Toxic Academia | Part 10: Semester 7 — the climax of my PhD experience
The story in this post is why I started this account, and it’s long. You will see why being anonymous is very important.
If this is the first post you’ve read from the Toxic Academia series, thank you for being there. And welcome. While this series is intended to be read sequentially, I will do my best to make this post make sense as a stand alone. If you find this story surprising, disgusting, and well — toxic, I encourage you to read the whole story.
If you’ve been following from the beginning, thank you. It means a lot to have someone spend their time reading my story. I promise the build up and the context is worth it.
This is a long one, buckle up. I guarantee your jaw will be on the floor after reading this, so please hang tight. Grab some coffee, tea, a blanket, and romanticize reading a blog post about a fucked up experience.
A short recap:
I’m a PhD student in a lab of several women (love it — I am also a woman). My PI is toxic in that he acts on impulse and emotion, but for the most part we have a good relationship. I have too many projects going on, which are in collaboration with another university where I have a Co-PI called Eileen. Here are the characters in this story:
- Rob: Rob is a scientist in Eileen’s lab, and he and I are working Project Alpha together. He and I have a very good and transparent working relationship. I can be candid with Rob, feel heard and respected. Also, I have not mentioned this yet but Rob and I are close to finishing and submitting Project Alpha. Yay!
- Mike: Mike is a post-doc in Eileen’s lab, and he is friends with Rob. Mike has also been someone I can be candid with, and feel heard and respected.
- Alan: Alan is a post-doc in Eileen’s lab. He sent me an inappropriate picture one time, and after setting very strict boundaries, he has not re-offended. Alan is micromanaging and unorganized, he is also an expert in the field. I do not feel like Alan respected me for a long time but I feel like he does now.
- Elizabeth: Elizabeth is my lab mate, and she joined our lab two semesters after I started my PhD. She also has Eileen as a Co-PI. We work on two projects together: Project Omega and Project Mega-Omega together. If you’ve read my previous stories, you’ve probably realized that Elizabeth and I have very different working styles and values.
I want to introduce another character I have not mentioned yet — this is Megan. Megan has been a PhD student in our lab two years longer than me. She does the same type of analyses that Elizabeth and I do, but since she’s been doing it the longest, she really is the expert. Her Co-PI is also Eileen, and so she also has worked with Rob, Mike and Alan.
Here goes nothing.
Spring semester, 2022. We start in January.
Elizabeth and I had been working on writing up a manuscript to publish our Project Omega work together — or rather, I’ve been writing up the manuscript because she didn’t work on it. Okay she wrote one paragraph over the entire fall semester, I’ll give credit where it’s due. I mentioned previously that our PI had instructed me to write up Elizabeth’s portion since she had not been working on it, and in doing so I noticed some things she made mistakes on and redid them. I shared the first draft with her and made note of the changes at the end of last semester, and never heard from her all winter break.
Once February came around, our PI asked for Elizabeth and I to find a time to meet with him in person about the manuscript, so we can discuss the first draft. Elizabeth responds that she will be unavailable during the time he suggests and to “feel free to go ahead without me!” Our PI insists we all meet together.
Project Mega-Omega
Project Omega is a project with a few samples intended to be a pilot project, which I call Project Mega-Omega. We got the remaining data for Project Mega-Omega last semester. Elizabeth is analyzing one type of data, I am analyzing a second type of data, and Mike is analyzing a third type of data. Alan ran the experiments.
Just like how Elizabeth did not assist with Project Omega last semester, she has made very little progress on Project Mega-Omega. This makes certain parts of my analysis impossible. One weekend I’m preparing for a lab meeting update for Eileen’s lab, and Elizabeth and I are supposed to present together. I reach out to her via email and talk to her in person multiple times the week before, explaining that I need some of her results, and she never gives them to me. The weekend before our Monday meeting, I text her that I really need her results so I can do my analysis (time is running out) and she responds “Going forward please do not text or email me during the weekend”. Ok so that’s how it’s going to be… noted. I guess I’m on my own.
We have lab meeting on Monday (it’s March now). Everyone expects Elizabeth and I to present together, so it’s awkward when I have to explain that we are not today. I share whatever updates I can share, and it’s obvious I’m stuck because I’m waiting on Elizabeth’s portion. Well she’s presenting today, so at least I’ll get to see with where she’s at on her analysis. Except she doesn’t present any analysis at all. She shows two different apps, and presents to the group that the softwares do the data analysis that we do, without coding. She presents them as if she built them. First of all, these “tools” are for data visualizing, not for robust analyses, so the way she is presenting them is misleading. Second of all she’s showcasing these tools as if she made them herself when she did not. Thirdly our jobs and careers depend on us being needed, so why is she presenting these tools as an alternative to us doing the analysis?
