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The best way to acquire knowledge from readings



The purpose of visualizing notes is to gain a deep understanding of what you've learned. If all of your notes are very long and you don't break down the knowledge into smaller parts, the understanding you can gain from visualization will be very limited. Real deep understanding doesn't come from the "relationship between two books" but from the "relationship between all the concepts in these two books."

You can only gain a deep understanding of the topics you care about through visual note-taking when you atomize your notes. Atomic note-taking does not mean you cannot have long notes. It means that each concept card should only contain one concept and be supported by its content. To ensure clarity, you should always describe the concept in one sentence and use that sentence as the title of the concept card.


I read a lot. For me, the most frustrating issue with reading is that great books often contain a high volume of content that is not easy to fully digest and integrate with my existing knowledge. Even when I fully digest the content, I often find it difficult to recall knowledge that I learned in the past purely from memory, which makes it hard to apply what I've learned to my current work.

I have met many people who face the same problem in learning, and this issue is what many note-taking (a.k.a. knowledge management) tools are trying to solve. Unfortunately, most of these tools put too much focus on how you store your notes (e.g., folders, graphs, relational databases, etc.) and neglect important aspects of learning such as acquisition (making sense of knowledge), retention (recalling past knowledge), and application (applying knowledge in a real-world scenario).

In this article, I will share a real-world example of how I developed an effective method for acquiring, retaining, and applying knowledge using Heptabase, a tool my team and I created for learning and research. While this is not the only workflow for learning, it has worked extremely well for me, and I believe almost anyone can apply it to their learning.

Method Overview​

The famous Feynman learning technique suggests that the best way to develop a deep understanding of a topic is to teach it to a child. I would say that whenever you want to teach something, you need to first figure out the structure of the knowledge and be able to articulate that structure clearly. The method that I developed can help you achieve that with five steps:

  1. Highlight all important paragraphs while reading.
  2. Dissect the content of a book into granular concepts.
  3. Map the relationships between these concepts.
  4. Group similar concepts together.
  5. Integrate these newly learned concepts with previously known concepts.

Here's a screencast of how I conduct this process. This screencast is not staged. It's a real example of how I develop an understanding of a book I read called Mindstorms: Children, Computers, and Powerful Ideas. You don't need to watch it fully (it's 4 hours long!), but quickly skimming through different parts of the video will give you a clear sense of how I extract core concepts from the book and develop my understanding of it. If you want to explore and play with the whiteboard I created in the video, here’s the link to it.

[2024/01/03 Update] I have created a tutorial showing and explaning how I conducted the five-step process in action using Heptabase. I highly recommend you check it out!

Step 1: Highlight all important paragraphs while reading.​

The first step in the process is to highlight important paragraphs from the book you have read and organize them by chapter.

Depending on the reader you use, the highlighting process may vary. If you are using a desktop reader, you can simply copy and paste the text into a Heptabase card. If you are using a Kindle or iPad reader, you can export all the highlights of the book into a Markdown file and then import it into Heptabase as a card. If you are reading a physical book, you can take notes in Heptabase whenever you finish reading a chapter.

It doesn't matter which tool you use to create highlights, as long as your output is one large card for the book that includes your highlights from different chapters.


Step 2: Dissect the content of a book into granular concepts.​

Once you have the book card ready, you can create a whiteboard and add that card through the import panel of the card library. In my example, I created a sub-whiteboard named Mindstorm under the parent whiteboard Reading Notes, and dragged my Mindstorms book card onto this sub-whiteboard.


Once I have the card ready, I open it on the right split panel so I can better see its content. I usually start by skimming through all the content to identify key concepts. When I decide that there's a concept I want to extract, I select the related blocks and drag them out onto the whiteboard to create a new card.


Simply creating a concept card is not enough. To ensure clarity, I always describe the concept in one sentence and use that sentence as the title of the concept card. Then, I reorganize the content of the card into a structure that makes sense to me, and perhaps even drag other related blocks from the original book card into this concept card.


Step 3: Map the relationships between these concepts.​

As I extract more concept cards from the original book card, I gradually add connections between them, or place similar concept cards next to each other. If I notice two concept cards are about the same idea, I merge them into one. At other times, I might break down a large concept card into several smaller ones to ensure granularity.


Step 4: Group similar concepts together.​

After extracting all the content from the original book cards into concept cards, I close the split panel and start working on mapping and grouping relationships. Often, I find multiple concept cards related to the same sub-topic. In such cases, I group those concept cards into a section and add a name to that section. Naming the section should be done as carefully as naming a concept card because these are the things that you recall first when you revisit this whiteboard in the future.


Completing steps two through four typically takes anywhere from an hour to a full day, depending on the length and depth of the book. Once you've produced the final whiteboard, the knowledge acquisition phase is complete. In this process, what's truly valuable is not the final whiteboard you produce, but the thought process you invest while establishing the knowledge structure and titling each concept card and section during steps two through four. Deep understanding and insights often come from the process of deconstructing, reassembling, and describing knowledge in your own words. Only after going through this process does the knowledge truly become your own.

After completing the final whiteboard layout (including all arrows and sections), I will open the original book card in the right split panel of the whiteboard and re-paste the links to all the concept cards and sections back onto this book card. In the figure below, you can see that each link in this book card displays the title of a concept card. This is why, in the second step, I summarize each concept card in one sentence and use that sentence as its title. Only by doing so can I see the core concepts of this book without having to open the links of these concept cards when reading the book card.


For example, if I name a concept card's title as "Engineers’ subculture," looking back a few months later, it would be hard for me to recall what this card is specifically about. But if I name the title of this concept card as "Engineers who find BASIC easy to learn formed a subculture that is influencing the world of education to favor students who are most like that subculture," even without reading the content, I can recall the core concept in the future just by its title.

