

I don’t have any specific examples, but the standard of code is really bad in science. I don’t mean this in an overly judgemental way — I am not surprised that scientists who have minimal code specific education end up with the kind of “eh, close enough” stuff that you see in personal projects. It is unfortunate how it leads to code being even less intelligible on average, which makes collaboration harder, even if the code is released open source.
I see a lot of teams basically reinventing the wheel. For example, 3D protein structures in the Protein Database (pdb) don’t have hydrogens on them. This is partly because that’ll depend a heckton on the pH of the environment that the protein is. Aspartic acid, for example, is an amino acid where its variable side chain (different for each amino acid) is CH2COOH in acidic conditions, but CH2COO- in basic conditions. Because it’s so relative to both the protein and the protein’s environment, you tend to get research groups just bashing together some simple code to add hydrogens back on depending on what they’re studying. This can lead to silly mistakes and shabby code in general though.
I can’t be too mad about it though. After all, wanting to learn how to be better at this stuff and to understand what was best practice caused me to go out and learn this stuff properly (or attempt to). Amongst programmers, I’m still more biochemist than programmer, but amongst my fellow scientists, I’m more programmer than biochemist. It’s a weird, liminal existence, but I sort of dig it.



Something I find cool about this book is that it’s so well known that people who haven’t even read it will often gesture towards it to make a point. It reminds me of how “enshittification” caught on because so many people were glad to have a word for what they’d been experiencing.
It’s a useful phrase to have. Recently a friend was lamenting that they’d had a string of bad jobs, and they were struggling to articulate what it was that they wanted from a job. They were at risk of blaming themselves for the fact that they’d struggled to find anything that wasn’t soul sucking, because they were beginning to doubt whether finding a fulfilling job was even possible.
They were grasping at straws trying to explain what would make them feel fulfilled, and I cut in to say “all of this is basically just saying you don’t care what job you have, as long as it’s a non-bullshit job”. They pondered it for a moment before emphatically agreeing with me. It was entertaining to see their entire demeanour change so quickly: from being demoralised and shrinking to being defiant and righteously angry at the fucked up world that turns good jobs into bullshit. Having vocabulary to describe your experiences can be pretty magical sometimes