If there are, again, ask what the rules are before proceeding.)
Your university's website probably has more information on this. If it's a larger university (and by the type of research you do, it probably is) the website and that information is likely available in both, German and English.
You can also ask your head of department, head of institute, the university's headmaster or any other of your boss's bosses, who the ombudsperson responsible for you is. If you ask them, you can (and probably should) do so without mentioning that (and why) you want to see the ombudsperson.
If you have problems finding an ombudsperson
I did a web search myself and found there is an official German organization called "Ombudsman für die Wissenschaft" (ombudsman for science), appointed by the renowned association DFG (Deutsche Forschungsgemeinschaft e.V.). The organization's website seems to be entirely in German, but they do have an English inquiry form for reporting conflicts and suspected violations of "good science" rules / suspected scientific misconduct.
They seem to be more focused on "good science" rules and scientific misconduct investigations than on conflicts, but according to their own examples in these presentation slides, they do consider "Inadäquate Doktorandenbetreuung" (inadequate / unsatisfactory support / supervision of PhD students) a violation of those "good science" rules, not just plagiarism, made up data, skewed results etc.
They also publish a "Liste der Ombudspersonen an deutschen Hochschulen und Forschungseinrichtungen" (list of ombudspersons at German universities and research facilities). I'm not sure how up-to-date that list is, but the people on it are probably still around. If they aren't active ombudspersons any more, they can probably tell you who's in charge of their chair nowadays.
Whether you confide in a local ombudsperson at your university or send an inquiry to the "Ombudsman für die Wissenschaft" organization is up to you. The DFS's white paper that lead to founding "Ombudsman für die Wissenschaft" is explicit about this:

Hochschul- oder Institutsangehörige werden ihre Probleme in der Regel bevorzugt einer örtlich erreichbaren Instanz mit Kenntnis der lokalen Verhältnisse vortragen wollen. Sie sollen dazu aber selbstverständlich nicht verpflichtet sein, wenn sie es vorziehen, sich unmittelbar an den [...] überregionalen „Ombudsman“ zu wenden.

(My translation: University and institute members will usually prefer to bring their issues forward to a locally available entity with knowledge about the local circumstances. Of course, they shall not be required to do so if they prefer to address the [...] supraregional ombudsman directly.)

Wow this is such a fantastic answer - thank you das-g! I have started drafting out an e-mail to the DFG about my situation. Even if they tell me there's nothing practical we can do, I think just having someone to talk to will help immensely, which also goes in the same direction as what tonysdg said. Thank you both!

You're welcome. I hope this helps you to get further advise. You might prefer to write to the "Ombudsman für die Wissenschaft" organization founded by the DFG instead of to the DFG itself. The DFG is AFAIK a large association with various activities, so if you write to the DFG, it could take them some time to get your inquiry to the right person. Also, while the DFG has most likely people willing to help, they are probably not trained in how to handle requests like yours and could (without ill intend) violate confidentiality or such.

Also, while the DFG is reknowned, your inquiry could get into hands of people with ill intend. Any large enough organization can have some rotten apples. Ombudspersons on the other hand are selected for their trustworthiness and follow an additional code of conduct. (E.g., they have to step down from a case if there is a conflict of interest for them.)

On the basis of the information you've given, I think you should look for a new supervisor as soon as possible. Regardless of whether you manage to adapt the focus of your work, your current supervisor does not sound like someone you want to work with.

I couldn't get anyone to teach me at the time, so the whole experience was pretty traumatic

No one should have to figure out how to humanely kill animals by trial and error.

he tells me quite bluntly - "this is what you are required to do as part of your PhD"

This is your project, and if you can find an alternative way of addressing the aims of the project then you are entitled to.

he's paying me every month (which he reminds me of, every month)

It sounds like he wants a technician, not a PhD student. Doing a PhD is not about unquestioningly doing the bidding of a supervisor.
Other answers have made good suggestions about how to make sure that you don't just have to throw away the progress that you have already made. But find another supervisor to continue your work under!

Agreed. It sounds like a toxic environment, best avoided. - "figure out how to humanely kill animals by trial and error." Honestly, it doesn't matter that it was killing animals. For any technique that's important to your Ph.D. research - even pipetting - you should be trained on how to perform it properly, or at the very least given the appropriate resources to teach yourself. You shouldn't potentially botch your data with trial and error mistakes if you don't have to. (e.g. Does stress change assay results in those tissues? If so, untrained hands have possibly confounded the experiment.)

I found this answer to be immensely helpful to me personally, thank you. Even though I marked another as the accepted answer, I just want to say thank you again.

No problem at all, glad to be of help. I hope you manage to resolve the situation!

Well, except that pretty much all PhD candidates are scutpuppies for their advisor's work.  Once you've got a specific thesis topic agreed upon, the work's gotta be done, and it's gotta be paid for.   The rest of your comments I fully agree with.

@CarlWitthoft That's not been my experience, but perhaps I've been lucky. Though I don't think it's controversial to say that there should be more to a PhD than just following instructions.

@CarlWitthoft no they are not. Many are, yes, but that's because their supervisors are, quite simply, bad mentors. A PhD should be a collaborative effort between the PhD student and the supervisor. Abusing a PhD student as a lab technician who has to follow orders instead of allowing them to go where their project leads them is unacceptable. Yes, it happens. Yes, it happens more often than it should. That does not make it OK and it doesn't make it normal.

You are two years into a four-year PhD, or perhaps you have completed four years out of six. It may seem long, but it's still early in your academic career.  It's not too late to quit and restart, and you might even be able to jumpstart into a new PhD position using the work you've already done.
That might be your best option.  Stop your current PhD.  Not abruptly, but accept you will have no more data, finish and submit publications in progress, and meanwhile search for a new supervisor/plan where you don't have to kill your conscience.  Your papers exist, and you have a valid explanation for a possible gap.
Change while you still can.

as a person that, 2 years into a 4 year PhD, has changed, I wholeheartedly subscribe the above.

Based on an older answer, OP is in the 4th year of a 6 year Ph.D.

...which doesn't really change that you are probably right in your suggestion...:)

I'm going to assume that this question is for real – that important research is being done, and live mice must be killed in order to conduct the research.
(Sorry for that caveat, but there's something rather fishy about this question, especially in light of Emilie's comment. If the O.P. was a newer user, I'd guess we were being trolled.)
Your question ends with:

we both know if I don't kill the mice, some one else is going to have to.

So why not have someone else kill the mice?
Part of this problem seems to stem from the early trauma you experienced by not being properly trained in the first place. So, lesson #1 for the research team would be to not make that mistake again. The advisor should admit that his callous attitude was a wrong one, and then help you solve the problem so that you can get on with your research.
Next, find someone who can kill the mice for you – perhaps even a student at the university. Train them to do it humanely. Explain the advances your research is expected to accomplish. Be more understanding than your advisor was with you. You might even consult with your university's psychology department, asking them for advice in training someone for such a grotesque undertaking.
If this course of action fails, then I'd be inclined to follow some of the other suggestions listed here: change advisors, find a new topic. But I wouldn't follow those routes until you at least tried to fix the problem in more constructive ways first. Otherwise, some unfortunate student is likely to follow in your footsteps and end up asking this same question two years from now, and then be even more shocked to find the question being closed as a duplicate of this one.

