Writing your first manuscript

Getting Started. It is time to think about writing when you have acquired some data in response to a specific hypothesis or question. It is not necessary to have all references read, all experiments done, nor all answers in hand before you start thinking about, and begin, writing. In fact, the writing process serves to focus on thinking in a more directed fashion, thereby identifying those areas that need additional attention. Start to think of your research as “packets” of information to help you focus. Identify a target journal for submission and consult instructions to authors before you begin. Many prolific authors adopt the practice of setting aside a finite amount of time, free from distraction, at the time of day they are most alert.

GENERAL WRITING ADVICE

Excerpt from Article: “Evidence-Based Grammar” Biotechniques 03/12/2014  by Amy Volpert

Researchers love comparisons and analogies. A comparison is essential for data analysis and validation—you can compare your sample to a standard or you can compare different treatments under the same conditions. Comparisons are also used to highlight the overall significance of a study, that is to say how the findings differ from or extend upon current knowledge.
“Like” vs. “Such as”

While “like” has become a place-holder in everyday speech, to the annoyance of many, it turns out that the word is also often used inappropriately in print. “Like” should be used when discussing something similar to, but not the same as, the desired item or result.

• Example: “The muscular/mesenchymal layer left behind also preserved it’s in vivo structure, with the mesenchymal cores of the villi sticking out like bristles on a brush and the crypt beds visible as tiny holes in between.”

In contrast, the phrase “such as” should be used when listing concrete possibilities; the phrase can commonly be replaced with “for example” in the text or “e.g.” in parenthesis.

• Example: “Organisms that are tolerant of extreme environmental stress, such as desiccation, accumulate large amounts of disaccharides in the dehydrated state.”

“Compared to” vs. “Compared with”

This is a more subtle distinction than in the case of “like” and “such as” above.

“Compared to” is correct when comparing items that are different or stating the similarities between items.

• Example: “Target titrations indicated some differences in plate-based sandwich assay performance compared to the bead-based test.”
  *Since the two types of assays are different, “compared to” is appropriate here.

“Compared with” should ideally be used when comparing similar items or stating the similarities and differences between items.

• Example: “The target sequence has GC content of 42.9%, compared with the mammoth mitogenome average of roughly 38%.”
  *Since two similar items (DNA sequences) are being analyzed, “compared with” is appropriate here.

Note: It is good to know this distinction between “compared to” and “compared with”, but in general practice, you can often get away with using the phrase you prefer.
“-er” vs. “-est”

In English, the suffix “-er” is used to compare one value relative to another (e.g., bigger, smaller). The suffix “-est”, however, is used to identify an extreme value (or subset of values) in a data set containing three or more elements (e.g., biggest, smallest).

The easiest way to think of this is that “-er” should be used when comparing two values relative to one another.

• Example: “We show that this protocol can generate observable changes in the amount of cartilage tissue formed in micromass, unlike lower efficiency, higher cytotoxicity techniques.”

On the other hand, “-est” should be used when identifying data points at either end of a range of values (assuming the data set has more than three items): “The expression of gene X was greatest in adult subjects compared to neonates or juveniles.”

• Example: “The algorithm should attempt to identify the deepest taxonomic rank possible.”

“Greater than” (>) vs. “Greater than or equal to” (≥) [or “Less than” (<) vs. “Less than or equal to” (≤)]

Everyone should know the difference between the phrases “greater than” (>) and “greater than or equal to” (≥), but when it comes to discussing data, it is important to double-check that you are using the right term (or symbol). It’s very easy to slip and say that a set of values is greater than 50 when the truth is that the set contains values of 50 or greater.

• Example: “A major limitation in miRNA library construction arises when the amount of input RNA <200 ng.”
  *This limitation would not be seen with 200 ng of input RNA.

• Example: “Sites with a maximum of 2 alleles and a minor allele frequency ≥2% were selected.”
  *A site with 0–2 alleles and a minor allele frequency equal to 2.0% could be selected.

We hope these examples start you thinking more about the way in which you word comparisons in your manuscripts. A simple turn of the phrase can have a profound impact on the way a reader or reviewer perceives your text.

More advice…..

1.  Pay attention to the four C’S

• Be careful. Text should be carefully crafted with attention to detail.
• Be clear. Text should be easy to read; avoid run-on sentences. Use proper grammar, and sentence and paragraph structure.
• Be concise. More verbiage is not necessarily better. Revise your writing to minimize superfluous words.
• Be correct. Make sure your information is accurate.

