I'm changing PhD programs, and I got a terrible recomendation letter form my advisor. I found out by accident. What do I do now? I'm shocked

Question

I’ll try to not be too specific for the sake of anonymity. I’m a STEM PhD student at one of the top-15 universities in the US. My own advisor said that I did great academically and made good progress on a hard research project. I also passed my candidacy. But my project turned out to be pretty unrealistic, and on top of that, I had a lot of personal issues that were out of my control. Because of that, while my research progress was fine, my performance was chaotic in terms of making quality presentations for regular reports (for my advisor) and meeting deadlines. I was also kind of a lone wolf in terms of how I worked: I still talked to people and asked for advice from other lab members as well as helped them whenever they needed help, but I guess that’s not the impression my advisor got since he only saw a small part of of it all.

Anyway, I’m applying to other PhD programs now, and he already submitted his letter to like 75% of the schools I was gonna apply to. One professor from a school outside the US was so shocked by the letter, he actually reached out to me and warned me. Apparently, the letter says that my advisor kicked me out, briefly mentions that I’m “smart and hard-working”, and then, goes on to list all my flaws and ends up saying that “I might deserve a chance to try my luck at PhD at least somewhere” and that my advisor “has reservations”. That’s shocking because he told me he’d focus on the positives and that he never writes negative rec letters. It sounded like it would be mediocre or even mildly good, but this is downright horrible. The letter doesn’t even say he actually recommends me, so I guess technically, it’s not even a recommendation. That can’t be ethical, can it? I’m not from the US, so maybe, I’m mistaken.

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

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

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

Edit 1: I was kicked out from the group, not the program. I'm still technically working in his group unofficially (on a new research avenue that I had proposed an that he agreed was a good idea) to get at least one paper out of it. But I'm still officially a PhD student. But all the other labs at this university are either not working in my subfield, or they are full. That's why I'm leaving the program on my own terms (technically) and applying elsewhere. I should have specified it, sorry.

Edit 2: I asked "Will this be a bad, medium level or good rec letter", and he said "Well, I don't write negative rec letters. I'll focus on the positives because no one is arguing that you're smart and hard-working and all that, but I'll have to mention why you're leaving if they ask". To me, that sounded like it would be a mediocre letter at worst and a pretty good one at best. If I hadn't asked, I wouldn't have doubts about the ethics of it all. I just expected him to be a bit more upfront. Normally, people refuse to write rec letters if they cant write strong ones. This one isn't even mediocre...

Edit 3: He was super friendly to me, so I don't think I made an enemy. And if I did, I didn't even know that.

Answer 1

I think you've learned you cannot use this person as a reference. It's unfortunate you learned when you did; there is probably nothing you can do to retract these letters and I'm not sure it benefits you to try.

I'd expect some mixed response to a letter like this. Some people are going to feel it's a huge red flag about you and appreciate the "head's up" from your advisor. Others, like the person who warned you, may feel that a letter like this actually reflects poorly on the writer as much as the applicant, and may consider it in the context of all your other application materials.

If you do successfully reach the interview stage for any program, you can expect this letter to come up. I'd recommend addressing that situation as gracefully as you can, acknowledge that you've heard about the contents of the letter from other recipients, state that you were surprised by the contents, and then do your best to explain the situation you find yourself in from your own perspective. I think it will reflect best on you if you're able to take responsibility rather than give blame for your predicament (whether or not that's entirely fair), and be forward-thinking: focus on how your accomplishments and your struggles to this point have prepared to to be successful in this new PhD program.

Overall, though, I do think your prospects are a bit grim unless there are other professors you trust that can give very strong recommendations in your favor and possibly vouch for you through less official channels. Graduate admissions is quite a dice roll: admissions committees try to dig through the entrails of an application to find some hint that one candidate or another is likely to be successful in the program. Amidst all these unclear signs, yours unfortunately has one clear data point even without this letter: you've been in a program before, and it didn't work. Offering you a position isn't necessarily about making a decision about whether you're likely to succeed given another opportunity, it's about making a decision about whether it's better to admit you over another very promising applicant who hasn't had the chance yet.

