Writing your manuscript
Writing your manuscript
A well-written paper will broaden the reach and impact of your data. These days, a compelling paper can also lead to invitations to give talks at conferences or write reviews, or serve as the cornerstone of a job or grant application, so it’s worth investing time in this part of the process. The guidelines below can help you construct a clear and captivating document so the data you’ve spent so much time collecting will really stand out.
Start with an outline to map out both the necessary background information to understand the context and motivation for your study as well as the logical flow of your results to help the reader understand the basis for new conclusions drawn. Keep in mind that the order in which experimental data are presented does not need to match the order in which they were obtained.
Be clear as to what your assumptions are, what hypotheses you’re testing, what alternative explanations for your data exist or can be ruled out, and when you’re proposing new ideas or models that reach beyond what has been directly demonstrated at this time.
Don’t be discouraged if you’re not a natural writer or native English speaker – the most effective text can be quite simple linguistically, as long as there’s a logical structure.
Ask colleagues from within the field to read the paper to look for inconsistencies or missing methodological details that could hamper review, and colleagues from related fields to read for jumps in logic or missing background information that could limit accessibility to the journal’s readership. And be prepared to return the favor!
At JBC, all the data needed to support your central conclusions should be in the main text, with the Supporting Information section used judiciously for information like data replicates, larger datasets, videos, and other content not suitable for layout in the article.
For additional JBC-specific information on manuscript preparation and journal style, please read our instructions to authors.
Download brief instructions on writing effective and informative titles and abstracts here.
Titles and abstracts
The title and abstract are the entry point to your paper, giving you the opportunity to capture a reader’s attention with a clear and compelling message, including an explanation of what your motivation was, what you’ve done and what it means. These strategies will help you maximize the reach of your manuscript and thus its potential for impact.
State the main finding of your work as a central thesis rather than multiple interconnected stories (i.e., ‘Dynamics alter the kinetics of enzyme X’ rather than ‘Motions in the C-terminal domain of enzyme X alter the off rate while flexibility in the N-terminal domain increases the on rate’). If the stories in the paper aren’t sufficiently related such that they can’t be condensed into a more general message, consider whether they belong in the same paper.
Keep it short! Studies suggest that papers with short titles are cited more often.
Draft several titles and read them aloud to see which ones flow easily.
Make sure the title truly fits with the focus of your paper: If you had drafted a provisional title before you started writing your paper, check that it still describes the central message when you finish.
Avoid specialized terms as much as possible. Check for journal-specific lists of abbreviations that can be used without definition; JBC's list is here.
Be sure your abstract includes:
Two or three introductory sentences explaining the general scientific context and the motivation for your research.
A specific statement of the research gap or question you sought to address or hypothesis you sought to test.
The central methods used and the key results obtained.
The major conclusions drawn, how they influence our understanding of the broader picture and any immediate implications that should be explored further.
Use 150-250 words to fully capture the paper’s content while being brief enough to be read quickly.
Let verbs (not nouns) do the work
Use strong verbs
Use simple words and expressions
Use the active voice
Avoid clunky and long word clusters
In formal writing, authors often tend to use nouns to express actions, a habit that can steal a statement’s momentum and sometimes even obscure the action. Consider, for example, An increase in catalytic rate was observed at 37°C. Although it’s a fairly simple, straightforward sentence, it’s slow to get to the point, and readers may be left wondering which of the two nouns (increase and catalytic rate) they should focus on. Rewording this to The catalytic rate increased at 37°C converts the noun increase to a verb directly relating the action and also making the sentence shorter.
Also beware of constructions like Copper acts as an activator for enzyme X; just converting the second noun (activator) to a verb (activate) greatly simplifies the sentence: Copper activates enzyme X.
Strong verbs are those that capture and engage readers by bringing an action or event to life. Conversely, weak verbs fail in that task. So how can we tell strong from weak verbs? A strong verb will produce a familiar and memorable image in the mind of a reader, whereas a weak verb will merely fulfill its grammatical role in the sentence.
