Monthly Archives: July 2018

07.18.18
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Zen and the art of revising (paper writing for PhD students pt 14)

[Previously in this series on how to write a scientific paper: how (and why) to write a crappy first draft

How to write a scientific paper, book cover

“If you feel the urge of ‘very’ coming on, just write the word ‘damn’ in the place of ‘very.’ The editor will strike out the word, ‘damn,’ and you will have a good sentence.”—William Allen White

If you have followed the advice in the last chapter, you should now be the proud owner of a crappy first draft of your scientific paper—a draft that serves as raw material, a draft that is for your eyes only, a draft that was written quickly and without too much care.

Now it is time for you to put on another hat and play a different role. It is time to look at your draft critically and to examine each and every sentence and paragraph ruthlessly so that you can cut out everything that doesn’t carry its own weight.

Before that, however, it might be a good idea to take some distance unless you are in a big hurry because a fresh pair of eyes can better spot what needs to be done.

How to revise your paper’s first draft? The process of editing and revising a scientific paper is iterative and it can take many rounds: my most-cited paper was at version number 27 or so when it was finally submitted. This may sound a bit excessive, but hey, it worked! You don’t always need to go to that length, though–just be sure to do several rounds of revisions, first alone and then with the help of your co-authors and/or your supervisor.

Just like with writing the draft, I recommend using a top-down approach when revising—begin with addressing broader issues before homing in on the details. First, read the draft quickly, without getting stuck on sentences, words, or other nitty-gritty details. Then, go through your findings: is the story logical, clear, and exciting? Does the abstract do its job and entice the reader? Is it clear what problem the paper solves? Is it clear what the solution is? Are concepts introduced in the right order? Is the paper balanced, or are there sections that are too long or sections lacking in detail?

Is it clear that your results are backed by solid evidence? Are the figures of a high quality and free of common errors such as microscopic label fonts? Does the paper begin with a proper lede – a sequence of sentences that frame the topic of the paper and entice the reader to read the rest of the story? Does the paper end on a high note?

The answers to the above questions may result in a need to “remix” the paper: to shuffle its contents around, to reorder things, and to completely rewrite some sections. This is normal: if you feel the need, just do it. Then, repeat the top-level analysis of your draft: answer the above questions again, and see if you can think of ways to improve the text further. If the answer is yes, do it. Repeat this loop until you are happy with the outcome and satisfied with the overall structure and flow of your paper. At this stage, you may even feel like returning to your research, say, to look for new results that back up your conclusion even more strongly. If so and if there is time, great, just do it, but please do remember to stop at some point because there will always be something new just around the corner. Leave some of that for the next paper.

When the overall structure is there, you should focus on the level of paragraphs and sentences. Use the same rules as for writing the paragraphs. For each paragraph, check that its topic is made clear in the first sentence or two. Check that the paragraph doesn’t stray away from the topic. If it does, cut it into two, or revise it. For each sentence, check that its meaning is clear, that it connects with the previous sentence, and that the rules outlined in the section on sentences below are fulfilled. Split sentences that are too long. Check the grammar. Use a spell checker.

Check your notation and nomenclature, and straighten them out if necessary. Do you always use the same word for describing a concept, or do you use several names for things? Is your notation consistent, do you always use the same symbols? Do you explain every symbol used in every equation?

Check your figures. Are your axis labels large enough to be seen without a magnifying class? (I repeat, this is the most common mistake in figures produced by PhD students, for reasons unknown to me: fonts whose size is measured in micrometers). Are your axis labels clear, and is the notation consistent with your body text? Are the colour schemes you use clear and informative, and most importantly, consistent across figures? Do the figure captions explain what should be learned from the figures, instead of only describing what is being plotted?

Then, finally, when all else seems in place, do a shortening edit, with the target of removing extra clutter and superfluous words. Make every sentence shorter that can be made shorter. Remove all adjectives, unless really necessary. Remove all repetition. Remove words that exaggerate things, because you sound more confident without them. Remove every instance of the word “very”, because you never need it. Remove the words “in order” from “in order to”.

When you are ready to show your improved draft to others, you can apply a technique that my research group has borrowed from the software industry: Extreme Editing.