Step 5: Integrate these newly learned concepts with previously known concepts​

Up to now, I have gained a deep understanding of the core concepts of the book Mindstorms by breaking down and connect its core concepts on a whiteboard. But just understanding this book is not enough; I also want to truly integrate all the knowledge I have learned in the past, present, and future. In other words, I want to integrate the concept cards of this book with the concept cards I wrote for other books and lectures in the past.

Before doing this, I want to share an important learning mindset: You can only gain a deep understanding of the topics you care about through visual note-taking when you atomize your notes.

Many people, when first using a visual note-taking app like Heptabase, continue to use the old way of note-taking and write one note for each book or lecture, resulting in very long notes that contain many concepts. When your notes are in this format, it's hard to gain value from visualization.

For instance, in the figure below, there are two book cards, each with a lot of content. Although the content of these two books is related, connecting these two book cards on a whiteboard does not provide any new value, as it is almost the same as putting them in the same folder.


The purpose of visualizing notes is to gain a deep understanding of what you've learned. If all of your notes are very long and you don't break down the knowledge into smaller parts, the understanding you can gain from visualization will be very limited. Real deep understanding doesn't come from the "relationship between two books" but from the "relationship between all the concepts in these two books." What you want to connect are not book cards, but individual concept cards that you extract from these books using the previous four steps.

For instance, I've recently been researching how to design a computer-driven dynamic medium, and both books Mindstorms and The Early History of Smalltalk are highly relevant to this research topic. To better conduct this research, I created a whiteboard called Dynamic Medium and reused concept cards related to Dynamic Medium from these two books, organizing them using a mindmap to establish a unique understanding framework.

It's because I extracted and atomized the most important knowledge and ideas from these two books into reusable concept cards in the past when I read them, so that I can now easily apply my previous learning to new research topics. My past knowledge no longer sits uselessly in folders, but instead becomes the foundation for my newest research work!


Note: Atomic note-taking does not mean you cannot have long notes. It means that each concept card should only contain one concept and be supported by its content. If the content is long but all of it can be used to support the concept in the title, then the card is still an atomic concept card.

How to Learn and Research​

After sharing how I implement the learning methodology in Heptabase, I would like to summarize the core ideas that underlie this methodology:

  • I believe that the essence of learning and research is to break down and extract the important concepts from books, literature, lectures, and experiences. Then, one should connect, understand, and internalize these concepts in one's own way to build a deep understanding of what is known and unknown to humans.
  • I believe all work plans and research papers are simply products of transforming this deep understanding into executable and communicable forms.

Under these core ideas, the processes of learning, research, planning, and output can be fully presented in the following diagram:


In this figure, on the left is source, which are the "literature cards" you wrote down while reading or attending lectures.

During my learning and research process, I extract useful concepts from these literature cards to create atomized "concept cards." Each concept card describes the concept in one sentence in the title and cites content from one or multiple pieces of literature to support this sentence. Every citation deepens my understanding and reflection of this concept.

As I learn and research, the original content of the literature cards will gradually be replaced by links to many concept cards. As I extract these concept cards from the literature cards step by step, I need to connect and fit them into a structure that makes sense to me. I can only truly understand and internalize a topic when I find such a structure for it.

In the future, whether I'm writing academic papers, work plans, or online articles, my process will involve linearly reassembling these concept cards into an "output card," which is an article meant for others to read. As I absorb and break down more and more "sources" during research, my "understanding" in the middle will deepen continuously, and the "output" on the right will naturally be of higher quality.

Closing thoughts​

Although the topic of this article is about my method for acquiring, retaining, and applying knowledge, I do want to stress the importance of choosing the right tool to do so, because the design of a tool can radically change the way we subconsciously approach learning and form good and bad habits for it.

Seymour Papert, one of the pioneers of artificial intelligence and the constructionist movement in education, discusses his thoughts on this in Mindstorms:

For me, writing means making a rough draft and refining it over a considerable period of time. My image of myself as a writer includes the expectation of an “unacceptable” first draft that will develop with successive editing into presentable form. But I would not be able to afford this image if I were a third grader. The physical act of writing would be slow and laborious. I would have no secretary. For most children rewriting a text is so laborious that the first draft is the final copy, and the skill of rereading with a critical eye is never acquired. This changes dramatically when children have access to computers capable of manipulating text. The first draft is composed at the keyboard. Corrections are made easily. The current copy is always neat and tidy. I have seen a child move from total rejection of writing to an intense involvement (accompanied by rapid improvement of quality) within a few weeks of beginning to write with a computer. Even more dramatic changes are seen when the child has physical handicaps that make writing by hand more than usually difficult or even impossible.

Word processors can make a child’s experience of writing more like that of a real writer. But this can be undermined if the adults surrounding that child fail to appreciate what it is like to be a writer. For example, it is only too easy to imagine adults, including teachers, expressing the view that editing and re-editing a text is a waste of time (“Why don’t you get on to something new?” or “You aren’t making it any better, why don’t you fix your spelling?”).

As with writing, so with music-making, games of skill, complex graphics, whatever: The computer is not a culture unto itself, but it can serve to advance very different cultural and philosophical outlooks.

When building Heptabase, we aimed to design an environment that empowers you to externalize the process of identifying, dissecting, connecting, and grouping the concepts you have learned. That's why we built features such as the ability to dissect cards, move blocks across cards, build card relationships on a whiteboard, and reuse cards across multiple whiteboards. Together, these features form an environment that leverages the human capability of visual comprehension and visual memory with the computer's capability of data persistence and retrieval. With continued use of the tool to create understanding of your learning, you will start subconsciously adopting the habit of using the learning method described in this article. This is what ultimately matters—not just helping you take notes, but helping you become better at learning.