how to write a scientific method paper

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10 Simple Steps to Writing a Scientific Paper

At any given time, Andrea Armani ’s lab at the University of Southern California has up to 15 PhD students, a couple of postdocs, nine undergrads, and an occasional high school student, all busy developing new materials for diagnostic and telecommunications devices.

When conducting scientific research, Armani believes it’s important to test a hypothesis—not prove it. She recruits students who are willing to adopt that “testing” mentality, and are excited to explore the unknown. “I want them to push themselves a little bit, push the field a little bit, and not be afraid to fail,” she says. “And, know that even if they fail, they can still learn something from it.”

Armani often coaches students through the process of writing their first scientific paper. Her 10-step formula for writing a scientific paper could be useful to anyone who has concluded a study and feels the dread of the blank page looming.

1. Write a Vision Statement

What is the key message of your paper? Be able to articulate it in one sentence, because it's a sentence you'll come back to a few times throughout the paper. Think of your paper as a press release: what would the subhead be? If you can't articulate the key discovery or accomplishment in a single sentence, then you're not ready to write a paper.

The vision statement should guide your next important decision: where are you submitting? Every journal has a different style and ordering of sections. Making this decision before you write a single word will save you a lot of time later on. Once you choose a journal, check the website for requirements with regards to formatting, length limits, and figures.

2. Don't Start at the Beginning

Logically, it makes sense to start a paper with the abstract, or, at least, the introduction. Don't. You often end up telling a completely different story than the one you thought you were going to tell. If you start with the introduction, by the time everything else is written, you will likely have to rewrite both sections.

3. Storyboard the Figures

Figures are the best place to start, because they form the backbone of your paper. Unlike you, the reader hasn't been living this research for a year or more. So, the first figure should inspire them to want to learn about your discovery.

A classic organizational approach used by writers is "storyboarding" where all figures are laid out on boards. This can be done using software like PowerPoint, Prezi, or Keynote. One approach is to put the vision statement on the first slide, and all of your results on subsequent slides. To start, simply include all data, without concern for order or importance. Subsequent passes can evaluate consolidation of data sets (e.g., forming panel figures) and relative importance (e.g., main text vs. supplement). The figures should be arranged in a logical order to support your hypothesis statement. Notably, this order may or may not be the order in which you took the data. If you're missing data, it should become obvious at this point.

4. Write the Methods Section

Of all the sections, the methods section is simultaneously the easiest and the most important section to write accurately. Any results in your paper should be replicable based on the methods section, so if you've developed an entirely new experimental method, write it out in excruciating detail, including setup, controls, and protocols, also manufacturers and part numbers, if appropriate. If you're building on a previous study, there's no need to repeat all of those details; that's what references are for.

One common mistake when writing a methods section is the inclusion of results. The methods section is simply a record of what you did.

The methods section is one example of where knowing the journal is important. Some journals integrate the methods section in between the introduction and the results; other journals place the methods section at the end of the article. Depending on the location of the methods section, the contents of the results and discussion section may vary slightly.

5. Write the Results and Discussion Section

In a few journals, results and discussion are separate sections. However, the trend is to merge these two sections. This section should form the bulk of your paper-by storyboarding your figures, you already have an outline!

A good place to start is to write a few paragraphs about each figure, explaining: 1. the result (this should be void of interpretation), 2. the relevance of the result to your hypothesis statement (interpretation is beginning to appear), and 3. the relevance to the field (this is completely your opinion). Whenever possible, you should be quantitative and specific, especially when comparing to prior work. Additionally, any experimental errors should be calculated and error bars should be included on experimental results along with replicate analysis.

You can use this section to help readers understand how your research fits in the context of other ongoing work and explain how your study adds to the body of knowledge. This section should smoothly transition into the conclusion.

6. Write the Conclusion

In the conclusion, summarize everything you have already written. Emphasize the most important findings from your study and restate why they matter. State what you learned and end with the most important thing you want the reader to take away from the paper-again, your vision statement. From the conclusion, a reader should be able to understand the gist of your whole study, including your results and their significance.

7. Now Write the Introduction

The introduction sets the stage for your article. If it was a fictional story, the introduction would be the exposition, where the characters, setting, time period, and main conflict are introduced.

Scientific papers follow a similar formula. The introduction gives a view of your research from 30,000 feet: it defines the problem in the context of a larger field; it reviews what other research groups have done to move forward on the problem (the literature review); and it lays out your hypothesis, which may include your expectations about what the study will contribute to the body of knowledge. The majority of your references will be located in the introduction.

8. Assemble References

The first thing that any new writer should do is pick a good electronic reference manager. There are many free ones available, but often research groups (or PIs) have a favorite one. Editing will be easier if everyone is using the same manager.

References serve multiple roles in a manuscript:

1) To enable a reader to get more detailed information on a topic that has been previously published. For example: "The device was fabricated using a standard method." You need to reference that method. One common mistake is to reference a paper that doesn't contain the protocol, resulting in readers being sent down a virtual rabbit hole in search of the protocol.

2) To support statements that are not common knowledge or may be contentious. For example: "Previous work has shown that vanilla is better than chocolate." You need a reference here. Frequently, there are several papers that could be used, and it is up to you to choose.

3) To recognize others working in the field, such as those who came before you and laid the groundwork for your work as well as more recent discoveries. The selection of these papers is where you need to be particularly conscientious. Don't get in the habit of citing the same couple of papers from the same couple of groups. New papers are published every day-literally. You need to make sure that your references include both foundational papers as well as recent works.

9. Write the Abstract

The abstract is the elevator pitch for your article. Most abstracts are 150–300 words, which translates to approximately 10–20 sentences. Like any good pitch, it should describe the importance of the field, the challenge that your research addresses, how your research solves the challenge, and its potential future impact. It should include any key quantitative metrics. It is important to remember that abstracts are included in search engine results.

10. The Title Comes Last

The title should capture the essence of the paper. If someone was interested in your topic, what phrase or keywords would they type into a search engine? Make sure those words are included in your title.

Andrea Martin Armani is an SPIE Fellow and the Ray Irani Chair in Engineering and Materials Science and Professor of Chemical Engineering and Materials Science at the USC Viterbi School of Engineering.

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• Int J Sports Phys Ther
• v.7(5); 2012 Oct

HOW TO WRITE A SCIENTIFIC ARTICLE

Barbara j. hoogenboom.

1 Grand Valley State University, Grand Rapids, MI, USA

Robert C. Manske

2 University of Wichita, Wichita, KS, USA

Successful production of a written product for submission to a peer‐reviewed scientific journal requires substantial effort. Such an effort can be maximized by following a few simple suggestions when composing/creating the product for submission. By following some suggested guidelines and avoiding common errors, the process can be streamlined and success realized for even beginning/novice authors as they negotiate the publication process. The purpose of this invited commentary is to offer practical suggestions for achieving success when writing and submitting manuscripts to The International Journal of Sports Physical Therapy and other professional journals.

INTRODUCTION

“The whole of science is nothing more than a refinement of everyday thinking” Albert Einstein

Conducting scientific and clinical research is only the beginning of the scholarship of discovery. In order for the results of research to be accessible to other professionals and have a potential effect on the greater scientific community, it must be written and published. Most clinical and scientific discovery is published in peer‐reviewed journals, which are those that utilize a process by which an author's peers, or experts in the content area, evaluate the manuscript. Following this review the manuscript is recommended for publication, revision or rejection. It is the rigor of this review process that makes scientific journals the primary source of new information that impacts clinical decision‐making and practice. 1 , 2

The task of writing a scientific paper and submitting it to a journal for publication is a time‐consuming and often daunting task. 3 , 4 Barriers to effective writing include lack of experience, poor writing habits, writing anxiety, unfamiliarity with the requirements of scholarly writing, lack of confidence in writing ability, fear of failure, and resistance to feedback. 5 However, the very process of writing can be a helpful tool for promoting the process of scientific thinking, 6 , 7 and effective writing skills allow professionals to participate in broader scientific conversations. Furthermore, peer review manuscript publication systems requiring these technical writing skills can be developed and improved with practice. 8 Having an understanding of the process and structure used to produce a peer‐reviewed publication will surely improve the likelihood that a submitted manuscript will result in a successful publication.

Clear communication of the findings of research is essential to the growth and development of science 3 and professional practice. The culmination of the publication process provides not only satisfaction for the researcher and protection of intellectual property, but also the important function of dissemination of research results, new ideas, and alternate thought; which ultimately facilitates scholarly discourse. In short, publication of scientific papers is one way to advance evidence‐based practice in many disciplines, including sports physical therapy. Failure to publish important findings significantly diminishes the potential impact that those findings may have on clinical practice. 9

BASICS OF MANUSCRIPT PREPARATION & GENERAL WRITING TIPS

To begin it might be interesting to learn why reviewers accept manuscripts! Reviewers consider the following five criteria to be the most important in decisions about whether to accept manuscripts for publication: 1) the importance, timeliness, relevance, and prevalence of the problem addressed; 2) the quality of the writing style (i.e., that it is well‐written, clear, straightforward, easy to follow, and logical); 3) the study design applied (i.e., that the design was appropriate, rigorous, and comprehensive); 4) the degree to which the literature review was thoughtful, focused, and up‐to‐date; and 5) the use of a sufficiently large sample. 10 For these statements to be true there are also reasons that reviewers reject manuscripts. The following are the top five reasons for rejecting papers: 1) inappropriate, incomplete, or insufficiently described statistics; 2) over‐interpretation of results; 3) use of inappropriate, suboptimal, or insufficiently described populations or instruments; 4) small or biased samples; and 5) text that is poorly written or difficult to follow. 10 , 11 With these reasons for acceptance or rejection in mind, it is time to review basics and general writing tips to be used when performing manuscript preparation.