In many cases it would be unethical not to kill the animals after the experiments have been conducted. For example, some neuroimaging techniques involve injecting a virus to the animal's brain.

There is a course that scientists can take called the FELASA, however at the time I started my PhD (and I dont know what the details are now) it was not a requirement to simply kill mice, and then work with them postmortem. The more invasive experiments, the ones that really bothered me, well - I don't know. I dont know what is and is not legal. But all that aside, you make a really excellent suggestion - teach the new students to do it, under the knowledge that I really hate it and one day they will take over from me. My boss cant argue if I dont do it so someone else can get experience...

This isn't an answer for everyone in this situation, but it seems very much an answer for you.
As you present it, you have skills in bioinformatics and don't like wetlab work (my wife is a vegetarian who had to do lots of work with mice during her PhD, so I very much understand the view). These two facts alone seem to present a reasonable solution. Having spent time in the bio-science world, my understanding is that bioinformatics is in much higher demand than wetlab experience. It is hard for me to imagine that there is not another PI at the university that would be extremely happy to have a full time bioinformaticist, who never even entered the wetlab, in their group.

First of all, let me tell you that I'm sorry this happened to you. Animal experiments are a necessary evil, but this is not the way to go about them. And when you are so desperate as it comes across from your question, remember: your first duty is to yourself. Not to your PI, and not even to your PhD project.
Before you look for any other solution, take a step back and look at the big picture. Is this line of work (still) good for you?
Do this when you have a bit of time for yourself, in a calm environment (go to the forest for a walk, do some sport first or mediate. Don't do it while stressed in the lab and thinking "I can't take one more minute of this"). Imagine yourself in 5 years. You have finished your PhD, you are a successful bioinformatitian, and you picked a position where you never have to touch a mouse again. You sit in a clean office doing gene pathways analysis on a computer, say. And every time somebody brings you an Excel sheet with data from n=20 mice, you know that for each of these quadruple mutants, they had to kill 200 littermates because they did not have the right genes. Will you be able to distance yourself sufficiently from this information that you can still do your job without it flashing traumatic images back with you and eating away at your happiness day after day?
If your head wants to go on, but your gut is churning every time you see preclinical data, you can try to solve this conflict by exposing yourself to the other end of the matter. Your university probably has a clinic attached - try to find out if there is any way to meet patients (maybe volunteer to help with some tasks in a clinical trial under the guise of acquiring more understanding about translational research) or look up stories and videos on the Internet about people healed by novel medicine. It was palpable contact with mouse suffering which traumatized you, and palpable contact with the positive outcome, seeing gleaming patients who would have died if not for animal research, has the best chance of calming your revulsion.
Assuming you want to stay in the area, your best option is probably to change advisors. It would be administratively easiest to see if you can change to another PI within the same group (assuming he's not the prof himself), but might still bring some friction on the people level - it is up to you to know if there is a suitable other PI, how are his connections with your current PI, is your current PI a resentful person, etc. Else you may look into other groups at the same university, or even move to another institution - may be very well worth the hassle, and as a bioinformatitian, you are in demand, you should be able to find a position easily.
Why change advisors? You accepted an answer suggesting an ombudsman, and this may be a good route short-term so you don't leave in bad blood. But 1) if somebody outside your group forces your advisor to concede something he doesn't want to (e.g. allowing you to stop the experiments, or to write the PhD based on your current work only), he will be angry and resent you, making your work with him extremely difficult. And 2) He has clearly shown that he cares more about his experiments than about the wellbeing of his coworkers, even when the situation gets as extreme as yours. This is the epitome of bad management - really, you deserve a better boss than he is.
If you conclude that you will always have trouble if you continue in the job, do not despair. I know, at first it feels like a failure, having to let go of your dreams is very painful. But the sunk "costs" of 1-2 years of working on something you don't finish as planned are not worth suffering for the next 35 years of your worklife. And they are not that much of a cost, if you factor in the experience you gathered even without getting this PhD as planned. Also, if 10 years later you realize you need to change careers, you will be biting yourself in the ass for not having changed now.
Stop focusing on this one path (staying in this PhD as it is) and trying to endure the raging inner conflict. The immense stress in situations like yours frequently leads to tunnel vision. Look at all the other options and allow yourself to accept them as viable options. Don't fall into the trap of "I have to finish this PhD, but I can't continue as now, so how do I change this project to fit my desires" and your boss resisting each of your tries to change it. If you find a way to change it - and it needs to be a good way, not out of the frying pan into the fire - great for you. If you don't, get out of the project and do something which brings you forward, even if not in the direction you imagined until now.
I wish you best of luck!

My sympathies as I cannot imagine doing what you had to. If you are open to starting mostly from scratch as you'd still like a similar academic career, on top of bioinformatics that was recommended elsewhere, consider looking into computational neuroscience.
Your wetlab experience would ease your work with the experimentalists greatly, and should count in your favor when applying elsewhere. Commonly, all you do is take experimental data, and try to explain it (typically, from a stochastic or machine learning angle). In particular on the ML side, you'll code and run your suggested models to produce a fit. You never touch a mouse, and this doesn't change in the different stages of your career: as a Ph.D. student, you work with your primary (theory) adviser and experimentalist faculty who provides your data; as a Postdoc, you typically are the theoretician attached to an experimental lab (or join a theory lab); and as faculty, you are the theory adviser of the Ph.D. student stage.
If you followed the deep learning success this year of a computer beating go, say, the firm who did this is rather keen on those students who drop out of their academic career in computational neuroscience (be it as a Ph.D., or a Postdoc). Facebook is another example of a place to target neuroscientists; and within Google, there are other groups too, not only DeepMind. So there are also exciting outside options should you eventually decide against being an academic for life.
Best of luck!

The past experience has left you traumatized.  Yes, you learned to cope somewhat, but you really haven't gotten over the experience either (it is apparent from your speech and actions).  It is probably not a big deal, but having to keep at the same work is wearing on you.
In Biology, lots of above board but could-be unsettling things are done in the pursuit of knowledge.  Biology researchers and professors have to deal with the outrage against these unsettling things till they get jaded.  Since you self-selected this field initially, odds are there is a bit less sympathy (right or wrong).
I suggest you leverage your school counseling system.  A licensed therapist can help you with coping strategies, and if that is not enough, can help you sort out the core issues which might permit you to have clarity and certainty before continuing or changing your current academic path.
Once you can decide if you can cope through your PhD (which might be a possibility with better coping tools), it is easier to leverage that degree in areas that don't require the data collection techniques you are performing now.
From your statements, it seems that the professor has indicated that getting off this path at this time jeopardizes your PhD.  Odds are that professor is right, and despite how the professor delivered the message, the fastest path to your degree is likely to continue what you are doing.

I am sorry I didn't see this question before; the accepted answer is excellent, and hopefully you've gotten everything straightened out by now.  I do want to add two additional ideas, for you, if things are still up in the air, and for others who may come across your question.

There are telephone translation services.  So, if you're ever in a situation where you need to talk to someone in a language you're not fully comfortable with, and you can't find a friend or colleague to interpret for you, don't hesitate to use a translation service.  In the U.S., hospitals, banks, courts, etc., have a contract with companies that handle a wide variety of languages.  Your university may be able to supply an interpreter at no cost to you (either in-person or by phone).
It sounds like you've had a traumatizing experience.  If you were in the U.S., it might make sense for you to see a doctor for an evaluation; if a problem, such as post-traumatic stress disorder, is found, it might make sense for you to get this documented with the university's office for students with disabilities; at the end of this big chain of IFs might be some accommodations, and some assistance with working out those accommodations with your advisor.
I don't know what the analogous procedures and structures are in the EU.  But I bet there's something analogous.
I once asked about this on SE and never got an answer.  Maybe it's time for a bounty....

