Once upon a time, I relied on marginalia to bridge ideas I had while reading. I'm old, whatever, get over it. Marginalia is the commentary written in the margins of physical books, articles, and other textual material.
A downfall of becoming a digital native is the genuine lack of the experience of marginalia in many applications. Certain pieces of software allow notes to be inserted at various points, sure, but they lack the immediacy of a person creating that physical marginalia. The neural connections don't get made as quickly, becoming more ephemeral digital replications. Often, these notes become hidden from view unless you remember to (or desire to) expose them. You typically choose to hide them while working on something that needs your full attention. You only have so much screen space, after all.
Compare that to marginalia in a physical medium. They can't be hidden. They force themselves upon you to remind you of a past reaction to a piece or a connection you drew between two points. When deliberately reading a physical medium, you will sit there, pen or pencil in hand, and prepared to create marginalia—an inch-and-a-half-wide diary of the intellect.
It isn't a secondary feature of an application to flip on and off or one you can choose to display or not. It's active participation with an item in physical space. Once made, marginalia remain.
This isn't "old man yells at clouds," this is a growing sense of frustration at realizing that I'm not sure how to bring this immediacy and active participation to the digital world. I'm not even sure it can be brought to the digital world. There is a disconnect between keyboards, screens, and minds that might never be reconciled—barring some physical brain-jack interface and an impossibly realistic simulation like in The Matrix. I want to hope, but decades of development and design in the digital document creation and editing space have only given us more complicated interactions, not a more holistic experience replicating the physical world. Even document readers like the Kindle can't compare.
And that's a shame. I wish I had a solution, but I'm not sure we will ever find one. The interface between the physical and the digital will always lose some data due to the "compression" of experience between the two. In this case, some of the lost data is that sense of immediacy and connection with our marginalia.