Would ending on bad terms with my undergrad PI ruin my graduate school experience/opportunities?

This forum made possible through the generous support of SDN members, donors, and sponsors. Thank you.

Latteandaprayer

Full Member
5+ Year Member
Joined
Sep 17, 2017
Messages
325
Reaction score
443
I don’t want to get too specific, but I think things are going to end badly with my PI. I’m staying here at this university for my MD/PhD, probably in the same field more or less. I’m going to try and keep things pleasant until I leave this June, but If things go south how much will that affect my PhD years? Would labs reject me? Would it follow me? My PI is friendly with all the faculty in his field, so I’m worried about it.

Members don't see this ad.
 
  • Care
Reactions: 1 user
I don’t want to get too specific, but I think things are going to end badly with my PI. I’m staying here at this university for my MD/PhD, probably in the same field more or less. I’m going to try and keep things pleasant until I leave this June, but If things go south how much will that affect my PhD years? Would labs reject me? Would it follow me? My PI is friendly with all the faculty in his field, so I’m worried about it.

Should not have an effect, unless the reason of your falling out was related to scientific integrity or honesty. Just don’t put your PI on your thesis committee.
 
Your PI will talk to people. Better to keep things as respectful and civil as you can (while doing whatever you need to do to move on). Best to talk to them now and set expectations. You don’t owe anyone anything (if you feel you owe them more work).
 
  • Like
Reactions: 1 users
Members don't see this ad :)
Sorry you're in this situation. PIs hold an immense amount of power over their trainees, even long after you've moved out of their lab. You will need a recommendation letter from this person if you apply for F grants and want that period of time you were in their lab significantly counted towards your research experience. If you stay in the same department for your PhD, you will be presenting department seminars and journal clubs with this person in the audience, where s/he and his/her friends can start grilling you on your background knowledge. You will have to be extra careful in who you choose as thesis committee members.

Obviously don't become a doormat, but there are very good reasons why trainees tread very carefully around their PIs and try their best to not burn bridges.
 
  • Like
Reactions: 1 user
Whatever happens 1) don't hinder or hamper yourself and 2) be amicable (though there are caveats to #2 in the sense of maliciousness... ie a PI doing something inappropriate to a student/trainee. In those cases, report it)

Best of luck.
 
  • Like
Reactions: 1 user
You have to get more specific in order for any of us to help you.
An experiment I’ve been trying for months has been failing from a technical standpoint (result looks physically bad, not that the data just disagrees with our hypothesis). I’ve been trying to troubleshoot it for months as well, reaching out to various labs on campus and in different countries to try and get some help. My PI is understandably frustrated with it, and has started accusing me of cutting corners and passing it off as me following the protocol. That isn’t true, so I offered to let him watch me do the entire 3-day protocol with him over my shoulder and I could even make a copy of the protocol so he can follow along with me. He said he couldn’t do that because of time, and I said okay, but lately these sort of accusations have been increasing in frequency and harshness. Like “How can you honestly say you’re following the protocol if it looks this bad?” and “Do you promise you’re actually following the protocol and not just trying to get out of here an hour earlier?”

I’m trying to keep things pleasant, I just smile and nod and say “I’m sure, if you want I can walk through the protocol with you to see if I’m making any mistakes” and the like, and I apologize for the frustration. However, I feel he’s either going to fire me or I’m going to quit because I can’t stand being accused of dishonesty and laziness when I’ve been putting in 50 hours a week and zoom calling people on my own time to figure out what’s going wrong. It’s another 3 months of this, and I honestly don’t want to come into work every day knowing that I’m going to get yelled at in front of my coworkers if it doesn’t look good again.

ETA: It sounds like I’m passing off all blame onto my PI, but for fairness it *is* a bad result and I am probably overlooking an important step or I’m just not good with my hands with this specific assay. It is obviously my fault that it isn’t working, but I’m not intentionally skipping steps or not being careful.
 
Last edited:
That sounds super frustrating. I wouldn't be so quick to put the blame on yourself however. I once ran a negative control that invalidated >3 months of data. Turned out that the specific batch of reagents I was using from sigma Aldrich was contaminated! That experience both highlighted the value of negative controls and the fact that sometimes an experiment just doesn't work and it's not necessarily your fault.

Is there a post doc or grad student who might have time to run the protocol with you to make absolutely sure that the protocol is being followed perfectly? With your PI, I would do my best to remain respectful and professional (even if your PI is not reciprocating) until you can officially move on.
 
  • Like
Reactions: 1 user
That sounds super frustrating. I wouldn't be so quick to put the blame on yourself however. I once ran a negative control that invalidated >3 months of data. Turned out that the specific batch of reagents I was using from sigma Aldrich was contaminated! That experience both highlighted the value of negative controls and the fact that sometimes an experiment just doesn't work and it's not necessarily your fault.