All of these answers are well thought, cogent remarks.  But what remains missing is a very straightforward question that you and your advisor should discuss:
Data collection aside, is this activity (sacrificing mice) critical to meet your academic and career goals? I had a similar, (yet decidedly more revolting) requirement, but argued successfully that my career goals did not necessitate that I personally do the job. There were others that could, and were happy to, assist.
If your advisor is difficult, he/she very well may remain adamant that you do the sacrificing.  But, if you sit down and calmly state your moral/ethical objections, alongside an argument that it is not integral to your academic development, you might be able to turn the tables.
Remember that most PIs seem to think that their students will become some kind of clone of themselves, and they want to prepare you to operate a lab just like their own.  From that perspective, of course you need to be able to sacrifice mice - that's part of the daily routine. His/Her statement that "this is what you are required to do as part of your PhD" perhaps anticipates this bias.
If you are unable to come to an agreement with that argument, I'd assume the only argument would be 'shortage of labor'.  But if there are others willing to complete this necessary evil in your behalf, I can't see a compelling reason why it must fall on you.
As for: OK, but "you won't have enough data for your PhD defense." -- at the end of the day, if its between quitting or lobbying for a reprieve -- double down.  Your PI has a vested interest in you completing the work, as you are most closely connected with it, and may bend upon ultimatum.  He or she may elect to take a deal rather than lose you once all cards are on the table.

If the project is important for the professor, one may ask a labor technician just to kill these mice, you taking over the remaining procedures. Of course, this is a high luxury to have a labor technician as an assistant for a PhD student, but should be possible if they do understand the need.
You can also ask to make this a shared project with some other PhD student. While it is not possible to get PhD degree just for killing mice, maybe that partner could also take over few other tasks and you would have the shared publication later.
Finally, as the competence of the professor is not questioned by this problem, it should be relatively easy to change the project, even by moving the to adjacent laboratory.

authors: Анна Катасонова


text:
Is it OK to send another reminder after prospective research leader stops responding to my email?
Long story short. I was look for some undergraduate level research for this July and August, so I contacted a professor like a month ago. Things went very well, and two weeks ago I even had a Skype conversation with one of their PhDs, from which I can tell that they are preparing to include me into their research group, because we talked about a lot of details like everyone's schedule, and they will presumably be my research leader in the future.
At the end of our remote meeting, the PhD told me they will send me a detailed schedule and research topic to me "in one or two weeks", and "feel free to shoot me an email in case I forgot about this". It has been over two weeks since then, so I sent an (extra polite) reminder three days ago, but I still haven't got any response yet.
Is it OK to sent another reminder to them? How long should I wait before doing so?
This is not a duplicate of How to get people to reply to emails and what to make of a no response?, because I am talking about a reminder to a previous reminder that is already sent. Also, the recipient is a PhD instead of a professor.

You can wait for another 1-2 days and send a reminder again. In the reminder, ask if there is any change in the prospect of the planned collaboration. You can also offer yourself to help with the situation, if they see you fit for this (even if the chances are small that you can actually help).
Of course, keep being polite (but do not over-do it).
Good note from @user2912328 in the comments: verify the correctness of the e-mail address of the PhD guy.
Note from me: please also verify the SPAM folder of your email. A friend of mine found (by mistake / luck) no less than 3 messages from me hidden there - while I was worried that he might be upset with me or something.

I agree with virolino. Wait for a few days more. People like me (a Phd student myself) are sometimes swamped with work. This is nothing against you or your qualifications but at the moment you are also work for this person so he/she might just not have had the time to reply.
Additionally, I'd double check if you have written to the correct email. Sometimes there are multiple persons with the same name at one University. Good luck with your research!

good one with verifying the correctness of the e-mail address. +1

As long as you remain polite, you can just send them a reminder now or in a couple of days. I would also suggest a phone call (if you have phone numbers, you can also call the group secretary) or contacting them through Skype.
All the signs are pointing to them wanting to include you in their research group; furthermore, researchers sometimes get overwhelmed with demands which leads to them not responding to emails that they really would like to respond to. I am reasonably sure this is happening here as well. If it makes you feel comfortable you can indeed, as per @virolino's suggestion, ask if there have been any changes in their plans.

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PhD study (University accreditation) and the ability to teach in the USA
I'm thinking of starting doctoral studies at York University (USA). I found this on the York University website information about accreditation:

YORK UNIVERSITY IS NOT ACCREDITED BY AN ACCREDITING AGENCY RECOGNIZED BY THE UNITED STATES SECRETARY OF EDUCATION

After finishing this doctorate at York University in the USA, could I work as a lecturer at the University or at others in the USA?
What is the general difference in the Universities accredited by the United States Secretary of Education, and those which are not?

Their "catalogue" is a one-page PDF listing degrees offered, including one in "Esthetics and Glory Science." Don't run. Fly away—and quickly.

Yet another sign: (almost?) all real US universities use a .edu domain, rather than .us.

Perhaps you should consider to study at the proper York University (outside of USA), which is fully accredited.

If the law doesn't provide a way for the real York University to prevent  this USA impostor from using its name, then the law needs to be changed.

For the second part of the question, the United States Secretary of Education does not accredit universities, but instead recognizes accrediting agencies which accredit universities.  The difference between universities accredited by recognized accrediting agencies and those not, is that Uncle Sam will never pay money to an unaccredited school.  You can not use federal financial aid or any veterans education benefits to attend York University.

Accreditation is supposed to enforce standards of quality in higher education institutions. If an institution does not have accreditation, then it is extremely suspect, and any degree you obtain from it is likely to be completely worthless. This is from the Wikipedia page on unaccredited institutions:

All fraudulent diploma mills are also unaccredited schools, although they may claim accreditation from an unrecognized agency. Accreditation from such organizations, known derisively as accreditation mills, is unrecognized by any government or reputable private entity, and any courses taken or degrees received from such a school are generally considered invalid.

As you noted, the "university" claims to be accredited by the "International Accreditation Organization". This has the hallmarks of an accreditation mill as described in above.
I would be extremely wary of this particular institution, and it is unlikely that any other academic institution would hire you on the basis of a degree from it.

York University is accredited by the IAO's (among others). Is this thing is worth?

@MarekWolny IAO is the only body they claim to be accredited by, and it is itself not recognised by any other body. That is, its accreditation seems to be worthless.

@MarekWolny I highly recommend you do not waste any time or money on this institution. Please look elsewhere!

The first hit on a search for "iao accreditation" was a list of fake college degree accreditation agencies.

Even if it were a legitimate accrediting body, the certificate says it's for "organizational management, business management, and business performance." I'd be wary of anyone presenting an accreditation certificate that doesn't mention anything about their education.

Accreditation does not enforce quality.  It is a protection racket.  When was the last time a low quality accredited school was kicked out?

@emory That's exactly why I said "supposed to".

@emory I agree that accreditation is poor quality control, but it at least assures that the institution exists and has vaguely appropriate facilities and faculty.  It does sort out a lot of scams, though unfortunately some scams still get though.   Your rhetorical question is just silly.  Did you really write that without bothering to google "college loses accreditation"?

