Guard your investment

Continue to save work frequently and make backups. The more time and energy you have invested in a document, the more important it is to protect that investment. A bit of paranoia can be healthy. Keep a duplicate copy. Remember to update the backup file each time you make significant changes.

FOLLOW STANDARD STRUCTURE

By this point in life, you've undoubtedly seen enough scientific documents to recognize that almost all of them follow a quite similar pattern, the so-called IMRAD format - an acronym for Introduction, Methods, Results And Discussion (Day and Gastel, 2006). Each main section is structured to address certain questions, and together they shape a critical argument.

Happily, this fairly rigid structure usually makes scientific writing easier, not more difficult. The next few pages offer a brief overview of what will be required. When you plunge in and begin to write, refer back here as necessary for inspiration and to stay on track.

Introduction

What is the problem, and why should anyone care? In other words, why was this work done? Deal with these questions briefly, interestingly, and as simply as possible. A well-written introduction should persuade colleagues and even non-specialists to begin reading the paper's text after their attention has been attracted by the title, abstract, tables, and figures.

A three-part introduction works well. First state the general field of interest. Concisely present what is already known about the subject of your investigation, referencing the most important publications. Don't try to mention everything, unless you are writing a review article or a thesis. One to three paragraphs should be enough for most journal articles.

Next, present others' findings that will be challenged or expanded. Explain how you are hoping to extend or modify what is already known or believed. Provide support for your argument.

Finally, specify the question that the paper addresses, and how it does so. This sentence is often phrased in hypothesis form. Indicate your experimental approach. Point out what is new and important about your work. When appropriate, briefly summarize the answer(s) you found.

Materials and methods

This section may have any of several names. Materials and/or Methods, Experimental Design, Protocol, and Procedure are some of the common ones. Sometimes it is divided into separately titled subsections, as well. Overall, it answers a simple question - how was the evidence obtained?

Begin by listing the supplies that were necessary for your work, including both animate materials such as experimental animals and inanimate ones such as chemicals. Explicitly note that use of animals and human subjects conformed to the legal requirements for the country in which the research was conducted.

Next, specify what was done, and for what purpose. Chronological order is a common way to proceed through this segment. Alternatively, parallel the sequence in which you present results. A flowchart may be useful for readers. Conclude with a discussion of any statistical procedures employed (but not the tests' outcomes, which belong in Results).

The key to a successful Methods section is to include the right amount of detail - too much, and it begins to sound like a laboratory manual; too little, and no one can determine what you actually did. For publication of a new discovery to be "valid" or scientifically accepted, it must appear in a form so that a reader could repeat the experiment. However, this really means not just any reader, but a trained investigator with considerable experience. Once again, it is important to know one's audience. As an additional guide, frequently refer to examples published in your chosen journal.

Increasingly, federally funded research in the United States is requiring studies to be conducted in accordance with Good Laboratory Practice (GLP) guidelines (Benson and Boege, 2002). The guidelines require preparation of standard operating procedures for all aspects of a project. Referring back to these procedures can be very helpful, both when preparing Materials and Methods and when documenting the data that were collected. Even when GLP guidelines are not required for a project, using this research approach can facilitate the writing task.

If you have followed a widely known method, simply name the principles on which it is based and cite the original publication or recent textbooks or handbooks that give full details. If you made changes to a published procedure, describe only the changes and reference the rest. Only if you have employed an entirely new process or technique must you describe it in full. In this last instance, you may wish to test the adequacy of your description by asking a colleague to do an experiment while following the technique as your text describes it.

Results

This section should be relatively easy. What was found or seen? Decide on a logical order for presentation (see Table 2.1). Present the results that have a bearing on the question you are examining, but do not interpret them here unless your journal combines Results and Discussion. Exclude irrelevant findings, but never omit valid results that appear to contradict your hypothesis. Suppressing such data is unethical, but when presenting them you may explain why you feel they are anomalous.

Tables and figures are usually an integral part of this section. Don't use the text to parrot the information they contain. Readers can see the data for themselves. Instead, point out salient features and note relationships between the various results.

Discussion and conclusions

What do your findings mean? Why are they important? Discussion and Conclusions sections exist to answer these questions. Often combined with each other

Table 2.1. Common patterns for organizing material

Pattern

Basis

Categorical

Chronological

Spatial

Functional

Importance

Problem-solutions

Specificity

Complexity

Pro and con

Causality

Deductive

Inductive

Groupings of like items Time sequence

Physical arrangement of entities How parts work

Usually with elements in order of decreasing consequence Predicament, possible answers, why each will/won't work, usually followed by specific recommendation General to particular, or particular to general Usually from simple to complex Both sides of an issue or decision Cause and effect

Conclusion first, then background leading up to it Individual facts first, leading to conclusion and sometimes with the Results as well, these sections generally parallel the organization used in earlier sections of the paper.

