Clear and Concise: General Suggestions for Manuscript Preparation

Today’s post is the first tutorial on some general good practices of scientific writing and manuscript preparation. Many of the suggestions are based on common errors I’ve seen so far in very rough drafts from my students. If you have other suggestions, please offer them in the comments section. This is part of a series of posts compiled on the page A Beginner’s Guide to Writing Scientific Manuscripts.

Congratulations, you have some research to report to the rest of the world. No one knows it better than you, and it’s your job to educate the rest of us. The whole point is to clearly convey what you did, what it means and why it’s important.

It may seem overwhelming where to begin, but the specifics of sections and formatting have largely been decided for you depending on the journal you have chosen* for your manuscript submission. Each scientific journal provides detailed ‘instructions to authors’ on their websites. It includes everything you need to know about putting your manuscript document(s) together- section headings, font and size, citation formatting and figure guidelines. Some even provide a useful template document for MS Word. It is imperative that you follow these guidelines explicitly (yes, all of them. yes, exactly) or your research manuscript will be bounced back to you by the editor without review until you make it conform to their requirements. If you have any questions about how your document should look, download an article from that journal and/or have a look at an available pre-publication accepted manuscript version; each readily available at the website for that journal.

Outside of the requirements of the journal, it’s up to your good practice and judgment to put together a written document that clearly conveys your research. There are typically character or page limitations so it is important to be concise. State your thoughts in the most direct and clear way. This style may not win you a Pulitzer prize, but your audience is reading for information content, not necessarily pleasure. Verbose descriptions or filler sentences that don’t really say much can be a frustrating waste of time for the reader.  At the other end of the spectrum, it shouldn’t be so terse as to be incomprehensible due to missing information or no connection with anything of greater significance. (It should be noted that your manuscript’s first readers will be an editor and reviewers that will decide whether your research ever sees the light of day beyond your lab notebook and documents on your computer. So, yeah, at the very least- it shouldn’t be difficult or frustrating to read.)

Another good piece of general advice is ‘be consistent.’ Consistency- in terms of abbreviation usage and nomenclature in the text and presentation in the figures. If you refer to an organism one way in one paragraph, it should be same in subsequent paragraphs, unless you are talking about a different organism. While synonyms can be useful to break up the monotony, for important things like technique names and critical variables, refer to them in the exact same way or the reader may think you’re talking about something else. It is also useful to consistently order/label samples in your figures. If untreated sample is a solid black line and treated sample is a dashed line in Panel A, then don’t switch them for Panel B. This consistency should propagate across figures as well. If wild type is to the left of the mutant in images or lanes on a gel for a figure, then don’t switch the orientation in subsequent figures.

Abbreviations- you should use them. For any uncommon and long gene/protein names or techniques names, use an abbreviation. Write out the full-length version of the name or technique at its first usage and follow it by the abbreviation in parentheses. Then, just use that abbreviation in the rest of the manuscript. The general rule is, if you’ll need to use cumbersome wording 3 times or more, use an abbreviation. There are a number of very commonly used abbreviations within a scientific field that are widely understood and do not need definitions (ex: DNA, RNA, ATP etc) and these are generally listed somewhere on the website for each journal. Manuscripts also have an abbreviations section somewhere at the very beginning or end where all abbreviations are defined in one place. If the reader missed the definition in the text, they can refer to the abbreviations section. Abbreviations should be used consistently and exactly as defined. (Ex: Photosystem II = PS II; not sometimes PSII or PsII etc).