In the software industry, extreme programming is one of the fashionable agile techniques, and part of this technique involves programming in pairs. So edit in pairs! Or, if there are more coauthors, involve as many of them as possible. Force your PhD supervisor to reserve several hours of uninterrupted quality time; you can argue that this co-editing session takes less time than several rounds of traditional red-pencil-comments.

This is how extreme editing works: go to a meeting room with a large enough screen and open the draft on the screen. Then, go through your text together, paragraph by paragraph and sentence by sentence. Be critical of each word and each sentence; look for sentences that are unclear and that can be misunderstood. Try to find ways of reducing clutter and shortening sentences. Cut out fat wherever needed. In my group, we jokingly keep a tally of points scored for every removed word. The winner is the one who has most ruthlessly killed the largest number of words that just tagged along, doing no real service to the text.

In the following two posts, I will present some more tips on how to revise your draft, first on the level of meaning and structure, and then on the level of sentences.

07.12.18
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How (and why) to write a crappy first draft (paper writing for PhD students pt 13)

For the previous episode in the series on how to write a scientific paper, see here.

“To write is human, to edit is divine” -Stephen King

The best and most productive writers do not write perfect first drafts. The best and most productive writers write crappy first drafts and they do this as quickly as possible. They then edit, revise, and polish their crappy first drafts until those are no longer crappy (and no longer drafts). Or until the deadline makes them stop, whichever comes first.

This is what you should do with your scientific paper too: write the first draft quickly, and then edit, revise, polish, rinse, and repeat, until you are satisfied with the outcome. Or until the deadline comes.

If you have followed the system outlined in this blog, you are now at the point where you are ready to write your very own crappy first draft. You have a story, you have a structure, and you have notes for each section and each paragraph. If you have read the previous chapter, you have some idea of how to organize the building blocks of paragraphs and sentences (recap: the first sentences/words tell what the paragraph/sentence is about; stick to this and keep it simple; put weighty stuff at the end). This is all you need to know for now; I’ll provide plenty of tips for editing later.

So at the time being, put all rules aside, and aim to produce to a complete first draft quickly. Embrace the words of Stephen King quoted above and forget perfection when it comes to the first draft—let it be human, let it be imperfect. Let it be crappy! Why? Because producing and then polishing a crappy first draft is much, much faster than agonizing over every word and sentence and making only perfect choices that take forever to make. When all that time is spent on editing and revising instead, the outcome is much better.

Now that you have to finally produce some text, this is where the pain of writing typically hits you. Coming up with plans and storylines can be fun; writing rarely is. Writing is hard work. Writing the first draft is particularly hard work because not being self-conscious of your words is hard, and because not letting your inner critic stop you in mid-sentence is hard. These demons are difficult to wrestle but wrestled they must be, otherwise, there is no progress and the pages remain blank.

How to ease this pain, especially if you are a novice and it feels overwhelming? How to write all that text that needs to be written before you have a paper? There are some techniques that may help you.

First, make the first draft your own little (crappy) secret. It is not for your supervisor’s or co-authors’ eyes—it is for no-one else’s eyes, it is only for you, and it serves as raw material for editing only. When your supervisor asks you for the first draft, you should give her your second draft instead—by all means, call it the first draft! Keeping your first draft private should make you less self-conscious, at least in theory: no-one else will ever see it.

Second, aim at producing more text than you need. Just let the words come! At this stage it’s OK to have sentences that are too long, it’s OK to repeat yourself, it’s OK to explain the same thing over and over again with different words. In particular, if you are writing, say, one of those 4-page letters with a restricted word count, do not worry about the length at all. Just write. Cutting text is easier than producing it, and the editing phase easily reduces the length of your text by 10-30%. In my experience, the more, the better the final product.

Third, to be productive, schedule writing time and stick to it. Never wait for inspiration to strike, because it rarely strikes those who just sit there waiting. The Muses dislike idleness; they tend to show up when you are already engaged in work. Just sit down, put your phone on silent, remove all clutter from your screen, shut down your Internet access, and do it. Write. A good target is something like 30-45 minutes of uninterrupted writing, followed by a break. For a really good day’s work, four to five of such sessions are already enough. Just keep on doing this daily until you find yourself at the end of your first draft.

