Scientific Research Papers Introduction

11 steps to structuring a science paper editors will take seriously

A seasoned editor gives advice to get your work published in an international journal

By Angel Borja, PhD     Posted on 24 June 2014

How to Prepare a Manuscript for International Journals — Part 2

In this monthly series, Dr. Angel Borja draws on his extensive background as an author, reviewer and editor to give advice on preparing the manuscript (author's view), the evaluation process (reviewer's view) and what there is to hate or love in a paper (editor's view).

This article is the second in the series. The first article was: "Six things to do before writing your manuscript."[divider]

The Author

Dr. Angel Borja is Head of Projects at AZTI-Tecnalia, a research center in the Basque Country in Spain specializing in marine research and food technologies. Formerly he was also Head of the Department of Oceanography and Head of the Marine Management Area. His main topic of investigation is marine ecology, and has published more than 270 contributions, from which 150 are in over 40 peer-reviewed journals, through his long career of 32 years of research. During this time he has investigated in multiple topics and ecosystem components, having an ample and multidisciplinary view of marine research.

Dr. Borja is the Editor of several journals, including Frontiers in Marine Ecosystem Ecology, Revista de Investigación Marina, Elsevier's Journal of Sea Research and Continental Shelf Research. In addition, he is a member of the editorial boards of Elsevier's Marine Pollution Bulletin, Ecological Indicators and Ocean & Coastal Management.

Read more about his work on ResearchGate, ORCID and LinkedIn, and follow him on Twitter (@AngelBorjaYerro).

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When you organize your manuscript, the first thing to consider is that the order of sections will be very different than the order of items on you checklist.

An article begins with the Title, Abstract and Keywords.

The article text follows the IMRAD format, which responds to the questions below:

  • Introduction: What did you/others do? Why did you do it?
  • Methods: How did you do it?
  • Results: What did you find?
  • And
  • Discussion: What does it all mean?

The main text is followed by the Conclusion, Acknowledgements, References and Supporting Materials.

While this is the published structure, however, we often use a different order when writing.

Steps to organizing your manuscript

  1. Prepare the figures and tables.
  2. Write the Methods.
  3. Write up the Results.
  4. Write the Discussion. Finalize the Results and Discussion before writing the introduction. This is because, if the discussion is insufficient, how can you objectively demonstrate the scientific significance of your work in the introduction?
  5. Write a clear Conclusion.
  6. Write a compelling introduction.
  7. Write the Abstract.
  8. Compose a concise and descriptive Title.
  9. Select Keywords for indexing.
  10. Write the Acknowledgements.
  11. Write up the References.

Next, I'll review each step in more detail. But before you set out to write a paper, there are two important things you should do that will set the groundwork for the entire process.

  • The topic to be studied should be the first issue to be solved. Define your hypothesis and objectives (These will go in the Introduction.)
  • Review the literature related to the topic and select some papers (about 30) that can be cited in your paper (These will be listed in the References.)

Finally, keep in mind that each publisher has its own style guidelines and preferences, so always consult the publisher's Guide for Authors.[divider]

Step 1: Prepare the figures and tables

Remember that "a figure is worth a thousand words." Hence, illustrations, including figures and tables, are the most efficient way to present your results. Your data are the driving force of the paper, so your illustrations are critical!

How do you decide between presenting your data as tables or figures? Generally, tables give the actual experimental results, while figures are often used for comparisons of experimental results with those of previous works, or with calculated/theoretical values (Figure 1).

Whatever your choice is, no illustrations should duplicate the information described elsewhere in the manuscript.

Another important factor: figure and table legends must be self-explanatory (Figure 2).

When presenting your tables and figures, appearances count! To this end:

  • Avoid crowded plots (Figure 3), using only three or four data sets per figure; use well-selected scales.
  • Think about appropriate axis label size
  • Include clear symbols and data sets that are easy to distinguish.
  • Never include long boring tables (e.g., chemical compositions of emulsion systems or lists of species and abundances). You can include them as supplementary material.

If you are using photographs, each must have a scale marker, or scale bar, of professional quality in one corner.

In photographs and figures, use color only when necessary when submitting to a print publication. If different line styles can clarify the meaning, never use colors or other thrilling effects or you will be charged with expensive fees. Of course, this does not apply to online journals. For many journals, you can submit duplicate figures: one in color for the online version of the journal and pdfs, and another in black and white for the hardcopy journal (Figure 4).

Another common problem is the misuse of lines and histograms. Lines joining data only can be used when presenting time series or consecutive samples data (e.g., in a transect from coast to offshore in Figure 5). However, when there is no connection between samples or there is not a gradient, you must use histograms (Figure 5).

Sometimes, fonts are too small for the journal. You must take this into account, or they may be illegible to readers (Figure 6).