Specific usage and nomenclature- organisms, genes, proteins. This nomenclature often gets mixed in biochemistry literature. The full proper names of any organisms should be given the first time they are mentioned with the genus name capitalized and italicized and the species name lowercase and italicized. (Ex: Drosophila melanogaster, Zea mays, Arabidopsis thaliana) Then, if you plan on referring to this organism other places throughout the manuscript, designate the shortened version in parentheses after the first usage. (Ex: …. Drosophila melanogaster (subsequently Drosophila)….) Just make sure you use exactly that shortened designation consistently throughout the rest of the manuscript because any deviation from that usage will make the reader wonder if you are referring to another species. The specific shortened designations can vary widely, some people just stick with Genus others G. species and for some reason some organisms are so commonly known by their genus name that it has become acceptable to write Genus (nonitalicized) like Arabidopsis. There are strict conventions for the proper designations of gene or protein names/abbreviations. In a more genetics/cell biology manuscript, the rules are stricter**, but in more biochemically-focus papers, we’re not such sticklers. That being said, again, consistency is key and it should be clear whether you are talking about a protein or a gene. Typically genes are italicized (Ex: adh, Adh, ADH) and proteins are nonitalicized and at least the first letter is capitalized (Ex: Adh, ADH).

Scientific writing is generally written in third person format without any personal pronouns. It may take some getting used to this style, but eventually you will find ways of writing methods and results without any mention of yourself. (Ex: The colonies were screened using PCR. vs. We isolated DNA and did PCR.) Also, the Methods and Results are typically written in past tense because you are reporting observations that were made before you started writing the manuscript. The Introduction and Conclusion sections can be a mix of both, but be careful how you marry tenses. If you are writing a statement that is a known fact in the field or some conclusion you are now making from your data, write about these things as if they were always true and in the present tense. (Ex: ADH requires an NAD cofactor for activity.) However, if your wording choice mentions them as a previous finding, the past tense may also be appropriate. (Ex: Cheng and co-authors (#) showed that pyrazole was a competitive inhibitor of ADH.) Sometimes the use of personal pronouns is used in the conclusion section as a way of really owning a claim, but these instances are generally few and far between (Ex: From blah, blah, blah results, we conclude the following model…).

Repetition is necessary. It may seem like you are repeating yourself in various places throughout the manuscript. While absolute monotony is discouraged, repeating key assumptions, rationales or findings in the abstract, introduction, results and conclusions is useful for guiding the reader through your work. Remember, no one else knows the topic as well as you. So, someone reading your work for the first time may not make the necessary connections from rationale to conclusion, especially if those things are only mentioned once and separated by very many sections and experiments. You have to help the reader along or they will get frustrated or start coming to their own alternative conclusions. If this happens during the review process, it means more work for you- re-writing and usually additional experimentation. If it happens after publication, readers will still have doubts about your work.

In this course, you are given small tasks throughout the semester to guide you to the ultimate finished product. Generally, here is the order in which researchers typically work on sections of a manuscript (Note: this is completely different from the order in which they are presented in manuscript form to be submitted to a journal!).