Is there a post doc or grad student who might have time to run the protocol with you to make absolutely sure that the protocol is being followed perfectly? With your PI, I would do my best to remain respectful and professional (even if your PI is not reciprocating) until you can officially move on.
We don’t have grad students or postdocs, I’m the senior member of the lab. My PI watched some steps when he had the time, and said that it looked fine. Obviously if those steps aren’t the issue then something else is.

I’m trying to keep things respectful, and I have no intention of “going off” on him or making rude comments. But I hate that he always does this in front of others, especially during lab meetings. It’s humiliating.

More importantly, I don’t want to end with him thinking I’m lazy and cutting corners, and telling other PIs that. What if they reject me, or treat me like a lazy researcher?
 
ETA: It sounds like I’m passing off all blame onto my PI, but for fairness it *is* a bad result and I am probably overlooking an important step or I’m just not good with my hands with this specific assay. It is obviously my fault that it isn’t working, but I’m not intentionally skipping steps or not being careful.
The situation you describe happens ALL the time.

You need to learn to "manage up" without being emotionally affected. This is one of the elementary skills required if you want to survive as a research scientist.

Here are the basic steps I recommend.
1) If you truly believe you followed the protocol correctly, the results are non-replicable. This happens all the time. Accept it as a reality.
2) Your boss is scared that his results are caught to be non-replicable.
3) You need to learn to be able to assuage people's fear, and avoid translating it into anger.
4) Non-replication is a technical issue. Either you made a mistake or the protocol itself has a problem that makes it hard to replicate, or the results were wrong or made up.
5) You need to calmly discuss with your boss and say, I'm trying my best for real, however, the results are not working out. The way you are talking to me make me feel like you don't trust me and are angry and are accusing me of being lazy, which I don't think the right way to solve this problem. Why don't we brainstorm to see which steps might be the weakest link, etc.
6) Your boss sounds like an ineffective manager, which is a dime a dozen in academia. However, your job as his trainee is to train him so that he can become an effective manager later.

Learn to fix interpersonal conflicts in a professional way is a foundational skill in science. If this is too hard consider getting some coaching.
 
Last edited:
  • Like
Reactions: 2 users
The situation you describe happens ALL the time.

You need to learn to "manage up" without being emotionally affected. This is one of the elementary skills required if you want to survive as a research scientist.

Here are the basic steps I recommend.
1) If you truly believe you followed the protocol correctly, the results are non-replicable. This happens all the time. Accept it as a reality.
2) Your boss is scared that his results are caught to be non-replicable.
3) You need to learn to be able to assuage people's fear, and avoid translating it into anger.
4) Non-replication is a technical issue. Either you made a mistake or the protocol itself has a problem that makes it hard to replicate, or the results were wrong or made up.
5) You need to calmly discuss with your boss and say, I'm trying my best for real, however, the results are not working out. The way you are talking to me make me feel like you don't trust me and are angry and are accusing me of being lazy, which I don't think the right way to solve this problem. Why don't we brainstorm to see which steps might be the weakest link, etc.
6) Your boss sounds like an ineffective manager, which is a dime a dozen in academia. However, your job as his trainee is to train him so that he can become an effective manager later.

Learn to fix interpersonal conflicts in a professional way is a foundational skill in science. If this is too hard consider getting some coaching.
You're right, thanks for the advice. This is something I'm gonna need to work on now and in my PhD years, since ideally I do want a research-heavy career. I'm mostly worried that he'll tell other PIs that I'm lazy/cutting corners, which might prevent them from accepting me or might make them distrust me if they do end up taking me. While I haven't expressed how my boss makes me feel when he does that, I have offered concrete solutions to the problem, like having him chaperone me during the protocol and discussing the steps in the protocol that seem to be critical and how I might be messing those steps up. I've gone into his office with the protocol and we talked about every single step, and we've tried tweaking some steps to see if they have any effect. I've always started conversations off with "I'm not sure what I did wrong this time, can we talk about the result, what's good about it, and how to make it look better next time?" (or the gist is that). I have never said "I don't know what's wrong here, because I did everything right and I made no mistakes."
 
Last edited:
You're right, thanks for the advice. I'm mostly worried that he'll tell other PIs that I'm lazy/cutting corners, which might prevent them from accepting me or might make them distrust me if they do end up taking me. While I haven't expressed how my boss makes me feel when he does that, I have offered concrete solutions to the problem, like having him chaperone me during the protocol and discussing the steps in the protocol that seem to be critical and how I might be messing those steps up. I've gone into his office with the protocol and we talked about every single step, and we've tried tweaking some steps to see if they have any effect. I've always started conversations off with "I'm not sure what I did wrong this time, can we talk about the result, what's good about it, and how to make it look better next time?" (or the gist is that). I have never said "I don't know what's wrong here, but I did everything right and made no mistakes."