“Begin with the end in mind” . When you begin writing about your research, begin with a specific target journal in mind. 12 Every scientific journal should have specific lists of manuscript categories that are preferred for their readership. The IJSPT seeks to provide readership with current information to enhance the practice of sports physical therapy. Therefore the manuscript categories accepted by IJSPT include: Original research; Systematic reviews of literature; Clinical commentary and Current concept reviews; Case reports; Clinical suggestions and unique practice techniques; and Technical notes. Once a decision has been made to write a manuscript, compose an outline that complies with the requirements of the target submission journal and has each of the suggested sections. This means carefully checking the submission criteria and preparing your paper in the exact format of the journal to which you intend to submit. Be thoughtful about the distinction between content (what you are reporting) and structure (where it goes in the manuscript). Poor placement of content confuses the reader (reviewer) and may cause misinterpretation of content. 3 , 5

It may be helpful to follow the IMRaD format for writing scientific manuscripts. This acronym stands for the sections contained within the article: Introduction, Methods, Results, and Discussion. Each of these areas of the manuscript will be addressed in this commentary.

Many accomplished authors write their results first, followed by an introduction and discussion, in an attempt to “stay true” to their results and not stray into additional areas. Typically the last two portions to be written are the conclusion and the abstract.

The ability to accurately describe ideas, protocols/procedures, and outcomes are the pillars of scientific writing . Accurate and clear expression of your thoughts and research information should be the primary goal of scientific writing. 12 Remember that accuracy and clarity are even more important when trying to get complicated ideas across. Contain your literature review, ideas, and discussions to your topic, theme, model, review, commentary, or case. Avoid vague terminology and too much prose. Use short rather than long sentences. If jargon has to be utilized keep it to a minimum and explain the terms you do use clearly. 13

Write with a measure of formality, using scientific language and avoiding conjunctions, slang, and discipline or regionally specific nomenclature or terms (e.g. exercise nicknames). For example, replace the term “Monster walks” with “closed‐chain hip abduction with elastic resistance around the thighs”. You may later refer to the exercise as “also known as Monster walks” if you desire.

Avoid first person language and instead write using third person language. Some journals do not ascribe to this requirement, and allow first person references, however, IJSPT prefers use of third person. For example, replace “We determined that…” with “The authors determined that….”.

For novice writers, it is really helpful to seek a reading mentor that will help you pre‐read your submission. Problems such as improper use of grammar, tense, and spelling are often a cause of rejection by reviewers. Despite the content of the study these easily fixed errors suggest that the authors created the manuscript with less thought leading reviewers to think that the manuscript may also potentially have erroneous findings as well. A review from a second set of trained eyes will often catch these errors missed by the original authors. If English is not your first language, the editorial staff at IJSPT suggests that you consult with someone with the relevant expertise to give you guidance on English writing conventions, verb tense, and grammar. Excellent writing in English is hard, even for those of us for whom it is our first language!

Use figures and graphics to your advantage . ‐ Consider the use of graphic/figure representation of data and important procedures or exercises. Tables should be able to stand alone and be completely understandable at a quick glance. Understanding a table should not require careful review of the manuscript! Figures dramatically enhance the graphic appeal of a scientific paper. Many formats for graphic presentation are acceptable, including graphs, charts, tables, and pictures or videos. Photographs should be clear, free of clutter or extraneous background distractions and be taken with models wearing simple clothing. Color photographs are preferred. Digital figures (Scans or existing files as well as new photographs) must be at least 300dpi. All photographs should be provided as separate files (jpeg or tif preferred) and not be embedded in the paper. Quality and clarity of figures are essential for reproduction purposes and should be considered before taking images for the manuscript.

A video of an exercise or procedure speaks a thousand words. Please consider using short video clips as descriptive additions to your paper. They will be placed on the IJSPT website and accompany your paper. The video clips must be submitted in MPEG‐1, MPEG‐2, Quicktime (.mov), or Audio/Video Interface (.avi) formats. Maximum cumulative length of videos is 5 minutes. Each video segment may not exceed 50 MB, and each video clip must be saved as a separate file and clearly identified. Formulate descriptive figure/video and Table/chart/graph titles and place them on a figure legend document. Carefully consider placement of, naming of, and location of figures. It makes the job of the editors much easier!

Avoid Plagiarism and inadvertent lack of citations. Finally, use citations to your benefit. Cite frequently in order to avoid any plagiarism. The bottom line: If it is not your original idea, give credit where credit is due . When using direct quotations, provide not only the number of the citation, but the page where the quote was found. All citations should appear in text as a superscripted number followed by punctuation. It is the authors' responsibility to fully ensure all references are cited in completed form, in an accurate location. Please carefully follow the instructions for citations and check that all references in your reference list are cited in the paper and that all citations in the paper appear correctly in the reference list. Please go to IJSPT submission guidelines for full information on the format for citations.

Sometimes written as an afterthought, the abstract is of extreme importance as in many instances this section is what is initially previewed by readership to determine if the remainder of the article is worth reading. This is the authors opportunity to draw the reader into the study and entice them to read the rest of the article. The abstract is a summary of the article or study written in 3 rd person allowing the readers to get a quick glance of what the contents of the article include. Writing an abstract is rather challenging as being brief, accurate and concise are requisite. The headings and structure for an abstract are usually provided in the instructions for authors. In some instances, the abstract may change slightly pending content revisions required during the peer review process. Therefore it often works well to complete this portion of the manuscript last. Remember the abstract should be able to stand alone and should be as succinct as possible. 14

Introduction and Review of Literature

The introduction is one of the more difficult portions of the manuscript to write. Past studies are used to set the stage or provide the reader with information regarding the necessity of the represented project. For an introduction to work properly, the reader must feel that the research question is clear, concise, and worthy of study.

A competent introduction should include at least four key concepts: 1) significance of the topic, 2) the information gap in the available literature associated with the topic, 3) a literature review in support of the key questions, 4) subsequently developed purposes/objectives and hypotheses. 9

When constructing a review of the literature, be attentive to “sticking” or “staying true” to your topic at hand. Don't reach or include too broad of a literature review. For example, do not include extraneous information about performance or prevention if your research does not actually address those things. The literature review of a scientific paper is not an exhaustive review of all available knowledge in a given field of study. That type of thorough review should be left to review articles or textbook chapters. Throughout the introduction (and later in the discussion!) remind yourself that a paper, existing evidence, or results of a paper cannot draw conclusions, demonstrate, describe, or make judgments, only PEOPLE (authors) can. “The evidence demonstrates that” should be stated, “Smith and Jones, demonstrated that….”

Conclude your introduction with a solid statement of your purpose(s) and your hypothesis(es), as appropriate. The purpose and objectives should clearly relate to the information gap associated with the given manuscript topic discussed earlier in the introduction section. This may seem repetitive, but it actually is helpful to ensure the reader clearly sees the evolution, importance, and critical aspects of the study at hand See Table 1 for examples of well‐stated purposes.

Examples of well-stated purposes by submission type.

The methods section should clearly describe the specific design of the study and provide clear and concise description of the procedures that were performed. The purpose of sufficient detail in the methods section is so that an appropriately trained person would be able to replicate your experiments. 15 There should be complete transparency when describing the study. To assist in writing and manuscript preparation there are several checklists or guidelines that are available on the IJSPT website. The CONSORT guidelines can be used when developing and reporting a randomized controlled trial. 16 The STARD checklist was developed for designing a diagnostic accuracy study. 17 The PRISMA checklist was developed for use when performing a meta‐analyses or systematic review. 18 A clear methods section should contain the following information: 1) the population and equipment used in the study, 2) how the population and equipment were prepared and what was done during the study, 3) the protocol used, 4) the outcomes and how they were measured, 5) the methods used for data analysis. Initially a brief paragraph should explain the overall procedures and study design. Within this first paragraph there is generally a description of inclusion and exclusion criteria which help the reader understand the population used. Paragraphs that follow should describe in more detail the procedures followed for the study. A clear description of how data was gathered is also helpful. For example were data gathered prospectively or retrospectively? Who if anyone was blinded, and where and when was the actual data collected?

Although it is a good idea for the authors to have justification and a rationale for their procedures, these should be saved for inclusion into the discussion section, not to be discussed in the methods section. However, occasionally studies supporting components of the methods section such as reliability of tests, or validation of outcome measures may be included in the methods section.

The final portion of the methods section will include the statistical methods used to analyze the data. 19 This does not mean that the actual results should be discussed in the methods section, as they have an entire section of their own!

Most scientific journals support the need for all projects involving humans or animals to have up‐to‐date documentation of ethical approval. 20 The methods section should include a clear statement that the researchers have obtained approval from an appropriate institutional review board.

