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I've always taken handwritten notes in class. It forces you to condense the information being presented quite a bit.

I've found that I use arrows, side boxes, lists, and all sorts of visual tricks along with writing to try to grasp the concept.

It's only my personal experience but it's always seemed to be more effective than trying to fuss with a laptop.

Handwritten notes allow you to use different modalities to interpret information, which promotes deeper understanding.
I don't know if it is because how I was raised or a limitation of my brain but past a certain difficulty of problem I am completely unable to solve it without pen and paper
Pen and paper don't need to be fought with to extend our brain's visual and mapping abilities. There are almost no friction to put thoughts down. It's much slower than imagining things but it doesn't rely on short term memory so we can build and think about more complex abstract thinking.
Type slowly and thoughtfully instead. Draw diagrams using an appropriate tool. Handwriting is tedious; pointless; painful to learn and bad for your hands.
> Handwriting is tedious; pointless; painful to learn and bad for your hands.

Can you cite any evidence for this claim?

I journaled daily for over a decade without any stress injuries whatsoever. In contrast, heavy laptop usage for a few years lead to severe RSI damage I'm only now recovering from.

For both keyboarding and handwriting, the stress can be high or low depending on your technique. Many people write with cramped hands, which is hard on them if they do much more than sign credit card receipts. But if you write with light pressure and a gently curved wrist, you can write all day without pain.
Handwritten notes are much more effective when having conversations and taking notes. Programmers often pull out their laptops or phones when talking with eachother, but when talking to scientists, they always seem to use paper, and so I've taken up that habit as well. (using bullet journalling mostly)

I then transcribe into a collected note markdown document in github, which forces me to complete the first spaced repetition of the information, which is a huge help in remembering it.

Then, I keep all notes in one document, so that when I review todos for the day, I have to scroll past / search through the other ones, completing more spaced repetition cues.

Is typing bad for my brain?
The only bad part of typing is it seems to allow a quicker conveyance of thought to word, which starts to make it sound like speech rather than concise text.

When I'm writing a note by hand, I tend to use BLUF or TLDR mode with bullets for supporting points. When typing, I can just about hit stream-of-consciousness rates of symbol transfer, which means I need to edit 2-3 times to get a concise email or document.