deep reading

Mastering the Content in PDFs: Using Hook and PDFpenPro for Deep Reading

This is a guest post by Luc P. Beaudoin, an adjunct professor of Cognitive Science and Education at Simon Fraser University and the developer of Hook and mySleepButton.

Often, we read papers to extract information from them. But sometimes we need to thoroughly understand a difficult document. This might be to use the information for work, write, teach, pass an exam, or simply to become more effective.

To master a difficult document, you need to take notes. It’s often useful to highlight and annotate a PDF directly in PDFpenPro. However, to take elaborate notes, it’s helpful to use a dedicated app, such as a writing app, an outliner, a drawing app, a spreadsheet, or a mind-mapping app.

Before you begin

This blog post focuses on deep reading for the purposes of mastering a document. It contains a tutorial and a worked example to help you experience, first hand, the benefits of using deep links for deep reading. 

We recommend reading Using Hook and PDFpenPro For Deep Linking: A Worked Example and following the steps described there before you move forward.

We’ll be using the resources included in this zip file, including the sample PDF titled Mental Perturbance.pdf, to discuss deep reading and how to take descriptive notes.

Deep reading and taking descriptive notes 

Assuming you have hooked a text app to the sample PDF titled Mental Perturbance.pdf, you’re ready to take notes. Your notes about a PDF should always contain the following:

  • The problem it addresses
  • Its key terms and concepts
  • Its major claims
  • Its ancillary claims
  • Its thesis and arguments

Feel free to copy these bullets into your notes document as a template.

Tip: I recommend creating a TextExpander snippet based on the Notes-template.txt document included in the zip file. That way, when you start a new notes document, you can simply type and expand the abbreviation. You can also add that file to Hook’s custom templates folder for use in Hook to New.

Normally it is best to fill out those bullets in your own words. But you can also copy the answers from the source PDF and paste the text in your notes. Either way, for every bullet you can add a deep hyperlink inside the note back to the PDF as illustrated below. In sum:

    1.    In the PDF, select the text you would like to refer to

    2.    Bring up Hook using keyboard shortcut ⇧⌘SPACE or the “Show Hook” button in the Menu bar

    3.    Click Hook’s Copy Link button (or use ⌘C)

    4.    Paste the link in your notes (TextEdit) or wherever you want to refer to the selection

You can change the text of the link in TextEdit to be more specific. The Mental Perturbance-notes.rtf file (included in the zip file) contains several deep links for you to try. When you click on the links, PDFpenPro will auto-scroll to the specific line in MentalPerturbance.pdf that is referenced.

Following are some example descriptive notes adapted from the MentalPerturbance.rtf file.

Note: Don’t worry about the content of these notes. Their main purpose is to illustrate structured note-taking with deep links.

Step 1 to deep reading a PDF: identify key terms

Two of several key terms in the PDF:

  1. Perturbance is a mental state in which insistent motivators or alarms distract or otherwise influence executive processes in a manner that is difficult for reflective processes to suppress or control.
  2. Perturbance, more generally, is the diminishment of the already limited human capacity to control one’s own attention with respect to a particular cluster of motives.
  3. Grief. When grieving, one tends to be assailed by memories and motives pertaining to the lost one.

Again, you’ll notice that when you click on those links, PDFpenPro will open the PDF, and scroll to the target inside the PDF. The Mental Perturbance-notes.rtf file lists several other key terms.

Step 2 to deep reading a PDF: identify a major claim

A major claim of our sample PDF is:

Susceptibility to perturbance is a necessary, inevitable consequence of being a truly autonomous agent as defined in this paper; it is not a feature but a byproduct of normal operation of the mind.

Try clicking on the two links above. You’ll see that Hook opens the PDF for you. The first link simply opens the file. The second one is a deep link that causes PDFpenPro to open the PDF and scroll exactly to where the target of the link resides.

Step 3 to deep reading a PDF: assess the document 

Once you have thoroughly analyzed a document you can assess it. A thorough assessment covers four sets of criteria:

  • Caliber is how the document fares against objective normative epistemic standards, such as generality, parsimony, coherence, clarity, explanatory power, veracity, and methodological rigor. Not all papers must abide by the same standards, however. For instance, legal documents differ from philosophical papers, which differ from scientific ones. But some criteria, such as coherence and clarity, are general.

  • Utility is how helpful the document is to you personally. This depends on your values, goals and projects. It is not normally something someone can answer for you (unless they know you). A document can be of very high caliber, but irrelevant to your needs. This requires understanding your projects. Software like OmniFocus, Things and TaskPaper, which support deep linking, can help with that.

  • Potency is the extent to which you can reshape your mind with the document (your comprehension, beliefs, habits, attitudes, etc.)

