When my supervisor pitched the PhD to me, it was all about analyzing "big data". I had BSc/MSc experience in wet-lab biology (mainly culturing cells), however I wanted to branch out into Bioinformatics since I am, and always have been, fairly good at programming in C, and data analysis in general.
I chose this particular PhD because the idea was we take a particular tissue from a mouse, run all kinds of different assays on the same pool of cells, and then create an analysis that would essentially get more information out of the data than any 1 assay alone could tell us, by integrating the data together in clever ways. That was the plan anyway.
What actually happened was that the protocol to get this tissue out of the mouse had yet to be developed, and without the tissue there would be no sequencing, and without sequencing there would be no data. So for the first year I had to roll up my sleeves (figuratively), and learn how to kill a mouse quickly and painlessly, to cut out and purify that 1 tissue I needed for sequencing. Again, in reality, this wasn't so simple. Although you don't/didn't need a licence in Germany/Europe to just kill a healthy mouse and take out some tissue (only to kill it in stressful ways, or if it's a mouse with a special phenotype), I feel you should still ideally be taught. Unfortunately, although other PhDs/Postdocs in my lab work with mice, I couldn't get anyone to teach me at the time, so the whole experience was pretty traumatic. I started off by filling up cages with CO2 (completely) and then putting the mice in, rather than what I now know you should do, which is to slowly increase the CO2. This will forever haunt me. I later learned to do cervical dislocation, which is better for everyone.
However, after I was able to sacrifice and extract the tissue I needed, I started getting asked to do more and more frankly grotesque experiments. Draining all the blood from a semi-conscious mouse. Implantation of electrodes. Cold room experiments. I can think of several more, but it's not really suitable for here. Of course this was all legal and above board - and important science that needed to be done - however I just cannot personally continue doing this sort of work. It all makes me feel slightly sick, and more importantly, I hate myself for doing it. What started off as probably 20-40 mice for the data I needed, is probably now at 500-600. Maybe more. I stopped counting.
But the reality I face now is that there are still 2 more years to my PhD to go, and I really don't/can't continue this for another 24 months. I have explained the situation to my PI, but he tells me quite bluntly - "this is what you are required to do as part of your PhD". On one occasion he said if I didn't do it, that's OK, but "you won't have enough data for your PhD defense."
That is total nonsense of course. I've already published and the data analysis - which I am now spending most of my time doing - has gone great. I'll be publishing some of the tools pretty soon too. The problem is that if I stop killing mice, my boss is going to really make things miserable for me for the next two years - and the end result of that might even be I'm asked to stop working on the PhD. I don't know exactly how or through what mechanism I would get kicked off the PhD, but my boss/PI is obviously a lot more senior than me and he's paying me every month (which he reminds me of, every month), and we both know if I don't kill the mice, some one else is going to have to.
What should I do?
EDIT: Out of respect for the German PhD system, I should point out that my supervisor isn't German - and I'm confident that another supervisor would have handled the issue very differently. Whilst I'm not confident it is an isolated case, I don't think in this scenario there was anything the Institute (or affiliated University) could have done better/differently.
Honestly, the take home message for me is that I wish I had asked this question sooner, had received all of the kind and encouraging words earlier, and then maybe I would have had the courage to do the right thing before it grew into something more difficult. Thank you all so much!
You are two years into a four-year PhD, or perhaps you have completed four years out of six. It may seem long, but it's still early in your academic career. It's not too late to quit and restart, and you might even be able to jumpstart into a new PhD position using the work you've already done.
That might be your best option. Stop your current PhD. Not abruptly, but accept you will have no more data, finish and submit publications in progress, and meanwhile search for a new supervisor/plan where you don't have to kill your conscience. Your papers exist, and you have a valid explanation for a possible gap.
Change while you still can.