You need to learn to be able to read people's feelings, assuage them, and effectively express your own feelings. The sooner you learn this the better off you are.
 
  • Like
Reactions: 1 user
You're right, thanks for the advice. This is something I'm gonna need to work on now and in my PhD years, since ideally I do want a research-heavy career. I'm mostly worried that he'll tell other PIs that I'm lazy/cutting corners, which might prevent them from accepting me or might make them distrust me if they do end up taking me. While I haven't expressed how my boss makes me feel when he does that, I have offered concrete solutions to the problem, like having him chaperone me during the protocol and discussing the steps in the protocol that seem to be critical and how I might be messing those steps up. I've gone into his office with the protocol and we talked about every single step, and we've tried tweaking some steps to see if they have any effect. I've always started conversations off with "I'm not sure what I did wrong this time, can we talk about the result, what's good about it, and how to make it look better next time?" (or the gist is that). I have never said "I don't know what's wrong here, because I did everything right and I made no mistakes."
I wholly agree with what @sluox has said and want to add that, unless he is making a completely unprovoked statement, I would also think about why he is accusing you of being lazy/cutting corners. If this is a him-problem (i.e. it's a totally baseless claim; he has a reputation for saying these things), then I wouldn't be as concerned about what he tells other PIs since your next PI/PIs can also comment on your work ethic. If it's something that your next PIs also pick up on, then that would be a little more concerning.

Side note: I went through a very similar situation as yours over the last 2 years (had successful experiments initially, but for whatever reason I couldn't replicate those experiments and tried tweaking it for a long time until recently when my lab manager and I successfully tweaked it - I was lucky enough to have a good PI who never accused me of anything and had me do other projects in the meantime as well). You aren't alone in this type of situation, and I hope that this doesn't discourage you from continuing the meaningful research that you are/will be doing.
 
The situation you describe happens ALL the time.

You need to learn to "manage up" without being emotionally affected. This is one of the elementary skills required if you want to survive as a research scientist.

Here are the basic steps I recommend.
1) If you truly believe you followed the protocol correctly, the results are non-replicable. This happens all the time. Accept it as a reality.
2) Your boss is scared that his results are caught to be non-replicable.
3) You need to learn to be able to assuage people's fear, and avoid translating it into anger.
4) Non-replication is a technical issue. Either you made a mistake or the protocol itself has a problem that makes it hard to replicate, or the results were wrong or made up.
5) You need to calmly discuss with your boss and say, I'm trying my best for real, however, the results are not working out. The way you are talking to me make me feel like you don't trust me and are angry and are accusing me of being lazy, which I don't think the right way to solve this problem. Why don't we brainstorm to see which steps might be the weakest link, etc.
6) Your boss sounds like an ineffective manager, which is a dime a dozen in academia. However, your job as his trainee is to train him so that he can become an effective manager later.

Learn to fix interpersonal conflicts in a professional way is a foundational skill in science. If this is too hard consider getting some coaching.

I have nothing to add but the above post is gold. I had a very similar conflict to what OP describes with my PhD thesis advisor and I would have handled it SO differently had I had some of the skills I learned a few years later in psych residency.
 
  • Like
Reactions: 1 user
I wholly agree with what @sluox has said and want to add that, unless he is making a completely unprovoked statement, I would also think about why he is accusing you of being lazy/cutting corners. If this is a him-problem (i.e. it's a totally baseless claim; he has a reputation for saying these things), then I wouldn't be as concerned about what he tells other PIs since your next PI/PIs can also comment on your work ethic. If it's something that your next PIs also pick up on, then that would be a little more concerning.

Side note: I went through a very similar situation as yours over the last 2 years (had successful experiments initially, but for whatever reason I couldn't replicate those experiments and tried tweaking it for a long time until recently when my lab manager and I successfully tweaked it - I was lucky enough to have a good PI who never accused me of anything and had me do other projects in the meantime as well). You aren't alone in this type of situation, and I hope that this doesn't discourage you from continuing the meaningful research that you are/will be doing.
As far as I can tell, he has no reason to be accusing me of this besides consistent failure that cannot be easily explained as a bad reagent or bad run. He is really good at communicating mistakes he sees, and has definitely made me aware of my own before, and this time it just sounds like he's out of ideas and is questioning if I'm telling the truth. That's fine, I understand it is frustrating, especially when he has to take my word alone. I don't have a history of covering anything up with him, and he knows I come to him whenever I make a mistake and admit to it. Nonetheless, I'll see if I can ask why he thinks I'm cutting corners (if he's noticed as a pattern, etc).