So, I had a few minutes' fun looking up on how much of a scam this "university" is. It is nothing more than a diploma mill. I hope these few tips may serve as useful warning signs for other dodgy institutions. From the university's website:

Duration of the Program
The normal duration of the PhD program for full-time students is 6
  semesters (24 months). Course work of 18 semester hours may normally
  be completed in three semesters (12 months). The dissertation may be
  completed in the remaining 3 semesters (12 months).

No PhD program is that short.
Additionally, any "university" whose website does not have a list of its departments and academic staff should be treated with great suspicion. I can find no information anywhere about its research departments or staff.
This is what the address of the place looks like on Google Street View (401 Kamakee Street #312, Honolulu, used to be the home of the "Apeautique medical spa"):

This is a diploma mill. Any institution capable of awarding a bona fide PhD degree must have a proper campus with sufficiently qualified and reputable academic staff (especially when they claim to award PhDs in civil engineering).

The university you link to is pretty obviously a diploma mill, and you should run as far and as fast as you can in the other direction.  Do not give them any money, and do not believe anything they say.
Let me just say generally that an online Ph.D. program is a pretty dubious endeavor in any circumstance, even if the school is accredited.  The chances that you can really get the deep immersion in the subject matter you need without meeting personally with faculty and fellow students are quite low.  You should be very skeptical that one will really open doors for you.

Recently, the New York Times did an expose on Axact's large scale diploma mill operation (link). It looks like IAO (the accrediting agency) has connections with this company

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Are References Confidential?
I am a postdoc who has been supervising a Master's student, who is applying for a PhD. The application uses an online system, and I have been notified that I have been designated as a referee. In general, will this be entirely confidential, such that the student will never see the reference I have written? Or will the student then see my reference on their application, with the ability to download it and read it?
Of course, I could ask my institution about this directly, and also this may vary between different universities, but I am wondering what the expected rule would be. My university is in the UK.

Based on how things work in my own (UK) department: PhD applicants don't necessarily see their letters of recommendation. I think that those handling the application would solicit letters of reference from those who have been noiminated, rather than asking the applicant to provide them.

In the UK all references can be revealed if the student makes an application to the University under the Data Protection Act for a copy of their application record. The record would contain full disclosure of their entire file including all correspondence, including emails, and minuted discussions of the application. This would have to be a formal application and would accrue a fee.
Normally, in all other circumstances, the references would be kept confidential. Most UK universities would warn referees about the Data Protection Act when requesting a reference.

If you are asked to submit letters via an online interface, there will normally be some indication of whether or not the candidate has waived her right to review the recommendation at a later date. If the letters are to be emailed to someone instead, then it's possible that such a waiver has not been made; in that case, you should contact the individual or organization requesting the letter if you want to ensure its confidentiality.

Is it possible to waive your rights under the Data Protection Act? If not, I would suggest this answer is not applicable to the UK.

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What is "Honorary Lecturer" in the UK universities?
I was browsing some UK universities, and I was surprised by the number of 'Honorary Lecturers'. I understand a 'honorary professor' position, normally given to an outstanding scientist outside the academia, but I wonder how a junior academic position (like lecturer) can be given with honorary title.
First, I thought it can be a political figure or something like than rather that someone with scientific achievements, but suprisingly, I found it is VERY popular to fall in this category.
For example, 10% of faculty members in UCL School of Life and Medical Sciences holds the positions of 'honorary lecturer', 'honorary senior lecturer', 'honorary reader', or 'honorary research associate'.

In this link they explain the subject in detail
In general regarding honorary academic titles for non-employees it is written:

To recognise the association, the College may confer an honorary academic title on a non-employee during the period of their association.... The title to be conferred will depend on the level of distinction and qualification of the candidate.

And specifically with regard to "honorary lecturer":

Honorary Lecturer: Must continue in teaching, research or joint industry/academic activity to an appropriately high level

Since links can become invalid over time, it is generally better to include a brief summary of what you found at the link to provide a more complete answer.

@earthling edited to add relevant quotes


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Does an admission committee assess Verbal/Analytical Writing scores differently for International applicants?
I have always wondered how admission committees in the US look at the Verbal/Analytical Writing scores for international applicants.
English is my third language, although the primary language of instruction in college. As I have studied in an engineering field, some of the words I encountered in the verbal section are completely new to me.
My verbal scores are what one would call "average", although being an international student I felt I did quite well considering my background.

Admission processes in the US is not standardized so no one can give you a definite answer. Some schools may consider the fact that English is not the applicant's first language, some do not. Some of the institutions are a lot more transparent and rigid when it comes to the scores' minimal requirements and it wouldn't hurt to ask the registration person.
There is an extra layer of complexity as well: even GRE itself is not uniformly regarded positively by admission committee members. Some may give it all the weight, some may consider it a flawed method and would rather use a more holistic evaluation.
As a former foreign student in the US and now a serving committee member in my department's admission committee (in the US), my personal advice is if your GRE verbal and writing are low, try to have a good TOEFL score (iBT > 100, CBT > 250, PBT > 600) as a back up. GRE verbal is notorious for testing words that are extremely infrequent in everyday life (even academic life) and most members in my committee do not consider it a specific enough test for identifying if someone lacks English communication skill. However, TOEFL is designed to assess people with English as second language and its scope is a lot closer to day-to-day communication. We tend to be more lenient with international applicants with strong TOEFL, well-written statement, but relatively weaker GRE verbal and writing scores.
As for the analytical score, I have not witnessed a big enough difference that would hint a special consideration.


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Dropping out and parting on bad terms with my PhD supervisor
I need to take responsibility for my actions. I need to take responsibility for my actions. There was a behavioral incident. I harassed him. He doesn't want to speak to me anymore.
I will mention that recently I was diagnosed a year ago with both autism and borderline personality disorder (BPD). It doesn't excuse anything. This isn't even the first time this has happened in my life. It's terrible. I've lost so many jobs at this point. There have been so many behavioral and conduct issues with everyone and everything. I'm 28 years old. I'm not a kid anymore. One previous supervisor called me a terrible employee when he fired me. Yea, I have a therapist and professional support. But I'm so legitimately terrified now about everything. I feel like I should just go start over and work at McDonald's.
How do I explain this to future employers? What should I do? Does it matter? Does any of it really matter? No sane person makes issues like this in life. This isn't about some academic issue. It seems like it's just much deeper in who I am as a person. I'm speaking with the department about the best ways to move forward.

General advice: Don't make any big, committal decisions while you're in an emotional state of mind like this. Breathe deeply, take things slowly. First understand yourself. Have a clear understanding of what you did, and why it was wrong. Talk with people. Friends, others in the department, etc. You're clearly having a lot of complex emotions right now, and that's going to take time to work through. Give yourself that time.

Yes, thank you @isaacg . It's just so difficult . I have support with therapists and professionals. Unfortunatley, in my life, compulsively messaging and harassing people has been a big issue for the past several years.

Please clarify your specific academic problem or highlight exactly what you need from academic viewpoint. ... You wrote "This isn't about some academic issue."

I'll clarify that this is about what's best to do in moving forward from a professional perspective in the case of future employers inquiring about what happened.

