"Write by hand and mark up your books" is excellent advice... that I no longer follow.

Marking up books didn't come naturally to me, but I did it for a while. Paper books are just decaying bundles of plant fiber — and the ideas within them are likewise ephemeral. The illusion of permanence must be confronted and reckoned with.

But for the last 15-20 years, I have been taking notes in text files that are saved to version control, which I find suits me better.

* Notes are not space-constrained by the space of the page margins, nor by the initial form they take on the paper page.

* Notes can be revised at will without requiring complete duplication to maintain optimal appearance and organization. There is no reason to resist revising notes — the history is completely preserved in old versions, so nothing will ever be destroyed even if deleted. Even though those old versions will almost certainly never be revisited, knowing that they exist frees the mind.

* I can indulge my perfectionism and write math notes in LaTeX, music notes in Lilypond, diagrams using SVG... The act of typesetting is itself a form of active engagement the source material, although it does not have all the advantages of hand-copying and can be time-consuming.

* Digital notes take up no physical space, compatible with a minimalist lifestyle. They can expand infinitely without needing to be stored or carted around.

* Digital notes don't need to be defended against physical threats such as fire, flood, or vermin. However digital notes still require precautions to preserve them in the form of a backup regime, so this is something of a wash.

* Ultimately, I don't expect anyone but me to be interested in my notes, and I don't owe anyone my notes. When I'm gone, the notes will vanish into nothingness — and since they are not constrained by being part of a legacy for heirs to pick through, they can take whatever form suits me best during my life.

I think the main point being conveyed is that writing by hand improves recollection. Whether it comes naturally or not, or whether it is a better system or not, of course is subjective. However there is truth in the notion.

When I draw something I can remember the shapes better than if I simply sit there and stare at it. Something with the hand-eye coordination triggers the brain into remembering.

Typing in contrast, one is not tracing the shapes of the letters (the thing to remember), but pushing buttons that are not physically related.

It’s the same thing as if you can touch and hold an object it becomes much more real than if you can see it in a picture or on a screen. Remembering is connected better to touch.