  1. Figures, Tables and Legends: All of that data from your notebooks need to come together in some fashion to tell a story to support your new conclusions. The order of the figures in your manuscript will probably NOT be the order in which you actually did them. Data in figures are used to make the frame for the way you will present your work. I hope your notebook is complete enough to provide the necessary details to render the data into figures. Do you remember what sample was in lane three on that gel you ran 6 months ago? Probably not; hope you wrote it down or you will have to repeat it. If you do have to repeat it, I hope the samples for that gel are in appropriately labeled tubes in a box in the freezer. The figure legends should clearly state what the reader is looking at. Sometimes key details of the method are mentioned when appropriate for evaluating the data. Do not write any lengthy analysis of the results. At this point the researchers that will be authors on the paper will agree upon overall conclusions based on the data and how they will presented in the manuscript.
  2. Title and Author List: The figures should give you an idea of the story you need to tell, so come up with a descriptive, but concise title that captures all of it. Considering the data to be used, the analysis of the results and the writing to be done, authors and their relative ranks in the list according to contribution should be decided.
  3. Materials and Methods: It’s a good section to start with and transition yourself from experimental mode to writing mode. Since you’ve already decided on the figures you need to tell your research story, simply write about the methods you used to generate those figures. Scientific literature varies widely on the useful content within this section. While this section is not a complete protocol, it should give enough highlights of the techniques (and details critical for your experiments) for someone of reasonable ability to repeat your work.
  4. Results: Now that you are in writing-mode, explain all of your results, referring to the data in figures and tables as necessary. This section can be divided into relevant subsections to group findings as they support the various conclusions of your work. It is important to briefly state the purpose for each experiment and the experimental results. Very briefly, conclusions may be mentioned, especially as they lead into later experiments. If this is a pure results section, you won’t want to expound at length on the conclusions or models drawn from your data, but you should say briefly what they mean so it’s not a frustrating cliffhanger for the reader until the next section. Some journals have combined results/conclusions sections and, in that case, it is appropriate to discuss the meanings of your results.
  5. Conclusions: After you have written up all of your results with supporting data in your figures and tables, use this section to talk about what it all means. You may have briefly mentioned the significance of your findings in the results, but here is a chance to put it all together again. This will be the last thing you leave your readers with, so make sure your conclusions are clear and supported by your data. If multiple conclusions are possible, then you’ll have to split the difference and give a little bit of space to each possibility that your experiments haven’t differentiated. Now is the time to relate your conclusions to other published work (which you will cite), supporting or possibly contradictory, as well as offer a possible future direction or application of the research. If you are specifically working on additional experiments along this vein, then it is OK to mention this here or just speak more generally about what your conclusions mean for your field. Research will always keep moving forward; there will always be more experiments to be done, but at some point, you need to stop and write it up. It’s up to you to define the scope of your work. Reviewers may suggest other reasonable experiments, but you can often successfully argue against them if they are beyond the scope you have defined.
  6. Introduction: The background information on your research topic should be sufficient enough for a reasonable person to understand the scope and significance, but not an overly exhaustive review. In theory, it can be written in parallel with your Results and Conclusions sections. It should be complementary to your Results and Conclusions. While it should start with the bigger picture of a research area and its significance, it should ultimately hone in on the problem addressed specifically by your experiments. Usually, the end of the Introduction has a small paragraph describing the current work with respect to techniques and purpose, but not completely giving away the final conclusions. The Introduction and Conclusions sections may need to be edited for content simultaneously so they can most appropriately complement each other.
  7. References: Should be included throughout the writing process- Methods, Results, Conclusions and Introduction. They should include enough information for a read to find the citation and relate it to the claim you have supported in your writing.
  8. Abstract: Take the most important points of the entire work and fit them neatly into a single paragraph of 250 words or less. Your audience should be able to read the abstract and know the gist of what you’re interested in, what you did and the conclusions you made.


*Deciding on a journal for submission is a tutorial topic unto itself. I’m avoiding this discussion at this point, since I’ve made the arbitrary decision for my students to prepare according to the Journal of Biological Chemistry.

**If anyone wants to list these rules in the comments section, please do. Gene names are generally italicized, but capitalization/lowercase varies in usage between prokaryotic and eukaryotic systems. As a biochemist, I try to focus on the protein so as not to have to worry about italicization at all.


2 thoughts on “Clear and Concise: General Suggestions for Manuscript Preparation

  1. sarahjose

    For plants, genes are always written in italics and capital letters, proteins are not italicised and are in capital letters, and mutants are in lower case and italics. Human genes and proteins are always in capitals too, but other species vary, for example mouse genes usually only have the first letter capitalised.

    I had to write my results in a journal format as an undergrad too. I think it is a great way of learning how to convey your information in an easily understandable (to other scientists!) way. We also had to do a lay summary, which was great in other ways. 🙂

    1. johnnaroose Post author

      These are the conventions that I learned as well. I just think its strange when there’s this clever gene name that’s kinda long that must be written in all caps and italicized. From the prokaryotic community, gene names are italicized but always lowercase (wild type and mutant).

      I like the lay summary idea as well! Will have to think of a clever way to work this in too.


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