I. Structure and Approach
The introduction is the broad beginning of the paper that answers three important questions for the reader:
- What is this?
- Why should I read it?
- What do you want me to think about / consider doing / react to?
Think of the structure of the introduction as an inverted triangle of information that lays a foundation for understanding the research problem. Organize the information so as to present the more general aspects of the topic early in the introduction, then narrow your analysis to more specific topical information that provides context, finally arriving at your research problem and the rationale for studying it [often written as a series of key questions] and, whenever possible, a description of the potential outcomes your study can reveal.
These are general phases associated with writing an introduction:
1. Establish an area to research by:
- Highlighting the importance of the topic, and/or
- Making general statements about the topic, and/or
- Presenting an overview on current research on the subject.
2. Identify a research niche by:
- Opposing an existing assumption, and/or
- Revealing a gap in existing research, and/or
- Formulating a research question or problem, and/or
- Continuing a disciplinary tradition.
3. Place your research within the research niche by:
- Stating the intent of your study,
- Outlining the key characteristics of your study,
- Describing important results, and
- Giving a brief overview of the structure of the paper.
NOTE: Even though the introduction is the first main section of a research paper, it is often useful to finish the introduction late in the writing process because the structure of the paper, the reporting and analysis of results, and the conclusion will have been completed. Reviewing and, if necessary, rewriting the introduction ensures that it correctly matches the overall structure of your final paper.
II. Delimitations of the Study
Delimitations refer to those characteristics that limit the scope and define the conceptual boundaries of your research. This is determined by the conscious exclusionary and inclusionary decisions you make about how to investigate the research problem. In other words, not only should you tell the reader what it is you are studying and why, but you must also acknowledge why you rejected alternative approaches that could have been used to examine the topic.
Obviously, the first limiting step was the choice of research problem itself. However, implicit are other, related problems that could have been chosen but were rejected. These should be noted in the conclusion of your introduction. For example, a delimitating statement could read, "Although many factors can be understood to impact the likelihood young people will vote, this study will focus on socioeconomic factors related to the need to work full-time while in school." The point is not to document every possible delimiting factor, but to highlight why previously researched issues related to the topic were not addressed.
Examples of delimitating choices would be:
- The key aims and objectives of your study,
- The research questions that you address,
- The variables of interest [i.e., the various factors and features of the phenomenon being studied],
- The method(s) of investigation,
- The time period your study covers, and
- Any relevant alternative theoretical frameworks that could have been adopted.
Review each of these decisions. Not only do you clearly establish what you intend to accomplish in your research, but you should also include a declaration of what the study does not intend to cover. In the latter case, your exclusionary decisions should be based upon criteria understood as, "not interesting"; "not directly relevant"; “too problematic because..."; "not feasible," and the like. Make this reasoning explicit!
NOTE: Delimitations refer to the initial choices made about the broader, overall design of your study and should not be confused with documenting the limitiations of your study discovered after the research has been completed.
ANOTHER NOTE: Do not view delimitating statements as admitting to an inherent failing or shortcoming in your research. They are an accepted element of academic writing intended to keep the reader focused on the research problem by explicitly defining the conceptual boundaries and scope of your study. It addresses any critical questions in the reader's mind of, "Why the hell didn't the author examine this?"
III. The Narrative Flow
Issues to keep in mind that will help the narrative flow in your introduction:
- Your introduction should clearly identify the subject area of interest. A simple strategy to follow is to use key words from your title in the first few sentences of the introduction. This will help focus the introduction on the topic at the appropriate level and ensures that you get to the subject matter quickly without losing focus, or discussing information that is too general.
- Establish context by providing a brief and balanced review of the pertinent published literature that is available on the subject. The key is to summarize for the reader what is known about the specific research problem before you did your analysis. This part of your introduction should not represent a comprehensive literature review--that comes next. It consists of a general review of the important, foundational research literature [with citations] that establishes a foundation for understanding key elements of the research problem. See the drop-down menu under this tab for "Background Information" regarding types of contexts.