Finally, you must pay attention to the use of decimals, lines, etc. (Figure 7)

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Step 2: Write the Methods

This section responds to the question of how the problem was studied. If your paper is proposing a new method, you need to include detailed information so a knowledgeable reader can reproduce the experiment.

However, do not repeat the details of established methods; use References and Supporting Materials to indicate the previously published procedures. Broad summaries or key references are sufficient.

Length of the manuscript

Again, look at the journal's Guide for Authors, but an ideal length for a manuscript is 25 to 40 pages, double spaced, including essential data only. Here are some general guidelines:

  • Title: Short and informative
  • Abstract: 1 paragraph (<250 words)
  • Introduction: 1.5-2 pages
  • Methods: 2-3 pages
  • Results: 6-8 pages
  • Discussion: 4-6 pages
  • Conclusion: 1 paragraph
  • Figures: 6-8 (one per page)
  • Tables: 1-3 (one per page)
  • References: 20-50 papers (2-4 pages)

Reviewers will criticize incomplete or incorrect methods descriptions and may recommend rejection, because this section is critical in the process of reproducing your investigation. In this way, all chemicals must be identified. Do not use proprietary, unidentifiable compounds.

To this end, it's important to use standard systems for numbers and nomenclature. For example:

Present proper control experiments and statistics used, again to make the experiment of investigation repeatable.

List the methods in the same order they will appear in the Results section, in the logical order in which you did the research:

  1. Description of the site
  2. Description of the surveys or experiments done, giving information on dates, etc.
  3. Description of the laboratory methods, including separation or treatment of samples, analytical methods, following the order of waters, sediments and biomonitors. If you have worked with different biodiversity components start from the simplest (i.e. microbes) to the more complex (i.e. mammals)
  4. Description of the statistical methods used (including confidence levels, etc.)

In this section, avoid adding comments, results, and discussion, which is a common error.[divider]

Step 3: Write up the Results

This section responds to the question "What have you found?" Hence, only representative results from your research should be presented. The results should be essential for discussion.

Statistical rules

  • Indicate the statistical tests used with all relevant parameters: e.g., mean and standard deviation (SD): 44% (±3); median and interpercentile range:  7 years (4.5 to 9.5 years).
  • Use mean and standard deviation to report normally distributed data.
  • Use median and interpercentile range to report skewed data.
  • For numbers, use two significant digits unless more precision is necessary (2.08, not 2.07856444).
  • Never use percentages for very small samples e.g., "one out of two" should not be replaced by 50%.

However, remember that most journals offer the possibility of adding Supporting Materials, so use them freely for data of secondary importance. In this way, do not attempt to "hide" data in the hope of saving it for a later paper. You may lose evidence to reinforce your conclusion. If data are too abundant, you can use those supplementary materials.

Use sub-headings to keep results of the same type together, which is easier to review and read. Number these sub-sections for the convenience of internal cross-referencing, but always taking into account the publisher's Guide for Authors.

For the data, decide on a logical order that tells a clear story and makes it and easy to understand. Generally, this will be in the same order as presented in the methods section.

An important issue is that you must not include references in this section; you are presenting your results, so you cannot refer to others here. If you refer to others, is because you are discussing your results, and this must be included in the Discussion section.[divider]

Step 4: Write the Discussion

Here you must respond to what the results mean. Probably it is the easiest section to write, but the hardest section to get right. This is because it is the most important section of your article. Here you get the chance to sell your data. Take into account that a huge numbers of manuscripts are rejected because the Discussion is weak.

You need to make the Discussion corresponding to the Results, but do not reiterate the results. Here you need to compare the published results by your colleagues with yours (using some of the references included in the Introduction). Never ignore work in disagreement with yours, in turn, you must confront it and convince the reader that you are correct or better.

Take into account the following tips:

1. Avoid statements that go beyond what the results can support.

2. Avoid unspecific expressions such as "higher temperature", "at a lower rate", "highly significant". Quantitative descriptions are always preferred (35ºC, 0.5%, p<0.001, respectively).

3. Avoid sudden introduction of new terms or ideas; you must present everything in the introduction, to be confronted with your results here.

4. Speculations on possible interpretations are allowed, but these should be rooted in fact, rather than imagination. To achieve good interpretations think about:

  • How do these results relate to the original question or objectives outlined in the Introduction section?
  • Do the data support your hypothesis?
  • Are your results consistent with what other investigators have reported?
  • Discuss weaknesses and discrepancies. If your results were unexpected, try to explain why
  • Is there another way to interpret your results?
  • What further research would be necessary to answer the questions raised by your results?
  • Explain what is new without exaggerating

5. Revision of Results and Discussion is not just paper work. You may do further experiments, derivations, or simulations. Sometimes you cannot clarify your idea in words because some critical items have not been studied substantially.[divider]

Step 5: Write a clear Conclusion

This section shows how the work advances the field from the present state of knowledge. In some journals, it's a separate section; in others, it's the last paragraph of the Discussion section. Whatever the case, without a clear conclusion section, reviewers and readers will find it difficult to judge your work and whether it merits publication in the journal.