While I know my next PI may speak highly of me (or might not, which I would deserve if I do have a pattern of carelessness or corner-cutting), I'm worried about finding my next PI if my current PI speaks badly of me or says that I cut corners and lie about it or something.
 
Last edited:
While I know my next PI may speak highly of me (or might not, which I would deserve if I do have a pattern of carelessness or corner-cutting), I'm worried about finding my next PI if my current PI speaks badly of me or says that I cut corners and lie about it or something.
(disclosure, also an incoming MD/PhD student, but I've talked extensively with lots of PDs and mentors, etc.) I wouldn't worry too much, especially since you'll be an MD/PhD student and have the support of the admin as well. Also wouldn't recommend confronting about why he thinks you're being lazy/cutting corners (but that's just because, based on what you've written, I would probably just chalk this up to it being a PI thing vs. it being a me thing). I would, however, still confront him like how sluox suggested in step #5.
 
Last edited:
I would add that some of this may be beyond your control. He doesn't sound like a PI you want to do your PhD with, so that's good to know. He may still think you're lazy...etc, because he's projecting some kind of quality on you, and maybe little you can do about this. My impression from your posts is that you're internalizing his judgements/attitude and it is affecting you mentally. Remember, you're doing your best and you are learning.

Biggest lesson is pick VERY carefully who you want to work with for your PhD. Someone with a successful track record of mentoring grad students and postdocs (it is a bit weird that this PI has neither).

I wouldn't worry too much how would this affect your future. You're past the hard step and are accepted to an Md/PhD. Tread carefully around him for the rest of the 3 months and frankly I would avoid direct confrontation. Do well on your lab rotations and take it from there.
 
  • Like
Reactions: 1 users
I would add that some of this may be beyond your control. He doesn't sound like a PI you want to do your PhD with, so that's good to know. He may still think you're lazy...etc, because he's projecting some kind of quality on you, and maybe little you can do about this. My impression from your posts is that you're internalizing his judgements/attitude and it is affecting you mentally. Remember, you're doing your best and you are learning.

Biggest lesson is pick VERY carefully who you want to work with for your PhD. Someone with a successful track record of mentoring grad students and postdocs (it is a bit weird that this PI has neither).

I wouldn't worry too much how would this affect your future. You're past the hard step and are accepted to an Md/PhD. Tread carefully around him for the rest of the 3 months and frankly I would avoid direct confrontation. Do well on your lab rotations and take it from there.
Okay, thanks. That’s a relief! Honestly my PI was very supportive and nice when I was an undergrad... but then it flipped when I graduated and became his lab tech. I guess his expectations are higher now, or something.
 
  • Like
Reactions: 1 user
Okay, thanks. That’s a relief! Honestly my PI was very supportive and nice when I was an undergrad... but then it flipped when I graduated and became his lab tech. I guess his expectations are higher now, or something.

I can imagine that if you're the most senior person in the lab. He is probably dependent on you for results (that's really his problem) and frustrated for an investment he made, especially that you're leaving now. That's one hypothesis of course, but it is always very useful to figure out intentions.

You'll find that attitudes change drastically i.e PI wanted you to join the lab, but once you join, think they are all game to do what they want. This is very common.

The most important criterion is track record of mentoring. Try to get impressions of current grad students/postdocs of any lab you're going to join. There is a lot of politics involved. Nice doesn't always end up well.
 
  • Like
Reactions: 1 users
Okay, thanks. That’s a relief! Honestly my PI was very supportive and nice when I was an undergrad... but then it flipped when I graduated and became his lab tech. I guess his expectations are higher now, or something.
I mean, he probably did have different expectations between when you were an undergrad and now, after several years of experience. All that being said, sometimes science doesn't work out as expected. There is so much out there as published data that is not reproducible. It's unfortunate, but that's the way it is. It sounds like you've done your due diligence and reached out to others for help, but its quite possible (nay, highly likely) that the technique is not reproducible. I mean, people will literally only use 1 specific reagent or only perform experiments a certain time of year to achieve a result and even then, its not a slam dunk. You can't be faulted for that. If anything, it sounds like the PI has unrealistic expectations and frankly, doesn't seem that invested. I mean, if I had a grant or paper due and the experiment wasn't working as expected, I'd confirm it by doing it myself. After all, I'm the one applying for funding, not the trainee or tech. But they can't be bothered? Umm... yeah.

I think you should stay amicable as best as possible, do your best, ignore the useless "feedback" from the PI and move on with your life when you school starts back up.
 
Last edited:
Top