I am so irritated. Elizabeth and I are supposed to be working together. She has consistently been undependable and unreliable. And now, she’s presenting some bullshit tools to replace us and acting like she made them. Someone asks about the tool she’s presenting that does analysis on the data type I specialize in, and she’s unable to answer the question, so she says “Oh I’m not sure, I’m sure my lab mate XX can answer.” Mmhmm. I answer the question, and I ask Elizabeth “Yeah, I’ve seen this tool before, you didn’t build this, did you?” she confirms she did not. Yeah let’s just clarify that at least. So again, no update on the project from Elizabeth. I need to find a time to talk to her about this, because I’ve been waiting on her for too long.
The next week:
It’s the day that we each meet one-on-one with our PI to provide updates. Which means Elizabeth will be in lab, and I can talk to her.
I absolutely hate confrontation. I get flustered, I cry easily, and I am not good at it. Elizabeth has been clear that she is not happy with me (at this point, I don’t understand why) and so I have a lot of anxiety about talking to her. It’s morning and most people have not arrived to lab yet. I go to Elizabeth’s office where there is one other graduate student present, and I ask if she has a couple of minutes. I explain that I am feeling stuck with the analysis, and I really cannot move forward without her doing her part. She explains that I can use the app she presented in Eileen’s meeting to get the data. The problem with this method is that we use a different set of statistical tests for our analysis, so this won’t work.
Trying to concede to the fact that she’s just not going to do the analysis, I say “Look I understand you’ve been busy, but I need to move this project along. Would you be willing to share the dataset with me and I can do the analysis myself?” I was not prepared for her response. She yelled at me, and said “No I will not share my dataset with anyone because I don’t want anyone redoing all of my analysis!” The other graduate student in the room looks up at me with wide eyes, and tears forming in mine, I run out of the room. I’m scheduled to meet with our PI soon, like in 10 minutes, and I am unable to compose myself before meeting with him.
I’m trying to process this interaction while the minutes pass by before my meeting. Now I know she’s upset with me for making changes to her analysis on the Project Omega manuscript. I touched on this before, the changes I made were small mistakes she made that I adjusted and remade the figures for. Because she became completely unresponsive over email, I waited until the first draft was finished, and then shared it with her and our PI explaining the changes I made — it wasn’t out of criticism, I just wanted to be transparent.
I meet with my PI and explain the situation. I tell him Elizabeth has not been doing her part, and I really need her results so I can finish my part of Project Mega-Omega. I explain the confrontation that just happened. He is empathetic, and says that he is going to ask Elizabeth to hand over the dataset to me so I can just keep moving the project forward. I thank him and go back to my office. Elizabeth is his next meeting.
It’s still morning when Elizabeth’s meeting with our PI is finished, and no one is in my lab office other than me. She comes into the room, and yells at me again. She says, “You got want you wanted! I’m done. I’m not doing this project anymore!” And storms out before I can respond. I pack up and go home.
A week goes by and I haven’t heard from Elizabeth and I don’t have her dataset. She’s not going to make it easy. So I do the thing, I email Elizabeth asking her for the dataset, and I CC our PI. I need some help from him. This is the response:
Elizabeth:
“That’s fine. I’ll transfer you all the data this week. Maybe we can discuss with [our PI] about not redoing each other’s analysis if possible.
Can you also share [your] data with me? I would like to try to integrate our datasets. There are new and improved tools to perform integration since you last tried.”
Me:
Sounds good, let’s meet with [our PI] to figure out the plan moving forward with the project.
Our PI:
This feuding has to stop. You are both in the right and you are both in the wrong, and I have no desire to be in the middle of it and more.
We’ll meet tomorrow at 10:30, and set a plan for you to work together to complete the study. It is clear that your personality differences will not support further collaboration, but you’ve come too far on this. I don’t think either of you understand why you’ve upset each other as much as you have, but first step is to see each other’s side.
So we meet. This meeting still bothers me to this day. It’s one of those memories that keeps me up at night, and makes my blood boil. This is how the meeting went.
Our PI confronts Elizabeth about her not making progress. She says she refuses to work with me anymore because I’m toxic to work with and I’ve affected her mental health. Tears are rolling down her face. At first, I feel sad, guilty. I think “oh my gosh, I didn’t realize how hard I was to work with her”. Then I start to reflect on how I could have been toxic. I did reach out to her multiple times, and on the weekend when it was urgent.