A common error in this section is repeating the abstract, or just listing experimental results. Trivial statements of your results are unacceptable in this section.

You should provide a clear scientific justification for your work in this section, and indicate uses and extensions if appropriate. Moreover, you can suggest future experiments and point out those that are underway.

You can propose present global and specific conclusions, in relation to the objectives included in the introduction.[divider]

Step 6: Write a compelling Introduction

This is your opportunity to convince readers that you clearly know why your work is useful.

A good introduction should answer the following questions:

  • What is the problem to be solved?
  • Are there any existing solutions?
  • Which is the best?
  • What is its main limitation?
  • What do you hope to achieve?

Editors like to see that you have provided a perspective consistent with the nature of the journal. You need to introduce the main scientific publications on which your work is based, citing a couple of original and important works, including recent review articles.

However, editors hate improper citations of too many references irrelevant to the work, or inappropriate judgments on your own achievements. They will think you have no sense of purpose.

Here are some additional tips for the introduction:

  • Never use more words than necessary (be concise and to-the-point). Don't make this section into a history lesson. Long introductions put readers off.
  • We all know that you are keen to present your new data. But do not forget that you need to give the whole picture at first.
  • The introduction must be organized from the global to the particular point of view, guiding the readers to your objectives when writing this paper.
  • State the purpose of the paper and research strategy adopted to answer the question, but do not mix introduction with results, discussion and conclusion. Always keep them separate to ensure that the manuscript flows logically from one section to the next.
  • Hypothesis and objectives must be clearly remarked at the end of the introduction.
  • Expressions such as "novel," "first time," "first ever," and "paradigm-changing" are not preferred. Use them sparingly.

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Step 7: Write the Abstract

The abstract tells prospective readers what you did and what the important findings in your research were. Together with the title, it's the advertisement of your article. Make it interesting and easily understood without reading the whole article.  Avoid using jargon, uncommon abbreviations and references.

You must be accurate, using the words that convey the precise meaning of your research. The abstract provides a short description of the perspective and purpose of your paper. It gives key results but minimizes experimental details. It is very important to remind that the abstract offers a short description of the interpretation/conclusion in the last sentence.

A clear abstract will strongly influence whether or not your work is further considered.

However, the abstracts must be keep as brief as possible. Just check the 'Guide for authors' of the journal, but normally they have less than 250 words. Here's a good example on a short abstract.

In an abstract, the two whats are essential. Here's an example from an article I co-authored in Ecological Indicators:

  1. What has been done? "In recent years, several benthic biotic indices have been proposed to be used as ecological indicators in estuarine and coastal waters. One such indicator, the AMBI (AZTI Marine Biotic Index), was designed to establish the ecological quality of European coasts. The AMBI has been used also for the determination of the ecological quality status within the context of the European Water Framework Directive. In this contribution, 38 different applications including six new case studies (hypoxia processes, sand extraction, oil platform impacts, engineering works, dredging and fish aquaculture) are presented."
  2. What are the main findings? "The results show the response of the benthic communities to different disturbance sources in a simple way. Those communities act as ecological indicators of the 'health' of the system, indicating clearly the gradient associated with the disturbance."

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Step 8: Compose a concise and descriptive title

The title must explain what the paper is broadly about. It is your first (and probably only) opportunity to attract the reader's attention. In this way, remember that the first readers are the Editor and the referees. Also, readers are the potential authors who will cite your article, so the first impression is powerful!

We are all flooded by publications, and readers don't have time to read all scientific production. They must be selective, and this selection often comes from the title.

Reviewers will check whether the title is specific and whether it reflects the content of the manuscript. Editors hate titles that make no sense or fail to represent the subject matter adequately. Hence, keep the title informative and concise (clear, descriptive, and not too long). You must avoid technical jargon and abbreviations, if possible. This is because you need to attract a readership as large as possible. Dedicate some time to think about the title and discuss it with your co-authors.

Here you can see some examples of original titles, and how they were changed after reviews and comments to them:

Example 1

  • Original title: Preliminary observations on the effect of salinity on benthic community distribution within a estuarine system, in the North Sea
  • Revised title: Effect of salinity on benthic distribution within the Scheldt estuary (North Sea)
  • Comments: Long title distracts readers. Remove all redundancies such as "studies on," "the nature of," etc. Never use expressions such as "preliminary." Be precise.

Example 2

  • Original title: Action of antibiotics on bacteria
  • Revised title: Inhibition of growth of Mycobacterium tuberculosis by streptomycin
  • Comments: Titles should be specific. Think about "how will I search for this piece of information" when you design the title.