Results, Discussion, and Conclusions

In most journals the results section is separate from the discussion section. It is important that you clearly distinguish your results from your discussion. The results section should describe the results only. The discussion section should put those results into a broader context. Report your results neutrally, as you “found them”. Again, be thoughtful about content and structure. Think carefully about where content is placed in the overall structure of your paper. It is not appropriate to bring up additional results, not discussed in the results section, in the discussion. All results must first be described/presented and then discussed. Thus, the discussion should not simply be a repeat of the results section. Carefully discuss where your information is similar or different from other published evidence and why this might be so. What was different in methods or analysis, what was similar?

As previously stated, stick to your topic at hand, and do not overstretch your discussion! One of the major pitfalls in writing the discussion section is overstating the significance of your findings 4 or making very strong statements. For example, it is better to say: “Findings of the current study support….” or “these findings suggest…” than, “Findings of the current study prove that…” or “this means that….”. Maintain a sense of humbleness, as nothing is without question in the outcomes of any type of research, in any discipline! Use words like “possibly”, “likely” or “suggests” to soften findings. 12

Do not discuss extraneous ideas, concepts, or information not covered by your topic/paper/commentary. Be sure to carefully address all relevant results, not just the statistically significant ones or the ones that support your hypotheses. When you must resort to speculation or opinion, be certain to state that up front using phrases such as “we therefore speculate” or “in the authors' opinion”.

Remember, just as in the introduction and literature review, evidence or results cannot draw conclusions, just as previously stated, only people, scientists, researchers, and authors can!

Finish with a concise, 3‐5 sentence conclusion paragraph. This is not just a restatement of your results, rather is comprised of some final, summative statements that reflect the flow and outcomes of the entire paper. Do not include speculative statements or additional material; however, based upon your findings a statement about potential changes in clinical practice or future research opportunities can be provided here.

CONCLUSIONS

Writing for publication can be a challenging yet satisfying endeavor. The ability to examine, relate, and interlink evidence, as well as to provide a peer‐reviewed, disseminated product of your research labors can be rewarding. A few suggestions have been offered in this commentary that may assist the novice or the developing writer to attempt, polish, and perfect their approach to scholarly writing.

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Scientific Papers

Scientific papers are for sharing your own original research work with other scientists or for reviewing the research conducted by others. As such, they are critical to the evolution of modern science, in which the work of one scientist builds upon that of others. To reach their goal, papers must aim to inform, not impress. They must be highly readable — that is, clear, accurate, and concise. They are more likely to be cited by other scientists if they are helpful rather than cryptic or self-centered.

Scientific papers typically have two audiences: first, the referees, who help the journal editor decide whether a paper is suitable for publication; and second, the journal readers themselves, who may be more or less knowledgeable about the topic addressed in the paper. To be accepted by referees and cited by readers, papers must do more than simply present a chronological account of the research work. Rather, they must convince their audience that the research presented is important, valid, and relevant to other scientists in the same field. To this end, they must emphasize both the motivation for the work and the outcome of it, and they must include just enough evidence to establish the validity of this outcome.

Papers that report experimental work are often structured chronologically in five sections: first, Introduction ; then Materials and Methods , Results , and Discussion (together, these three sections make up the paper's body); and finally, Conclusion .

• The Introduction section clarifies the motivation for the work presented and prepares readers for the structure of the paper.
• The Materials and Methods section provides sufficient detail for other scientists to reproduce the experiments presented in the paper. In some journals, this information is placed in an appendix, because it is not what most readers want to know first.
• The Results and Discussion sections present and discuss the research results, respectively. They are often usefully combined into one section, however, because readers can seldom make sense of results alone without accompanying interpretation — they need to be told what the results mean.
• The Conclusion section presents the outcome of the work by interpreting the findings at a higher level of abstraction than the Discussion and by relating these findings to the motivation stated in the Introduction .

(Papers reporting something other than experiments, such as a new method or technology, typically have different sections in their body, but they include the same Introduction and Conclusion sections as described above.)

Although the above structure reflects the progression of most research projects, effective papers typically break the chronology in at least three ways to present their content in the order in which the audience will most likely want to read it. First and foremost, they summarize the motivation for, and the outcome of, the work in an abstract, located before the Introduction . In a sense, they reveal the beginning and end of the story — briefly — before providing the full story. Second, they move the more detailed, less important parts of the body to the end of the paper in one or more appendices so that these parts do not stand in the readers' way. Finally, they structure the content in the body in theorem-proof fashion, stating first what readers must remember (for example, as the first sentence of a paragraph) and then presenting evidence to support this statement.

The introduction

• First, provide some context to orient those readers who are less familiar with your topic and to establish the importance of your work.
• Second, state the need for your work, as an opposition between what the scientific community currently has and what it wants.
• Third, indicate what you have done in an effort to address the need (this is the task).
• Finally, preview the remainder of the paper to mentally prepare readers for its structure, in the object of the document.

Context and need

At the beginning of the Introduction section, the context and need work together as a funnel: They start broad and progressively narrow down to the issue addressed in the paper. To spark interest among your audience — referees and journal readers alike — provide a compelling motivation for the work presented in your paper: The fact that a phenomenon has never been studied before is not, in and of itself, a reason to study that phenomenon.

Write the context in a way that appeals to a broad range of readers and leads into the need. Do not include context for the sake of including context: Rather, provide only what will help readers better understand the need and, especially, its importance. Consider anchoring the context in time, using phrases such as recently , in the past 10 years , or since the early 1990s . You may also want to anchor your context in space (either geographically or within a given research field).

Convey the need for the work as an opposition between actual and desired situations. Start by stating the actual situation (what we have) as a direct continuation of the context. If you feel you must explain recent achievements in much detail — say, in more than one or two paragraphs — consider moving the details to a section titled State of the art (or something similar) after the Introduction , but do provide a brief idea of the actual situation in the Introduction . Next, state the desired situation (what we want). Emphasize the contrast between the actual and desired situations with such words as but , however, or unfortunately .

One elegant way to express the desired part of the need is to combine it with the task in a single sentence. This sentence expresses first the objective, then the action undertaken to reach this objective, thus creating a strong and elegant connection between need and task. Here are three examples of such a combination:

To confirm this assumption , we studied the effects of a range of inhibitors of connexin channels . . . on . . .

To assess whether such multiple-coil sensors perform better than single-signal ones , we tested two of them — the DuoPXK and the GEMM3 — in a field where . . . To form a better view of the global distribution and infectiousness of this pathogen , we examined 1645 postmetamorphic and adult amphibians collected from 27 countries between 1984 and 2006 for the presence of . . .

Task and object

An Introduction is usually clearer and more logical when it separates what the authors have done (the task) from what the paper itself attempts or covers (the object of the document). In other words, the task clarifies your contribution as a scientist, whereas the object of the document prepares readers for the structure of the paper, thus allowing focused or selective reading.

For the task,

• use whoever did the work (normally, you and your colleagues) as the subject of the sentence: we or perhaps the authors;
• use a verb expressing a research action: measured , calculated , etc.;
• set that verb in the past tense.

The three examples below are well-formed tasks.

To confirm this assumption, we studied the effects of a range of inhibitors of connexin channels, such as the connexin mimetic peptides Gap26 and Gap27 and anti-peptide antibodies, on calcium signaling in cardiac cells and HeLa cells expressing connexins.

During controlled experiments, we investigated the influence of the HMP boundary conditions on liver flows.

To tackle this problem, we developed a new software verification technique called oblivious hashing, which calculates the hash values based on the actual execution of the program.

The list below provides examples of verbs that express research actions:

For the object of the document,

• use the document itself as the subject of the sentence: this paper , this letter , etc.;
• use a verb expressing a communication action: presents , summarizes , etc.;
• set the verb in the present tense.

The three examples below are suitable objects of the document for the three tasks shown above, respectively.

This paper clarifies the role of CxHc on calcium oscillations in neonatal cardiac myocytes and calcium transients induced by ATP in HL-cells originated from cardiac atrium and in HeLa cells expressing connexin 43 or 26. This paper presents the flow effects induced by increasing the hepatic-artery pressure and by obstructing the vena cava inferior. This paper discusses the theory behind oblivious hashing and shows how this approach can be applied for local software tamper resistance and remote code authentication.

The list below provides examples of verbs that express communication actions:

Even the most logical structure is of little use if readers do not see and understand it as they progress through a paper. Thus, as you organize the body of your paper into sections and perhaps subsections, remember to prepare your readers for the structure ahead at all levels. You already do so for the overall structure of the body (the sections) in the object of the document at the end of the Introduction . You can similarly prepare your readers for an upcoming division into subsections by introducing a global paragraph between the heading of a section and the heading of its first subsection. This paragraph can contain any information relating to the section as a whole rather than particular subsections, but it should at least announce the subsections, whether explicitly or implicitly. An explicit preview would be phrased much like the object of the document: "This section first . . . , then . . . , and finally . . . "

Although papers can be organized into sections in many ways, those reporting experimental work typically include Materials and Methods , Results , and Discussion in their body. In any case, the paragraphs in these sections should begin with a topic sentence to prepare readers for their contents, allow selective reading, and — ideally — get a message across.

Materials and methods

Results and discussion.

When reporting and discussing your results, do not force your readers to go through everything you went through in chronological order. Instead, state the message of each paragraph upfront: Convey in the first sentence what you want readers to remember from the paragraph as a whole. Focus on what happened, not on the fact that you observed it. Then develop your message in the remainder of the paragraph, including only that information you think you need to convince your audience.

