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Four or five thoughts on scientific writing

18 Aug 2016

2640 words

A few days ago I handed in my bachelor’s thesis in physics and I had a few thoughts while writing it. Some of these thoughts only apply to literature that features a lot of mathematical equations, but some apply to all academic writing, or all writing in general.

“Cite before you write” is difficult

I have the impression that a common mistake for undergrads writing their first scientific paper is that they start writing and only insert citations later. This takes a lot of time because they have to go through the whole text and remember where they read each argument they mention. Additionally, it leads to worse quality citations because many students will get lazy and only insert citations until their supervisors stop complaining.

Like anyone who thinks they’re smart, I figured I wouldn’t make this mistake when I’m writing my bachelor’s thesis. But there I was, multiple pages written, a rough outline of the entire document finished, and I still had approximately zero citations in the text.

This surprised me because, whenever I research a topic online and take notes about it for myself, I never fail to cite sources. I gather links to sources, put them at the bottom of a markdown file, and write my notes around those links.

Why did I do it wrong in the context of my thesis? The problem wasn’t that I didn’t know citing as I write would be a good idea – I’d explicitly planned to do it. My best guess is that there was too much friction in the process. In the markdown example, all I have to do is copy the link to the source, paste it into the document, and put some identifier for the link at the beginning of the line (e.g. [example]: http://example.com "Optional title"). To get a proper citation into BibTeX, I have to find the paper on Google Scholar, click “Cite”, click “BibTeX”, copy the content of the entry, open the bibliography file, paste it in, change the identifier if it looks gross, go back to my document, and enter \cite{identifier}. It’s no surprise that people get lazy if that’s what they have to do for each source.

A solution to this problem is using citation management applications. There is, for example, Zotero, which can store all your papers in a handy library. It even gives you a button for your browser to quickly add new references without digging through cite-menus on Google Scholar. Using such an app, you just add every paper you look at into your library and, from there, export your bibliography file. Then you can copy or drag the citations from your Zotero library without having to think about the details.

I find it surprising that I hadn’t heard much or thought about them until a few weeks before my deadline.

On formal tone

I was surprised to see how much the tone of scientific papers differs from that of textbooks. So far I’d only ever read textbooks, and a lot of why I was excited to write my bachelor’s thesis was that I liked the styles of some textbooks. Authors like David Griffiths or David Halliday1 write in a way that is both whimsical and easy to understand.

Here are some fun examples:

Before leaving our review of the notion of temperature, we should dispel the popular misconception that high temperature necessarily means a lot of heat. People are usually amazed to learn that the electron temperature inside a fluorescent light bulb is about 20,000°K. “My, it doesn’t feel that hot!”2

I would be delinquent if I failed to mention the archaic nomenclature for atomic states, because all chemists and most physicists use it (and the people who make up the Graduate Record Exam love this kind of thing). For reasons known best to nineteenth century spectroscopists, $l=0$ is called s (“sharp”), $l=1$ is p (for “principal”), $l=2$ is d (“diffuse”), and $l=3$ is f (“fundamental”); after that I guess they ran out of imagination, because now it continues alphabetically (g, h, i, but skip j—just to be utterly perverse, k, l, etc.). The shells themselves are assigned equally arbitrary nicknames, starting (don’t ask me why) with K: The K shell is $n=1$, the L shell is $n=2$, M is $n=3$, and so on (at least they’re in alphabetical order).3

And then I looked at articles and didn’t find a single joke in them! In fact the more papers I read, the more it felt like I was reading an entirely new language. Sentences are much longer than in non-academic writing. Most authors avoid using contractions (e.g. “can’t”, “isn’t”). Nobody puts any emotion into their writing, eliminating all traces of informality from the text. To say something “ran out” as in the second example above would probably already be too informal. It seems uncommon to add analogies to complicated explanations to make them intuitively easier to understand.