Example 3

  • Original title: Fabrication of carbon/CdS coaxial nanofibers displaying optical and electrical properties via electrospinning carbon
  • Revised title: Electrospinning of carbon/CdS coaxial nanofibers with optical and electrical properties
  • Comments: "English needs help. The title is nonsense. All materials have properties of all varieties.  You could examine my hair for its electrical and optical properties! You MUST be specific. I haven't read the paper but I suspect there is something special about these properties, otherwise why would you be reporting them?" – the Editor-in-Chief.

Try to avoid this kind of response! [divider]

Step 9: Select keywords for indexing

Keywords are used for indexing your paper. They are the label of your manuscript. It is true that now they are less used by journals because you can search the whole text. However, when looking for keywords, avoid words with a broad meaning and words already included in the title.

Some journals require that the keywords are not those from the journal name, because it is implicit that the topic is that. For example, the journal Soil Biology & Biochemistry requires that the word "soil" not be selected as a keyword.

Only abbreviations firmly established in the field are eligible (e.g., TOC, CTD), avoiding those which are not broadly used (e.g., EBA, MMI).

Again, check the Guide for Authors and look at the number of keywords admitted, label, definitions, thesaurus, range, and other special requests. [divider]

Step 10: Write the Acknowledgements

Here, you can thank people who have contributed to the manuscript but not to the extent where that would justify authorship. For example, here you can include technical help and assistance with writing and proofreading. Probably, the most important thing is to thank your funding agency or the agency giving you a grant or fellowship.

In the case of European projects, do not forget to include the grant number or reference. Also, some institutes include the number of publications of the organization, e.g., "This is publication number 657 from AZTI-Tecnalia."[divider]

Step 11: Write up the References

Typically, there are more mistakes in the references than in any other part of the manuscript. It is one of the most annoying problems, and causes great headaches among editors. Now, it is easier since to avoid these problem, because there are many available tools.

In the text, you must cite all the scientific publications on which your work is based. But do not over-inflate the manuscript with too many references – it doesn't make a better manuscript! Avoid excessive self-citations and excessive citations of publications from the same region.

Minimize personal communications, do not include unpublished observations, manuscripts submitted but not yet accepted for publication, publications that are not peer reviewed, grey literature, or articles not published in English.

You can use any software, such as EndNote or Mendeley, to format and include your references in the paper. Most journals have now the possibility to download small files with the format of the references, allowing you to change it automatically. Also, Elsevier's Your Paper Your Way program waves strict formatting requirements for the initial submission of a manuscript as long as it contains all the essential elements being presented here.

Make the reference list and the in-text citation conform strictly to the style given in the Guide for Authors. Remember that presentation of the references in the correct format is the responsibility of the author, not the editor. Checking the format is normally a large job for the editors. Make their work easier and they will appreciate the effort.

Finally, check the following:

  • Spelling of author names
  • Year of publications
  • Usages of "et al."
  • Punctuation
  • Whether all references are included

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In my next article, I will give tips for writing the manuscript, authorship, and how to write a compelling cover letter. Stay tuned![divider]

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ECO 101

Scientific Writing Made Easy: A Step-by-Step Guide to Undergraduate Writing in the Biological Sciences

Authors

  • Sheela P. Turbek,

    1. Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Boulder, Colorado, USA
    Search for more papers by this author
  • Taylor M. Chock,

    1. Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Boulder, Colorado, USA
    Search for more papers by this author
  • Kyle Donahue,

    1. Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Boulder, Colorado, USA
    Search for more papers by this author
  • Caroline A. Havrilla,

    1. Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Boulder, Colorado, USA
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  • Angela M. Oliverio,

    1. Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Boulder, Colorado, USA
    2. Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado, USA
    Search for more papers by this author
  • Stephanie K. Polutchko,

    1. Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Boulder, Colorado, USA
    Search for more papers by this author
  • Lauren G. Shoemaker,

    1. Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Boulder, Colorado, USA
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  • Lara Vimercati

    1. Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Boulder, Colorado, USA
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  • Note: Charlene D'Avanzo is the editor of Ecology 101. Anyone wishing to contribute articles or reviews to this section should contact her at the School of Natural Sciences, Hampshire College, 893 West Street, Amherst, MA 01002. E-mail: cdavanzo@hampshire.edu

Abstract

Scientific writing, while an indispensable step of the scientific process, is often overlooked in undergraduate courses in favor of maximizing class time devoted to scientific concepts. However, the ability to effectively communicate research findings is crucial for success in the biological sciences. Graduate students are encouraged to publish early and often, and professional scientists are generally evaluated by the quantity of articles published and the number of citations those articles receive. It is therefore important that undergraduate students receive a solid foundation in scientific writing early in their academic careers. In order to increase the emphasis on effective writing in the classroom, we assembled a succinct step-by-Step guide to scientific writing that can be directly disseminated to undergraduates enrolled in biological science courses. The guide breaks down the scientific writing process into easily digestible pieces, providing concrete examples that students can refer to when preparing a scientific manuscript or laboratory report. By increasing undergraduate exposure to the scientific writing process, we hope to better prepare undergraduates for graduate school and productive careers in the biological sciences.