Sorry to hear of your difficulties. As you say, "this isn't about some academic issue," and so it's not really something we as the Academia site can really help with. As for dealing with future employers, I recommend checking out our sister site, [Workplace.SE]. They have many similar questions in their archives, such as this one.

TIP:  Obviously, you need professional medical help.  However, for purposes of this site, I can tell you that if you can find a remote job, such as software engineering or even answering phones, there is much less stress. That said, it may be hard with your current track record but start small, maybe part-time or even volunteer.  If you have a circle of friends that can help, it'd be a great place to start.

Thanks. One thing I should mention is that I took a leave of absence last year (2022). During this time off, I did some volunteer research under another professor at another university, and he said he'd be willing to serve as a reference. This means I may  be able to avoid mentioning the PhD supervisor who no longer wants to speak to me.

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Can I request that my PI remove a poorly-behaving member from my research group?
I am a third year student at a R2 university that puts an emphasis on undergraduate research. This university requires all students to participate in an off-campus research project during junior year (after taking a qualitative research methods course and writing a project proposal the preceding semester). I completed this class with my research group a few weeks ago and am doing the project over the summer.
For my semester abroad research project, I was placed in a group with a student I am going to call Parker. Parker has fairly severe ADHD. Over the course of the preparatory class, they wrote a total of 6 sentences--four of which were plagiarized. For reference, the final proposal turned out to be approximately 40 pages. In our daily team meetings, they are constantly watching videos on their laptop. The group has spoken to the instructor of the preparatory course (not PI) about these issues and he seems fairly dismissive. According to him, Parker brings a unique perspective to the project which makes up for their lack of substantive contribution (to me, this reeks of BS). I could understand this position if Parker was consistently interacting with us, but they are not. Even during weekly group meetings with the PI they are playing games or watching videos. The PI doesn't seem to care either.
We've tried talking to Parker about these issues and it always ends poorly. In their eyes, we are "singling them out" and "not letting go of the past". I think this leads to everyone treating them with kid gloves. The first instance of plagiarism should have warranted at minimum a stern warning from the PI and department head. By the third they should have easily been booted from the class, in my opinion. Neither instance was even noted when I caught it and brought it up with the instructor. This makes me fairly anxious and angry, as I am aiming for a career in academia and do not want my record marred by coauthoring a plagiarized paper.
I'm at a bit of a loss regarding what to do about Parker's behavior when we are abroad. Our research involves direct interaction with the public, and frankly Parker has not shown me that they are capable of doing that in an appropriate manner (they insulted one of my classmates with a stutter during his presentation FCS). Given the pattern of our professor blaming the entire group for Parker's behavior, I'm extremely worried about what will happen if they get in a spat with a visitor or otherwise misbehave. I feel like I'm being treated as a babysitter.
The rest of my group (sans Parker) shares my position in all of this, so we have decided to draft a team contract to review with the PI before we go abroad. Herein lies my question. As a undergraduate students, how reasonable is it for my group to request to remove a student (with significant accommodations) from our research team should certain conditions be met? We will, of course, give a singular warning, but none of us want to work with Parker if they aren't going to act appropriately or contribute to the project. I signed onto this project to do research, not look after someone who can't be trusted to do the same.
If anyone has any insight into any part of my situation, I would love to hear it.

First, know that this is very common. Whenever you put a bunch of inexperienced young people to work together in a group, you will get the normal issues arising from people learning how to work as a team. You get people who want to be the "ideas person" and do no work (ie a designer, not a digger of ditches), you get the lazy ones, you get the control freaks, etc. Part of the job of being an advisor to a group of young people is teaching them how manage these issues, e.g. there will be no "ideas person" in this group, everybody has to work, how deadlines will be implemented, etc. It's concerning that the people in charge of training you have been dismissive.
Not only can you report Parker, but you should. There are many possible outcomes, all of them good: They can

Shape up and start working
Promise to change, not change, and get dismissed from the group.
Realize there's work to be done and quit right away.

In my experience dealing with dozens of undergraduate groups, I bet you a beer that they will choose #3. But you have nothing to lose and all to gain.

While I agree that you should report this to the PI, I don't these outcomes are by any means comprehensive. Another possibility is the PI doesn't do anything and you have to deal with Parker the whole summer.

The question was "can I request...", not "what are all of the possible scenarios?"


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Academic position salaries in the UK
In job ads in the UK, a range is often mentioned as a salary, e.g. from 30k to 35k pounds per year. What exactly does this mean?

Is the salary negotiable?
Does the salary remain the same throughout the contract/employment?
Is it increasing progressively?
When and how does one reach the upper bound? In permanent positions, what happens after the upper bound has been reached?

Also, is there a difference in the calculations between fixed-term and permanent positions?

There is typically a fixed pay scale (see the UCU page, for example), but where on that scale someone starts may be subject to negotiation.
Within each job "band" (lecturer, senior lecturer) there is progression up the scale on a regular basis (usually, and usually one point per year). Typically people are promoted from one band to the next before reaching the top of the scale, but in principle you would just stop. Different institutions may place the boundaries of the job "band" in different places, but the number quoted in the advert usually corresponds to those edges.
On being promoted to full professor different rules apply, which seem to vary by institution.
There is no difference between fixed term and permanent positions.
Often a probation period will apply - there may be different rules in that time.
The salary scales are not accurate for all institutions - for example, London salaries are increased to account for the increased cost of living.

Still, the last spine seems to be around 60k£/year, which is lower than german/swiss/canada/US counterparts, from the information I could gather, mainly from academia.se itself, which would be around 100k/year. Do I have the wrong impression or UK salaries are indeed lower?

Remember that doesn't include full professors at all, where the salary can go much higher. I don't have good data for other countries, but http://www.eui.eu/ProgrammesAndFellowships/AcademicCareersObservatory/CareerComparisons/SalaryComparisons.aspx has comparisons (that are nearly 10 years old), including weightings against cost of living. Anecdotally I believe US and Swiss salaries are much higher (but in the latter case so is cost of living) but German salaries are comparable or slightly lower.


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After an unsuccessful application for a permanent academic position in the UK, should I call and ask details about the selection procedure?
I applied for an permanent lecturer position in the UK and received an answer of the type "we regret to inform you...". My question is, should I call the university and ask more details about the selection procedure such as how many candidates were shortlisted, what was my overall ranking among the candidates, etc., or is there a typical number of candidates (e.g. 2-3? 9-10?) that are called for an interview?
I am asking because I guess this would give an idea about my relative qualifications and whether it is worth applying in a "similar" opportunity, or to stop applying for this level and aim lower for the time being, at least until I improve my cv.

Well, was it a top middle or low ranking University? Were they focused on reaching over teaching etc.. It might be that you are applying for top Universities and your C.V. is not strong enough. I know someone who had to apply for a "up and coming" University, in order to build their C.V. after getting rejected from the higher universities.

It never hurts to ask

A middle-tier university for the computer science domain, as far as I could tell; my point of reference is this http://www.theguardian.com/education/ng-interactive/2014/jun/03/university-guide-2015-league-table-for-computer-science-and-information-systems. I could not tell the focus because in the job specification was stating that the duties included both research and teaching. I would guess my CV is adequate because I saw in their site that there are lecturers in the university with more and with less publications than mine.

I should say that the title of your question does not really match the body. The title sounds like you are looking for data, the body asks whether it is appropriate to ask the people at the university you applied for.