The conclusion

At the end of your Conclusion , consider including perspectives — that is, an idea of what could or should still be done in relation to the issue addressed in the paper. If you include perspectives, clarify whether you are referring to firm plans for yourself and your colleagues ("In the coming months, we will . . . ") or to an invitation to readers ("One remaining question is . . . ").

If your paper includes a well-structured Introduction and an effective abstract, you need not repeat any of the Introduction in the Conclusion . In particular, do not restate what you have done or what the paper does. Instead, focus on what you have found and, especially, on what your findings mean. Do not be afraid to write a short Conclusion section: If you can conclude in just a few sentences given the rich discussion in the body of the paper, then do so. (In other words, resist the temptation to repeat material from the Introduction just to make the Conclusio n longer under the false belief that a longer Conclusion will seem more impressive.)

The abstract

Typically, readers are primarily interested in the information presented in a paper's Introduction and Conclusion sections. Primarily, they want to know the motivation for the work presented and the outcome of this work. Then (and only then) the most specialized among them might want to know the details of the work. Thus, an effective abstract focuses on motivation and outcome; in doing so, it parallels the paper's Introduction and Conclusion .

Accordingly, you can think of an abstract as having two distinct parts — motivation and outcome — even if it is typeset as a single paragraph. For the first part, follow the same structure as the Introduction section of the paper: State the context, the need, the task, and the object of the document. For the second part, mention your findings (the what ) and, especially, your conclusion (the so what — that is, the interpretation of your findings); if appropriate, end with perspectives, as in the Conclusion section of your paper.

Although the structure of the abstract parallels the Introduction and Conclusion sections, it differs from these sections in the audience it addresses. The abstract is read by many different readers, from the most specialized to the least specialized among the target audience. In a sense, it should be the least specialized part of the paper. Any scientist reading it should be able to understand why the work was carried out and why it is important (context and need), what the authors did (task) and what the paper reports about this work (object of the document), what the authors found (findings), what these findings mean (the conclusion), and possibly what the next steps are (perspectives). In contrast, the full paper is typically read by specialists only; its Introduction and Conclusion are more detailed (that is, longer and more specialized) than the abstract.

An effective abstract stands on its own — it can be understood fully even when made available without the full paper. To this end, avoid referring to figures or the bibliography in the abstract. Also, introduce any acronyms the first time you use them in the abstract (if needed), and do so again in the full paper (see Mechanics: Using abbreviations ).

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Writing the Scientific Paper

When you write about scientific topics to specialists in a particular scientific field, we call that scientific writing. (When you write to non-specialists about scientific topics, we call that science writing.)

The scientific paper has developed over the past three centuries into a tool to communicate the results of scientific inquiry. The main audience for scientific papers is extremely specialized. The purpose of these papers is twofold: to present information so that it is easy to retrieve, and to present enough information that the reader can duplicate the scientific study. A standard format with six main part helps readers to find expected information and analysis:

• Title--subject and what aspect of the subject was studied.
• Abstract--summary of paper: The main reason for the study, the primary results, the main conclusions
• Introduction-- why the study was undertaken
• Methods and Materials-- how the study was undertaken
• Results-- what was found
• Discussion-- why these results could be significant (what the reasons might be for the patterns found or not found)

There are many ways to approach the writing of a scientific paper, and no one way is right. Many people, however, find that drafting chunks in this order works best: Results, Discussion, Introduction, Materials & Methods, Abstract, and, finally, Title.

The title should be very limited and specific. Really, it should be a pithy summary of the article's main focus.

• "Renal disease susceptibility and hypertension are under independent genetic control in the fawn hooded rat"
• "Territory size in Lincoln's Sparrows ( Melospiza lincolnii )"
• "Replacement of deciduous first premolars and dental eruption in archaeocete whales"
• "The Radio-Frequency Single-Electron Transistor (RF-SET): A Fast and Ultrasensitive Electrometer"

This is a summary of your article. Generally between 50-100 words, it should state the goals, results, and the main conclusions of your study. You should list the parameters of your study (when and where was it conducted, if applicable; your sample size; the specific species, proteins, genes, etc., studied). Think of the process of writing the abstract as taking one or two sentences from each of your sections (an introductory sentence, a sentence stating the specific question addressed, a sentence listing your main techniques or procedures, two or three sentences describing your results, and one sentence describing your main conclusion).

Example One

Hypertension, diabetes and hyperlipidemia are risk factors for life-threatening complications such as end-stage renal disease, coronary artery disease and stroke. Why some patients develop complications is unclear, but only susceptibility genes may be involved. To test this notion, we studied crosses involving the fawn-hooded rat, an animal model of hypertension that develops chronic renal failure. Here, we report the localization of two genes, Rf-1 and Rf-2 , responsible for about half of the genetic variation in key indices of renal impairment. In addition, we localize a gene, Bpfh-1 , responsible for about 26% of the genetic variation in blood pressure. Rf-1 strongly affects the risk of renal impairment, but has no significant effect on blood pressure. Our results show that susceptibility to a complication of hypertension is under at least partially independent genetic control from susceptibility to hypertension itself.

Brown, Donna M, A.P. Provoost, M.J. Daly, E.S. Lander, & H.J. Jacob. 1996. "Renal disease susceptibility and hypertension are under indpendent genetic control in the faun-hooded rat." Nature Genetics , 12(1):44-51.

Example Two

We studied survival of 220 calves of radiocollared moose ( Alces alces ) from parturition to the end of July in southcentral Alaska from 1994 to 1997. Prior studies established that predation by brown bears ( Ursus arctos ) was the primary cause of mortality of moose calves in the region. Our objectives were to characterize vulnerability of moose calves to predation as influenced by age, date, snow depths, and previous reproductive success of the mother. We also tested the hypothesis that survival of twin moose calves was independent and identical to that of single calves. Survival of moose calves from parturition through July was 0.27 ± 0.03 SE, and their daily rate of mortality declined at a near constant rate with age in that period. Mean annual survival was 0.22 ± 0.03 SE. Previous winter's snow depths or survival of the mother's previous calf was not related to neonatal survival. Selection for early parturition was evidenced in the 4 years of study by a 6.3% increase in the hazard of death with each daily increase in parturition date. Although there was no significant difference in survival of twin and single moose calves, most twins that died disappeared together during the first 15 days after birth and independently thereafter, suggesting that predators usually killed both when encountered up to that age.

Key words: Alaska, Alces alces , calf survival, moose, Nelchina, parturition synchrony, predation

Testa, J.W., E.F. Becker, & G.R. Lee. 2000. "Temporal patterns in the survival of twin and single moose ( alces alces ) calves in southcentral Alaska." Journal of Mammalogy , 81(1):162-168.

Example Three

We monitored breeding phenology and population levels of Rana yavapaiensis by use of repeated egg mass censuses and visual encounter surveys at Agua Caliente Canyon near Tucson, Arizona, from 1994 to 1996. Adult counts fluctuated erratically within each year of the study but annual means remained similar. Juvenile counts peaked during the fall recruitment season and fell to near zero by early spring. Rana yavapaiensis deposited eggs in two distinct annual episodes, one in spring (March-May) and a much smaller one in fall (September-October). Larvae from the spring deposition period completed metamorphosis in earlv summer. Over the two years of study, 96.6% of egg masses successfully produced larvae. Egg masses were deposited during periods of predictable, moderate stream flow, but not during seasonal periods when flash flooding or drought were likely to affect eggs or larvae. Breeding phenology of Rana yavapaiensis is particularly well suited for life in desert streams with natural flow regimes which include frequent flash flooding and drought at predictable times. The exotic predators of R. yavapaiensis are less able to cope with fluctuating conditions. Unaltered stream flow regimes that allow natural fluctuations in stream discharge may provide refugia for this declining ranid frog from exotic predators by excluding those exotic species that are unable to cope with brief flash flooding and habitat drying.

Sartorius, Shawn S., and Philip C. Rosen. 2000. "Breeding phenology of the lowland leopard frog ( Rana yavepaiensis )." Southwestern Naturalist , 45(3): 267-273.

Introduction

The introduction is where you sketch out the background of your study, including why you have investigated the question that you have and how it relates to earlier research that has been done in the field. It may help to think of an introduction as a telescoping focus, where you begin with the broader context and gradually narrow to the specific problem addressed by the report. A typical (and very useful) construction of an introduction proceeds as follows:

"Echimyid rodents of the genus Proechimys (spiny rats) often are the most abundant and widespread lowland forest rodents throughout much of their range in the Neotropics (Eisenberg 1989). Recent studies suggested that these rodents play an important role in forest dynamics through their activities as seed predators and dispersers of seeds (Adler and Kestrell 1998; Asquith et al 1997; Forget 1991; Hoch and Adler 1997)." (Lambert and Adler, p. 70)

"Our laboratory has been involved in the analysis of the HLA class II genes and their association with autoimmune disorders such as insulin-dependent diabetes mellitus. As part of this work, the laboratory handles a large number of blood samples. In an effort to minimize the expense and urgency of transportation of frozen or liquid blood samples, we have designed a protocol that will preserve the integrity of lymphocyte DNA and enable the transport and storage of samples at ambient temperatures." (Torrance, MacLeod & Hache, p. 64)

"Despite the ubiquity and abundance of P. semispinosus , only two previous studies have assessed habitat use, with both showing a generalized habitat use. [brief summary of these studies]." (Lambert and Adler, p. 70)

"Although very good results have been obtained using polymerase chain reaction (PCR) amplification of DNA extracted from dried blood spots on filter paper (1,4,5,8,9), this preservation method yields limited amounts of DNA and is susceptible to contamination." (Torrance, MacLeod & Hache, p. 64)

"No attempt has been made to quantitatively describe microhabitat characteristics with which this species may be associated. Thus, specific structural features of secondary forests that may promote abundance of spiny rats remains unknown. Such information is essential to understand the role of spiny rats in Neotropical forests, particularly with regard to forest regeneration via interactions with seeds." (Lambert and Adler, p. 71)

"As an alternative, we have been investigating the use of lyophilization ("freeze-drying") of whole blood as a method to preserve sufficient amounts of genomic DNA to perform PCR and Southern Blot analysis." (Torrance, MacLeod & Hache, p. 64)

"We present an analysis of microhabitat use by P. semispinosus in tropical moist forests in central Panama." (Lambert and Adler, p. 71)

"In this report, we summarize our analysis of genomic DNA extracted from lyophilized whole blood." (Torrance, MacLeod & Hache, p. 64)

Methods and Materials

In this section you describe how you performed your study. You need to provide enough information here for the reader to duplicate your experiment. However, be reasonable about who the reader is. Assume that he or she is someone familiar with the basic practices of your field.