An introduction to the guide

While writing is a critical part of the scientific process, it is often taught secondarily to scientific concepts and becomes an afterthought to students. How many students can you recall who worked on a laboratory assignment or class project for weeks, only to throw together the written report the day before it was due?

For many, this pattern occurs because we focus almost exclusively on the scientific process, all but neglecting the scientific writing process. Scientific writing is often a difficult and arduous task for many students. It follows a different format and deviates in structure from how we were initially taught to write, or even how we currently write for English, history, or social science classes. This can make the scientific writing process appear overwhelming, especially when presented with new, complex content. However, effective writing can deepen understanding of the topic at hand by compelling the writer to present a coherent and logical story that is supported by previous research and new results.

Clear scientific writing generally follows a specific format with key sections: an introduction to a particular topic, hypotheses to be tested, a description of methods, key results, and finally, a discussion that ties these results to our broader knowledge of the topic (Day and Gastel 2012). This general format is inherent in most scientific writing and facilitates the transfer of information from author to reader if a few guidelines are followed.

Here, we present a succinct step-by-step guide that lays out strategies for effective scientific writing with the intention that the guide be disseminated to undergraduate students to increase the focus on the writing process in the college classroom. While we recognize that there are no hard and fast rules when it comes to scientific writing, and more experienced writers may choose to disregard our suggestions these guidelines will assist undergraduates in overcoming the initial challenges associated with writing scientific papers. This guide was inspired by Joshua Schimel's Writing Science: How to Write Papers that Get Cited and Proposals that Get Funded—an excellent book about scientific writing for graduate students and professional scientists—but designed to address undergraduate students. While the guide was written by a group of ecologists and evolutionary biologists, the strategies and suggestions presented here are applicable across the biological sciences and other scientific disciplines. Regardless of the specific course being taught, this guide can be used as a reference when writing scientific papers, independent research projects, and laboratory reports. For students looking for more in-depth advice, additional resources are listed at the end of the guide.

To illustrate points regarding each step of the scientific writing process, we draw examples throughout the guide from Kilner et al. (2004), a paper on brown-headed cowbirds—a species of bird that lays its eggs in the nests of other bird species, or hosts—that was published in the journal Science. Kilner et al. investigate why cowbird nestlings tolerate the company of host offspring during development rather than pushing host eggs out of the nest upon hatching to monopolize parental resources. While articles in the journal Science are especially concise and lack the divisions of a normal scientific paper, Kilner et al. (2004) offers plenty of examples of effective communication strategies that are utilized in scientific writing. We hope that the guidelines that follow, as well as the concrete examples provided, will lead to scientific papers that are information rich, concise, and clear, while simultaneously alleviating frustration and streamlining the writing process.

Undergraduate guide to writing in the biological sciences

The before steps

The scientific writing process can be a daunting and often procrastinated “last step” in the scientific process, leading to cursory attempts to get scientific arguments and results down on paper. However, scientific writing is not an afterthought and should begin well before drafting the first outline. Successful writing starts with researching how your work fits into existing literature, crafting a compelling story, and determining how to best tailor your message to an intended audience.

Research how your work fits into existing literature

It is important to decide how your research compares to other studies of its kind by familiarizing yourself with previous research on the topic. If you are preparing a laboratory write-up, refer to your textbook and laboratory manual for background information. For a research article, perform a thorough literature search on a credible search engine (e.g., Web of Science, Google Scholar). Ask the following questions: What do we know about the topic? What open questions and knowledge do we not yet know? Why is this information important? This will provide critical insight into the structure and style that others have used when writing about the field and communicating ideas on this specific topic. It will also set you up to successfully craft a compelling story, as you will begin writing with precise knowledge of how your work builds on previous research and what sets your research apart from the current published literature.

Understand your audience (and write to them)

In order to write effectively, you must identify your audience and decide what story you want them to learn. While this may seem obvious, writing about science as a narrative is often not done, largely because you were probably taught to remain dispassionate and impartial while communicating scientific findings. The purpose of science writing is not explaining what you did or what you learned, but rather what you want your audience to understand. Start by asking: Who is my audience? What are their goals in reading my writing? What message do I want them to take away from my writing? There are great resources available to help science writers answer these questions (Nisbet 2009, Baron 2010). If you are interested in publishing a scientific paper, academic journal websites also provide clear journal mission statements and submission guidelines for prospective authors. The most effective science writers are familiar with the background of their topic, have a clear story that they want to convey, and effectively craft their message to communicate that story to their audience.