For example, when you revise the sentence The N-terminal domain of enzyme A connected with the variable region in Enzyme B to The N-terminal domain of enzyme A latched on to the variable region in Enzyme B, the relatively bland verb connected becomes the more dynamic verb latched on.
A similar revision in the aforementioned sentence The catalytic rate increased at 37°C to The catalytic rate accelerated at 37°C also conjures up a more striking image.
The latter is a good example that strong verbs also add variety: usage of increased (which is not a weak verb per se) is totally fine unless you use it two or more times in the same paragraph, in which case you want to think about enlisting a more dynamic verb. So a good dose of strong verbs both enlivens your writing and helps you and the reader get out of a rut of recurring expressions.
Some writers find it tempting to use unfamiliar or “big” words when common and short words will do a much better job. Such examples include utilize (which typically denotes finding a new use for something) for use, methodology for method, following for after, and so forth.
There’s nothing wrong with occasionally using longer, less familiar words for variety or flourish. But it’s worth bearing in mind that most scientific writing is already very heavy on long and complex words. When you choose simpler words whenever you can, your readers are more likely to stay with you.
The same goes for lengthy expressions where shorter ones will do. Obvious candidates are redundant expressions like past history for simply history and wordy phrases that have a way of sneaking in every so often: due to the fact that rather than because, during the course of rather than during, and so on. Getting rid of excess verbiage frees up valuable space for important details, especially in the abstract in which word limits mandate economical writing.
Imagine you’re riding in a car and the driver is speeding. Which of the two phrases would you use to warn the driver? Change speed or Slow down?
It would seem obvious that you would choose the more precise Slow down, yet in scientific writing, authors frequently use imprecise verbs to describe an action or observation: Ligand A modulated receptor B. Does modulated really tell us what ligand A did to receptor B? It does not, because modulated could mean many things: for instance, ligand A might activate, inhibit, or block receptor B. Revising this to Ligand A reversibly inhibited receptor B gives the reader a much clearer idea of what happened in this interaction.
Similarly, Exposing the cells to factor A led to large changes in gene expression, including genes in pro-inflammatory and oxidative stress pathways tells the reader fairly little. Refining this statement to Exposing the cells to factor A increased expression of genes involved in pro-inflammatory and oxidative stress pathways by up to 100-fold removes a lot of vagueness and adds precision (if you have the data to support these statements).
Being active usually beats being passive, a fact that also applies to writing. A study of the effects of constrained residues on protein folding was conducted is much more blurry and sluggish than We conducted a study of the effects of spatially constrained residues on protein folding (or even better, We investigated the effects of spatially constrained residues on protein folding).
The first sentence, written in the passive voice, distances the author from the reader because it fails to make clear who conducted the study, and it also unnecessarily puts the action was conducted into the sentence’s power position, that is, at the end. The revised sentence uses the active voice, which clearly identifies the authors as the actor and puts the research topic protein folding into the power position.
Scientific writing is often dense with specialized terms, so it’s all the more important not to overwhelm the reader with long chains of them. Can you read Crystallization of motor protein X was used for spontaneous power stroke angular velocity profile determinations without feeling lightheaded?
Even if some readers could unpack this long chain of nouns and adjectives, you probably have only very few missteps left until they eventually lose interest and stop reading your work. If you find yourself in the habit of assembling long word chains, you may want to pause after writing three nouns and adjectives in a row before adding another one. That’s because three is roughly the number of individual words most people can readily absorb as a unit.
Sorting words into smaller packages and hyphenating words that modify the same noun is a fairly easy remedy to fix unwieldy noun clusters: We used protein crystallization to determine the angular-velocity profiles of spontaneous power stroke in motor protein X. The resulting sentence is a little longer but much more comprehensible.
Green, A. E. (2013) Writing Science in Plain English, University of Chicago Press, Chicago
Schimel, J. (2012) Writing Science: How to Write Papers That Get Cited and Proposal That Get Funded, Oxford University Press, New York
Zeiger, M. (2000) Essentials of Writing Biomedical Research Papers, 2nd Ed., McGraw-Hill, New York