Autumn colours for complexity aficionados (photos)

Here is a collection of photos taken on long stroller walks with the little one sleeping, taken in Espoo, Finland, where the autumn is slowly approaching. I took a few photos for fun and then couldn’t stop looking at things from the can-you-spot-the-complexity perspective. There are lots of interesting patterns out there, from spiral waves and spreading fronts to symmetrical shapes. So here’s some natural Nordic complexity, enjoy!

How to write the cover letter (paper writing for PhD students pt 17)

Previously in this series on how to write a scientific paper: ten tips for editing your sentences.

Now that you have revised and polished your draft and are the happy owner of a shiny new manuscript, one more step remains before you can submit it to a journal: writing the cover letter.

The cover letter is, in my view, mostly a historical remnant. Having to write one is, consequently, rather annoying. I can see that there may be some reason for cover letters for journals where the papers are too long to be skimmed by the editors, but even then, I doubt whether cover letters are of any use. Let me explain.

The point of the cover letter is to convince the editor that your manuscript is solid and important and that it fits their journal. But this is something that the abstract should do in the first place, especially if it follows the broad-narrow-broad formula outlined earlier in this series. The paper itself should do the job, too. In particular, the paper’s introduction should contain all the information that the editor needs to decide whether the paper is in the journal’s scope. It should also be enough for gauging whether the results sound believable and important enough for the paper to be sent to referees, instead of bluntly desk rejecting it. So why repeat all this information in a redundant letter?

So a big thank you to those journals who no longer ask for a cover letter.

Was I an editor, hard pressed on time, whose journal demands cover letters, I would highly appreciate a cover letter that is focused and short, say three to four paragraphs, max one page, preferably less. Here are two ways to write a short cover letter with only a few paragraphs and less than a page of text.

The better but slightly more adventurous way is to follow the inverted-pyramid schema that journalists commonly use for news stories. Most scientists are not used to writing this way! When following the inverted pyramid, you should begin with the most important thing and then proceed towards less important things, the nice-to-know details of the story, one by one and in order of decreasing importance. Tell what you have found in the very first sentence or two, then tell why your finding matters, and only then say something about how you obtained your results. Do not write a detailed explanation of your methods unless they are the key point of the paper; the editor is probably too busy to care, and if not, the details can be found in your manuscript. This way of structuring the letter is particularly suitable for those top-tier journals whose editors desk-reject most of the papers that they receive— they do not have the patience to search for the main point if it is buried somewhere on page two of your letter. They want to hear it first and then decide.

As a side note, the inverted-pyramid structure should always be used for press releases; those are read by journalists, not scientists, and journalists only get confused if they have to wade through lengthy introductory material before the main point arrives.

The other, more traditional way is to structure your cover letter in the same way as the abstract, or the Introduction section. Begin with the broad context, and then narrow the scope down and proceed towards your specific research question. After stating the question, tell what you have found out and how, and why what you have found out matters. But please be swift and move quickly: the first paragraph for context and question, second paragraph for the key result, and the third paragraph for significance.

You can also consider writing a hybrid version of the traditional cover letter and the inverted-pyramid lede. First, state your key result in a single-sentence paragraph: “In this manuscript, we show that X”. Then, follow the structure of the abstract and explain the context and the question in the second paragraph, a more detailed explanation of the result in the third paragraph, and an account of its significance in the fourth paragraph.

Whichever structure you choose, put emphasis on the implications and impact of your results. The why-does-it-matter part matters more than the how-did-you-do-it part, even if you have used particularly inventive methods. Do not exaggerate; rather, tell honestly what your work means. Whenever you feel like typing the word “very”, take a deep breath, command your fingers to stop, and jump directly to the next word.

Cover letter: if you have to write one, keep it simple, keep it short, put important stuff first, tell why your work matters.

 

Ten tips for editing your sentences (paper writing for PhD students pt 16)

Previously in this series on how to write a scientific paper: ten tips for revising your first draft

I have also condensed this post into a downloadable cheatsheet—click here for it!

