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Academic Writing Using Emacs’ Org Mode
This living note explains why MS Word and similar word processors are not the best tools for academic writing. Then, it offers an alternative toolset to replace Word.
Table of Contents
Incompetency of word processors for academic writing
When I started my PhD, I used Microsoft (MS) Word to prepare my homework assignments, technical reports, and pretty much any other writing assignments. I also used other tools, such as One Note and Evernote, to take notes. These tools had several fundamental flaws that eventually led me to dump them. The following subsections explain these issues.
High price tag
MS Word is expensive. The last time I checked, a single-user Word license was $160. This price may be reasonable for those living in rich countries, but it is a problem for those living in developing countries. It is also annoying that the license you get is not really perpetual. Although you can always use it, the software gets updated every few years, and if you don’t pay for a new license, you have to stick with your old copy. Realistically, you will have to update your software at some point!
Paying for a basic academic writing tool is a serious problem against the fair share of science and education. Paying for MS Office (either directly or using it through your institution) helps sustain its monopoly, meaning that access to it becomes necessary for young researchers. As such, people in poor economic conditions would either pay a high price for it or use an illegal copy of the software.
Fee, cross-platform word-processing software (e.g., LibreOffice and WPS) exist that can completely replace Word. Being free is great! However, this software does not resolve the other issues that Word suffers from.
Listen to your grandma:
Focus on formatting rather than writing
MS Word and all other WYSIWYG (what you see is what you get) software put a large emphasis on formatting while writing. This is a big source of distraction, as it shifts your focus from what is important (writing) to what is not (formatting).
My early publications, including a few journal articles and a master thesis, all were written using Word. When I was typing my Master’s thesis, I struggled to arrange all the figures and tables in the right place, trying to minimize the white space in my manuscript. If you are writing a five-page report, it may be fine. However, it can easily become a huge problem if you work on a large document with many figures, tables, and equations.
Fragile hyperlinks
My experience combining Word with citation management tools such as Zotero has not been pleasant. Inconsistency in hyperlinks, especially when working on large documents, is too frequent. On several occasions, I had to re-insert all the citations in a manuscript because all the Zotero hyperlinks broke after I exchanged the manuscript with a coauthor. I still do not know for sure why the hyperlinks broke. Maybe because my coauthor used different word-processing software or an older version of Word. Regardless of the cause, it was an annoying situation. At that moment, I had two choices: (1) use my older copy of the manuscript, which had the working hyperlinks, and redo all the coauthor’s edits myself into the old version, or (2) re-insert all the citations in the text manually. Neither solution was cheap.
Of course, this can also happen to other types of cross-referencing, such as figures, tables, equations, and section headings. One way to avoid the problem is to type all entity numbers in plain text without hyperlinks. This will eliminate the problem of accidentally breaking hyperlinks. However, it creates another problem that hyperlinked cross-referencing was invented to resolve! That is, all the entity numbering will require manual updates if the order of things has to change or if an entity needs to be added or removed.
Me when I have to redo all the hyperlinks in a 100+ page document:
Sluggish performance
Word processing software usually becomes very slow and sluggish if the file size becomes large, e.g., due to a large number of figures. This will make the writing process very painful and frustrating and sometimes causes your computer’s operating system to crash.
Not easy to switch styles
It is time-consuming to put a Word document into a specific journal style. If you already know which journal you want to submit your manuscript to, this may not be a big problem. However, there is always a chance that you are uncertain about your journal in advance, or your first submission might fail (God forbid), and you need to submit the same paper to another journal. Even if you learn how to import styles from a Word template to another document, you still need to reformat the document frequently after adopting a new style. You probably need to reshuffle the figures, tables, equations, etc., to minimize the white space in your document.
Lack of customizability
These tools need a fully customizable interface. For instance, there was no convenient way to switch to a dark background and light foreground in Word until recently. Now, they have added a dark mode option, and that is it. You cannot go beyond this single option.
The ability to customize the interface is critical for academics who spend a significant amount of their time typing in their reports or manuscripts in front of a computer. They need to create a space for themselves that appeals to their preference and minimizes the strain on their eyes. A pleasant working environment will improve their productivity and performance.
Poor window management
Over the years, I have not been able to integrate MS Word (and other word processing software) with my other programming tools, e.g., Spyder. I had to switch frequently between many different windows, which was inefficient. Researchers usually write while interacting with some sort of computer programs that run their analytics, e.g., R, Python, etc. Switching between different program windows while working on different documents and programs is not convenient. Tiling windows is not a good solution because it reduces the width of your Word window and makes it difficult to read your own (or others) writing.
To address this problem, many researchers use multiple computer displays so that they can see all their workspace at the same time. However, that may not be a good solution. Letting your eyes travel horizontally in a wide range can strain them greatly. Working on narrow screens (e.g., using a display in portrait mode) could also be a problem because you have to reduce the width of your documents.
Word has a partial solution for this problem. You can use the “web layout” instead of the “print layout.” This mode can help you zoom in on your document without needing to scroll horizontally. This feature, however, has two issues. First, if you have a figure in your document, the horizontal scrolling will appear anyway. Second, if you have comments in your document, the comment pane will occupy a large portion of the document’s width. In either case, the “web mode” feature becomes almost useless.
Not available on Linux
It is a huge problem that MS Word is unavailable across all computer platforms. A few years ago, a web-based version of Word was launched, but it excludes many of the important features of the desktop version. This problem is related to the unfair availability and accessibility of resources in science and education and the monopoly that feeds the scientific dictatorship.
