Assume for a minute that that best way to take notes is on paper with pens, pencils etc., and not in a digital device. (I might return to this later).

I'm torn between two extremes for note-taking. One one hand, I find it useful in the short-term to make scrappy, ephemeral notes: ad-hoc daily TODO lists; mind maps and experiments, that I intend to throw away. There are lots of styles of stationary to support this: ring-bound notebooks that are easy to tear leaves from; or literally the back of envelopes.

The other extreme is the "preserve everything" mentality. For my PhD, I have a single, hard-backed notebook that I try to do all my PhD note taking in. I date each entry. There's a history I can refer to, no matter whether what I'm writing is seemingly ephemeral or not.

So I do both. Sometimes I want to refer back to something I did which was ephemeral and I've lost it or thrown it away. And having lots of mis-matched stationary for ephemeral storage is a bit messy, and works against the other extreme to a certain extent.

I've started to wonder whether strictly doing one or the other (and most likely, the "preserve everything" approach) might be a good idea. In practise that would mean settling on a particular notebook format, and disposing of anything else; having separate notebooks by topics (PhD, work, …) with a "catch-all" for the rest.

Does anyone have any advice or useful resources to read on this topic?


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I did pretty much what you describe when I did my physics PhD about a decade ago: one main notebook (or a series of them, as time went on) which contained the more coherently-formed notes, ideas, observed results (important stuff!), etc., while at the other end I'd scribble on loose-leaf paper to work out equations or try to flesh out half-baked ideas into more complete forms - or until I could see they wouldn't work. In the reminaing cases, I'd often rewrite clean-up versions in my notebook to "preserve" them.

The loose-leaf scribbles were semi-organized. I'd always have a date and a sequence number at the top of the page, which gives me some way to search through them if I ever needed to. There were a few occasions that demanded that, typically involving refreshing my memory when writing up a paper.

I still work more-or-less like this. I've been a little lax on keeping my scratch-pads organized, and I discard them more often, but I still use them. (Perhaps I've become more confident about "preserving" the right things in my notebook.) Personally, I don't think I could compress down to a "single-tier" approach. There's definite utility in being able to rough out concepts on some kind of scratch pad before "preserving them for posterity". Sometimes it's clear that you can toss the scratch-pad afterwards, but other times you can't be sure until, say, years down the track (e.g., after everything's been published... or abandoned). And I think it's beneficial to have the main notebook have more refined, consise content than otherwise having to wade through all the scribbles to get to the good stuff.

I don't know if that's useful info, but at least it confirms you aren't the only one to come to this way of working, so it can't be all bad.

Comment by Brendon Higgins,
comment 2
I know you weren't looking for specific tools, but maybe VimWiki would be neat to check out. It has a diary feature that I didn't ever intend to use... but now I use it daily! It lets me do both of what you mentioned: I have article pages with extensive information on a subject, but if I also think 'hey, that might be useful later' then I shove it in today's diary and tag it with something relevant. If I ever need to expand on it I can move it into its own article; otherwise, the rough information is still sitting there for consumption just in case.
Comment by Ghelc,
comment 3

WARNING: I've not done any PhD and have no interest to do that, but the things I deal with (i.e., universe of knowledge) is not any less than doing a PhD, at least I think so. :)

What problem you want to solve, for that I think a good ToDo manager software will be enough.

Presently, I use "" (available from F-droid) on my Android mobile which serves my all needs (finally after 10yrs of searching). It stores it's tasks list on a JSON file which can be backed up & restored easily, it also supports CalDAV, Google Tasks, EteSync. It provides timely notifications/reminder. It also comes with a very useful widget.

Now for note taking:

I use folder/directory & file (plain text) approach, as being a distro-hopper (& experimental) I cann't expect my notes be accessible (read-writable) by any system unless I follow this strategy. Also some good simple text processing tools like "grep", "find", "diff" etc are available in all GNU Linux systems I've encountered so far. The directories & files are easy to backup also for personal users.

I maintain a separate directory to keep internet links lists (subject wise) mentioning related info as little as possible.

I create a root directory for each new subject, create text files for each chapter/topic thereunder. I write some files in Markdown now-a-days if needed.

If at all needed I also create some schematic drawings (SVG/PNG/JPEG) and keep under the subject directory and mention the relative path to that graphic file on related text files (I never create symbolic/hard links to make it multi-system compatible).

Also keep the essential files downloaded from internet under the related subject directory and mention the relative path to it on related text file/topic.

The real problem is with the mathematical equations, as of now. For that you can use LibreOffice. Although there are some hard ways if you already know that.

Here are some good links for further study:

If you want Adaptive Hypermedia system you can use any of the popular wiki software available. I would like to suggest DokuWiki, MoinMoin, PmWiki etc.

So far, real Hypermedia creation-preservation-distribution platform for individual user (Personal Knowledge Management) is not yet available, at least I don't know. If you know please inform me. :)

Comment by Tusar,
comment 3
Comment by User,