- Clearly state the hypothesis that you investigated. When you are first learning to write in this format it is okay, and actually preferable, to use a past statement like, "The purpose of this study was to...." or "We investigated three possible mechanisms to explain the...."
- Why did you choose this kind of research study or design? Provide a clear statement of the rationale for your approach to the problem studied. This will usually follow your statement of purpose in the last paragraph of the introduction.
IV. Engaging the Reader
The overarching goal of your introduction is to make your readers want to read your paper. The introduction should grab the reader's attention. Strategies for doing this can be to:
- Open with a compelling story,
- Include a strong quotation or a vivid, perhaps unexpected anecdote,
- Pose a provocative or thought-provoking question,
- Describe a puzzling scenario or incongruity, or
- Cite a stirring example or case study that illustrates why the research problem is important.
NOTE: Choose only one strategy for engaging your readers; avoid giving an impression that your paper is more flash than substance.
Freedman, Leora and Jerry Plotnick. Introductions and Conclusions. University College Writing Centre. University of Toronto; Introduction. The Structure, Format, Content, and Style of a Journal-Style Scientific Paper. Department of Biology. Bates College; Introductions. The Writing Center. University of North Carolina; Introductions. The Writer’s Handbook. Writing Center. University of Wisconsin, Madison; Introductions, Body Paragraphs, and Conclusions for an Argument Paper. The Writing Lab and The OWL. Purdue University; “Writing Introductions.” In Good Essay Writing: A Social Sciences Guide. Peter Redman. 4th edition. (London: Sage, 2011), pp. 63-70; Resources for Writers: Introduction Strategies. Program in Writing and Humanistic Studies. Massachusetts Institute of Technology; Sharpling, Gerald. Writing an Introduction. Centre for Applied Linguistics, University of Warwick; Samraj, B. “Introductions in Research Articles: Variations Across Disciplines.” English for Specific Purposes 21 (2002): 1–17; Swales, John and Christine B. Feak. Academic Writing for Graduate Students: Essential Skills and Tasks. 2nd edition. Ann Arbor, MI: University of Michigan Press, 2004; Writing Your Introduction. Department of English Writing Guide. George Mason University.
Citation: Mensh B, Kording K (2017) Ten simple rules for structuring papers. PLoS Comput Biol 13(9): e1005619. https://doi.org/10.1371/journal.pcbi.1005619
Editor: Scott Markel, Dassault Systemes BIOVIA, UNITED STATES
Published: September 28, 2017
Copyright: © 2017 Mensh, Kording. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Funding: The authors received no specific funding for this work.
Competing interests: The authors have declared that no competing interests exist.
Good scientific writing is essential to career development and to the progress of science. A well-structured manuscript allows readers and reviewers to get excited about the subject matter, to understand and verify the paper’s contributions, and to integrate these contributions into a broader context. However, many scientists struggle with producing high-quality manuscripts and are typically untrained in paper writing. Focusing on how readers consume information, we present a set of ten simple rules to help you communicate the main idea of your paper. These rules are designed to make your paper more influential and the process of writing more efficient and pleasurable.
Writing and reading papers are key skills for scientists. Indeed, success at publishing is used to evaluate scientists  and can help predict their future success . In the production and consumption of papers, multiple parties are involved, each having their own motivations and priorities. The editors want to make sure that the paper is significant, and the reviewers want to determine whether the conclusions are justified by the results. The reader wants to quickly understand the conceptual conclusions of the paper before deciding whether to dig into the details, and the writer wants to convey the important contributions to the broadest audience possible while convincing the specialist that the findings are credible. You can facilitate all of these goals by structuring the paper well at multiple scales—spanning the sentence, paragraph, section, and document.
Clear communication is also crucial for the broader scientific enterprise because “concept transfer” is a rate-limiting step in scientific cross-pollination. This is particularly true in the biological sciences and other fields that comprise a vast web of highly interconnected sub-disciplines. As scientists become increasingly specialized, it becomes more important (and difficult) to strengthen the conceptual links. Communication across disciplinary boundaries can only work when manuscripts are readable, credible, and memorable.