It's helpful to both writer and reader to organize this section chronologically: that is, describe each procedure in the order it was performed. For example, DNA-extraction, purification, amplification, assay, detection. Or, study area, study population, sampling technique, variables studied, analysis method.

Include in this section:

• study design: procedures should be listed and described, or the reader should be referred to papers that have already described the used procedure
• particular techniques used and why, if relevant
• modifications of any techniques; be sure to describe the modification
• specialized equipment, including brand-names
• temporal, spatial, and historical description of study area and studied population
• assumptions underlying the study
• statistical methods, including software programs

Example description of activity

Chromosomal DNA was denatured for the first cycle by incubating the slides in 70% deionized formamide; 2x standard saline citrate (SSC) at 70ºC for 2 min, followed by 70% ethanol at -20ºC and then 90% and 100% ethanol at room temperature, followed by air drying. (Rouwendal et al ., p. 79)

Example description of assumptions

We considered seeds left in the petri dish to be unharvested and those scattered singly on the surface of a tile to be scattered and also unharvested. We considered seeds in cheek pouches to be harvested but not cached, those stored in the nestbox to be larderhoarded, and those buried in caching sites within the arena to be scatterhoarded. (Krupa and Geluso, p. 99)

Examples of use of specialized equipment

• Oligonucleotide primers were prepared using the Applied Biosystems Model 318A (Foster City, CA) DNA Synthesizer according to the manufacturers' instructions. (Rouwendal et al ., p.78)
• We first visually reviewed the complete song sample of an individual using spectrograms produced on a Princeton Applied Research Real Time Spectrum Analyzer (model 4512). (Peters et al ., p. 937)

Example of use of a certain technique

Frogs were monitored using visual encounter transects (Crump and Scott, 1994). (Sartorius and Rosen, p. 269)

Example description of statistical analysis

We used Wilcox rank-sum tests for all comparisons of pre-experimental scores and for all comparisons of hue, saturation, and brightness scores between various groups of birds ... All P -values are two-tailed unless otherwise noted. (Brawner et al ., p. 955)

This section presents the facts--what was found in the course of this investigation. Detailed data--measurements, counts, percentages, patterns--usually appear in tables, figures, and graphs, and the text of the section draws attention to the key data and relationships among data. Three rules of thumb will help you with this section:

• present results clearly and logically
• avoid excess verbiage
• consider providing a one-sentence summary at the beginning of each paragraph if you think it will help your reader understand your data

Remember to use table and figures effectively. But don't expect these to stand alone.

Some examples of well-organized and easy-to-follow results:

• Size of the aquatic habitat at Agua Caliente Canyon varied dramatically throughout the year. The site contained three rockbound tinajas (bedrock pools) that did not dry during this study. During periods of high stream discharge seven more seasonal pools and intermittent stretches of riffle became available. Perennial and seasonal pool levels remained stable from late February through early May. Between mid-May and mid-July seasonal pools dried until they disappeared. Perennial pools shrank in surface area from a range of 30-60 m² to 3-5- M². (Sartorius and Rosen, Sept. 2000: 269)

Notice how the second sample points out what is important in the accompanying figure. It makes us aware of relationships that we may not have noticed quickly otherwise and that will be important to the discussion.

A similar test result is obtained with a primer derived from the human ß-satellite... This primer (AGTGCAGAGATATGTCACAATG-CCCC: Oligo 435) labels 6 sites in the PRINS reaction: the chromosomes 1, one pair of acrocentrics and, more weakly, the chromosomes 9 (Fig. 2a). After 10 cycles of PCR-IS, the number of sites labeled has doubled (Fig. 2b); after 20 cycles, the number of sites labeled is the same but the signals are stronger (Fig. 2c) (Rouwendal et al ., July 93:80).

Related Information: Use Tables and Figures Effectively

Do not repeat all of the information in the text that appears in a table, but do summarize it. For example, if you present a table of temperature measurements taken at various times, describe the general pattern of temperature change and refer to the table.

"The temperature of the solution increased rapidly at first, going from 50º to 80º in the first three minutes (Table 1)."

You don't want to list every single measurement in the text ("After one minute, the temperature had risen to 55º. After two minutes, it had risen to 58º," etc.). There is no hard and fast rule about when to report all measurements in the text and when to put the measurements in a table and refer to them, but use your common sense. Remember that readers have all that data in the accompanying tables and figures, so your task in this section is to highlight key data, changes, or relationships.

In this section you discuss your results. What aspect you choose to focus on depends on your results and on the main questions addressed by them. For example, if you were testing a new technique, you will want to discuss how useful this technique is: how well did it work, what are the benefits and drawbacks, etc. If you are presenting data that appear to refute or support earlier research, you will want to analyze both your own data and the earlier data--what conditions are different? how much difference is due to a change in the study design, and how much to a new property in the study subject? You may discuss the implication of your research--particularly if it has a direct bearing on a practical issue, such as conservation or public health.

This section centers on speculation . However, this does not free you to present wild and haphazard guesses. Focus your discussion around a particular question or hypothesis. Use subheadings to organize your thoughts, if necessary.

This section depends on a logical organization so readers can see the connection between your study question and your results. One typical approach is to make a list of all the ideas that you will discuss and to work out the logical relationships between them--what idea is most important? or, what point is most clearly made by your data? what ideas are subordinate to the main idea? what are the connections between ideas?

Achieving the Scientific Voice

Eight tips will help you match your style for most scientific publications.

• Develop a precise vocabulary: read the literature to become fluent, or at least familiar with, the sort of language that is standard to describe what you're trying to describe.
• Once you've labeled an activity, a condition, or a period of time, use that label consistently throughout the paper. Consistency is more important than creativity.
• Define your terms and your assumptions.
• Include all the information the reader needs to interpret your data.
• Remember, the key to all scientific discourse is that it be reproducible . Have you presented enough information clearly enough that the reader could reproduce your experiment, your research, or your investigation?
• When describing an activity, break it down into elements that can be described and labeled, and then present them in the order they occurred.
• When you use numbers, use them effectively. Don't present them so that they cause more work for the reader.
• Include details before conclusions, but only include those details you have been able to observe by the methods you have described. Do not include your feelings, attitudes, impressions, or opinions.
• Research your format and citations: do these match what have been used in current relevant journals?
• Run a spellcheck and proofread carefully. Read your paper out loud, and/ or have a friend look over it for misspelled words, missing words, etc.

Applying the Principles, Example 1

The following example needs more precise information. Look at the original and revised paragraphs to see how revising with these guidelines in mind can make the text clearer and more informative:

Before: Each male sang a definite number of songs while singing. They start with a whistle and then go from there. Each new song is always different, but made up an overall repertoire that was completed before starting over again. In 16 cases (84%), no new songs were sung after the first 20, even though we counted about 44 songs for each bird.

After: Each male used a discrete number of song types in his singing. Each song began with an introductory whistle, followed by a distinctive, complex series of fluty warbles (Fig. 1). Successive songs were always different, and five of the 19 males presented their entire song repertoire before repeating any of their song types (i.e., the first IO recorded songs revealed the entire repertoire of 10 song types). Each song type recurred in long sequences of singing, so that we could be confident that we had recorded the entire repertoire of commonly used songs by each male. For 16 of the 19 males, no new song types were encountered after the first 20 songs, even though we analyzed and average of 44 songs/male (range 30-59).

Applying the Principles, Example 2

In this set of examples, even a few changes in wording result in a more precise second version. Look at the original and revised paragraphs to see how revising with these guidelines in mind can make the text clearer and more informative:

Before: The study area was on Mt. Cain and Maquilla Peak in British Columbia, Canada. The study area is about 12,000 ha of coastal montane forest. The area is both managed and unmanaged and ranges from 600-1650m. The most common trees present are mountain hemlock ( Tsuga mertensiana ), western hemlock ( Tsuga heterophylla ), yellow cedar ( Chamaecyparis nootkatensis ), and amabilis fir ( Abies amabilis ).