Although we do not know exactly what portion of academics use Linux, we know for sure that this portion is not insignificant. Approximately 55.7% of professional developers reported using Linux, according to the Stack Overflow developer survey of 2020. This suggests a significant portion of the academic community, especially those involved in computer science and related fields, likely uses Linux given their overlap with professional developers (TrueList).
In broader terms, Linux adoption in the academic sphere is supported by its dominance in areas requiring high computational power and flexibility, such as research and development environments. Around 83% of developers reported using Linux in a 2019 survey, which includes a substantial number of academic researchers (WorldMetrics). Additionally, Linux is favored for its open-source nature, which allows customization and efficiency in various academic tasks, ranging from data analysis to software development (ACRL News).
Although I have not put this reason at the top of my list (because I thought my audience, mostly students, did not care much about these philosophical issues), it is the biggest reason to dump MS Word.
Inconsistent formatting
Every year, I review about 10 master’s thesis and 100 other documents such as homework assignments, final exams, and project reports. Almost all of these documents are written using Word, and almost all of them have numerous formatting inconsistencies. That is, the document uses inconsistent font types, font sizes, line spaces, page margins, etc. Such inconsistency is a direct consequence of Word’s (and similar software’s) WYSIWYG (what you see is what you get) nature. This philosophy implies you must rely on your eyes to discover the inconsistency. There is actually an inconsistency in the current paragraph. Could you find it?
It was very painful for me to check formatting consistency in my Master’s thesis, as it was a large MS Word document. I often made errors of leaving a word or sentence with inconsistent formatting within the text, which was caught later only by chance.
The toolset I introduce in this article resolves all the issues discussed in this section. The rest of this note will walk you through these tools and a minimalist approach to get started.
Alternative tools
I believe the only way to address the problems we discussed in Section is to abandon the WYSIWYG philosophy and use a markdown language. Markdown languages use plain text and keep formatting procedures separate from the contents. This separation lets us focus on the content and logical structure of our writing rather than spending a lot of time on formatting. It also lets us use any text editor we want rather than the rigid and inflexible environment imposed by word processors.
If you insist on using a WYSIWYG, it’s fine. But, at least consider one of the free, open-source tools rather than MS Word. Some of these tools that I have tried, ordered according to my personal preference, are:
However, if you are open to new experiences, please continue reading as I will tell you about the Org Mode of Emacs that you can use for:
- writing manuscripts and reports,
- creating presentations,
- creating websites,
- coding, and more.
What is Emacs’ Org Mode?
Emacs is a free, open-source text editor for computer coding and scripting in any programming language. You can learn more about Emacs here.
Org Mode is a markup language designed for note-taking, which is also a major programming mode in Emacs. Org Mode is also a powerful tool for authoring academic documents. Using it, we can avoid almost all the problems with WYSIWYG word processors. Here is a non-exhaustive list:
- It automatically formats your manuscript and minimizes its white spaces. This saves you a lot of time if you are working with large technical documents.
- It exports your manuscript to useful formats including \(\LaTeX\), ODT, HTML, and PDF. This is particularly useful if you use a document for different media, e.g., blog posts, presentations, etc.
- It does not require you to copy figures into your document every time you update them. Figures are saved separately, making it convenient for publishers to reformat your work if needed.
- Since the figures are not embedded in the document, the text file size is small, regardless of the number of pages you have written. This makes your document very light and easy to work with even on extremely slow/old computers. You probably have experienced how slow word processors can get if the document is large with high-resolution figures. This problem will not be relevant if you use Org Mode because your manuscript will be in plain text.
- Since your org files are all plain text, you can open and edit them on any device, making your work absolutely portable and widely accessible.
- Emacs is a free, open-source software. So, it frees you of any paid services.
- Using Emacs improves your workflow productivity through smart keyboard shortcuts. After using it for a few years now, I hardly need to use a pointing device (mouse or trackball).
- Its user interface is fully customizable and distraction-free. This is very useful for people who spend a lot of time on a computer. An enjoyable work environment boosts productivity. For instance, I have designed my Emacs interface (Figure 1) so that it has no menu bar, toolbar, window title, etc. It has only a thin status bar, which gives me quick information about the document (file size, line number, remaining battery, time, etc.). When I am working on a manuscript, I will see nothing but the manuscript, which allows me to immerse myself in the work and focus.
Figure 1: My Emacs’ custom interface
- Org Mode can be used for heavy note-taking. For over a decade, I have stored all my notes in one org (plain text) file. The file size is not even close to 1MB yet. The file is organized in a very manageable hierarchy and can be exported partially or as a whole, which is very convenient.
- Org Mode provides a robust and reliable cross-referencing system for citations, figures, tables, sections, footnotes, etc.
- Emacs provides very smart window management that lets you see all your programs in one integrated window. You can see in Figure 1 that I am using it on a very tall portrait display. I can zoom infinitely in (see Figure 2) and still get my whole text without needing to scroll horizontally. As mentioned, this feature exists in Word but does not work properly, as expected from Microsoft!
Figure 2: Emacs’ zoom (like any other general text editor’s) enlarges text without adding to the width of the text. Unlike MS Word or Google Docs, Emacs lets us see and read the text without needing to scroll horizontally.
Getting started
To get started, we first need to install Emacs. You can download and install Emacs from https://www.gnu.org/software/emacs/.
You can then open Emacs by searching for it in your applications. The following video can help you get started.
For a more detailed tutorial on how to use Emacs (beyond academic writing), watch this video: