Video summary

The Powerful Way to take Notes as A PhD Student

Main summary

Key takeaways

Wellness and Self-Improvement

Overview

Dr. Miles explains how he built a PhD-level note-taking and knowledge management workflow—based on the Zettelkassen method—to handle high research volume, improve long-term retrieval, and turn ideas into actionable research.

Key wellness / self-care mindset (cognitive load)

  • Reduce overwhelm by building a system, not relying on memory or “stacks of notes.”
  • Lower friction to reuse knowledge (e.g., web access, consistent structure) so future review doesn’t feel like a “nightmare.”
  • Avoid long-term wasted effort from highlighting/notes you can’t effectively retrieve or understand later.

Core productivity / knowledge management strategies

Build a note system designed for long-term retrieval (not exam cramming)

  • Undergrad methods (highlighting textbooks, notebooks you never reopen) didn’t scale to PhD volume.
  • The goal shifts from “studying for exams” to a knowledge management system that preserves ideas and the relationships between them.

Use the Zettelkassen-inspired “3 principles” for note quality

  1. Write notes in your own words
    • Prefer full sentences over bare bullet fragments (bullets lose context later).
  2. Keep notes “irreducible”
    • Capture an idea as its simplest complete form—not just a list of factors and not a full essay.
  3. Connect every new idea to existing ideas
    • Link it into your knowledge network so you can find it months or years later.

Stop relying on highlighting alone—replace it with “fleeting notes”

  • While reading a paper (often PDFs), capture fleeting notes immediately when something sparks insight.
  • Each fleeting note has two parts:
    • Source/cause (what triggered the idea)
    • Digested meaning (your own reframing + what it implies)
  • Emphasis: highlighting often doesn’t improve retention, and may even hurt long-term retention, according to cited studies.

Move from fleeting notes to permanent notes (and then to knowledge outputs)

Conceptual workflow:

  1. Capture: extract fleeting notes while reading a source.
  2. Create permanent notes: promote the best ideas into a lasting “permanent note” repository.
  3. Expand permanent notes: rewrite/condense, add context, and record how the idea relates to your research direction.
  4. Link permanently: connect notes to other permanent notes to build a network (not isolated pages).

Additional detail:

  • Permanent notes maintain traceability: you can jump back to the original source and the fleeting note context quickly.

Use properties/filters + a lightweight task workflow

  • Store notes with attributes/properties (e.g., related future experiments).
  • Use an inbox → to-do (Kanban) flow:
    • New items go to inbox, then move into a to-do list for later reading/processing.

Software-agnostic advice: don’t wait for “perfect tools”

  • The key isn’t the platform (Protolist / Obsidian / Rome / Notion / etc.).
  • The key is to build a system that matches how you work:
    • “Take bits you like from other systems, discard what you don’t.”

How he implements it (Protolist as an example)

  • Reads PDFs online and captures fleeting notes tied to specific pages.
  • Fleeting notes can be:
    • Promoted into permanent notes
    • Cited inside permanent notes to show where the idea came from
  • Uses linking and hierarchy:
    • Notes can be set so one becomes a “child,” inheriting/bringing in relevant fleeting notes to refine understanding.
  • Maintains searchable, filterable organization using a table-like setup.

Motivation / long-term sustainability tip

  • Knowledge building is iterative: invest small time daily for consistency.
  • The payoff: permanent notes become starting points for papers, thesis sections, or essays.

Presenters / sources

  • Presenter: Dr. Miles (former PhD student in physics / nano physics & nano optics)
  • Method/source referenced: Zettelkassen method (developed by Niklas Luhmann, referenced as originally from the 1960s)
  • Other sources referenced: studies suggesting highlighting may not improve retention and can hurt long-term retention (a paper link was mentioned; not named in the subtitles)
  • Software/tools mentioned: Protolist (his app), Obsidian, Rome, Notion, pen & paper, slip boxes (general analog systems), Google Drive, Kindle, Python (for earlier tooling), Kanban board (as a workflow style)

Original video