But then, I think about how she has treated me. She has yelled at me twice, I’ve never raised my voice at her. Am I being gaslighted? Because I feel like she has been toxic and affected my mental health. I had not mentioned this before in my blogs, but I was dealing with some really upsetting family situations in the last few weeks, and out of stress from everything I had started seeing a therapist and stopped eating — I lost 15 pounds in two weeks.
Flustered, all I get out is “I’m really sorry I made you feel that way. To be honest, I’ve felt like I’ve had challenges working with you because-” then I’m interrupted by our PI to say that Elizabeth and I can hash it out later. He doesn’t have time for this. Um, isn’t this meeting supposed to be about overcoming our issues, with you as a mediator? What continues to make me mad reflecting on this situation is that Elizabeth got the chance to say how she felt, and I didn’t have the chance to do the same. And no, we did not hash things out later. We end the meeting and the plan is that Elizabeth will give me her dataset by the end of the week, and she will no longer be working on the project — her choice, despite our PI urging her to continue. He even pulled out the “I’m your boss and you don’t get a say” card and she refused.
Is this the climax you’ve been waiting for? Oh, no no no. It gets much, much worse.
Friday afternoon that week
It’s the end of the week and I still don’t have Elizabeth’s dataset. Is anyone surprised? Anyone?
Our PI walks into our lab office and says “Hey, Megan noticed something in Elizabeth’s dataset. You may want to go talk to them — hopefully it’s just a small mistake.” Alarmed, I do. Megan and Elizabeth explain that they noticed one of the samples which was supposed to come from a male, is showing biologically that they’re female. That’s odd. The first thing for us on the data analysis side is to recheck everything — all of our labels, to make sure we didn’t make a mistake. It’s entirely possible, and with a dataset this big, understandable. Elizabeth says she will check the other samples over the weekend and I explain that I’ll do the same with mine. Megan then tells us a disturbing story about how on one of her projects with Alan, he gave her the sex of each donor and she noticed one donor’s sex did not match the data. Alan said it was just a typo. Later, he told her he accidentally messed up that sample. Okay these things happen — Alan is in charge of a lot of samples, and nobody is perfect. Hopefully it’s something we can resolve in our Project Mega-Omega data.
I check the sex in my dataset. Over 60% of my samples have the wrong sex. Did I really mess up labeling the samples that bad?! OMG something must be wrong with my code. I check, and recheck, and I check the sexes another way — no. And what’s worse, samples that were meant to be from the same person, are showing up to be different sexes. So for example, Sample 1 and Sample 2 are from Person A — but Sample 1 is showing male biology, and Sample 2 is showing female biology. It is all a big mess. Not only that, but we were meant to have 10 females and 9 males, but we have 11 females and 8 males, so it’s not even a matter of simple swapping.
This is very bad. Mike has data from these samples too, and his analysis is written up in a manuscript that has already been submitted to a journal. His data came from the exact same samples as Elizabeth, so if hers are messed up, his must be messed up too. I email our PI, Elizabeth (sorry it’s the weekend) and Megan the disturbing result I found. Before sharing this with our collaborators, we have to be really sure and have compelling evidence. Because if these samples are actually messed up, this entire $500k project will have to be scrapped. Our PI advises me to learn how to obtain genotypes from the data. It takes me a few days, but I do it. I compare the genotypes of the samples in my dataset — there are samples which look correct, in that they came from the same person and all of the genotypes match. But for the other 60% of samples, they’re mixed up. FUCK.
I meet with my PI and my Co-PI Eileen and show them the evidence of sample mix ups based on 3 types of evidence. Because I have the best relationship with Alan out of everyone (surprise, Elizabeth was unable to work with Alan), I should be the one to tell him. We need to give him a chance to sort things out. So I do. I email him, and I tell him the issues. I do my best to be diplomatic and state the facts, in addition to sharing the analysis I did to confirm that at the very least, my dataset is fucked. We meet on Zoom the next day, and of course he is very flustered because things are pointing to him making the mistakes. He tells me he has looked through all of his notes and spreadsheets and will continue to do so. I ask him to send them to me. This is a Friday.