Your task here is to interpret your results against a background of existing knowledge. Explain what is new in your work, and why it matters. Discuss both the limitations and the implications of your results, and relate your observations to other relevant studies. State new hypotheses (clearly labeled as such) when they are warranted. Include recommendations when appropriate.

When writing this section, watch for symptoms of megalomania. Avoid exaggerated or extravagant claims for your work. Carefully distinguish between facts and speculation. Be wary about extrapolating your results to other species or conditions. Rein in the natural human tendency to want to point out the shortcomings of another investigator's report. Indicate what the next steps might be to resolve any apparent conflicts. Frankly admit anomalies. Discuss any possible errors or limitations in your methods and assumptions. And finally, don't stack in so many alternative hypotheses to explain the results that readers become buried in the pile. Hailman and Strier (1997) state that as a general rule, the discussion should never be the longest section in a paper.

Acknowledgments

Acknowledgments usually appear between the Discussion and Reference sections. (Note that some journals spell the title of this section with two "e"s, others with three.) Include any substantial help received from organizations or individuals, whether they provided grants, materials, technical assistance, or advice. (Some journals specify that funding bodies be named on the title page instead.) Concisely thank those who went out of their way to help, and describe their contribution. Do not list people who did not contribute directly to the reported work or those who did no more than their routine laboratory, secretarial, or office work. As a courtesy, ask consent from anyone you name; some journals require signed permissions from everyone who is acknowledged.

References

In this section, include all the references you cited (specifically referred to) in the text, tables, and figures, but not references that were only useful background reading for you.

For your first draft, use the name-and-year (Harvard) system for citations rather than a consecutive number (Vancouver) style. It is easier to compile a final reference list from names than from numbers, and the Harvard system minimizes the chances that reference citations will become scrambled during reorganizations of the text.

There are literally hundreds of variations of literature reference style. Some excellent computerized bibliographic programs are available to help you consistently apply proper formatting to your final draft.

Note that some journals limit the number of references you can cite; check the Instructions to Authors. One common restriction is 40 references for full articles and 10 for brief communications, but some journals specify even fewer.

Abstracts and summaries

Abstracts are usually inserted right after the title page in the completed document. They are easier to prepare when your document is finished, but a first draft now may help you stay focused.

Some journals use the term "summary" to describe abstracts of their articles, but a summary is not the same as an abstract. An abstract is an abbreviated version of the paper, written for people who may never read the complete version. A summary restates the main findings and conclusions of a paper, and is written for people who have already read the paper. Include a summary only if the journal requires it.

Abstracts come in several varieties. Informative abstracts include some data and are commonly used with documents that describe original research. They address the same questions as the body of the paper, but briefly and without supporting tables or figures. Indicative abstracts (also called descriptive or topical) contain general statements about the subjects covered. Often used for review articles or books, they usually can be created simply by turning the table of contents into sentences.

Both informative and indicative abstracts are typically limited to between 100 and 250 words, and different points are emphasized in proportion to the emphasis they receive in the text itself. They are generally written as a single paragraph.

Structured abstracts are often longer, sometimes allowing as many as 400 words. These abstracts group series of points below headings such as Objective, Design, Setting, Patients, Treatment, Results, Conclusions, and Clinical Relevance. Experts disagree whether structured abstracts are on the way to disappearance or are evolving into a new kind of publication, with the main text available only in electronic form.

Staying within an abstract's word count specifications is a challenge for almost every writer. Be as brief and specific as possible, but write complete sentences that logically follow one another. Use the third person, active verbs, and the past tense unless it becomes unacceptably awkward to do so. The title and abstract are always read together, so there is no reason to repeat words or paraphrase the title in the abstract.

Write the abstract so that it can stand on its own merits, because many readers of your abstract will never see your entire text. If possible, avoid citing others' work here; when a citation is essential, include a short form of the bibliographic details. Likewise, avoid unfamiliar terms, acronyms, abbreviations, or symbols; if they must be used, define them at first mention in the abstract, then again at first mention in the text. And finally, never introduce information in the abstract that is not covered in the paper.

The title

From the moment when the first words are written, every document needs a rough working title for identification purposes. However, a working title is rarely suitable for the final paper. Refine it now. Is it interesting, concise, and informative? Is it accurate enough for use in indexing systems and bibliographic databases? Will potential readers be able to judge your paper's relevance to their own interests on the basis of the title alone?