Ok, I just rephrased the question title, thanks xLeitix

In my department, most of the people who apply for positions don't have a "ranking among the candidates". We don't make an ordered ranking of all the candidates.  Rather, members of the personnel committee look for candidates who seem especially good, good enough to be brought to the attention of the whole committee.

You can call and ask, but you are unlikely to get anything useful. You will most likely hear that your CV was very good, but that there were stronger applicants. If the head of the search is really good, they might actually look at your CV again and pick a weaker aspect of it (no matter how strong a applicant is, there is always a weaker aspect of the CV).
If you want to know about your relative qualifications, ask whoever is writing your references. If they do not know about the UK system, find a colleague that does and ask them.

@george yes, those people or anyone else who knows your work well and you respect.

When you say "ask whoever is writing your references", you mean the people that I have declared as references in the CV? I am asking because while I have communicated with them prior to including their contact details in the application, I have not asked them to ask a reference letter: no such thing was asked in the job ads and I figured that the university would contact them over phone or email in case they would like to invite me for an interview. This could be another question, but, since you mentioned it, should I also include reference letters with the application?

You should not include reference letters with an application unless they explicitly ask you to do so (which would be unusual).

You can always a wait a few months and see who was actually hired and what their qualifications were.


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Frequency of appointments with Ph.D. supervisor
I am a recent PhD student. My adviser is really a very nice, kind, and open-minded person. They are always open to discuss about subjects of my interest.
As I am almost at the half of my first year, my rhythm of working has evolved from making lectures to doing something concrete. So, I have started to contact my adviser more often in the last month.
How often a PhD student can see his supervisor? Is it really disturbing to send them some results to take their opinion every week? For the moment, my adviser does not seem to be disturbed but are there some "implicit" norms that have escaped me?

If you are in the US, taking classes, and not yet working on your own research, once a month could be fine. Just be sure that you are making progress appropriately. If you are working on your own research, a once a week shorter check-in meeting is better for both of you.

Anecdotal evidence: I meet mine every week generally.

My personal experience: my adviser and I meet every single day (whether I want to or not haha). We don't always talk about research or ask questions, but he does make himself available during our daily check-in, and if I have things I want to discuss I can bring them up. Our lab is considered somewhat abnormal with how often we see our adviser, and it's something of a joke in the rest of the department, but it's a really great system for us students!

I once read about a university rule stating that a supervisor has to meet his/her PhD students at least once a year. I saw real world examples who violated this rule.

The frequency that students and advisors meet depends a lot on the particular student and advisor, and also varies highly by time.  In my experience, once a month is quite a bit on the low side, but not unusually so.  A more typical pacing is once a week or once every two weeks.
The reason for this frequency is not for the sake of "norms", but rather is a good spacing for giving enough time for the student to accomplish something but not so much so that the student is likely to end up wasting a lot of time or becoming very frustrated going down a bad path that the advisor might have been able to detect and help remedy.
If your advisor is meeting with you once a month and happy with your progress, then perhaps you are simply doing very well at self-direction.  It is quite reasonable, however, to ask for more frequent supervision if you think that you will benefit, and as a new Ph.D. student, I think that you likely should do so.

Let me give you an answer from the "high side", just to remind you that Academia varies more than you think it does.
I typically meet my PhD students from three times a week to once a day, at least for a short meeting (or just for a coffee or lunch). Among the many reasons for such high-frequency meetings, I wish to highlight the following:

I see here on Academia.SE many PhD students asking questions, like yours, which really should be addressed to their own advisors. So, I make clear with my PhD students that questions pertaining our relationship and their activities should be first addressed to me, whenever the need arises, because it's my duty, as advisor, to answer them. Should I eschew from answering this kind of questions, they'd better call me "unadvisor".
There are fields, especially among experimental sciences, where a PhD student cannot work independently on a research topic, but he or she are instead part of a group which works on a certain number of already ongoing experiments. Frequently, these experiments should follow a certain schedule, especially when devices and instruments should be built by other co-workers, or when there is an ongoing international collaboration (e.g. devices and instruments might need to be exchanged between institutes at certain dates). Therefore, I want to be sure that PhD students can complete the assigned tasks on time, and correctly.
In certain experiments, mistakes are always around the corner and results need to be cross-checked between different people, even between senior researchers. Therefore, I want to cross-check the results from my PhD students as soon as the data are available.
Personal issues can lower scientific productivity (see e.g. How to handle pressure from collaborators when life circumstances make it impossible to get work done?): I think these kind of issues should be discussed as soon as possible with the advisor, and I ask my students to do so.

I really appreciate advisers with such restrict advising policies like yours. Your PhD students should be lucky indeed that are working with you.

Thanks so much for this clear response. As I am doing a theoretical study without experiments, my case differs a little bit I think.

I think the existing answers are quite comprehensive, but I want to reiterate that you should be asking your advisor what is expected. What I'd like to add is another example of how the relationship can vary.
With my advisor, we would often meet informally several times a day. This was often while critical experiments were happening, or just to bounce ideas off of each other. As my advisor requested for everyone, our lab as a whole kept this culture, where we all were available in the lab for each other. We were also welcome to stop by our advisor's office whenever something needed to be discussed, as he kept an open door. I found this to be very positive and enabled faster progress on our projects.


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How to avoid plagiarism when working on an idea not developed from a student who quit the PhD program?
I am doing a PhD in economics. I had an idea on an issue of my interest. With making some research, I found out that there was a previous student at my university, who did not finish his PhD, but he made an unpublished paper on the idea that I had, which has been presented at a conference, and it is not a working paper which is registered to any database.
Probably I will do something different, but build my stuff purely on this idea, but do I risk to make something just slightly different from his stuff? In this case, is it plagiarism and also unethical? How should I handle this case?

Upload that unpublished paper under the author's name here.

Why don't you contact the student who left, and propose him to be a co-author of the paper you plan to write?

Copyright draws no distinction between "personal documents" and "work presented at a conference".  Regarding Ryder's book, I find it implausible that he was copying text from Popov's preprint without permission.  It's much more likely that Ryder wrote chapter 6 himself but was giving Wess and Popov credit for some of the ideas and explanations he used.  (It's conceivable that Ryder got permission to copy some text, but there's no way Cambridge University Press would let him do it without permission, and I can't believe he just slipped this past his editor.)

It is easy to discharge your ethical obligations here: you treat the unpublished paper like you would any other source, i.e., citing it carefully and making sure not to rewrite sentences or rehash ideas without explicit attribution (include direct quotes if necessary, and probably don't include too many of those without a very compelling reason).
As you point out, the more serious risk is that you are starting thesis work on a problem on which someone else did a substantial amount of work on (though you worked on it independently) and that you may come out with little which is essentially new.  You're right that this is a risk: it's a risk for all thesis work everywhere.  Again my advice is to not treat this any differently than work that has been published: clearly you need to go substantially beyond it, or you don't have a thesis.  Whether the prior work of this other person shows that this is a fruitful area for you to continue in or whether it is evidence that all the good stuff has already been done is one of those tough calls that your thesis advisor should help you with.
Finally, of course it is a shame if two people have done good work on something and neither of them publishes it.  If it turns out that you do your thesis work on something else, then as a separate project (or perhaps better: a later project), you may want to explore a publication which is a synthesis of your work and this other person's.  Offering him coauthorship would be appropriate, but if he is really out of academia then it becomes a service to the profession for you to publish the work, while accurately conveying its provenance.  It's just that that kind of publication would probably not meet the requirements for a PhD thesis (and even if it did, it would not be a good launching of your career).