After: The study took place on Mt. Cain and Maquilla Peak (50'1 3'N, 126'1 8'W), Vancouver Island, British Columbia. The study area encompassed 11,800 ha of coastal montane forest. The landscape consisted of managed and unmanaged stands of coastal montane forest, 600-1650 m in elevation. The dominant tree species included mountain hemlock ( Tsuga mertensiana ), western hemlock ( Tsuga heterophylla ), yellow cedar ( Chamaecyparis nootkatensis ), and amabilis fir ( Abies amabilis ).

Two Tips for Sentence Clarity

Although you will want to consider more detailed stylistic revisions as you become more comfortable with scientific writing, two tips can get you started:

First, the verb should follow the subject as soon as possible.

Really Hard to Read : "The smallest of the URF's (URFA6L), a 207-nucleotide (nt) reading frame overlapping out of phase the NH2- terminal portion of the adenosinetriphosphatase (ATPase) subunit 6 gene has been identified as the animal equivalent of the recently discovered yeast H+-ATPase subunit gene."

Less Hard to Read : "The smallest of the UR-F's is URFA6L, a 207-nucleotide (nt) reading frame overlapping out of phase the NH2-terminal portion of the adenosinetriphosphatase (ATPase) subunit 6 gene; it has been identified as the animal equivalent of the recently discovered yeast H+-ATPase subunit 8 gene."

Second, place familiar information first in a clause, a sentence, or a paragraph, and put the new and unfamiliar information later.

More confusing : The epidermis, the dermis, and the subcutaneous layer are the three layers of the skin. A layer of dead skin cells makes up the epidermis, which forms the body's shield against the world. Blood vessels, carrying nourishment, and nerve endings, which relay information about the outside world, are found in the dermis. Sweat glands and fat cells make up the third layer, the subcutaneous layer.

Less confusing : The skin consists of three layers: the epidermis, the dermis, and the subcutaneous layer. The epidermis is made up of dead skin cells, and forms a protective shield between the body and the world. The dermis contains the blood vessels and nerve endings that nourish the skin and make it receptive to outside stimuli. The subcutaneous layer contains the sweat glands and fat cells which perform other functions of the skin.

Bibliography

• Scientific Writing for Graduate Students . F. P. Woodford. Bethesda, MD: Council of Biology Editors, 1968. [A manual on the teaching of writing to graduate students--very clear and direct.]
• Scientific Style and Format . Council of Biology Editors. Cambridge: Cambridge University Press, 1994.
• "The science of scientific writing." George Gopen and Judith Swann. The American Scientist , Vol. 78, Nov.-Dec. 1990. Pp 550-558.
• "What's right about scientific writing." Alan Gross and Joseph Harmon. The Scientist , Dec. 6 1999. Pp. 20-21.
• "A Quick Fix for Figure Legends and Table Headings." Donald Kroodsma. The Auk , 117 (4): 1081-1083, 2000.

Wortman-Wunder, Emily, & Kate Kiefer. (1998). Writing the Scientific Paper. Writing@CSU . Colorado State University. https://writing.colostate.edu/resources/writing/guides/.

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Writing a scientific paper.

• Writing a lab report
• INTRODUCTION

Writing a "good" methods section

"methods checklist" from: how to write a good scientific paper. chris a. mack. spie. 2018..

• LITERATURE CITED
• Bibliography of guides to scientific writing and presenting
• Peer Review
• Presentations
• Lab Report Writing Guides on the Web

The purpose is to provide enough detail that a competent worker could repeat the experiment. Many of your readers will skip this section because they already know from the Introduction the general methods you used. However careful writing of this section is important because for your results to be of scientific merit they must be reproducible. Otherwise your paper does not represent good science.

• Exact technical specifications and quantities and source or method of preparation
• Describe equipment used and provide illustrations where relevant.
• Chronological presentation (but related methods described together)
• Questions about "how" and "how much" are answered for the reader and not left for them to puzzle over
• Discuss statistical methods only if unusual or advanced
• When a large number of components are used prepare tables for the benefit of the reader
• Do not state the action without stating the agent of the action
• Describe how the results were generated with sufficient detail so that an independent researcher (working in the same field) could reproduce the results sufficiently to allow validation of the conclusions.
• Can the reader assess internal validity (conclusions are supported by the results presented)?
• Can the reader assess external validity (conclusions are properly generalized beyond these specific results)?
• Has the chosen method been justified?
• Are data analysis and statistical approaches justified, with assumptions and biases considered?
• Avoid: including results in the Method section; including extraneous details (unnecessary to enable reproducibility or judge validity); treating the method as a chronological history of events; unneeded references to commercial products; references to “proprietary” products or processes unavailable to the reader. 
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Pulmonology (previously Revista Portuguesa de Pneumologia) is the official journal of the Portuguese Society of Pulmonology (Sociedade Portuguesa de Pneumologia/SPP). The journal publishes 6 issues per year, mainly about respiratory system diseases in adults and clinical research. This work can range from peer-reviewed original articles to review articles, editorials, and opinion articles. The journal is printed in English, and is freely available in its web page as well as in Medline and other databases.

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The Impact Factor measures the average number of citations received in a particular year by papers published in the journal during the two preceding years. © Clarivate Analytics, Journal Citation Reports 2022

CiteScore measures average citations received per document published.

SRJ is a prestige metric based on the idea that not all citations are the same. SJR uses a similar algorithm as the Google page rank; it provides a quantitative and qualitative measure of the journal's impact.

SNIP measures contextual citation impact by wighting citations based on the total number of citations in a subject field.

• Introduction
• Basics of the scientific method and study design
• Structure and content of the methods section
• Study design
• Ethical considerations
• Selection of participants – selection criteria and selection methods
• Data collection – variables, methods and instruments
• Data analysis
• Bibliography

The methods section is the most important part of a scientific paper because it provides the essential information that allows the reader to judge the validity of the results and conclusions of the study reported. Therefore, in this section the authors should provide a clear and precise description of how the study was performed and the rationale for the methodological choices and characteristics of the study design. This section should be written in a clear and concise manner, but should always present enough information so that: (1) the study could be replicated by other researchers, in order to evaluate the reproducibility of results (it should not be a step-by-step tutorial but should be a systematic and complete description of what was done), and (2) the readers are able to judge the validity of results and conclusions presented. This will typically be the first section to be written in a paper (although many times the last to be finalized after corrections and reviews of authors and reviewers), mainly because it should be already thought of and written as a part of the research protocol/proposal, prepared at the initial phase of the research work, and because it sets the stage for the results and conclusions presented in a paper. From a journalistic point of view this section should answer questions like “who”, “what”, “where”, “when”, “why” and “how”; and should do it having into account the difficult balance between completeness (sufficient details to allow replication and validity verification) and brevity (the impossibility of describing every technical detail and the need to strictly follow the guidelines/instructions for authors provided by journals and recommendations regarding word count limits). In this article, we describe and discuss some general recommendations that should help preparing the methods section of our manuscripts; and we propose a general structure and recommended content for this section. Because this section is so intimately related to the foundations of science, the scientific method and the study design, we begin by reviewing some general concepts and principles and then follow with the presentation of a proposal for its structure and content.

Although many authors and schools of thought have different definitions and understandings regarding this matter, it is fair and generally consensual to say that science is a systematic endeavor aiming at the acquisition, development and updating of knowledge; and knowledge could be defined as a set of models that aim to describe, understand, explain, control and eventually modify the real world. 1–4 The practice of science, generically named scientific research, aims to define questions and find answers that may contribute to the building of knowledge using the so called scientific method. The scientific method, particularly in the natural sciences, mainly relies on the empirical observation of the world, as objective and unbiased as possible, and the adequate use of processes as deduction, induction 1–3 and abduction, 4 in order to generate and test hypothesis and subsequently models that allow us to describe, explain and modify the real world. In general, scientific research questions look for the estimation of population parameters or the confirmation or discovery of relationships, eventually of a causal nature, among objects (physical matter, processes, interventions or concepts). In a quantitative research paradigm the objects are regarded as variables that researchers may measure and/or control, and a variable is simply defined as a characteristic that may vary among the subjects or units of observation under study. When estimating parameters or assessing relationships, that quantitatively translate the answer to the research question, researchers are interested in minimizing random errors and systematic errors. Random errors are associated with usual sources of variability, generally measurement and sampling variability, that may affect the estimation 5,6 ; and they directly affect the precision of the parameter estimates presented. Systematic errors or bias are associated with phenomena that may affect the validity of the estimation and conclusions. 5–9 Validity simply refers to the ability that a method or a study has to measure or estimate what it really intends to measure or estimate. Thus, validity refers to the credibility of the study design and results and the degree to which these results can be applied to the general population of interest. 5,6 Internal validity refers to the credibility of the study itself and is determined by the degree to which study conclusions correctly depict the truth in the study. 5,6 External validity refers to whether the results of a study can be generalized to a larger population of interest. 5,6

Random errors are controlled or dealt with mainly by an adequate choice of measurement methods and instruments, an adequate choice of sampling methods and sample size and an adequate use of statistical methods for data analysis and presentation. 5

Selection bias refers to systematic errors associated with the selection of study participants or units of observation. 5,6,12

Information bias refers to systematic errors associated with the measurement or classification of study variables (typically classified into three main groups: dependent variables – outcome or response variables; independent variables – predictive, exposure or intervention variables and confounding variables – confounders or extraneous factors) and the methods and instruments used for that purpose. 5,6

Confounding refers to a phenomenon where certain variables (confounding variables) that are associated simultaneously with the outcome and predictors under study interfere with the valid estimation of the true predictor's effect on the outcome. 5–8 Confounding is, of course, of particular importance in causal research. Sadly, the real world is much more complex than we would like, so simple, unambiguous, direct relationships between objects can be difficult to ascertain. Thus, in causal research, the validity of a study is judged by the degree to which its outcomes can be attributed to manipulation of independent variables and not to the effects of confounding variables. It is important to emphasize that confounding variables are hardly ever fully controlled; and in many instances the influence of those variables is not fully appreciated by researchers. Therefore, the study design must be defined so as to control as many extraneous factors as possible, so that any potential cause-and-effect relationship between two objects can be judged validly.