Monday next week, it 8:30 AM and I run to Kroger to get some flowers because my lab mate is defending her thesis. After I check out, I hear someone say my name, and I turn around. It’s Alan. WTF. He walks out of the store with me and flustered, explains he normally shops for groceries here in the morning — I’ve been shopping here for three years and have not once ever seen him. I look down and see he has one bag with maybe some milk and a box of crackers. He is clearly stressed out over the whole situation and explains that he is very scared of getting fired and his career is ruined. I tell him we will figure it out, and hurry off to my car, shaking. Did he follow me here?
The Meeting
The cat is out of the bag. A Zoom meeting is scheduled with me, my PI, Elizabeth, Alan, Eileen, and Mike. Eileen’s husband is a PI in a other lab and he has been equally involved in the project as Eileen, let’s called him Ian. Megan also joins, since she can speak to Alan’s previous mix up of samples. The project Megan is currently working on with Alan was also discovered to have many more mix ups. The sex’s looked correct, but when Megan genotypes her samples, she found they were messed up too. By the way, we did the same analysis on datasets processed by others — publicly available data from other labs, and another scientist in Eileen’s lab, to show negative controls and how the genotypes should look. So Megan eventually brings this up in the meeting too.
I go over the issues and the evidence for the mix ups. We decide that we need to do the same checks with Elizabeth’s dataset, since they have the same exact samples as Mike, and Mike is getting ready to publish his part of the analysis on these samples. We try to discuss how this could have happened — I share my theory, and Mike gets very heated and says “that is impossible!” It’s heated and there are a lot of emotions. Ian also completely dismisses me. He doesn’t believe my results and tries to come up with reasons for why I am seeing what I am seeing without mix ups being the explanation. Mike and Ian are in denial. At the end of the meeting, Mike agrees to share his data with Elizabeth, and she does another kind of analysis to check her and his data. We also agree that I need to check Elizabeth’s dataset the same way I checked mine. Hopefully we can get to the bottom of this.
This meeting was very heated. I’m sick with how Ian and Mike dismissed the evidence for these issues. Their explanations do not make any sense and I feel that they are not handling this ethically. That night, I email my PI saying that I will no longer work with those labs (Eileen and Ian). It states:
I think it is clear I am not satisfied with the [other] group regarding moving forward with publishing the paper with concrete evidence that the samples are compromised.
I think today’s meeting has confirmed, in my opinion, that my values do not (and have not) aligned with the group. I would like to consider potential options for the remainder of my PhD, as I am concerned about my association with potentially compromised published work. I have given this a lot of thought over the past few weeks, so I want you to know I am not speaking strictly from emotion based on today’s meeting alone.
My PI encourages me to reconsider.
Checking… 1, 2, 3
Elizabeth finds the same issues in Mike’s dataset that she found in hers and shares it in an email that night. Mike confirms he independently did the same check and found the same issues Elizabeth found. I email our PI:
I am finding it to be difficult in this situation, derailing such a big project and Mike’s paper. After looking through last night’s emails this morning, it seems that Mike is accepting of the problems, I’m guessing he will pull the paper. Unfortunately, I firmly believe it is best for me to step away from this group.
First and foremost, I want to say that I believe Eileen was the most receptive in hearing us out, I want to credit her for that. I believe she is genuine and she is deserving, it is unfortunate that Ian and Mike were not the same. I felt the others were more willing to choose ignorance over due diligence, and the fact that we had to force their hand into due diligence, makes me feel the values in the group are unethical. Mike knew there were some problem samples in the beginning, but he did not share that with us until a few weeks ago despite us having the same samples. I find it hard to believe that he did not think to check the samples for this most recent manuscript. I suspect he either knew there could be a problem and chose not to check them, or he did check them and decided to proceed forward with the paper (I’m hoping the former).
I think any desire I would have to continue this collaboration would be purely to please Eileen, as I feel that she has been a victim in this. However, this is not enough for me to stay with her. She has not followed through on her promise on the [Project Alpha] paper, and I suspect it is because it doesn’t match the [previously relevant] publication which I am told, is also compromised science.
As you can see, more has been going on behind the scenes. Fortunately my PI understands and helps me pivot. But for now, I have to continue assessing the data to see the extent of the issues.
For me to do the same analysis on Elizabeth’s data that I did on mine, I need certain files from her. These are files which are generated after the first step of the analysis (from the raw data), which is a very long step. Turns out she deleted those files. Great. She will need to redo Step 1.