Once again, it's time to check your journal's Instructions to Authors and to look over the publications in recent issues. Note capitalization style, title length, and general form. For journals in some fields, writers are being encouraged to use a declarative title written as a sentence or fragment that includes what the paper says, not just what it covers; in other fields, neutral descriptive titles remain the norm. Sometimes, they coexist. For example, in the international weekly journal, Nature, one can find both:

Declarative: Selective elimination of messenger RNA prevents an incidence of untimely meiosis

Descriptive: Mechanism of DNA translocation in a replicative hexa-meric helicase

Most journals prefer short titles, typically not over 100 characters (and sometimes considerably fewer), including the spaces between the words. This usually works out to only 10-12 words. Delete trivial phrases (such as "Notes on" or "A study of"), but do not use uncommon abbreviations or stack nouns and adjectives together without their prepositions.

Poor: A Study of Chipmunk Muscle Tissue Ion Channel Amino Acid Activation Parameters

Better: Amino Acid Activation of Ion Channels in Chipmunk Muscle Tissue

Most editors frown upon fanciful titles. Some also object to two-part titles, with a main title and a subtitle. Titles that end with a question mark are seldom acceptable.

Risky choices:

German Saxifrage Pollens are Superior to Those in Austria.

Does Saxifraga Pollen in Germany Resemble That in Austria?

Pollen Between a Rock and a Hard Place: German and Austrian Saxifrages

Widespread acceptability: Pollen Morphology of German and Austrian Saxifraga Species

When writing a series of papers on a subject, title each separately. Numbered series with the same title and differing subtitles are a headache to everyone, especially if the papers have slightly different sets of coauthors. Editors are unhappy with the implication that acceptance of one paper obligates them to publish successive ones. Readers, librarians, and cataloguers deal with unnecessary confusion, especially if Part 4 is published before Part 2, or Part 3 is rejected entirely. If you feel it is vital that everyone knows the papers are a series, link them by mentioning the others in a footnote on the title page or by citing them in the Introduction. If the typescript on hand is interdependent with another unpublished paper, remember to include copies of that other paper for reviewers when you send the document to an editor.

Exercise 2.2. Title choices

How could the following manuscript titles be improved? Explain the reasons for your choices.

1.

Plantar's Wart Removal: Report of a Case of Recurrence of Verruca after Curative Excision

2.

Characteristics of Columbine Flowers are Correlated with Their Pollinators

3.

Panda Mating Fails: Veterinarian Takes Over

4.

Gleanings On The Bionomics And Behavior Of The East Asiatic Nonsocial Wasps. III. The Subfamily Crabroninae With A Key To The Species Of The Tribe Crabronini Occurring In Formosa And The Ryukyus, Contributions To The Knowledge Of The Behavior Of Crabronine Fauna, And Changes In The Taxonomic Position Of Three Species Of Crabronini Occurring In Japan

5.

Report of New Health Data Results from the 1999 National ASAP-FYI-ERGO Health Study: Lung Cancer in Women Mushrooms

Other title page items

The title page really doesn't need to be compiled until the final document is assembled. However, for a psychological sense of completeness, writers often like to put one on the first draft. Most journals specify what information should appear -commonly, authors' names, degrees, job titles, and the name and addresses (postal and electronic) of the author to whom correspondence, proofs, and reprint requests should be sent. Keywords and funding sources may be mandatory, and some journals request a text word count.

Keywords or key phrases serve as reference points to indicate document contents for indexing and cataloguing. Check your journal's Instructions to Authors for their location in the typescript. The number of keywords that can be included is usually specified; three to ten are common limits.

If guidance from the journal is lacking, it is generally prudent to choose keywords and terms from the Medical Subject Headings used in Index Medicus, or from lists such as those published in Biological Abstracts and Chemical Abstracts. Choose the most important and most specific terms you can find in your document, including more general terms only if your work has interdisciplinary significance. Unless the target journal specifies otherwise, words that appear in the title do not need to be included among the keywords.

USE TENSE TO SHOW THE STATUS OF WORK

The use of present or past forms of verbs has a very special meaning in scientific papers. Proper tense use derives from scientific ethics. The use of past or present verb forms is a way of indicating the status of the scientific work being reported.

Because of these conventions regarding tense use, a scientific paper usually should seesaw back and forth between the past and present tenses. An Abstract or Summary refers primarily to the author's own unpublished results, and uses the past tense. Most of the Introduction section emphasizes previously established knowledge, given in the present tense. Both the Materials and Methods and the Results sections describe what the author did and found. They appear in the past tense. Finally, the Discussion emphasizes the relationship of the author's work to previously established knowledge. This section is the most difficult to write smoothly because it includes both past and present tenses.

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