After you have finished with your first pass and are now happy with the overall shape of things, it is time to polish the micro-level structure of words, sentences, and paragraphs. Once again, your overall goal should be simplicity, clarity, and readability. You can achieve this goal by cutting out everything that is not necessary. Condense and straighten your sentences so that they are short, to-the-point, and easy to follow. When editing your sentences, pay attention to these points:

  1. Ensure that each sentence in a paragraph belongs to that paragraph: the first sentence defines the topic of the paragraph, and the rest stick to the topic. If a sentence goes off in a tangential direction, delete it or move it elsewhere; if the paragraph is long and its topic appears to change on the way, split the paragraph into two or more.
  2. Check that your sentences follow one another logically and that there are no jarring, abrupt changes in direction. Tie your sentences together with transitional words. Begin your sentences by addressing the words or concepts that finished the previous sentence, or use conjunctions that refer to the previous sentence (however, in addition, to the contrary, and so on).
  3. Check sentence length; aim at short, precise sentences. Try to make every sentence shorter by rephrasing the idea using fewer words and cutting out words that do no work. Those lazy words include repetitions and unnecessary adverbs and adjectives—almost always, if you remove “very”, your sentence will be tighter. Also look out for wordy expressions involving the passive voice or nominalizations of perfectly good verbs (see below). Tighten your sentences, remove redundancy. Rejoice for every word that you cut!
    If your sentence still feels too long after tightening, look for ways of splitting it. Long sentences are taxing to read because the reader has to hold a great number of words in her short-term memory: about 25 words is already at the limit. You do not need to count words for spotting sentences that are too long, though. You can spot those sentences visually (if a sentence spans several lines, it is too long) or, better, by reading your text aloud. Wherever you stumble or run out of breath, you have a problem.
  4. Make meaning early in the sentence, and keep your subject and verb close. If the first words tell who does what, it is easier to decipher the rest of the sentence. If the main point of the sentence becomes clear in the beginning, even wordy sentences can be comprehensible. But if the meaning of your sentence is only unlocked by its 27th word, the long and winding road there will be littered with the remains of readers who have perished from utter mental exhaustion.
  5. Use active voice and avoid the passive (for exceptions, read on). There is a long tradition in the scientific literature to use the passive voice, probably because the passive voice sounds more distanced and impersonal—somehow more “academic”. But when anyway writing about abstract concepts, there is no reason for making them any more abstract, impersonal, or distant! So it is time to get rid of this tradition: avoid the passive wherever you can.
    How to spot the passive when editing? Easy—if your sentence ends with the actor (“by X”) or if you can insert “by zombies” to the end of the sentence without violating grammar. Whenever you spot a passive sentence, try to rephrase it and activate the verb. “X influences Y” is better and shorter than “Y is influenced by X”. If you use active verbs, your sentences will be stronger, shorter and more readable.
