You know, you would think for something as basic as writing down what you're doing there would be an optimized way passed down like some sort of tribal knowledg

You know, you would think for something as basic as writing down what you're doing there would be an optimized way passed down like some sort of tribal knowledge. But from having asked around, the note taking process spans the entire spectrum from old school big research notebooks, collated three ring binders, instances of mediawiki, evernote, to just a bunch of .txt files scattered throughout their filesystem. However Evernote is probably the most common--being able to easily copy-paste plots and images seems to ease a big pain point. For paper notes, I know exactly what you're talking about. I think such a non-linear problem can be solved with different note taking methods as "short, medium, and long-term storage". I find my research notebook useful as a dated "what am I doing right now", free-form input useful for equations and diagrams, and short term to-do lists (which are more useful for outlining the steps needed to actually get something done). However, it's not very easy to lookup info by topic and it's time consuming to write out detailed explanations in long-hand. I haven't had much luck with the bullet journal system or similar because it's just hard to keep those indices up to date. At this point I find it most useful to type up the "cooked" knowledge into vimwiki at various points. These semi-fully formed digital notes can then be used as the building blocks for the "long-term storage" of more durable works like journal articles or papers.