You cite your source and give proper credit, even if it is an obscure unpublished manuscript.  Your advisor shouldn't let you defend such a dissertation unless you really have made a substantial contribution of your own.

I would like to add that it is a good idea to try to obtain a permission from the former student to reproduce that unpublished paper. You can put it on your website say. Citing something that is impossible to find is only barely helpful to the reader.

It is not at all uncommon for ideas to hit two entirely different and unrelated people at the same time, and they work those ideas up entirely independently.
So, well-along in the process, you discover that someone else is doing the same work. This is not plagiarism.  I cannot begin to tell you how many patents are filed virtually simultaneously for the same design, developed entirely separately.  Ideas are wandering around out there, and if you had the idea, chances are someone else did too.
It BECOMES plagiarism if, now that you've seen this other work, you co-opt it and claim it as your own.
Your problem is to fend off the appearance or "stink" of plagiarism, because the other researcher was in a very close milieu to you, and it would be easy to impute that you had opportunity. My advice:  include an acknowledgement of the other work, with a brief precis of how it is similar and how it is different:  i.e. you arrive at the same conclusion via dissimilar methods.
The strategy here is for you to do the "entanglement" of the two ideas yourself, control how it is presented and perceived, as you and this other researcher co-attributed, following independent but similar lines, instead of letting the greater community decide something decidedly less charitable for you later.


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Forwarding Email of a future employer to my Supervisor. Broken code of confidentially?
I am applying for postdoc positions. A faculty member sent me an Email encouraging me to apply for his open position. He disclosed with me the name of two famous companies that are involved in his project. He also mentioned the name of a famous scientific problem he is currently working on, as a part of this project.
I forwarded his Email to my supervisor, asking for his advice on this position. Have I done something illegal, in terms of breaking the code of confidentially?

Why do you think there would be confidential information involved?

Because, the faculty has shared with me the name of companies he is working with. He has also shared with me the name of scientific problem he is currently working on.

Was the information you shared in the public domain already?

It is hard to imagine how a perspective employee could be required to keep names confidential.

I am not a lawyer, but unless you signed a nondisclosure agreement or made some other legally binding promise not to disclose the information, you almost certainly didn't do anything illegal by forwarding the email. Related: https://en.m.wikipedia.org/wiki/Email_disclaimer. Keep in mind that illegal and improper/unethical are two different things, so it's still quite possible that what you did will upset the sender of the email.

@Don Romik: What you explained completely makes sense, and brung me some relief!

In which country/state are you located? Laws differ between different jurisdictions. However, I agree with @Don Romik. His information applies to a majority of jurisdictions, and forwarding an email will not be considered any breach by a court, unless you did it with malicious intent, which then would fall upon faculty to proove, and they would simply loose.

Legally, no. Ethically, no. He felt free to reveal it to you, you felt free to reveal it to someone else. And nothing he revealed seems that earthshaking to me: Lots of people work on famous problems, lots of people work with major corporations.


text:
How should one handle peers, competition and other social pressure while studying theoretical CS/Maths?
I'm currently a 20 year old undergrad studying CS at a reputed institute in my city. I'm one of the very few from my batch who's interested in studying theoretical CS and mathematics (about 10 students from a batch of 200) and want to pursue research as a career.
Thing is, out of these 10 students, I'm the dumbest. I score the least in a graph theory exam, I cannot come up with creative solutions to problems in complexity theory as quick as they can (sometimes I keep on thinking for days, if not weeks, and still cannot come up with anything useful), I'm the student who the professor looks at and wonders: why are they here? To be very honest, I don't really like programming or web development. I like to spend time thinking about stuff, solving problems by hand, and learning fascinating things in logic and modern algebra. I'm weak at exams, true, but then I'm mostly clueless and disinterested in web development classes, where I can score easily but not learn something that I couldn't have learnt by watching tutorials on the Internet. I'm obviously looked down by my peers, too; and my grades are, well... not too great. In my current semester, I'm studying four theory courses (Complexity Theory, Graph Theory, Abstract Algebra and Cryptography) and one introductory CS security course. I'm going through the most difficult time of my academic curriculum so far; getting around 3-4 hours of sleep every day, with most of my day spent in attending classes and solving assignments. I'd like to drop a course from my current roster, but I'm afraid that since that'd show up in my transcript after I graduate, it might ruin my chances of getting into a respected grad school or landing a job.
I was recently diagnosed with manic depression, and while there are a few personal problems I have (premature balding, asocial lifestyle etc.) that might have caused that, some amount of the aforementioned issue might have also contributed to the cause. Anyway, I'm not asking for any consolation.
What I'm asking is: if anyone who's been through similar experiences while pursuing academia, how did you cope up? Even if you weren't like me (chances are pretty high that you weren't like me, CS theory/Math students are usually very intelligent), what do you advice? Should I stop studying theoretical CS due to my frequent failures? I mean, I don't believe in that kind of stuff, but usually if you fail too much at a certain thing, maybe that's some sort of sign or something? I don't really have a lot of friends, and no one from my family has received as much education as I have (so far), so I don't really have anyone I can ask for advice.

"getting around 3-4 hours of sleep every day". This is not helping. If you don't sleep well you will be dumber, cognitive abilities get impaired, and it is a vicious circle from there on.

I can't agree with @Davidmh enough. If you don't work as quickly as your peers, you shouldn't feel bad about taking a reduced workload. Sacrificing sleep to try to keep up will not end well.

Also, I was one of the bright, natural CS/Math students during my undergrad, and I can tell you it's not the best indicator of a good future researcher. In grad school and beyond, quick clever solutions get less common, and the norm shifts to solutions coming from patience and accumulated knowledge.

In addition to the great advice, I want to draw attention to one small line: not dropping a course because it would look bad to future schools. Challenge that assumption - I can find absolutely nothing to back up such a belief. Most universities have clear "add/drop" dates, and no special meaning is given. You are allowed to go, "eh, I'll take this course a different semester" without dirty looks or grand future consequence in every place I've ever heard of.

This is an issue in many elite programs. DO not compare yourself to others. People are different.

sometimes I keep on thinking for days, if not weeks, and still cannot come up with anything useful — So now you know what research is like. (Only sometimes it's months.)

I'd just like to add to this rather concerning paragraph: If you don't already do so, you should seek professional help for manic depressions - This is a serious condition. To the premature balding: Well, that is less serious and I can assure you that no-one really cares - But it gives you a nice excuse to wear hats/basecaps/whatever you like ;)

@Davidmh is right. When it comes to intellectual work sacrificing sleep daily to get more hours in is not a valid strategy. Frankly I'd consider if your depression might be misdiagnosed sleep deprivation.

If you don't like to code, but like the theory then I would suggest changing to a math based major (computational math, math theory, applied math). Being majorly disinterested in classes will not help you succeed and really it sounds a lot like you are setting yourself up to fail (whether consciously or sub you need to decide for yourself). Talk to a counselor at your school, they are there to help you through these things.

You're destroying your intellectual faculties with just 3-4 hours sleep.