  • Appeal reflects how much the ideas in the paper, the prose or even the author appeal to you. This is actually something to watch out for because bad ideas can be very seductive; and sometimes the truth is unpleasant.

Based on its acronym, I call this the “CUP’A assessment schema”. Appeal (’A) is set aside because it can be so misleading.

While this assessment schema draws on previous literature, it is an integrative, cognitive science-based alternative to schemas used in education and philosophy, such as the CRAAP test (Currency, Relevance, Accuracy, Authority, Purpose/point of view.) 

These previous schemas do not consider potency and appeal, and in my opinion do not deal with caliber in a sufficiently general and detailed manner. Also, they had not adequately been integrated with software. Nor were they based on integrative theories of mind. The CUP’A criteria are discussed at length in Cognitive Productivity books.

The Mental Perturbance-notes.rtf file demonstrates how one might assess the Mental Perturbance paper. Again, the assessment contains several hyperlinks. Here are some examples.

Caliber questions

When assessing the caliber of a document, one needs to compare it to related idea products. For the example paper, one might ask, How does the perturbance theory compare to related theories? Some answers might be:

Again, each hyperlink above brings you to a specific location in the PDF.


I think it is important to single out an aspect of caliber that is somewhat related to utility: the significance of the work. Whereas personal utility concerns how helpful the information is to you, general significance pertains to the usefulness of a paper for the broader world. A PDF can be useless to you but useful for one or more communities, and vice versa.

An example assessment of significance of the perturbance paper is that the paper can be used by scientists, psychologists and others to:

  • Understand and treat insomnia, or more specifically insomnolence 
  • Explain how emotional memories can be potentiated. When an insistent motivator hijacks one’s brain (i.e., causing one to focus on the motivator and its object), the agent repeatedly recalls information pertaining to the motivator. For instance, in limerence or grief, one may repeatedly recall interactions with the love object. This strengthens those memories.

In “How to Read a Book” (p. 47), Adler & Van Doren discuss how to evaluate the significance of a book, by having you ask the question, “What of it?

[Assuming the information is true] Why does the author think it is important to know these things? Is it important to you to know them? And if the book has not only informed you, but also enlightened you, it is necessary to seek further enlightenment by asking what else follows, what is further implied or suggested.

What is true of assessing books is also true of assessing noteworthy papers.

Step 4 to deep reading a PDF: practice productively

In a previous blog post, I wrote:

“Good students know that in order to be transformed by information, they need not only to read it but to practice using it. And so they explain the information to themselves and others, they write about it, they work through examples, and they practice answering questions about the material.”

This is similar to the learning strategy, proposed by the Nobel Prize winning physicist Richard Feynman, known as the Feynman Technique. It’s a great way to detect and rectify one’s knowledge gap. If you can’t adequately answer basic questions about a paper, then you don’t understand it.

Whether you use flashcard software such as Anki or RemNote, or co-opt a note-taking app for this purpose, using deep links can help you practice more productively. When you are constructing flashcards, you can include links to the specific location in the PDF that contains the answer to your questions.

Here is an example for learning from the perturbance paper.

Example Question: How can the concept of perturbance be applied in insomnia?

Here is an answer that is a bit technical; but what matters here is the links, and that if you practice answering such questions you will better understand the answers:

  1. The brain contains a sleep control system that continuously determines whether to promote sleep or wakefulness.
  2. Perturbance involves insistent motivators, which tend to grab attention, and/or global alarms. Both of these states promote wakefulness, so that the organism can deal with the presumably urgent and important situation. To put it differently, perturbance is insomnolent, meaning it tends to delay the onset of sleep. See this section of the PDF you downloaded.
  3. If one’s insomnia is due to perturbance, then decreasing mental perturbance should counteract insomnolence, and promote sleep (assuming the person is otherwise predisposed to sleep). That is one of the ways in which the “cognitive shuffle” is supposed to help one fall asleep. Actively imagining things that are unrelated to the perturbance is supposed to deactivate the perturbant motivators. That’s the thinking behind the mySleepButton® iPhone app, which is another CogSci Apps invention. mySleepButton helps you administer shuffle your thoughts.

You can find other example productive practice questions in the Mental Perturbance.pdf file.

Deep linking, true competence

To truly master a difficult paper, reading it is not enough. You need to have analyzed it, evaluated it, and practiced it. Writing about a paper helps you understand it. That’s partly why professors get their students to write papers. 

Creating deep links forces you to identify the key content in a paper, thereby distilling it to its essence. Having included deep links in your notes and flashcards, later you can quickly access key passages in the PDF. This saves you time and helps you master the document.

As a result, when the time comes to write your exam, give a presentation, discuss the paper with others, or use its knowledge gems to solve an urgent real-world problem, you will not need to consult your notes. The knowledge will be in your head. And that is the hallmark of cognitive productivity.