Answer 2

Sorry you are going through this. Life can be unfair at time.

You ask several parts and questions in your post:

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

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

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

Sorry, but it is ethical. In hindsight, ask if the person will write a positive letter of recommendation. Not necessarily kind, but ethical, sure. If they truly think what they are writing is true and not doing to be vindictive. No way you can prove the previous point one way or other nor is there anybody you can reasonably argue the point with for any outcome that would help you.

Also, some countries give more negative references than others. Search this site for examples of this different cultures. US tends to be positive only or omission of negative traits, but some people like your advisor give negative letters.

Edit: It is ethical to write negative letters. Saying one would write a positive letter and then writing a negative letter is not ethical. But, there is likely nothing you can do about it.

So, your other questions:

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

First, breath and seek out some outside perspective. It's not the end of the world. Find someone you trust who can help you process this. Ideally, someone who is not a another grad student and has perspective. Perhaps a therapist at your current school or another committee member. Perhaps a professor in your department you trust that you know from classes. This is context specific and we cannot help you online with the specifics.

Second, yes, make sure you tell a coherent "story" about why you are changing programs in your letter. Get references from people you trust.

Third, if you're leaving your program, people will know you're not a good fit. It's up to you to tell them why and have references who support your story. There are several other similar questions on this site that can help you with this.

Fourth, individual applications are school specific. You would need to checkout those programs systems to see.

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

I would do this if you can.

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

I'm sorry to hear this happened to you.

Edit based upon additional comments from the OP: You were kicked out the professor's group. In hindsight, do not use them as a reference for anything.

And, you also need to tell a story of how the new programs would help you and you would fit in. Ideally, you would have professional contacts in similar lab groups at other universities and one of those professors might be willing to take you on.

Or, you might need to consider a non-academic career.

Answer 3

my background - industry for 20+ years. Friends in tenured academia positions.
One of the first things you may want to do is use a site like checkmyreferences.com to see what's going on as an overall picture. This also would allow you to check other references to verify that they are as solid as you think are. People can be funny in that they will say one thing (IE avoid conflict) and do another (you asked for a recommendation and I don't really want to say them No). You admit to being a lone wolf, if you don't work well with others, its not the end of the world, however most places don't want lone wolfs, they end up being a PITA and unless you can be a superstar doing your work, it won't be worth most peoples time to even interview you.

Did your advisor know about your personal issues and how/why they were impacting your work product? While you don't necessarily have an obligation to share your personal details, when they impact work like they have for you, its helpful to have people understand why you are acting and performing the way you are, especially if its not your norm. Otherwise people can only (and will) draw conclusions based on what they see you do and how you interact.

You have a major set back here since your advisor is basically providing a dis-recommendation for you and they are your immediate supervisor. You may have to look at how you can get into their good graces and how could you rejoin the group. IE What can YOU do to fix your advisors opinion so they write a recommendation that helps you move on.

You may need to approach your advisor and discuss some of the more obvous issues, ones that either they tried to address with you already (hopefully they did?) or noted verbally to you. IE whatever is in the discommendation that you theoretically would already know and wouldn't indicate that you now know the contents of his discommendation due to another professor sharing them with you.

Lastly you may need to take a year or two time hit, to put something in your subfield or similar between you and this advisor. IE distance yourself so that you can rebuild your professional reputation.

Ethics- i would be unethical to write a recommendation that was not honest and representative of how the advisor perceives you. Its just poor form to say you will write a recommendation and then write (based on your info) a discommendation. Generally in the US recommendations are understood to be "recommends" you for work. It should be balanced and fair, however should generally be positive leaning.
I've had to say no to several people who were expecting a recommendation, and I told them I couldn't in good conscience write one given their overall performance.