St Andrews Lynx

Whatever you do, don't treat this person as your enemy! Academia is a small world: your PI may decide to take 2 students after all, you may end up in the same teams for coursework, or you may put off the PI/lab members by being too mean and thus not get accepted. First - come up with a solid back-up plan for alternative rotations. It could be that you don't get on as well in this lab as you thought, or the PI's funding falls through and they end up not taking anyone this year. Treat all rotations seriously and be open-minded. Second - do the best you can in the rotation. It's not just about putting in the most hours or getting the most experiments done. You want to come across as a conscientious (future) labmate who tidies up after themselves, follows the rules, matches the group personality, etc. A lot of the decision-making for selecting new grad students is based upon personality, values and perceived fit, which is hard to change if you don't match up to what the PI is after and doesn't necessarily mean you're a bad scientist if they don't accept you.

There's a RadioLab episode from 2012 about lucid dreaming - the idea that you can take control of your dreams/nightmares while you're in the middle of them. That may be something to look in to. http://www.radiolab.org/story/182747-wake-up-dream/ It's great that you've sought professional help and I'm sure that over time you'll see the positive effects increase.

That set-up is fairly common in the physical sciences: 1st years spend their 1st semester either rotating through several labs, or doing what the OP has to do (sit in group meetings, talk to group, etc), then they pick their advisor at the end of the semester. In that situation I'd take plenty of classes. Talk to the current grad students anyway, even if they're not on your precise fellowship. It'll give you an idea about departmental culture and the classes that are worth taking.

The best way to put out a fire is to starve it of oxygen. If there's a student trolling for attention (which it certainly sounds like this one is)...minimise the attention you give them. It sounds like the only reason this student has joined the Feminist class is to be edgy and controversial - not because they need the course/grades or want to learn about the subject. Deal with them the way you'd deal with a student who is dominating the discussions. "Thank you for your contribution, is there anybody else who would like a chance to speak?" As a TA don't get side-tracked into arguing with this student, and don't let the other students get side-tracked into arguing with them to the point where the class is derailed. Don't act like you're shocked or upset by what they say - thank them politely for offering their opinions and move on. It's possible this student doesn't believe what they are saying anyway...but if they are, you aren't going to "save" them through force of argument. Follow what others have said about grading their papers or dealing with hate speech. But understand what they're really after...and don't give it to them.

Maybe incrementally. It helps when your letter writers are known to the admissions committee - their word in your favour counts for a bit more. But your advisor may already been known and respected at the other schools you are applying to. I wouldn't expect anything more than that. Now, if you want to do your PhD with your undergrad PI then my advice would to be talk to them directly. PIs sometimes get to have a say on applicants who are interested in working for them - but not at every school.

I'm a grad student at a public university. As university employees our emails aren't truly "private" - if there was some kind of ethics investigation (for example) we could have our emails examined as evidence. So yeah, I would never assume an email I sent is "confidential".

Forget about background noise from admins, parents, friends in the program who had a bad time: your advisor's opinion is the one that matters. Concentrate your energy on keeping on his good side and doing what he expects you to do. If anybody on the committee asks about delays to your writing, reply with 1-2 sentences accepting full responsibility (don't go into excuses or allocation of blame) and a polite apology for any inconvenience caused to them. I had kinda a hard time deciphering your post - what exactly is going on and what you are most afraid of. It might be helpful if in your own time you break this morass of fears/challenges into a list. Rank them by their power to affect your dissertation endgame. How are you going to deal with each individual hurdle? (e.g. parents getting angsty isn't going to affect your dissertation; so practice conversation-ending platitudes)

My understanding is that confidentiality applies to (i) what is in the applicant files (content of statements, proposals and rec letters) (ii) what the committee members have said about the candidates ("X is our top choice"/"Y has some red flags in their rec letters") during the decision-making process (iii) who has received a formal offer (prior to them accepting/declining it). The political stuff, which I agree should be kept quiet. More general information - which could be in the public domain already - I suspect is less confidential. It could be well known that this scholar is on the market and has been public about applying for your school. You also don't know what exactly your boss said to this grad student, and what the grad student inferred/misheard/assumed (they might be guessing that your boss doesn't like this scholar). You seem to be over-responding to a minor event. Your supervisor didn't go maliciously leak intel to this other grad student to undermine you. Even if he did...you can't let every slight in academia reduce you to a crying wreck.

At this point I'd try getting your Graduate Program Director or Program Admin involved. See if a "no credit" can be negotiated. Before that do your best to get the anger out of your system: be prepared to acknowledge responsibility and propose a concrete plan for getting back on track/meeting basic program requirements. It's usually a hassle for professors/graduate programs to fail out their students for messing up coursework. Lots of additional paperwork involved, etc. The upside is that it is possible to negotiate your way back from the brink, and for the admin team to want that outcome as much as you do.

Honestly, it does sound like you're over invested in this professional relationship. The dude is your boss, not your friend, and he doesn't owe you a particular emotional response. And yes, while you are important to him...you aren't necessarily the most important thing right now. I can see how if your advisor was stressed by work, having his advisee go off on a heated tangent about feeling under-appreciated/how he should conduct his mentor-mentee relationships...would be exasperating. It doesn't mean that he did a good job of handling the situation, rather you should let it slide if you generally get on well. I doubt he meant it as a personal attack. The relationship with my supervisor changed over the course of my PhD. They went from being hands-on (I'd see them on a daily basis) to hands-off (weeks without interactions). Sometimes people change as the nature of their responsibilities change...and you've got to adjust to that.

Three years is a long time. Focus on continually improving as a researcher & scholar, and don't worry too much about grades in coursework (those aren't the most important things in grad school). If your advisor says nothing, then my guess is it isn't a big issue for him.

The only thing I'd like to add beyond what has been said (excellently) above is with Point 3. It could have been that your advisor forgot he promised you meetings, or that they realised upon discussion that it'd be in violation of departmental policy/spirit-of-policy to meet with you. Or they have a busy semester with teaching/grant deadlines/conference travel so think it's unlikely they could fit in time anyway. I wouldn't think of it as "a refusal to meet with you", since that implies more negativity than what I suspect was intended. It is what it is.

If I was in that situation I'd take the free registration, introduce myself confidently as a postdoc and then feign TOTAL IGNORANCE if called out. "Oh, my boss Prof X handled my registration." (Honestly, given how cheap most academics are they'll probably be impressed with your ability to get something for free) If it only costs $20 to register as a non-student or something like that then just tell your PI you'll pay for the registration yourself. If it costs something like $200 and the PI would otherwise be paying for your registration...then either swallow the lie or don't go.

Have you applied or been formally admitted to the program yet? I can't quite tell from your post. I've you've not applied yet, the PI might be assuming you are going to apply to the Chem PhD program and then carry out biophysics-esque research in their lab. If you're applying/accepted to the Biology PhD program then as others have said you need to check if the faculty has a dual appointment, etc. There should be a graduate handbook and course listings online for both the Chem & Biology programs (you can also look on the Chem Dept website to see if your prospective PI is listed as affiliated faculty there). I suspect if your background is in Bio then the course requirements for a Chem degree could be challenging (or an unnecessary time sink), but there are often options to take classes in other departments that could count towards your degree (this is something you'd need to talk about with a graduate advisor/administrator).