    You do not need to always use the active voice, though. There are times when the passive voice works better; some concepts and elements sound out of place if made actors. It is OK to use the passive voice when the researcher wants to remove herself (or other researchers) out of the picture. Common examples include “it has been experimentally confirmed that” or “it has been argued that” (in particular if you disagree with the argument but do not want to name the culprits). Also, if you want to stress whatever is being acted upon, that is, the receiver (or victim) of action, use the passive voice. “The climate is influenced by greenhouse gases” stresses the word “climate”, whereas “greenhouse gases influence the climate” focuses more on the greenhouse gases.
  6. Avoid nominalizations—turning verbs into nouns. Nominalizations take the life out of perfectly good verbs. And because what was once a happy, active verb has now been shrunk into a sad noun that just sits there, doing nothing, a replacement verb is required. These are usually clunkier and duller, like “carry out”, “perform”, “conduct”, or plain “to be”. In addition to sounding like company-speak, these verbs make your sentences longer than they need to be.
    When you happen to come across nominalizations, rescue and release the original verb from captivity and let it roam free again! Say “we compared” instead of “we performed a comparison”, say “we examined” instead of “we conducted an examination”, and say “we analysed” instead of “we carried out an analysis”.
    How to spot a nominalised verb? Nouns that have a captive verb inside, waiting to escape its torment, often sound like French or Latin—they end with “-ion”, “-ence”, or ”-ment”. Adjectives can also be nominalized into nouns, and there can even be chains where “to differ” becomes “different” that becomes “difference”. The difference between these forms is that “X differs from Y” is much simpler than “there is a difference between X and Y”. And shorter by 21 characters!
  7. Avoid words that end in “-ive”—those are adjectives that have a verb inside, struggling to get out. Release the verb! Instead of “X is indicative of Y”, say “X indicates that Y.”
  8. Comb your text for clunky expressions that are simpler and shorter in plain English. Plain “because” is much more effective than “as a consequence of” or “due to the fact that”. “Although” works better than “despite the fact that.” Do not say “for the purpose of” when you can simply say “to”, or “for”. Search for “in order to” in your text; replace with “to”. Search for “such as” in your text; delete these words and rewrite the sentence without them and it will sound better. For more examples—and a convenient search-and-replace list—see http://plainenglish.co.uk/files/alternative.pdf.
  9. Search for “moreover” in your text. Delete it. Rewrite the sentence using perfectly good simple words – “besides”, “in addition”, “also”– that are common in everyday speech. No-one says “moreover” anywhere else than in scientific journals; people probably use this word only because they saw someone else use it.
  10. Avoid using jargon and complicated words as a blanket, to feel secure. Excessive amounts of jargon often result from thinking that for something to sound academic and scientific, it has to be complicated, full of expressions that no-one uses in everyday speech. This is wrong. The more simple and the more clear your writing is, the more authority it has. It is more difficult to trust a writer who hides her point behind a facade of long sentences and complicated words; these feel like smoke and mirrors, tricks to hide the absence of depth. You do not appear more intelligent if your writing is too complex, to the contrary of what many seem to believe. However, if you use words that everyone can understand to explain complicated issues, Richard Feynman would be proud of you. Science is difficult enough as it is—do not make it any more complicated with your writing.
  11. Bonus tip: learn from the masters. Get The Elements of Style by Strunk & White, and do as the masters tell you. Your readers will thank you for it.