The claim that gives significance to your work has to be supported by data and by a logic that gives it credibility. Without carefully planning the paper’s logic, writers will often be missing data or missing logical steps on the way to the conclusion. While these lapses are beyond our scope, your scientific logic must be crystal clear to powerfully make your claim.
Here we present ten simple rules for structuring papers. The first four rules are principles that apply to all the parts of a paper and further to other forms of communication such as grants and posters. The next four rules deal with the primary goals of each of the main parts of papers. The final two rules deliver guidance on the process—heuristics for efficiently constructing manuscripts.
Principles (Rules 1–4)
Writing is communication. Thus, the reader’s experience is of primary importance, and all writing serves this goal. When you write, you should constantly have your reader in mind. These four rules help you to avoid losing your reader.
Rule 1: Focus your paper on a central contribution, which you communicate in the title
Your communication efforts are successful if readers can still describe the main contribution of your paper to their colleagues a year after reading it. Although it is clear that a paper often needs to communicate a number of innovations on the way to its final message, it does not pay to be greedy. Focus on a single message; papers that simultaneously focus on multiple contributions tend to be less convincing about each and are therefore less memorable.
The most important element of a paper is the title—think of the ratio of the number of titles you read to the number of papers you read. The title is typically the first element a reader encounters, so its quality  determines whether the reader will invest time in reading the abstract.
The title not only transmits the paper’s central contribution but can also serve as a constant reminder (to you) to focus the text on transmitting that idea. Science is, after all, the abstraction of simple principles from complex data. The title is the ultimate refinement of the paper’s contribution. Thinking about the title early—and regularly returning to hone it—can help not only the writing of the paper but also the process of designing experiments or developing theories.
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. For example, a technology paper may describe both its new technology and a biological result using it; the bridge that unifies these two facets is a clear description of how the new technology can be used to do new biology.
Rule 2: Write for flesh-and-blood human beings who do not know your work
Because you are the world’s leading expert at exactly what you are doing, you are also the world’s least qualified person to judge your writing from the perspective of the naïve reader. The majority of writing mistakes stem from this predicament. Think like a designer—for each element, determine the impact that you want to have on people and then strive to achieve that objective . Try to think through the paper like a naïve reader who must first be made to care about the problem you are addressing (see Rule 6) and then will want to understand your answer with minimal effort.
Define technical terms clearly because readers can become frustrated when they encounter a word that they don’t understand. Avoid abbreviations and acronyms so that readers do not have to go back to earlier sections to identify them.
The vast knowledge base of human psychology is useful in paper writing. For example, people have working memory constraints in that they can only remember a small number of items and are better at remembering the beginning and the end of a list than the middle . Do your best to minimize the number of loose threads that the reader has to keep in mind at any one time.
Rule 3: Stick to the context-content-conclusion (C-C-C) scheme
The vast majority of popular (i.e., memorable and re-tellable) stories have a structure with a discernible beginning, a well-defined body, and an end. The beginning sets up the context for the story, while the body (content) advances the story towards an ending in which the problems find their conclusions. This structure reduces the chance that the reader will wonder “Why was I told that?” (if the context is missing) or “So what?” (if the conclusion is missing).
There are many ways of telling a story. Mostly, they differ in how well they serve a patient reader versus an impatient one . The impatient reader needs to be engaged quickly; this can be accomplished by presenting the most exciting content first (e.g., as seen in news articles). The C-C-C scheme that we advocate serves a more patient reader who is willing to spend the time to get oriented with the context. A consequent disadvantage of C-C-C is that it may not optimally engage the impatient reader. This disadvantage is mitigated by the fact that the structure of scientific articles, specifically the primacy of the title and abstract, already forces the content to be revealed quickly. Thus, a reader who proceeds to the introduction is likely engaged enough to have the patience to absorb the context. Furthermore, one hazard of excessive “content first” story structures in science is that you may generate skepticism in the reader because they may be missing an important piece of context that makes your claim more credible. For these reasons, we advocate C-C-C as a “default” scientific story structure.