Introduction

The Introduction sets the tone of the paper by providing relevant background information and clearly identifying the problem you plan to address. Think of your Introduction as the beginning of a funnel: Start wide to put your research into a broad context that someone outside of the field would understand, and then narrow the scope until you reach the specific question that you are trying to answer (Fig. 1; Schimel 2012). Clearly state the wider implications of your work for the field of study, or, if relevant, any societal impacts it may have, and provide enough background information that the reader can understand your topic. Perform a thorough sweep of the literature; however, do not parrot everything you find. Background information should only include material that is directly relevant to your research and fits into your story; it does not need to contain an entire history of the field of interest. Remember to include in-text citations in the format of (Author, year published) for each paper that you cite and avoid using the author's name as the subject of the sentence:

“Kilner et al. (2004) found that cowbird nestlings use host offspring to procure more food.”

Instead, use an in-text citation:

“Cowbird nestlings use host offspring to procure more food.”

(Kilner et al. 2004)

Upon narrowing the background information presented to arrive at the specific focus of your research, clearly state the problem that your paper addresses. The problem is also known as the knowledge gap, or a specific area of the literature that contains an unknown question or problem (e.g., it is unclear why cowbird nestlings tolerate host offspring when they must compete with host offspring for food) (refer to the section “Research how your work fits into existing literature”). The knowledge gap tends to be a small piece of a much larger field of study. Explicitly state how your work will contribute to filling that knowledge gap. This is a crucial section of your manuscript; your discussion and conclusion should all be aimed at answering the knowledge gap that you are trying to fill. In addition, the knowledge gap will drive your hypotheses and questions that you design your experiment to answer.

Your hypothesis will often logically follow the identification of the knowledge gap (Table 1). Define the hypotheses you wish to address, state the approach of your experiment, and provide a 1–2 sentence overview of your experimental design, leaving the specific details for the methods section. If your methods are complicated, consider briefly explaining the reasoning behind your choice of experimental design. Here, you may also state your system, study organism, or study site, and provide justification for why you chose this particular system for your research. Is your system, study organism, or site a good representation of a more generalized pattern? Providing a brief outline of your project will allow your Introduction to segue smoothly into your 'Materials and Methods' section.

A hypothesis is a testable explanation of an observed occurrence in nature, or, more specifically, why something you observed is occurring. Hypotheses relate directly to research questions, are written in the present tense, and can be tested through observation or experimentation. Although the terms “hypothesis” and “prediction” are often incorrectly used interchangeably, they refer to different but complementary concepts. A hypothesis attempts to explain the mechanism underlying a pattern, while a prediction states an expectation regarding the results. While challenging to construct, hypotheses provide powerful tools for structuring research, generating specific predictions, and designing experiments.
Example:
Observation: Brown-headed cowbird nestlings refrain from ejecting host offspring from the nest even though those offspring compete for limited parental resources.
Research question: Why do nestling cowbirds tolerate the presence of host offspring in the nest?
Hypothesis: The presence of host offspring causes parents to bring more food to the nest.
Prediction: Cowbird nestlings will grow at a faster rate in nests that contain host offspring.

Materials and Methods

The 'Materials and Methods' section is arguably the most straightforward section to write; you can even begin writing it while performing your experiments to avoid forgetting any details of your experimental design. In order to make your paper as clear as possible, organize this section into subsections with headers for each procedure you describe (e.g., field collection vs. laboratory analysis). We recommend reusing these headers in your Results and Discussion to help orient your readers.

The aim of the 'Materials and Methods' section is to demonstrate that you used scientifically valid methods and provide the reader with enough information to recreate your experiment. In chronological order, clearly state the procedural steps you took, remembering to include the model numbers and specific settings of all equipment used (e.g., centrifuged in Beckman Coulter Benchtop Centrifuge Model Allegra X -15R at 12,000 × g for 45 minutes). In addition to your experimental procedure, describe any statistical analyses that you performed. While the parameters you include in your 'Materials and Methods' section will vary based on your experimental design, we list common ones in Table 2 (Journal of Young Investigators 2005) that are usually mentioned. If you followed a procedure developed from another paper, cite the source that it came from and provide a general description of the method. There is no need to reiterate every detail, unless you deviated from the source and changed a step in your procedure. However, it is important to provide enough information that the reader can follow your methods without referring to the original source. As you explain your experiment step by step, you may be tempted to include qualifiers where sources of error occurred (e.g., the tube was supposed to be centrifuged for 5 minutes, but was actually centrifuged for 10). However, generally wait until the Discussion to mention these subjective qualifiers and avoid discussing them in the 'Materials and Methods' section.