How much do we known about the topic under study?

Will there be an intervention? Will all subjects get it? Do we control who gets the intervention? Is it feasible to randomly assign subjects to the intervention?

How often and when will data be collected from subjects?

How can factors that may potentially interfere in the relationship between predictors and outcomes be minimized or controlled?

The answer to these questions comprises the justification for the study design selected and should be always succinctly explained. The different study designs and methodological characteristics will affect the validity of the study results. Thus, although a more thorough description of the various types of study designs is beyond the focus of this article, it is very important that researchers know the basics regarding study design and are able to adequately describe it. 5

In conclusion, the choice of the most appropriate study design and the adequate planning and implementation of the research methods are the foundations of good research work; and their main purpose is exactly to minimize random and systematic errors that may affect the answer to the research question. Thus, the methods section in a paper should essentially report in a concise but complete manner how well random and systematic errors were considered and controlled by researchers, so that the validity and precision of the estimates that quantitatively translate the answer to the research question may be judged by the readers.

In most journals the “Methods” section is designated as “Materials and Methods” or “Participants and Methods” emphasizing the two main areas that should be addressed. First, “Materials” refers to what was observed (e.g.: humans, animals, tissues, cells, etc.) and the interventions (e.g.: drugs, devices, etc.) and instruments (e.g.: measurement technologies) used in the study. Second, “Methods” refers to how subjects or objects were selected, manipulated or observed to answer the research question, how measurements were performed and how the data were analyzed. 13–15

Study design;

Selection of participants – selection criteria and selection methods;

Data collection – variables, methods and instruments and

Data analysis.

Each one of these subsections could have additional subheadings as appropriate. It should be stressed that the proposal that follows is deemed to be broad and general in scope, and should always be completed with some other specific indications in the context of the particular type of study reported. To master the writing of the methods section it is important (1) to look at many other examples of methods sections in articles with similar scopes and aims as ours and (2) to use some of the many reporting guidelines that are available for the most common study types 16,17 (e.g.: CONSORT for clinical trials 18 ; STROBE for observational studies 19 ; STARD for diagnostic research 20 ; PRISMA for systematic reviews and meta-analysis 21 ; etc.).

The writing of Methods section should be direct, precise and in the past tense. Complex sentence structures should be avoided, as well as descriptions of unimportant aspects or too much details. In general the description of procedures and measurements should be organized chronologically; and, in each subsection, content should be organized from the most to the least important. 13–15

The definition of the descriptive vs. analytical nature of the study. Descriptive studies aim to describe population parameters or associations (hypothesis generating studies) and analytical studies try to answer causal questions (hypothesis testing studies).

Reporting the comparative vs. non-comparative nature of the study (is there a group comparison?).

Reporting the interventional vs. non-interventional nature of the study (is there an intervention to be evaluated?).

Reporting the existence of control over the interventions or factors under study and the existence of randomization. These two criteria allow the classification of studies into three main groups: experimental, quasi-experimental and observational studies. In experimental studies the researchers have direct control over the interventions or factors under study and allocate them to the subjects using a random process – randomization (e.g.: randomized controlled trials). In quasi-experimental studies researchers control the interventions or factors under study but they do not implement randomization procedures (e.g.: non-randomized clinical trials). In observational studies researchers are unable to directly control the interventions or factors under study and do not implement randomization procedures (e.g.: cohort studies, case–control studies, etc.).

Reporting the type of randomization procedures when those are implemented (e.g.: parallel groups vs. cross-over, balanced vs. unbalanced groups, complete vs. incomplete designs, factorial designs, etc.).

Reporting, in observational studies, if the participant selection was based on the predictor variables (cohort studies) or the outcomes (case–control studies) under assessment.

Reporting the cross-sectional vs. longitudinal nature of the study (having into account the existence of an assumed or factual follow-up period).

Reporting the prospective vs. retrospective nature of the study (having into account the point in time where the predictors are measured in relation to the outcomes or the point in time where recruitment of participants starts).

The different study designs and methodological characteristics will affect the validity of the study results. Thus, although a more thorough description of the various types of study designs is beyond the focus of this article, it is very important that researchers know the basics regarding study design and are able to adequately describe it. 5,6

A clear presentation of the ethical considerations is mandatory in all animal or human studies. Although it may not be a subsection by itself, as an alternative it could be a part of the subsection “Selection of participants”, this presentation is important and should take into account the international guidelines on good clinical and research practices. 22–25 In general, references regarding the informed consent obtained on human subjects and the approval of the research protocol by an ethical committee or an institutional review board should be presented. In Portugal, submission of the research protocol to the national data protection agency (Comissão Nacional de Protecção de Dados – CNPD) could also be necessary. 26 In the case of experimental studies on human subjects (clinical trials) the approval by a national ethical committee is legally mandatory. 27 If the study raises any additional specific ethical concern this should be adequately described (e.g.: studies on especially vulnerable subgroups). 28 Although not directly linked with the ethical considerations, it is important to stress that for experimental studies on human subjects (clinical trials) authors should give an appropriate reference to the registration of the study protocol on a clinical trials registration database. 29 Most journals today only accept for publication clinical trials previously registered.

The participants selected for inclusion in a study and the methods of selection will ultimately determine the limits that are placed on the generalizations that can be made regarding the study results. Judging the external validity of a study (i.e.: assessing to whom the study results may be applied) requires that a comprehensive description of the selection criteria and selection methods and descriptive data regarding the study sample be provided. 5

This subsection could begin with a brief presentation of the study setting, in order to contextualize the study presented. This should include the setting, location(s) and relevant dates of the study, indicating, for example, periods of recruitment, exposures or interventions, follow-up and data collection.

Specification criteria (selection criteria),

Methods for selection of participants (sampling) and

Recruitment process.

First, a full and thorough description of the criteria for selection of participants – inclusion and exclusion criteria – should be presented and its rationale explained. 5 Authors should clearly indicate the target population and the accessible population in the study.

A general description of the characteristics of participants is also important and could also be added, but this is a matter of discussion because many authors and journals believe this should be a part of the results section. For human subjects it is important to describe general demographic and clinical characteristics. For animal subjects it is important to adequately describe the species, weight, strain, sex, age and eventually details regarding special characteristics or living conditions.

In studies involving animal models or mechanical models, a detailed description must be provided regarding the preparations made prior to beginning the experimental protocol. In addition, all aspects of animal or tissue preparation required prior to initiation of the research protocol must be described in detail. With any animal preparation or mechanical model there must be enough detail provided so that the reader can duplicate it or evaluate its relevance.

Second, the methods for selection of participants should be carefully explained. This should include an account of how the subjects were identified and how they were sampled from the target population under study (sampling methods). 5 When selecting subjects from a target population, probabilistic sampling methods (random samples) are preferred because they more appropriately guarantee representativeness of the sample. When reporting probabilistic sampling methods authors should describe the sampling frame, the instruments used for the random selection process and, if appropriate, the use of complex sampling methods with stratification or clustering and weighting procedures. Although probabilistic methods are preferred, for practical reasons, non-probabilistic sampling methods (non-random samples) are much more common (e.g.: consecutive samples, convenience samples, systematic samples, etc.). Although non-random sampling methods do not guarantee the representativeness of the sample, they do not necessarily prevent us from validly answering the research question. It should be stressed that non-probabilistic sampling methods are in many instances appropriate. For example, most of randomized clinical trials do not select participants through a random sampling process, and they still are able to appropriately answer the causal question regarding efficacy of therapeutic interventions, relying on the random allocation of alternative interventions (randomization), even when the participants selection was non-random. When answering causal questions the crucial point is to be able to generate comparable study groups and make fair comparisons (equipoise) between groups and, at least in this case, representativeness of the sample, although also important, is regarded as secondary.

The third topic to be addressed in the “Selection of participants” subsection is the recruitment process. 5 Authors should describe in detail how recruitment was undertaken and particularly how effective it was. They should present a complete account of the subjects selected from the sampling frame, those that accepted and those that refused to participate, ideally with a summary of reasons for refusal and a brief characterization of the subjects refusing to participate. Methods implemented to reduce refusal rate should also be described.

