3 Useful Concepts for Organizing a Journal Manuscript

Research is a messy process, but reporting on it requires some organization for the sake of the reader

Robert Lawrence
MetaScientific
4 min readJul 23, 2024

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Investing some time and thought into how you want to organize a research manuscript before you start putting the words down can make things easier for you downstream. Here are three useful organizational concepts taken largely from the 2017 editorial in PLOS, Ten simple rules for structuring papers, by Mensh, et al. [1].

Concept 1| The Rule of One

Research is an unwieldy process, and writing about it can be too. But this should not be the experience of those reading about your research. And so before the writing begins, the manuscript author needs to define what the take home message is. In the words of Mensh, et al.:

“Focus on a single message; papers that simultaneously focus on multiple contributions tend to be less convincing about each and are therefore less memorable…This Rule of One is the most difficult rule to optimally implement because it comes face-to-face with the key challenge of science, which is to make the claim and/or model as simple as the data and logic can support but no simpler. In the end, your struggle to find this balance may appropriately result in ‘one contribution’ that is multifaceted.”

The importance of developing a single message was iterated in another commentary on manuscript writing titled, Successful Scientific Writing and Publishing: A Step-by-Step Approach, by Iskander, et al. [2].

“Scientific articles should have a clear and concise take-home message. Typically, this is expressed in 1 to 2 sentences that summarize the main point of the paper.”

Developing the take-home message can also help you decide what title to choose for your manuscript. And using this message to similarly guide and focus each subsequent section of the manuscript can prevent you from meandering too far into the weeds and too far over the word limit.

Concept 2| The Context-Content-Conclusion (C-C-C) Scheme

This is a sequential framework for organizing paragraphs, sections, and the manuscript as a whole, being mindful of placing context, content, and conclusions at the respective beginning, middle, and end. This kind of structure may seem basic and obvious, but when you get buried under pages of half-edited text in Word, it can easily get lost.

A. Context (Once upon a time…): We all know that the outlined structure of any manuscript begins with an Introduction, where all essential background information is provided to the reader. Similarly, each section should have its own introductory paragraph, and, wherever possible, each paragraph should be introduced with a topic sentence. The goal with each of these is to provide the appropriate context for what comes next.

B. Content (…and he huffed, and he puffed…): Once you’ve set the table, you can feast on the meal. Or, to be less metaphorical, after you have provided sufficient background and introduction, you can then unleash all the details. This is the main content of your paragraph, your section, and your story as a whole.

C. Conclusion (…and they lived happily ever after.): Whenever possible, adding a concluding sentence on a paragraph that ties things together can really help the flow. Concluding paragraphs in each section do the same.

Once you start looking for it, you can find versions of the C-C-C scheme all over in good literature, storytelling, and films (although maybe not in artsy films by people like Terrence Malick who take less traditional approaches). This concept also aligns nicely with another piece of advice common to writing and presentation:

“Tell them what you are going to tell them, then tell them, and then tell them what you told them.’ — Unknown origin

Concept 3 | Logic > Chronology

Extenuating circumstances might dictate the order in which you carry out certain experiments in the lab. But let logic dictate the order in which you present your methods and results in your manuscript. As Mensh, et al., stated:

“It is natural to want to record these efforts on paper and structure a paper chronologically. But for our readers, most details of our activities are extraneous. They do not care about the chronological path by which you reached a result; they just care about the ultimate claim and the logic supporting it. Thus, all our work must be reformatted to provide a context that makes our material meaningful and a conclusion that helps the reader to understand and remember it.”

As you are mapping out the most logical way to present your findings, it can be helpful to start by first making your figures and legends, and let that be your guide. Again, quoting from Iskander, et al.:

“One strategy for writing the results section is to start by first drafting the figures and tables…Identify the figures and tables that best describe the findings and relate to the study’s purpose, and then develop 1 to 2 sentences summarizing each one.”

References:

  1. Mensh B, Kording K. Ten simple rules for structuring papers. PLoS Comput Biol. 2017 Sep 28;13(9):e1005619. PMID: 28957311
  2. Iskander JK, Wolicki SB, Leeb RT, Siegel PZ. Successful Scientific Writing and Publishing: A Step-by-Step Approach. Prev Chronic Dis. 2018 Jun 14;15:E79. PMID: 29908052

Robert Lawrence is a science editor at Baylor College of Medicine. You can find his published work at www.robertlawrencephd.com

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Robert Lawrence
MetaScientific

Data visualization and science writing. Science editor in academia and biochem PhD. Published work at: www.robertlawrencephd.com