• Site characterization:
Study organism used, its origin, any pre-experiment handling or care
Description of field site or site where experiment was performed
• Experimental design:
Step-by-step procedures in paragraph form
Sample preparation
Experimental controls
Equipment used, including model numbers and year
Important equipment settings (e.g., temperature of incubation, speed of centrifuge)
Amount of reagents used
Specific measurements taken (e.g., wing length, weight of organism)
• Statistical analyses conducted (e.g., ANOVA, linear regression)

The 'Materials and Methods' section should be written in the past tense:

“On hatch day, and every day thereafter for 9 days, we weighed chicks, measured their tibia length, and calculated the instantaneous growth constant K to summarize rates of mass gain and skeletal growth.”

(Kilner et al. 2004)

While it is generally advisable to use active voice throughout the paper (refer to the section “Putting It All Together,” below), you may want to use a mixture of active and passive voice in the 'Materials and Methods' section in order to vary sentence structure and avoid repetitive clauses.

Results

The Results section provides a space to present your key findings in a purely objective manner and lay the foundation for the Discussion section, where those data are subjectively interpreted. Before diving into this section, identify which graphs, tables, and data are absolutely necessary for telling your story. Then, craft a descriptive sentence or two that summarizes each result, referring to corresponding table and figure numbers. Rather than presenting the details all at once, write a short summary about each data set. If you carried out a complicated study, we recommend dividing your results into multiple sections with clear headers following the sequence laid out in the 'Materials and Methods' section.

As you relate each finding, be as specific as possible and describe your data biologically rather than through the lens of statistics. While statistical tests give your data credibility by allowing you to attribute observed differences to nonrandom variation, they fail to address the actual meaning of the data. Instead, translate the data into biological terms and refer to statistical results as supplemental information, or even in parenthetical clauses (Schimel 2012). For example, if your dependent variable changed in response to a treatment, report the magnitude and direction of the effect, with the P-value in parentheses.

“By day 8, cowbirds reared with host young were, on average, 14% heavier than cowbirds reared alone (unpaired t16 = −2.23, P = 0.041, Fig. 2A).”

(Kilner et al. 2004)

If your P-value exceeded 0.05 (or your other statistical tests yielded nonsignificant results), report any noticeable trends in the data rather than simply dismissing the treatment as having no significant effect (Fry 1993). By focusing on the data and leaving out any interpretation of the results in this section, you will provide the reader with the tools necessary to objectively evaluate your findings.

Discussion and conclusion

The Discussion section usually requires the most consideration, as this is where you interpret your results. Your Discussion should form a self-contained story tying together your Introduction and Results sections (Schimel 2012). One potential strategy for writing the Discussion is to begin by explicitly stating the main finding(s) of your research (Cals and Kotz 2013). Remind the reader of the knowledge gap identified in the Introduction to re-spark curiosity about the question you set out to answer. Then, explicitly state how your experiment moved the field forward by filling that knowledge gap.

After the opening paragraph of your Discussion, we suggest addressing your question and hypotheses with specific evidence from your results. If there are multiple possible interpretations of a result, clearly lay out each competing explanation. In the cowbird example, a higher feeding rate in the presence of host offspring could indicate either (1) that the parents were more responsive to the begging behavior of their own species or (2) that the collective begging behavior of more offspring in the nest motivated the host parents to provide additional food (Kilner et al. 2004). Presenting and evaluating alternative explanations of your findings will provide clear opportunities for future research. However, be sure to keep your Discussion concrete by referring to your results to support each given interpretation.

Intermingled with these interpretations, reference preexisting literature and report how your results relate to previous findings (Casenove and Kirk 2016). Ask yourself the following questions: How do my results compare to those of similar studies? Are they consistent or inconsistent with what other researchers have found? If they are inconsistent, discuss why this might be the case. For example, are you asking a similar question in a different system, organism, or site? Was there a difference in the methods or experimental design? Any caveats of the study (e.g., small sample size, procedural mistakes, or known biases in the methods) should be transparent and briefly discussed.

The conclusion, generally located in its own short section or the last paragraph of the Discussion, represents your final opportunity to state the significance of your research. Rather than merely restating your main findings, the conclusion should summarize the outcome of your study in a way that incorporates new insights or frames interesting questions that arose as a result of your research. Broaden your perspective again as you reach the bottom of the hourglass (Fig. 1). While it is important to acknowledge the shortcomings or caveats of the research project, generally include these near the beginning of the conclusion or earlier in the Discussion. You want your take-home sentences to focus on what you have accomplished and the broader implications of your study, rather than your study's limitations or shortcomings (Schimel 2012). End on a strong note.

Putting it all together

No matter how many boards you stack on top of each other, you still need nails to prevent the pile from falling apart. The same logic applies to a scientific paper. Little things—such as flow, structure, voice, and word choice—will connect your story, polish your paper, and make it enjoyable to read.