In a TED talk, linguist John McWhorter proposes that texting doesn’t harm teenagers’ writing skills because they subconsciously treat it like a form of speech rather than writing. Since writing a text message doesn’t feel like composing an essay, using lol and rofl won’t destroy the child’s ability to spell. I suspect that this compartmentalization of different means of communication is part of why formality is so important in academic writing: “Normal” written language can be imprecise but still easy to understand, if the reader and writer have shared background knowledge. Academic papers usually communicate complicated ideas where precision is important. It’s not hard to imagine that funny metaphors can easily lead to misunderstandings. So, while I don’t see how contractions would cause any problems on their own, the rule “be careful with funny metaphores” is harder to follow than “nothing even remotely informal ever”. If following either rule will lead to a well-argued paper, the latter is more efficient. Similarly, if it’s forbidden to write in terms of analogies, it’ll be easier not to be tempted to think in terms of bad analogies.

So simply writing in a way that feels very formal and fancy is a good way to make sure one’s writing stays precise without having to think about it too much.

But (1), on the other hand, “regular language” is a good tool for communication, too. We’ve all been trained to speak and write from very early on, and if you’re forced to write an basically a different language, it can slow down your thoughts and make you less efficient. Contractions aren’t “formal”, but they can make sentences more fluent and easy-to-parse. And analogies can offer valuable support for complicated explanations to steer the reader’s mind in the right direction such that they have an easier time following the text.

But (2), using formal language is not a fool-proof way to make sure all of your thinking is precise. I recently read a paper that contained the sentence, “At the inner boundary there are basically two types of reasonable boundary conditions: …” Saying words like “basically”, or “essentially”, or “reasonable” may sound fancy, but doesn’t actually explain anything.

But (3), using formal language can actually be harmful for clarity. You know how saying “I did X” sounds informal? A lot of the time, authors use “We did X” instead. This strikes me as a weird custom for papers that only have one author, but it’s still reasonably clear what the author means. It gets problematic when they start using the passive voice to sound fancy. Using the passive voice is almost always a bad idea. The reader needs to know who does what. “The stress tensor is given by …” Is that the definition? Does this follow from something? Are we assuming this? Using the passive voice is an easy way to accidentally leave out crucial information that the readers then have to figure out themselves.

Nobody ever quotes anything

I was wondering why there were so few quotations in the papers I read. Searching the internet revealed arguments like the following:

Unlike other styles of writing, scientific writing rarely includes direct quotations. Why?

  • Quotations usually detract from the point you want to communicate.
  • Quotations do not reflect original thinking.

Inexperienced writers may be tempted to quote, especially when they don’t understand the content. However, the writer who understands her subject can always find a way to paraphrase from a research article without losing the intended meaning – and paraphrasing shows that the writer knows what she is talking about.4

I get that you want to make sure the author understands the concepts they’re writing about and didn’t just copy–paste stuff from other papers without having read them first. But even so, it strikes me as wildly inefficient for them to paraphrase the same thoughts over and over in every paper they write on the same topic. You wouldn’t believe how many times I’ve read about the viscosity prescription being the big unsolved problem of accretion disc physics.

If you’re literally repeating what someone else already said, there is not much value in trying to come up with a new way to phrase it, unless you have a great new explanation. If everyone just quoted one really good explanation, they wouldn’t have to waste their time rewriting the same information and could instead spend their time doing more research.

Next, if you paraphrase everything you read in a paper and then just say, “see <Some paper>”, it can be hard for the reader to find the exact spot you’re referencing. Also, the reader has to have a copy of each paper you’re citing on hand, and find the statement you’re paraphrasing to check whether you actually understood the source material correctly. This is not optimal. On the web, this can be easily solved by putting a quotation of the relevant section, plus a reference to the original article, into a footnote. Then the reader can immediately see the sentence/paragraph what you’re referring to without having to seek out the source article. I can imagine the reason that this hasn’t caught on yet is that it doesn’t work well on paper. If you only have a limited amount of space, you don’t want to dilute your own text with foreign material – and, contrary to the web, footnotes must always take up physical space on the page.