2. Use your tools wisely. Search results are only as good as your design and interpretation. All databases are limited by the information entered into the program.

• Sequence identification and analysis programs. Be aware of the limitations of the programs you use, and that the results you obtain may be affected by the way you design your search. The results you obtain will require study and interpretation on your part. Keep any such pitfalls in mind as you write your text.
• Publication databases. Databases are limited by the literature entered into the programs. Papers published before a certain date may not be included. Not all journals will be represented. Be aware of these limitations, and make every effort to uncover the important papers you need to cite. Read the papers before you cite them, and accurately represent the findings and conclusions.

3. Get critical feedback.

• From yourself: let the draft sit for a while before you revise it.
• From others: in addition to your major advisor, ask others in the lab to read your text for general, as well as specific, impressions.
• Be prepared to write multiple versions.

4. Image is everything

• While presentation never replaces content, the more professional your presentation, the better the reception it will receive. This is true for presentations as well as manuscripts. Hand drawn slides and transparencies send a message that you didn’t respect the venue and/or audience enough to prepare in advance. Manuscripts and proposals are the same way; errors and carelessness in documents lead the reader to wonder if the quality of thought behind the data is the same. Reviewers appreciate a well thought out piece of writing.
• Know and follow formats and good editorial practices. Consult the instructions to authors; this is especially important for journals in the field of genetics that are likely to have specific instructions about the designations for genes, alleles, proteins, organisms, cloned DNA fragments, reporter constructs, transgenic animals, etc. Always properly and completely format manuscripts to the specifications of the journal.
• Know the literature in the field. Keep up to date in your own small sphere of research; this includes knowledge of the “classics”.
• Cite previously published works correctly; journals have different formats for literature cited.

WRITING YOUR FIRST JOURNAL ARTICLE

Scientific papers typically have the following sections:

I. Abstract
II. Introduction
III. Materials and Methods
IV. Results
V. Discussion
VI. Literature cited
VII. Figures and Tables

One suggested sequence for writing:

It is often difficult for young scientific writers to get started. While the author is aware of the general thrust and major points of his research, the challenges of organization, focus, and presentation can be overwhelming. There are many successful strategies for writing, but here is one sequence that works for many inexperienced writers.

Abstract. The key points of the paper are briefly summarized in this section.

Introduction. Introductions are brief reviews of the significance of the work to be presented and of the background necessary to understand it. Although all will not be appropriate to every paper, the following is a list of questions the introduction might address. What is the significance of this research? Why should anyone care? What is the overall theme of this piece of writing? What is its goal? What is the state of knowledge (brief and targeted review)? What are the gaps/weaknesses of the present state of knowledge? How does this work contribute to its advancement? What does this work accomplish? A good introduction funnels the reader’s attention from the general to the specifics of the paper.

Materials and Methods. This is a section of a paper or thesis that can be worked on at any time. For a paper or presentation, refer to published protocols as appropriate to support general text; this section should not be very long. Provide detail of important modifications, or unpublished or novel methods. This section in a thesis will be more comprehensive to allow exact replication. Pay attention to proper abbreviations, terminology, nomenclature, and designations. Working on Materials & Methods text is always a good diversion when writer’s block hits!

Results. The results section of a full-length paper is typically comprised of subsections, one for each major hypothesis/question/goal of the paper. Such subsections may or may not be subtitled in a given journal format. Each subsection will begin with a restatement of the specific information, question or hypothesis addressed by that portion of the research. If necessary, a very brief recap of the rationale may be presented. A detailed analysis of each figure and table is presented, including any considerations of limitations or sources of error. The subsection concludes with a statement of what the results tell the reader about the hypothesis or questions posed. As you move to the next subsection of the results, it is important to make use of transition sentences to create a logical progression from one point to the next.

Figures and Tables. The answer to the question “What data have I actually generated?” will help focus the rest of the paper. Spend time considering how the data can be presented in the clearest and most logical fashion. Each of your figures/tables should correspond to a major point in the paper. Figures must always be of high quality and the major finding unambiguous. Format figures/tables as specified for the target journal; there will be journal-specific instructions for size, fonts, legends. Proper preparation of figures and tables is a time-consuming task.

Discussion/Conclusion. Most discussions begin with a brief recap of the entire work, including questions and findings. The main body of this section will be interpretations of the results in the context of the body of existing knowledge. This is also the appropriate place to discuss new models, theories, or questions that arise from the research. Discussions typically end with a brief projection of the next logical extension of the research (future directions).

Literature Cited. Be judicious in literature cited; reference only those publications that are directly germane to the text.