The C-C-C scheme defines the structure of the paper on multiple scales. At the whole-paper scale, the introduction sets the context, the results are the content, and the discussion brings home the conclusion. Applying C-C-C at the paragraph scale, the first sentence defines the topic or context, the body hosts the novel content put forth for the reader’s consideration, and the last sentence provides the conclusion to be remembered.
Deviating from the C-C-C structure often leads to papers that are hard to read, but writers often do so because of their own autobiographical context. During our everyday lives as scientists, we spend a majority of our time producing content and a minority amidst a flurry of other activities. We run experiments, develop the exposition of available literature, and combine thoughts using the magic of human cognition. 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 (see Rule 7). 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.
Rule 4: Optimize your logical flow by avoiding zig-zag and using parallelism
Only the central idea of the paper should be touched upon multiple times. Otherwise, each subject should be covered in only one place in order to minimize the number of subject changes. Related sentences or paragraphs should be strung together rather than interrupted by unrelated material. Ideas that are similar, such as two reasons why we should believe something, should come one immediately after the other.
Similarly, across consecutive paragraphs or sentences, parallel messages should be communicated with parallel form. Parallelism makes it easier to read the text because the reader is familiar with the structure. For example, if we have three independent reasons why we prefer one interpretation of a result over another, it is helpful to communicate them with the same syntax so that this syntax becomes transparent to the reader, which allows them to focus on the content. There is nothing wrong with using the same word multiple times in a sentence or paragraph. Resist the temptation to use a different word to refer to the same concept—doing so makes readers wonder if the second word has a slightly different meaning.
The components of a paper (Rules 5–8)
The individual parts of a paper—abstract, introduction, results, and discussion—have different objectives, and thus they each apply the C-C-C structure a little differently in order to achieve their objectives. We will discuss these specialized structures in this section and summarize them in Fig 1.
Fig 1. Summary of a paper’s structural elements at three spatial scales: Across sections, across paragraphs, and within paragraphs.
Note that the abstract is special in that it contains all three elements (Context, Content, and Conclusion), thus comprising all three colors.
Rule 5: Tell a complete story in the abstract
The abstract is, for most readers, the only part of the paper that will be read. This means that the abstract must convey the entire message of the paper effectively. To serve this purpose, the abstract’s structure is highly conserved. Each of the C-C-C elements is detailed below.
The context must communicate to the reader what gap the paper will fill. The first sentence orients the reader by introducing the broader field in which the particular research is situated. Then, this context is narrowed until it lands on the open question that the research answered. A successful context section sets the stage for distinguishing the paper’s contributions from the current state of the art by communicating what is missing in the literature (i.e., the specific gap) and why that matters (i.e., the connection between the specific gap and the broader context that the paper opened with).
The content (“Here we”) first describes the novel method or approach that you used to fill the gap or question. Then you present the meat—your executive summary of the results.
Finally, the conclusion interprets the results to answer the question that was posed at the end of the context section. There is often a second part to the conclusion section that highlights how this conclusion moves the broader field forward (i.e., “broader significance”). This is particularly true for more “general” journals with a broad readership.
This structure helps you avoid the most common mistake with the abstract, which is to talk about results before the reader is ready to understand them. Good abstracts usually take many iterations of refinement to make sure the results fill the gap like a key fits its lock. The broad-narrow-broad structure allows you to communicate with a wider readership (through breadth) while maintaining the credibility of your claim (which is always based on a finite or narrow set of results).
Rule 6: Communicate why the paper matters in the introduction
The introduction highlights the gap that exists in current knowledge or methods and why it is important. This is usually done by a set of progressively more specific paragraphs that culminate in a clear exposition of what is lacking in the literature, followed by a paragraph summarizing what the paper does to fill that gap.
As an example of the progression of gaps, a first paragraph may explain why understanding cell differentiation is an important topic and that the field has not yet solved what triggers it (a field gap). A second paragraph may explain what is unknown about the differentiation of a specific cell type, such as astrocytes (a subfield gap). A third may provide clues that a particular gene might drive astrocytic differentiation and then state that this hypothesis is untested (the gap within the subfield that you will fill). The gap statement sets the reader’s expectation for what the paper will deliver.