First, a paper needs to flow. The reader should easily be able to move from one concept to another, either within a sentence or between paragraphs. To bolster the flow, constantly remind yourself of the overarching story; always connect new questions with resolutions and tie new concepts to previously presented ideas. As a general rule, try to maintain the same subject throughout a section and mix up sentence structure in order to emphasize different concepts. Keep in mind that words or ideas placed toward the end of a sentence often convey the most importance (Schimel 2012).

The use of active voice with occasional sentences in passive voice will additionally strengthen your writing. Scientific writing is rife with passive voice that weakens otherwise powerful sentences by stripping the subjects of action. However, when used properly, the passive voice can improve flow by strategically placing a sentence's subject so that it echoes the emphasis of the preceding sentence. Compare the following sentences:

“The cowbird nestlings tolerated the host nestlings.”

(active)

“The host nestlings were tolerated by the cowbird nestlings.”

(passive)

If host nestlings are the focus of the paragraph as a whole, it may make more sense to present the passive sentence in this case, even though it is weaker than the active version. While passive and active voices can complement each other in particular situations, you should typically use the active voice whenever possible.

Lastly, word choice is critical for effective storytelling (Journal of Young Investigators 2005). Rather than peppering your report or manuscript with overly complicated words, use simple words to lay the framework of your study and discuss your findings. Eliminating any flourish and choosing words that get your point across as clearly as possible will make your work much more enjoyable to read (Strunk and White 1979, Schimel 2012).

Editing and peer review

Although you have finally finished collecting data and writing your report, you are not done yet! Re-reading your paper and incorporating constructive feedback from others can make the difference between getting a paper accepted or rejected from a journal or receiving one letter grade over another on a report. The editing stage is where you put the finishing touches on your work.

Start by taking some time away from your paper. Ideally, you began your paper early enough that you can refrain from looking at it for a day or two. However, if the deadline looms large, take an hour break at the very least. Come back to your paper and verify that it still expresses what you intended to say. Where are the gaps in your story structure? What has not been explained clearly? Where is the writing awkward, making it difficult to understand your point? Consider reading the paper out loud first, and then print and edit a hard copy to inspect the paper from different angles.

Editing is best done in stages. On the first run-through of your paper, make sure you addressed all of the main ideas of the study. One way to achieve this is by writing down the key points you want to hit prior to re-reading your paper. If your paper deviates from these points, you may need to delete some paragraphs. In contrast, if you forgot to include something, add it in. To check the flow of your paragraphs, verify that a common thread ties each paragraph to the preceding one, and similarly, that each sentence within a paragraph builds on the previous sentence. Finally, re-read the paper with a finer lens, editing sentence structure and word choice as you go to put the finishing touches on your work. Grammar and spelling are just as important as your scientific story; a poorly written paper will have limited impact regardless of the quality of the ideas expressed (Harley et al. 2004).

After editing your own paper, ask someone else to read it. A classmate is ideal because he/she understands the assignment and could exchange papers with you. The editing steps described above also apply when editing someone else's paper. If a classmate is not available, try asking a family member or a friend. Having a fresh set of eyes examine your work may help you identify sections of your paper that need clarification. This procedure will also give you a glimpse into the peer review process, which is integral to professional science writing (Guilford 2001). Don't be discouraged by negative comments—incorporating the feedback of reviewers will only strengthen your paper. Good criticism is constructive.

Conclusion

While the basics of writing are generally taught early in life, many people constantly work to refine their writing ability throughout their careers. Even professional scientists feel that they can always write more effectively. Focusing on the strategies for success laid out in this guide will not only improve your writing skills, but also make the scientific writing process easier and more efficient. However, keep in mind that there is no single correct way to write a scientific paper, and as you gain experience with scientific writing, you will begin to find your own voice. Good luck and happy writing!

Additional resources

For those interested in learning more about the skill of scientific writing, we recommend the following resources. We note that much of the inspiration and concrete ideas for this step-by-step guide originated from Schimel's Writing Science: How to Write Papers that Get Cited and Proposals that Get Funded.

  1. Journal of Young Investigators. 2005. Writing scientific manuscripts: a guide for undergraduates. Journal of Young Investigators, California.
  2. Lanciani, C. A. 1998. Reader-friendly writing in science. Bulletin of the Ecological Society of America 79: 171–172.
  3. Morris, J., T. Jehn, C. Vaughan, E. Pantages, T. Torello, M. Bucheli, D. Lohman, and R. Jue. 2007. A student's guide to writing in the life sciences. The President and Fellows of Harvard University, Massachusetts.
  4. Schimel, J. 2012. Writing science: how to write papers that get cited and proposals that get funded. Oxford University Press, Oxford.

Acknowledgments

We thank Nichole Barger and the University of Colorado, Boulder 2016 graduate writing seminar for helpful discussions that greatly enhanced the quality of this essay.

Potential Conflicts of Interest

None.

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Literature Cited

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