My PhD supervisor had me do all my writing in pencil. I still do it to this day. Being able to erase is great, but I prefer the permanence and limitless space of paper.
Additionally, some research results should be stored in an immutable material.
(We called it 'ink killer' in school, you were however not allowed to use it the first few years after switching to ink from pencil.)
addendum: And you can get ballpens with the ink as well.
It's clumsy AF - the Excel part works, the Word part could be better - but it's a working solution of sorts, with everything synced across all my devices so I can make some notes on my Macbook while out and then pick up the thread at my desk later.
I tried all the usual alternatives - Trello, Org Mode, paper notebooks, real white boards, and so on - and so far this is the most productive.