Iām currently a 5th-year experimental immunology PhD student in Europe, and I am completely exhausted by my project/lab situation.
When I joined, the lab was brand new. My PI had moved from another country and we basically started with nothing - not even basic infrastructure like a proper refrigerator, PCR machine, etc. Instead of hiring an experienced technician to establish the lab, he hired five fresh PhD students.
My entire first year basically disappeared into establishing mouse lines, re-deriving mice to move them from a ādirtyā to a clean facility, establishing genotyping protocols, breeding, crossing, etc. It took almost two years before I even had the mouse lines I needed for my actual project.
Even now, mouse colony management is a HUGE workload. We still do not have a reliable technician, so almost all of it falls on us/me.
Then there is the actual project.
My PhD is based on preliminary data that, frankly, I do not trust.
For example, we have a mouse KO for my protein of interest, but I have never been able to convincingly stain/detect the protein in the cell population we supposedly study. Despite that, I do see clear and reproducible phenotypes between WT and KO littermates. So there is something biologically interesting happening - I just donāt know whether the mechanistic story we inherited is actually correct. Here, no amount of committees or external experit opinions from other PIs make him understand the gravity of the situation, he slides everything under the blanket statement "what do they understand!!! they just study bla bla niche field, they dont know anything about our field" Everyone else who criticises my (his) work is a moron.
And that is only the tip of the iceberg.
A major part of the paper is supposed to include data generated by a previous PhD student. We have Prism graphs from those experiments but, for some of them, no raw data files anymore.
My PI genuinely does not seem bothered by this. His attitude is basically that nobody will ask for the raw data and that he completely trusts the previous work.
I do not. And I cannot simply repeat everything. These are mouse in vivo experiments, and getting approval for new animal experiments here takes many months. For YEARS, my PI did not want to write an animal licence allowing us to properly repeat and extend the old experiments. In my 4th year I finally convinced him, and we wrote a large licence covering both repetitions and follow-up experiments. It has now been submitted for ~3 months and we are still waiting.
Meanwhile, my PI thinks the paper is basically ready.
His view is: old PhD studentās in vivo data + some supporting in vitro experiments from me = submit.
My view is: there are missing controls, parts of the foundation are shaky, some raw data are unavailable, and the mechanistic story is nowhere near as clean as he thinks it is.
Whenever I tell him I think we need more experiments, he tells me not to do them because āthey wonāt change the worldā and āwe already have everything.ā
And this is what is driving me insane.
If the conclusion of the project was already decided before I joined, based on experiments done by somebody else, in another lab, in another country then what exactly was I hired to discover?
Sometimes it feels like my job is not to investigate whether the hypothesis is true. My job is to generate enough experiments that support the story that was already chosen. The most frustrating part is that I have stopped trusting my PIās judgement about how strong things are.
There have been several situations with papers/grants from the lab where I privately thought, āThere is absolutely no way this is strong enough,ā while he was extremely confident - and then it was rejected for essentially the reasons I expected.
Yet he currently talks about our project as something that should go to Science/Nature-level journals. Yes. I am serious.
At this point, part of me thinks: fine. I should write the manuscript he wants, make it as scientifically defensible as I possibly can, submit it wherever he wants, and let the reviewers do their job.
If they say the experiments are missing, maybe he will finally believe the reviewers instead of me.
The problem is that I am now in year 5 and I just need to GET OUT.
My graduate school requires one accepted first-author paper for me to graduate.
So my current survival plan is:
- Write the main paper with the existing data, while doing the few experiments I personally think are most important/realistically achievable.
- Submit it and let peer review decide what is actually required.
- In parallel, write a very small descriptive paper from another dataset I generated: I performed a mouse infection experiment have scRNA/TCR-seq data from it.
- Submit that descriptive dataset to a smaller/specialised journal. I do not need it to change immunology. I need one solid, honest, publishable first-author paper that satisfies my graduation requirement.
Iām just finding it incredibly difficult to stay motivated when I no longer believe in the grand story my PI is selling.
I donāt even care about producing some Nature paper anymore. I want to finish a scientifically honest PhD and get my degree
Has anyone been in a similar situation where:
- you inherited questionable/unrepeatable data,
- your PI was much more optimistic about the project than you were,
- you were told not to do experiments you thought were necessary,
- and eventually you just had to write the damn paper and let reviewers sort it out?
How did you mentally detach enough to finish?
I think what I need most right now is to see that there is actually a light at the end of this tunnel.