But yeah, I’m always happy when I look at how Gwern cites sources using enormous footnotes.

TeXmacs is better than LaTeX (even though it has bugs)

TeXmacs is a WYSIWYG text editor that makes it easy to write sort of LaTeX-looking documents without the hassle of having to look at the source code and output files separately. What sets TeXmacs apart from other word processors is that you still get a lot of the benefits you expect from plain text editors. For example, one thing I like about writing in markdown is that I can see formatting control characters, like * for denoting the start and end of italics. Most WYSIWYG editors only show you the currently selected formatting options in a toolbar somewhere, which leads to the classic “Write an italicized word, write a normal word, delete the normal word, retype the normal word, argh now the new word is italicized too”-problem. In TeXmacs, when the cursor is in a region with formatting applied, it draws a little box around that region, so you can always tell what’s happening. Typesetting formulas in TeXmacs is the most pleasant experience I have ever had in my entire life and I never want to go back to writing LaTeX equations.

Unfortunately, when I started writing, I discovered bugs that occasionally made TeXmacs freeze up and I had to restart it. It seemed relatively dangerous to make myself dependent on a program that sometimes freezes, but, in retrospect, I should’ve stuck with it. I switched to LaTeX and it felt like placing individual atoms of ink on the paper. This decision probably cost me a lot of time and writing quality, since I had less time for editing.

I tried talking to people at my university about TeXmacs and most of them said, “I’m pretty happy with LaTeX,” or, “I’m pretty fast at typing LaTeX,” but once you see how fast you can really be, you will not want to go back.

My hope is that if many people use TeXmacs, it’ll get more code contributions and become less buggy, because that’s supposedly how open-source works.

Putting each sentence on a single line in your text file is a good idea

Say you use LaTeX for your writing anyway, or you write in markdown. There are two common ways to write plain-text documents:

  1. One line per paragraph. Each paragraph is contained in a single “line” of text, followed by an empty line. Most text editors wrap lines dynamically, such that these one-line paragraphs just look like normal paragraphs.

  2. Hard wrapped lines. Some people like to use old text editors like Vim. Vim isn’t very good at handling long lines that have to be displayed on multiple lines on the screen. So, instead of putting an entire paragraph into a single line, Vim users configure their text editor to insert line breaks after, e.g., 80 characters. This makes the files nice to look at in old text editors, but it makes editing more complicated: Whenever you change something at the beginning of a paragraph, the line breaks in the rest of the paragraph may no longer be in appropriate places, so you have to reformat the entire paragraph.

After switching to LaTeX, I wanted to try a technique I read about a few years back: Inserting a hard line break after each sentence or sub-clause. This sounds like a strange idea because it makes the right edge of your text look all jaggedy, but it is actually really useful.

LaTeX and markdown ignore single line breaks in the text, so the output you create is going to look the same as when you use methods 1 or 2. But if you place line breaks after periods, or important commas, it suddenly becomes much easier to delete, edit, and re-order individual sentences. Another nice feature is that you can easily see when you’re accidentally starting each sentence with the same words. And your version control system is going to love keeping track of your writing because version control systems natively operate on lines and not sentences. And you can now see how long your sentences are, because they’re visually separated from each other. This can help prevent the common problem where scientists write extremely long sentences.

Note that I’m only recommending putting line breaks in the source documents. Don’t put line breaks in published texts.

  1. Every author of good textbooks is called David. It’s true. 

  2. Chen, Francis F. 1974. Introduction to Plasma Physics. Springer, New York. 

  3. Griffiths, David J. 2004. Introduction to Quantum Mechanics. 2nd edition. Upper Saddle River, NJ: Pearson Prentice Hall. 

  4. The University of Washington Psychology Writing Center on using quotes in scientific writing