The structure of each introduction paragraph (except the last) serves the goal of developing the gap. Each paragraph first orients the reader to the topic (a context sentence or two) and then explains the “knowns” in the relevant literature (content) before landing on the critical “unknown” (conclusion) that makes the paper matter at the relevant scale. Along the path, there are often clues given about the mystery behind the gaps; these clues lead to the untested hypothesis or undeveloped method of the paper and give the reader hope that the mystery is solvable. The introduction should not contain a broad literature review beyond the motivation of the paper. This gap-focused structure makes it easy for experienced readers to evaluate the potential importance of a paper—they only need to assess the importance of the claimed gap.
The last paragraph of the introduction is special: it compactly summarizes the results, which fill the gap you just established. It differs from the abstract in the following ways: it does not need to present the context (which has just been given), it is somewhat more specific about the results, and it only briefly previews the conclusion of the paper, if at all.
Rule 7: Deliver the results as a sequence of statements, supported by figures, that connect logically to support the central contribution
The results section needs to convince the reader that the central claim is supported by data and logic. Every scientific argument has its own particular logical structure, which dictates the sequence in which its elements should be presented.
For example, a paper may set up a hypothesis, verify that a method for measurement is valid in the system under study, and then use the measurement to disprove the hypothesis. Alternatively, a paper may set up multiple alternative (and mutually exclusive) hypotheses and then disprove all but one to provide evidence for the remaining interpretation. The fabric of the argument will contain controls and methods where they are needed for the overall logic.
In the outlining phase of paper preparation (see Rule 9), sketch out the logical structure of how your results support your claim and convert this into a sequence of declarative statements that become the headers of subsections within the results section (and/or the titles of figures). Most journals allow this type of formatting, but if your chosen journal does not, these headers are still useful during the writing phase and can either be adapted to serve as introductory sentences to your paragraphs or deleted before submission. Such a clear progression of logical steps makes the paper easy to follow.
Figures, their titles, and legends are particularly important because they show the most objective support (data) of the steps that culminate in the paper’s claim. Moreover, figures are often viewed by readers who skip directly from the abstract in order to save time. Thus, the title of the figure should communicate the conclusion of the analysis, and the legend should explain how it was done. Figure making is an art unto itself; the Edward Tufte books remain the gold standard for learning this craft [7,8].
The first results paragraph is special in that it typically summarizes the overall approach to the problem outlined in the introduction, along with any key innovative methods that were developed. Most readers do not read the methods, so this paragraph gives them the gist of the methods that were used.
Each subsequent paragraph in the results section starts with a sentence or two that set up the question that the paragraph answers, such as the following: “To verify that there are no artifacts…,” “What is the test-retest reliability of our measure?,” or “We next tested whether Ca2+ flux through L-type Ca2+ channels was involved.” The middle of the paragraph presents data and logic that pertain to the question, and the paragraph ends with a sentence that answers the question. For example, it may conclude that none of the potential artifacts were detected. This structure makes it easy for experienced readers to fact-check a paper. Each paragraph convinces the reader of the answer given in its last sentence. This makes it easy to find the paragraph in which a suspicious conclusion is drawn and to check the logic of that paragraph. The result of each paragraph is a logical statement, and paragraphs farther down in the text rely on the logical conclusions of previous paragraphs, much as theorems are built in mathematical literature.
Rule 8: Discuss how the gap was filled, the limitations of the interpretation, and the relevance to the field
The discussion section explains how the results have filled the gap that was identified in the introduction, provides caveats to the interpretation, and describes how the paper advances the field by providing new opportunities. This is typically done by recapitulating the results, discussing the limitations, and then revealing how the central contribution may catalyze future progress. The first discussion paragraph is special in that it generally summarizes the important findings from the results section. Some readers skip over substantial parts of the results, so this paragraph at least gives them the gist of that section.
Each of the following paragraphs in the discussion section starts by describing an area of weakness or strength of the paper. It then evaluates the strength or weakness by linking it to the relevant literature. Discussion paragraphs often conclude by describing a clever, informal way of perceiving the contribution or by discussing future directions that can extend the contribution.