It’s been several days, and everyone is upset and anxious. Elizabeth has not redone Step 1, and I’m being bombarded with everyone asking me for the result. I’m going to be frank. Elizabeth does not know how to code. I don’t know how she made it this far, but it’s becoming more clear and I think this is why she has not been doing the project. And it’s clear she’s struggling with Step 1, but instead of asking for help, she tells me she’s not going to do it. I speak with our PI — and he says “Just do it, Elizabeth is just not good at doing this kind of stuff and it’s just easier if you do it.” Um, what? I’ve been doing 90% of everything. Elizabeth deleted her files, it is on HER to regenerate them. I have a very heated phone call with Elizabeth, where she again is refusing to do it. Furious, I tell her “No, you deleted the files, you need to redo it”. Eventually, our PI tells her she has to redo it. Begrudgingly, I help show her how and she takes it from there.
After pulling her teeth, Elizabeth finally sends me the files I need to evaluate the genotypes of her data. We confirm they are mixed up. Which means Mike’s data is mixed up. Which means his project, which has now been accepted by the journal, is messed up. I send the results to everyone involved, including Mike, confident he will be an ethical scientist and pull his paper before it becomes public.
Mike wants to meet with Megan and I. He shows us that he “cleaned up the data” in a way he feels is kosher. He explains that he wrote up a letter to the reviewers of the journal about needing to fix some things. Look. I’ve been analyzing this data for a long time, and a mix up this bad cannot be “cleaned up”, it just can’t. If it could, I would have cleaned up my own data because now I’ve wasted over a year on a project that was supposed to be a chapter for my thesis. Megan and I explain our concerns, and Mike ensures us that he will make sure that the published work will be correct before it goes live. He also hears Megan’s suggestion to get more samples and redo the project, since he already has the pipelines in place and can do it relatively quickly with confidently labeled samples. He agrees, and we sign off.
What just happened
There are a lot of emotions. Project Omega and Project Mega-Omega are canceled. The manuscript for Project Omega is cancelled, those samples were messed up too. Megan is set to defend her thesis in a few months, and a project she spent three years on is also canceled. I have 3 other projects in that lab. Project Alpha was thankfully not processed by Alan, and is okay. The two other projects that were processed by Alan were also found to have severe sample mixups, so those are canceled. In total, we discovered 6 active projects were ruined by Alan. After this situation, I never saw or heard from Alan again.
I just spent two years of my PhD juggling 4 projects, 3 of which were found to have mixed up samples. Why didn’t I check the genotypes sooner? Checking genotypes on this kind of data is not common, and besides, aren’t we supposed to trust the people processing our samples? I feel lost, depressed.
I find Elizabeth, and I want to just be okay. I tell her that I’m really sorry that I was difficult to work with and affected her mental health. I told her that I hope she could forgive me, and that I want to be friends and I don’t want there to be anymore tension. She also apologizes, she says that she’s sorry for how she treated me and she also wants to just be okay and be friends. It feels genuine, we hug, and a huge weight lifts off my chest.
But wait, there’s more.
A week goes by, its nearing the end of the Spring semester and Elizabeth and I are friendly. It feels like the storm is over.
Our lab is located on the floor of a building with a few other labs, and it sometimes feels like a small town with the way gossip travels. So of course, everyone has heard murmurs of the project scandal.
One afternoon I’m chatting with my lab mate, let’s call her Paige. It’s late, so Paige and I are the only ones in the office. We talk a little about what has happened, and I open up to her and explain that yeah it’s been obvious that Elizabeth and I were not getting along, but we finally made up and I am really happy about it.
Paige looks at me and takes a moment to respond. “Remember that really difficult coding boot camp class we all have to take? Well, turns out Elizabeth got caught cheating in that class, multiple times. And our PI knows but managed to keep her out of trouble. If I were you, I wouldn’t let your guard down with Elizabeth.”
What? How does she know?
“Elizabeth asked me for my code for that class, and I gave it to her. I remember that class being really hard and I was just trying to be nice but obviously I shouldn’t have done that. I know she cheated with my code because I saw her submissions — she didn’t even change anything on it to make it look any different! It’s so frustrating because I work my ass off for that class and got a B! I heard her computer science cousin did the last two assignments for her.”
Apparently, she cheated on multiple assignments and got caught by the TA using the autograder to assess the originality of the work. I’ve heard this story now from multiple people. The TA and the professor met with our PI and I don’t know how it happened, but our PI refused to allow any consequences to happen to Elizabeth.
I’m in shock. I remember Elizabeth asking for my code and I told her no — I’m glad I listened to my gut.
After all of the ethical issues arising from our project, how can our PI allow this?
There’s more that unfolds, a stab in the back. But that’s later.
Until then , remember that your gut is more trustworthy than the person who upsets it.
XX Rosie Frank