Fourth, if you get stuck, try changing the way you write. Take a pen and a notepad and walk away from the computer. Sit down somewhere, get a cup of decent coffee, and sketch your sentences on paper. Try to write as if you would be making lecture notes or just jotting down ideas. When unstuck, go back to your computer and use the material in your notes to continue. Or, instead of a notepad, try dictation, or go for a walk and play out imagined conversations in your head where you explain whatever it is that you are supposed to be writing to someone.

If you are very self-conscious and find it hard to make progress because of that nasty voice in the back of your head, you might want to try something along the lines of the Morning Pages technique. This technique provides desensitization by stream-of-consciousness writing: every morning you take a pen, a journal, and write longhand three whole pages, filling them with anything that comes to your mind. This may feel rather difficult at first; just keep on doing it. Morning Pages were introduced by Julia Cameron in her book The Artist’s Way as a tool for artists to connect with their creativity and overcome whatever fears hold them back. If you’d like to use this technique to help you write your paper, you can fill those three pages with thoughts on your research. See where this leads you.

If nothing else helps and it feels impossible to make progress, stop for a while and think about why this would be. What would need to change for the words to emerge from wherever it is that words come from? Usually, if I find myself in this situation, the answer is that the problem lies not with words or with writing but with thinking: there is something that I don’t yet understand, some pieces that don’t yet fit. Then, the solution is to stop writing (this part of the text, at least) and to solve the underlying problem instead. So take a time-out, and look for understanding first; the words will come more easily when you have found it.

Next: how to edit the first draft of your scientific paper

07.04.18
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Paragraphs, sentences, and a toy model of your reader’s mind (Paper writing for PhD students pt. 12)

coverdraft2

[For the previous post in the series, see here]

“Words are to sentences what atoms are to molecules: the basic building blocks that control structure and function. If we extend that analogy, paragraphs become cells: the fundamental unit of life. A cell gains life from its structure, a structure that creates internal cohesion and external connection, allowing it to function as part of a larger organism.” —Joshua Schimel, Writing Science

Finally, after all this planning and outlining, it is time to start filling in the blanks. It is time to write words that form sentences that form paragraphs that form sections that form your story.

Because of the top-down approach that has brought you here, coming up with words and sentences should be easier than having to start with a blank page. You should already have an outline of the paper as well as notes for each paragraph—now you only need to turn those notes into full sentences!

From the point of view of the reader, the best sentences are those that are easy to understand, that make the story flow, that tell the right things in the right order, so that the reader can always expect what comes next. From the point of view of the writer, this is achieved if the writer feels empathy for the reader. A good writer tries to look through the reader’s eyes, taking the reader’s hand and guiding her through the text, making the reader’s job as easy as possible.

To guide the reader through the text, the writer has to gently manipulate the short-term memory of the reader. It has been argued that one’s short-term memory can only hold seven things—such as digits—at a given time. When it comes to concepts that are more complex than digits, even seven sounds like an awful lot to me. There is only so much one can hold in his head.

When a piece of text feels too hard to grasp, this is often not only because the ideas therein are difficult. Instead, there may be a problem with the sentences that should deliver those ideas. This has to do with the order in which the concepts that the sentences contain are placed into the short-term memory of the reader. Bad writing randomly jumps from one thought to another. This creates a traffic jam of thoughts and ideas without giving a clue as to how they relate to one another.

What, then, is the right order of things? How to choose what comes first in a paragraph or in a sentence? To answer this question, we have to understand how the reader processes information—how the reader reads. To this end, let’s construct a toy model of the reader—think of the reader as an automaton of sorts, with three types of memories that you can manipulate. Each type of memory plays a role in interpreting and understanding the paragraphs and sentences that the reader encounters.

The first, long-term memory contains the key concepts that are required for understanding the paper. Using the film script analogy, these are, if you like, the world of your story and its inhabitants. This memory is initialized in the Introduction, and populated with more characters and events as the reader reads. Whenever new concepts become established in the paper, they are added to this memory.