For example, the first paragraph may summarize the results, focusing on their meaning. The second through fourth paragraphs may deal with potential weaknesses and with how the literature alleviates concerns or how future experiments can deal with these weaknesses. The fifth paragraph may then culminate in a description of how the paper moves the field forward. Step by step, the reader thus learns to put the paper’s conclusions into the right context.
Process (Rules 9 and 10)
To produce a good paper, authors can use helpful processes and habits. Some aspects of a paper affect its impact more than others, which suggests that your investment of time should be weighted towards the issues that matter most. Moreover, iteratively using feedback from colleagues allows authors to improve the story at all levels to produce a powerful manuscript. Choosing the right process makes writing papers easier and more effective.
Rule 9: Allocate time where it matters: Title, abstract, figures, and outlining
The central logic that underlies a scientific claim is paramount. It is also the bridge that connects the experimental phase of a research effort with the paper-writing phase. Thus, it is useful to formalize the logic of ongoing experimental efforts (e.g., during lab meetings) into an evolving document of some sort that will ultimately steer the outline of the paper.
You should also allocate your time according to the importance of each section. The title, abstract, and figures are viewed by far more people than the rest of the paper, and the methods section is read least of all. Budget accordingly.
The time that we do spend on each section can be used efficiently by planning text before producing it. Make an outline. We like to write one informal sentence for each planned paragraph. It is often useful to start the process around descriptions of each result—these may become the section headers in the results section. Because the story has an overall arc, each paragraph should have a defined role in advancing this story. This role is best scrutinized at the outline stage in order to reduce wasting time on wordsmithing paragraphs that don’t end up fitting within the overall story.
Rule 10: Get feedback to reduce, reuse, and recycle the story
Writing can be considered an optimization problem in which you simultaneously improve the story, the outline, and all the component sentences. In this context, it is important not to get too attached to one’s writing. In many cases, trashing entire paragraphs and rewriting is a faster way to produce good text than incremental editing.
There are multiple signs that further work is necessary on a manuscript (see Table 1). For example, if you, as the writer, cannot describe the entire outline of a paper to a colleague in a few minutes, then clearly a reader will not be able to. You need to further distill your story. Finding such violations of good writing helps to improve the paper at all levels.
Successfully writing a paper typically requires input from multiple people. Test readers are necessary to make sure that the overall story works. They can also give valuable input on where the story appears to move too quickly or too slowly. They can clarify when it is best to go back to the drawing board and retell the entire story. Reviewers are also extremely useful. Non-specific feedback and unenthusiastic reviews often imply that the reviewers did not “get” the big picture story line. Very specific feedback usually points out places where the logic within a paragraph was not sufficient. It is vital to accept this feedback in a positive way. Because input from others is essential, a network of helpful colleagues is fundamental to making a story memorable. To keep this network working, make sure to pay back your colleagues by reading their manuscripts.
This paper focused on the structure, or “anatomy,” of manuscripts. We had to gloss over many finer points of writing, including word choice and grammar, the creative process, and collaboration. A paper about writing can never be complete; as such, there is a large body of literature dealing with issues of scientific writing [9,10,11,12,13,14,15,16,17].
Personal style often leads writers to deviate from a rigid, conserved structure, and it can be a delight to read a paper that creatively bends the rules. However, as with many other things in life, a thorough mastery of the standard rules is necessary to successfully bend them . In following these guidelines, scientists will be able to address a broad audience, bridge disciplines, and more effectively enable integrative science.
We took our own advice and sought feedback from a large number of colleagues throughout the process of preparing this paper. We would like to especially thank the following people who gave particularly detailed and useful feedback:
Sandra Aamodt, Misha Ahrens, Vanessa Bender, Erik Bloss, Davi Bock, Shelly Buffington, Xing Chen, Frances Cho, Gabrielle Edgerton, multiple generations of the COSMO summer school, Jason Perry, Jermyn See, Nelson Spruston, David Stern, Alice Ting, Joshua Vogelstein, Ronald Weber.
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