First, slow != dumb (your words). In fact, these are two completely different cognitive processes. WISC, a widely used IQ test, measures IQ as a composite of four scores. Two of them are working memory and processing speed, which is your general ability to quickly solve problems. Another two scores are Verbal Comprehension index and Perceptual Reasoning Index, which measure loosely your problem solving skills and pattern recognition. Many score high on one, and not the other.
Some problems are hard, and it is very difficult to learn how to solve them. But, after solving (or understanding solutions to) many, many of them, you develop the feel how to approach a new problem. If you are passionate about the field, so much so that you have enough discipline to practice and work hard day after day, the results will come.
Last, take care of yourself. And you might want to read up on imposter syndrome, https://counseling.caltech.edu/general/InfoandResources/Impostor . A very common occurrence in academia, it is a mindset where people downplay their own successes, focus only on their struggle, fail to see others' struggles. For example, just from your post: you are more educated that the rest of your family, you have been admitted to a top school, are eager to tackle some of the most difficult problems, and have a very heavy class load. These are your successes. Give yourself credit for it. Focus on the struggle: you tend to call yourself names, and over-generalize several setbacks (bad grades), while seeing others in glorified way. A more constructive would be to look for a solution for your current struggle that takes an advantage of your strengths: maybe dropping a class, if you can, to give yourself more in-depth studying time.

Having taken the courses you mentioned in college, you feel about how I would expect someone to feel in your position.  If you feel you're overwhelmed its because for your workload you can easily be overwhelmed.  I agree with @Davidmh and @afaust on their points.
Also remember you're comparing yourself against 10 other students (who i assume) have similar interests.  If you were all equal, you might expect yourself to get the best/right answer 10% of the time.  So it would feel as though everyone else is always doing something better than you.  The only objective measure i see in your post is that you got the lowest score on a test.  Everything else is just feelings.
Also, think about the pool you're in. Say the baseline for your opinion of yourself was high school.  You went to a college where the bar for average people was raised. Then you went on to a program that sounds similar to mine so I assume the average raised more.  Now you're taking courses that are again challenging courses so the average raises more.  Judging by where you are now, I suspect you were at the top in high school and now see yourself as failing because you aren't 'the best.'
If you can't cope with the fact that you're competing with more and more qualified people, you need to dial it back a bit and get to point where you're feeling good again.  Other people may downvote this, but you should drop a course, get some sleep, and get your bearings.  Try the course next time its available.

+1 for "drop a course, get some sleep, and get your bearings. Try the course next time its available." Personally, I'm deliberately taking a lighter courseload than I could because I know it would be very difficult for me to manage additional classes. Knowing that I can do what I've signed up for allows me to be successful and feel good about school at the same time.

First: I wholeheartedly agree with the answers by Davidmh, afaust and Carlos Bribiescas.
Since your title asks about handling peers and your questions included "How do you cope?", I want to answer that aspect:
Don't see the others only as rivals. They are your peers and you are in this together. Think about joining/forming a study group.
I'm socially shy and a bit awkward, but my first year professors got me into the habit of looking for or forming study groups and whether I was the fastest or slowest student in my study group I always profited a lot by seeing other people's approaches, by learning to explain my reasoning and by having others help me stay focused.
I participated in study groups of 2 to 4 students for many but not all of my classes, and having a study group was a real bonus every time.
I did some classes solo and did well, but the material of classes I took with a study group came so much easier to me that I really can't recommend it enough.
One thing to keep in mind when doing study groups: Besides any questions you might have from the lecture, do discuss (and maybe solve) homework problems until you're satisfied that everybody understood enough to write a solution, but never let anybody take home any homework solutions from the study group - if you can, meet in an empty classroom, use the board, and erase when you're done. The purpose of the study group is to work on an understanding of how to do the problems but the actual doing has to be done by each student on their own, in order to get the practice in and also to avoid plagiarism issues.

One thing that impresses me about you, based upon what you've written, is that you seem to be able to handle more adversity than the average person. Unfortunately, you don't realize it. There are several very basic things that you should probably focus intensely on:

Stop knocking yourself because you are obviously stronger than you think. When you berate yourself, you are wasting time and being counterproductive.
Spend some quick and intense effort thinking about what kind of occupation you'd like. Spend some time looking at this resource.
Realize that you might very well be a "deep thinker". You reject easier, more superficial solutions quickly because you want to find the BEST solution. Many times, if not most times, "creative" solutions are in the eye of the beholder.

I think you have a lot more going for you than you realize. Sit back and, logically and objectively, analyze your situation.

A person says s/he is diagnosed with manic depression and there are a lot of very important details that might drive to a very unhappy state of mind. But the advice is to get some sleep and don't force yourself too much, be nice to yourself, you are beautiful.
Using these examples, I can tell you my own experience in academia (with a phd, did some post-doc bla bla) I had the same pace like you but my story ended up not so bitter as you might anticipate however ridiculously difficult in the making. I'm now kind of known internationally in some small circle and it came much after the time I was struggling desperately inside academia so I don't care now but once in a while I review a few papers for the fun of it.
This pattern probably going to be like this. While it might seem very attractive as you can get away with minimum human contact and sticking to your own imaginary world and enjoying algebraic constructions, academia unfortunately gets more and more socially demanding and on a subjective note with very unpleasant pretentious geniuses around you. After some masters or phd you will find yourself OK, what now? and then people will start saying well you should have done some networking too, or better talk to that department head, this professor and suddenly you would find yourself in a self-pitching game. Well the idea was to avoid that stuff WTF? Then your options would be much fewer than now.
Also it gets more and more demanding in terms of non-research like stuff, grants or teaching or this paper form, that email etc. So the initial kick that almost you get from other substances wears off very quickly. The internet is filled with grad student stories and most of them are not dealing with half of your challenges and still having those hard times. Do the math(excuse the pun).
So this utopia of oh maybe you would do amazing things is nothing more than buy a ticket, you might win the lottery. You don't even know what you might be working on. And that is the danger. You like the idea of research but you don't even know if you would like the topic or not. Imagine the frustration now and fold it many times if you get stuck in a topic that you don't like. On top of all those "succesful" people stress, you would be extra depressed that you don't want to work on bla bla.
My strong recommendation is that don't see research as a place where people let each other alone and it is relatively peaceful for introverts. It is definitely not. And if you can try to comfort yourself and achieve smaller things, having smaller steps and most importantly if you can keep yourself happier bit by bit, two steps forward a few back, 5-2+3-6+2+1-7 ... you get the idea, keeping the total a bit on the positive side then you don't need this stuff. You can think about stuff outside academia anyways. You can even make money as analyst or some other thing that you can utilize your analytical skills.
Lastly, instead of hanging out with the academia, you can use your thinking skill to create something that might lead to a path that you can walk on. Not some grad student's errands. And don't underestimate those Web development stuff. you sound like an academician already. Watch those youtube videos and try to do them then complain about triviality.
You'll see pretty clever stuff also in those things. Clever people are everywhere and even better; math people are still people. Open any bell curve look at it carefully. That small percent that on the right side still denotes the intelligent people. I've seen some math people in quite good institutions whose IQ might be somewhere between a paper weight and a toaster. They know the lingo for sure but what they do with  that information is still the same.
If you find out that you get your kick out of a specific topic then consider academia and find out if there is a demand for it. Otherwise do it outside academia. There are more people like you out there than inside the academia. I think this would make a nice problem for you about the distribution of the risk and your chances.

I had trouble following this answer.

The field you are known internationally in must be Rambleogy!