The second, intermediate-term memory contains concepts essential for connecting the dots currently in front of the reader—for making sense of things in the current paragraph and in the current sentence. In particular, this memory contains the topic of the current paragraph (or the reader’s interpretation of it). Not all concepts remain in this memory for long: many are flushed out at the end of each paragraph. If you know time series analysis, you can think of this memory as a sliding window of sorts.

The third, short-term memory holds the concepts that are required for making sense of the current sentence, as in “what is the subject of the sentence, what is the verb, what is the object”, or, “what does what to what”. In addition to grammar, the short-term memory is essential for relating the concepts encountered in the sentence to one another. As the reader reads, the words and concepts of a sentence are placed in this memory in their order of appearance. This memory is flushed at the end of each sentence.

How do these memories work? When the reader reads, she consumes the words from the left to the right and interprets them with the help of all the memories. The long-term and intermediate-term memory help to extract the meaning in the sentences. They also and set the reader’s expectations, “bias the reader” if you will, and determine how words and concepts are interpreted. The short-term memory is used to parse the current sentence and to connect its words to one another.

If all goes well and the reader understands the words in front of her, the concepts that those words hold are first put into the short-term memory, to be flushed out at the end of the sentence. The higher-level concepts formed by the words in the short-term memory are placed in the intermediate-term memory, to be used in deciphering the rest of the paragraph. At the end of each paragraph, this intermediate-term memory is given a vigorous shaking so that those concepts that are unnecessary baggage fall out, never to be seen again. But those that stay and prove to be useful may transcend to the first, long-term memory.

But if the reader encounters something that is inexplicable—something that doesn’t match with anything in any memory stack—an error occurs, and the reader is lost. Or, worse, if the reader uses a wrong concept to parse the current sentence, she can become entirely derailed.

Because of the way this parsing automaton operates, the first words of a sentence are tremendously important, as is the first sentence of a paragraph.

The first words of a sentence initialize the short-term memory, determining how the rest of the sentence is understood—they define the topic of the sentence. Then, when the reader reads on, the words that she encounters are seen interpreted through the lens of the topic. As more and more words accumulate in the memory, the reader is trying to tie them together and make sense of the sentence. The more words there are, the more difficult this gets (think combinatorial explosion). In particular, if the sentence is constructed such that its meaning hinges on the last word(s), it becomes taxing to read.

So, from the point of view of our short-term memory model, the perfect sentence begins with words that clearly define its topic, and is not too long. Any superfluous words like “very” wherever it appears or the “in order” in “in order to” just make the reader’s job more difficult by increasing the number of possible combinations. Also, it helps if the order of words allows one to parse the sentence up to the current word, so do keep the subject and verb close. And one more thing: place familiar words and concepts at the beginning of the sentence, and use them to explain any words or concepts that might be unfamiliar to the reader that appear later on in the sentence.

When it comes to paragraphs, the first sentence of a paragraph establishes its topic, and this topic is stored the intermediate-term memory for interpreting the rest of the of the paragraph. So always make sure that the first sentence of each paragraph is well-chosen and clearly tells the reader what the paragraph is about. This sentence sets the expectations of the reader and determines how the reader will attempt to interpret everything that follows. Always stick to the topic in the rest of the paragraph—an unexpected, unconnected sentence breaks the flow and leaves the reader baffled. But a sentence that makes sense in light of the topic will be interpreted properly, setting expectations for the next sentence as well.

One way to make the topic of the paragraph clear is to begin with a phrase that acts as a signpost that clearly tells the reader where the paragraph is going. Examples include “To measure how X depends on Y, we constructed an elaborate apparatus…” and “In conclusion, in this paper, we have shown that…” When the reader knows what to expect, interpreting the rest of the paragraph is easier.

But not only beginnings are important—endings matter, too, just like for stories. Because the end of a paragraph and the end of a sentence signal a break, the reader has more time to think about the last few words. Therefore, the last words carry extra weight in the mind of the reader, almost unconsciously.  Place important things in these stress positions, things that you want to emphasize.

Next: how to write your first draft.