Next: how to write the cover letter

Newsflash: the book based on this series is now available in most digital stores—click here for direct links!

Ten tips for revising your first draft (paper writing for PhD students, pt 15)

Previously in this series on how to write a scientific paper: Zen and the art of revising and, if you didn’t read this yet, how (and why) to write a crappy first draft

“Don’t use big words. They mean so little.” -Oscar Wilde

When editing and revising your paper’s first draft, my suggestion is to do two passes: first, a pass that focuses on the broader issues of structure and content, and then a second pass that focuses on the nitty-gritty, sentence-level details. In this post, I will present ten tips for revising your draft that can be used as a checklist for the first pass; this list contains issues that I frequently come across when working with students and revising papers.

If you have read this series this far, you won’t be surprised to see that most of the issues have to do with clarity and focus.

  1. Check that the abstract follows the hourglass structure: broad context, narrower context, the research question, your result, implications of your result on your (sub)field, its broader implications. Also, do make sure that your abstract is as jargon-free as possible: only use words that most readers can understand.
  2. Check that your paper is focused. Choose the point of the paper and its key conclusion before you begin writing, stick to your choice, and write the paper so that the reader gets the point already in the abstract and in the introduction. Leave out results that are not required for supporting the key conclusion, or safely tuck them away in the supplementary information document. When editing, if you feel that your paper loses its focus at some point, take a step back and do a major rewrite.
  3. Check that there is a clear question and a clear answer. A good paper states and then solves a problem; your results are meaningful only if they solve a meaningful problem. Remember that your paper is neither an account of your work nor a lab diary; it should be a story of an important problem and its solution. Emphasise the problem, both in the Introduction where it should really stand out, and in the Results section and the Discussion. Make it clear to the reader how each result contributes to solving the problem, and what the implications of solving the problem are.
  4. Check that the figures tell your story. If you just glance through the figures and skim their captions, do you get the point of the paper and its take-home message? If not, go back and revise—after all, skimming is what most of your readers do.
  5. Check that the reader can replicate your results. Verify that your Methods section (and the supplementary sections if any) contains everything that the reader needs to know. Also, check that you provide links to your code and your data if it can be released without violating anyone’s privacy.
  6. Check that you end the paper with something worth remembering. This means something concrete. “More research is needed” is a platitude and a vague one at that; better, go for something like “because of the results of this paper, we are now in a position to tackle problem X with method Y, bringing us closer to the ultimate goal of Z”. This is far more concrete and memorable. Endings have power; do not waste this power.
  7. Check that you provide enough background information: your reader does not know what you know. Assuming that your reader knows much more than you and therefore omitting background information is a very common problem with students. A typical example would be a Methods section that directly launches into what you have done without first telling why. Although it is evident to you that to get from A to B you need to do X, this is probably far less obvious to the reader. If you only tell the reader that you did X, she is confused. Why did you do X? Never assume that the reader knows your motivation, or the details of every method you used, or why your research question is important. Tell her.
    Many students seem to think that they know little while everyone else knows a lot—therefore they shouldn’t explain things that everyone probably already knows. It is only later in their careers when they realise that no-one really knows that much! Besides, there will be readers from adjacent (sub)fields and readers who are just learning the tricks of the trade. Use a colleague who works on something slightly different than you as a test reader—ask her which parts of the text are hard to follow, and revise accordingly.
  8. Make sure that you take the reader’s hand and lead her through the text with signposts. Or, in other words, check that your writing is not confusing. Writing is, in part, psychology, and it aims to modify your reader’s state of mind and to influence what your reader thinks. Feel empathy for your readers and try to get inside their heads, assuming that they know nothing or very little. Your empathy should be reflected at the level of sentences and paragraphs: present familiar things first before moving to new concepts, use leading sentences, glue your sentences together with expressions that guide the reader. Use subheadings. Gently lead the reader from result to result, from paragraph to paragraph, and from sentence to sentence. Never leave it to the reader to connect the dots— always connect them for her. Err on the side of caution: papers where things have been over-explained are rare (if they exist at all), but papers that are all too difficult to follow are frustratingly common.
  9. Check that you are consistent with nomenclature and notation. Because you have been immersed all too long in the world of your paper, this problem may be hard to spot for you—using an outside reader as a guinea pig is recommended. Problems with notation are easier to detect; problems with naming things are more difficult. Often, while doing research and while conceptualising the paper, there is a number of concepts floating around, and the very same things can have many names in your thinking. Writers of fiction are allowed to use synonyms for variation, but science should be precise: in the final version of your paper, everything should be called by one name only. While it may be evident to you that the thing you call the weight matrix is the same as the thing that was called the correlation matrix in the previous paragraph, your reader quickly gets confused. Never refer to the same thing with multiple terms.
  10. If you feel that it is impossible to get some part of your text just right, this is often a sign, a message from you to you. When you are stuck with a paragraph that just won’t yield, stop trying to force it. Instead, ask yourself: why is this so difficult? Search your feelings. What would make the paragraph easy to write, what are you missing? Often, you will notice that you are not faced with a writing problem at all—rather, you miss some important piece of understanding. Perhaps your result is not clear after all, or you have not thought enough about some tricky issue and that is why you cannot express it in words. So take a time out, and look for understanding first; the words will come more easily when you have found it.

New to this series? It begins here: Why can writing a paper be such a pain?

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.

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

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.