# Software for notes and academic writing

I am not aware of any linking notetaking editors, including Markdown editors like Zettlr and Obsidian and outliners like Logseq and Roam, that can be used to take ideas from a linked network of short notes to long-form academic writing.

I've talked with many people since the explosion of notetaking apps a few years ago about the process of incorporating linked notes with more traditional writing processes. I'll set out some descriptions of concepts/categories in order to make my points. Please understand that I don't think this is the only way to think about the writing process, or that it is even the best way, but it's a way that will allow me to explain what I see as the main problems with using current notetaking applications to produce effective academic writing. I'm sure others have their own equally valid ways of breaking down this process, but perhaps just go with me for a bit here so I can explain myself. I'm happy to adopt other terms or structures once my ideas are communicated.

## Three stages of writing

Formal or academic writing is a complex, iterative process, but let's crudely break it into three stages: source notetaking, generating and organizing ideas, and drafting and editing output.

- Source notetaking is understanding and summarizing others' ideas. It can be thought of as including non-writing activities such as locating sources, organizing meta-data, getting citation information, as well as writing source notes (in ZK terms, this would include fleeting and literature notes). The audience for the notes in this stage is the author (or authors, in the case of collaborative work, authors, but let's ignore that complication for now). The main difference between the notes of this stage and the next are that these notes generally require less revision and reorganization after they are first completed.
- Writing and organizing ideas includes generating your own ideas (including your ideas about others' ideas) and organizing those ideas into an original argument. This is often quite tricky and will require repeated reorganization as your original ideas are refined, revised, etc. If writing was a one-way process (which it isn't, but bear with me), the output of this writing stage would be an outline or structured set of ideas that constitute your entire argument with supporting evidence, but it wouldn't be in a form that effectively communicated those ideas to others, since they wouldn't be conveyed in full sentences, with full explanations and descriptions of evidence, and it wouldn't be correctly formatted. The audience for the notes in this stage is the author. These notes, unlike source notes, are frequently revised, reorganized, and updated as an author's ideas change.
- Drafting and editing involves transforming the structured argument based on your own ideas from stage 2 above into a final output by 1) communicating your ideas clearly in full sentences and 2) converting the text in your application (whether in files or an outline database) into properly formatted text, including any citations, footnotes, headings, or other elements of academic writing. The audience for the output of this stage is other readers.

Each of these very broad stages includes a lot of very different actitivites. The activities are grouped based on a small number of things that seem central to the "output" of the stage and thus the best type of software for managing those activities.

A personal knowledge base or Zettlekasten is constituted by the notes created in the first two stages above. For these systems to work as intended, the notes from the first two stages must reflect the "best" version of the author's knowledge, thinking, and analysis.

I understand that terms such as "stage" and "output" imply a one-way process. These terms are a bit misleading because, although writing does broadly move through these stages from a macro perspective, in practice, there is tons of back-and-forth movement between the stages. Writing is recursive until the author decides that a piece is complete enough to submit/publish.

## The problem: interaction between the writing stages

Most people who produce longform writing with writing systems that start with note blocks (aka Zettles aka atomic notes) do so like this: They start in one piece of software; call it a "notes app". In the notes app, they write notes (both source notes and notes on original ideas), connect the notes to each other with tags/links/namespaces/folders, and eventually organize the notes to some degree to create an outline and/or loose first draft. Then, they transfer some set of semi-organized notes from the notes app to another program, call it a "drafting app", for producing a full draft that can be given proper formatting and citations.

The main problem with this practice is that as people write their drafts, developing their ideas from words or phrases into full sentences, often they revise their initial ideas, and this can demand significant reorganization of their argument. If the argument is organized in one application (notes app), and the drafting takes place in another application (drafting app), then:
- Any improved ideas generated during drafting must be put manually put any into the organizing application, which is a high-effort and high-friction process, OR...
- the improved ideas or organization are never put back into the notes app, which means that the writer can no longer trust the notes app to be a knowledge base with the most updated and organized version of their ideas and supporting evidence for those ideas. The notes app is a temporary workspace for ideas that are later improved and revised rather than an ever-evolving knowledge base of ideas that you might return to over and over again for future projects.

## Three types of text

One way to think about how software can deal with these issues is by thinking of three types of text produced when working with these apps.

Text1 includes things like asterisks, brackets, underscores, or other elements that exist to tell the program how to format or link other text. Depending on the software, some or all of these characters are visible some or all of the time. This text provides functionality, doesn't really reflect the content of the final output, and isn't intended for output to the final written product.

Text2 isn't intended for the final product, but isn't there to provide functionality as Text1 is. Instead, Text2 refers to the ideas that are refined during stage 2, "generating and organizing ideas". Text2 is used for things like making categories or taxonomies, or for briefly summarizing ideas in ways that are easy to read, organize, and reorganize, and just as likely to be words or phrases as full sentences.

Text3 is produced and revised during stage 3, "drafting and editing output". Text3 is intended to constitute the final written output and includes the main body text of the draft as well as some of the text in other structural elements such as footnotes and headings. Text3 is primarily written as full sentences and includes citation markers that, after output, will be transformed into proper citation and formatting. Although some content from initial notes will end up in Text3, this category is reserved for text that exists in a form where it can be drafted, edited, revised, and otherwise prepared for final output without having to move it once again from its initial location to somewhere else in a document.

## Outliners vs. text editors

My experience is that outliners and mindmapping programs are better at early stages of writing because they are good at working efficiently with Text2. It's much easier to reorganize brief summaries of ideas than the fully explicated versions of those same ideas (Text3) that are needed for a final output. Part of the reason for this, which is hard to replicate in a pure markdown editor, is the usefulness of a visual hierarchical structure in organizing ideas, which isn't really replicated by headers alone.

Text editors, on the other hand, are better at moving text through the various activities that are part of stage 3, drafting and editing output, including producing Text3 and converting text to a properly formatted final output.

If you are working in a field where the output is already highly structured by convention, such as a hard science, then organizing your ideas is less difficult and the inability to easily drag and drop Text2 in new structures is less of a drawback. If you are working in a field that is less well-defined, allows more variation in writing organization, or is interdisciplinary, then organizing Text2 in a low-friction way is much more important.

I currently write in a program that lets me mark certain text as Text2 vs Text3, and I can filter to output Text3 to Markdown, and then use Zettlr to convert it to final output. But Zettlr is not (for me) currently suitable for efficiently working with Text2. However, my current system is not what I want. I organize writing and draft in a mindmapping program, take and link source notes in an outliner, and format and polish in Zettlr. I am not building a knowledge base of ideas that I can return to, and the overall workflow is not smooth.