In addition to the three main topics described above, in comparative studies it is also important to describe some particular methods of group allocation and/or participant selection that aim to improve their comparability. In experimental studies (randomized controlled trials) a thorough account of randomization procedures should be presented including 18 : methods used to generate the random allocation sequence, details on any restrictions to randomization (stratification or blocking), methods for allocation concealment and implementation details of the randomization process. In this type of studies this is often an independent subsection of the methods section. In observational studies (e.g.: cohort studies, case–control studies, etc.) authors should describe and give details regarding the implementation of methods such as stratification and matching, whenever those are used. 19

Finally, in longitudinal studies a full description should be presented of the follow-up procedures implemented, often as a separate subsection. This should include a description of the completeness and quality of participants follow-up (number and reasons for losses of follow-up, drop-outs, drop-ins, etc.) and, in comparative studies, methods implemented to guarantee equality of follow-up conditions, for example, blinding of researchers or healthcare professionals responsible for the follow-up and the adequate control of co-interventions. 5

The next step in the methods section is to describe the data collection process, including the variables measured and the methods and instruments used for their measurement. In a quantitative research paradigm the adequate and unbiased empirical observation and measurement of variables is the cornerstone of the scientific method; thus this subsection deserves careful and thorough consideration.

Variables are observable objects that are measured, manipulated, or controlled in a study. Variables can be concrete concepts, such as height, weight, and blood pressure, or abstract concepts, such as stress, coping or quality-of-life. Variables should be operationally defined by indicating how the variable will be observed and measured in the study. Abstract variables (constructs), such as quality-of-life or stress, should be defined both conceptually and operationally. The conceptual definition explains the theoretical meaning of the variable, while the operational definition specifies how it will be measured. For example, when measuring quality-of-life, researchers could present a brief conceptual definition of the construct, but should always add details regarding its operational definition, by indicating the model and instrument applied to measure quality-of-life, for example, by using the SF-36 health questionnaire.

Predictor (independent, exposure or intervention) variables,

Outcome (dependent) variables,

Confounding (extraneous) variables or

Interaction (effect modifier) variables.

When describing the variables in a study the authors do not need to give a full and complete description of all variables measured, however the main predictors and all outcome variables should be described with sufficient detail as to allow replication and assessment of the quality of the measurement or classification. For these variables a full account of their conceptual definition, operational definition, classification or diagnostic criteria applied (if appropriate), methods of measurement, instruments used and a brief description of the evidence regarding their validity and reproducibility should be presented. This detailed presentation should be extended to any other variable of particular importance for the study or with uncommon measurement procedures or instruments. 5

For those variables where it is deemed necessary, the description of the measurement methods and instruments should include the manufacturer and model, calibration procedures, evidence regarding the validity and reproducibility of instruments and how measurements were made. The instruments used to measure variables must be reliable and valid. Validity is the extent to which an instrument measures what it reports to measure. Reliability refers to the consistency with which an instrument measures a study variable. Internal consistency (e.g.: Cronbach's alpha), test–retest reliability, and inter-rater reliability are examples of methods used to assess the reliability of an instrument, particularly in the context of abstract concepts (constructs) measurement. These psychometric or clinimetric properties of instruments determine the overall study validity. It is important to select and describe instruments that have established reliability and validity in the population that the investigator plans to study (e.g.: older adults or children) and use instruments that are properly translated, adapted and validated for the study population. Although not formally prohibited, the use of instruments that were not previously submitted to an adequate translation, adaptation and validation process impose important limitations to the credibility and validity of the study results and its use should be always indicated.

Finally, particular methods to control bias associated with the measurement or classification of study variables should be described. For example, implementation of blinding procedures for participants and for researchers collecting data (especially outcomes measurement) should be indicated and explained.

In the last part of the methods section authors should describe with sufficient detail the statistical methods used for the study data analysis, including descriptive statistics and methods for statistical inference. 5 This presentation should have a close link to the aims of the study and should precisely establish what will be presented in the results section.

This subsection should include an initial general sentence regarding the descriptive statistics used, having into account the main types of variables analyzed (e.g.: means or medians, standard deviations or quantile ranges, absolute frequencies and proportions, etc.). Next, a brief description of inferential methods used should follow, including the indication of confidence intervals calculated, an account of the statistical hypothesis tests applied and the indication of any uni- or multi-variable regression or modeling procedures employed. A special note should be added regarding the use of confidence intervals as the best method to express the precision of parameter estimates presented in a study. Their presentation is increasingly deemed essential and they are more informative than the classical p -values of hypothesis testing.

Describing the specifics regarding methods used to account for confounding in observational studies (e.g.: multi-variable regression methods for effect measures adjustment, propensity scores, 30 causality modeling using directed acyclic graphs and structural models, 31–33 etc.).

Describing methods to examine subgroups, interactions and effect modification in experimental and observational studies. 34

Describing any interim analysis, stopping rules and adjustments that may be used, particularly in experimental studies. 18

Describing any particular adjustments made taking into account the sampling methods and weighting procedures used.

Describing methods used to account for missing data.

Describing methods used for sensitivity analysis.

Also important in this section is to describe the estimates and explanation of methods for the sample size and power determination. 5 The determination of the sample size before the beginning of the study is crucial to ensure the appropriate power of hypothesis testing and the precision of parameter estimates. In many instances, particularly in observational studies, a formal sample size calculation is not possible for practical reasons (for example, the study sample is assembled retrospectively or is already fixed before the beginning of the study). Even in these situations it is advisable to present results of a formal power analysis, in order to give an indication of the power of hypothesis tests and the magnitude of differences that researchers are able to detect in those settings. Some authors prefer to incorporate the paragraph regarding sample size determination as a part of the “Selection of participants” subsection.

Finally, an indication of the level of type I errors (alpha level) assumed in all statistical hypothesis testing (usually, a 5% alpha level is assumed) and an indication of the statistical software package used for analysis (with a reference) should be presented in this subsection.

The methods section is the most important part of a scientific paper because it provides the crucial information that allows the reader to judge the validity of the results and conclusions of the study reported. Therefore, in this section, the authors should provide a clear and precise description of how the study was performed and the rationale for the methodological choices and characteristics of the study design. A clear and precise account of how a study was performed, and the rationale for specific study methods are the crucial aspects of scientific writing. A proposal for the structure and content of the methods has been presented and explored giving a general guidance for the writing and assessment of the quality of this section and of the study reported. We hope that somehow this paper may comprise a useful tool for authors, reviewers and readers of scientific papers, and in particular those of the Portuguese Journal of Pulmonology (Revista Portuguesa de Pneumologia) .

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WRITING A SCIENTIFIC RESEARCH ARTICLE | Format for the paper | Edit your paper! | Useful books | FORMAT FOR THE PAPER Scientific research articles provide a method for scientists to communicate with other scientists about the results of their research. A standard format is used for these articles, in which the author presents the research in an orderly, logical manner. This doesn't necessarily reflect the order in which you did or thought about the work.  This format is: | Title | Authors | Introduction | Materials and Methods | Results (with Tables and Figures ) | Discussion | Acknowledgments | Literature Cited | TITLE Make your title specific enough to describe the contents of the paper, but not so technical that only specialists will understand. The title should be appropriate for the intended audience. The title usually describes the subject matter of the article: Effect of Smoking on Academic Performance" Sometimes a title that summarizes the results is more effective: Students Who Smoke Get Lower Grades" AUTHORS 1. The person who did the work and wrote the paper is generally listed as the first author of a research paper. 2. For published articles, other people who made substantial contributions to the work are also listed as authors. Ask your mentor's permission before including his/her name as co-author. ABSTRACT 1. An abstract, or summary, is published together with a research article, giving the reader a "preview" of what's to come. Such abstracts may also be published separately in bibliographical sources, such as Biologic al Abstracts. They allow other scientists to quickly scan the large scientific literature, and decide which articles they want to read in depth. The abstract should be a little less technical than the article itself; you don't want to dissuade your potent ial audience from reading your paper. 2. Your abstract should be one paragraph, of 100-250 words, which summarizes the purpose, methods, results and conclusions of the paper. 3. It is not easy to include all this information in just a few words. Start by writing a summary that includes whatever you think is important, and then gradually prune it down to size by removing unnecessary words, while still retaini ng the necessary concepts. 3. Don't use abbreviations or citations in the abstract. It should be able to stand alone without any footnotes. INTRODUCTION What question did you ask in your experiment? Why is it interesting? The introduction summarizes the relevant literature so that the reader will understand why you were interested in the question you asked. One to fo ur paragraphs should be enough. End with a sentence explaining the specific question you asked in this experiment. MATERIALS AND METHODS 1. How did you answer this question? There should be enough information here to allow another scientist to repeat your experiment. Look at other papers that have been published in your field to get some idea of what is included in this section. 2. If you had a complicated protocol, it may helpful to include a diagram, table or flowchart to explain the methods you used. 3. Do not put results in this section. You may, however, include preliminary results that were used to design the main experiment that you are reporting on. ("In a preliminary study, I observed the owls for one week, and found that 73 % of their locomotor activity occurred during the night, and so I conducted all subsequent experiments between 11 pm and 6 am.") 4. Mention relevant ethical considerations. If you used human subjects, did they consent to participate. If you used animals, what measures did you take to minimize pain? RESULTS 1. This is where you present the results you've gotten. Use graphs and tables if appropriate, but also summarize your main findings in the text. Do NOT discuss the results or speculate as to why something happened; t hat goes in th e Discussion. 2. You don't necessarily have to include all the data you've gotten during the semester. This isn't a diary. 3. Use appropriate methods of showing data. Don't try to manipulate the data to make it look like you did more than you actually did. "The drug cured 1/3 of the infected mice, another 1/3 were not affected, and the third mouse got away." TABLES AND GRAPHS 1. If you present your data in a table or graph, include a title describing what's in the table ("Enzyme activity at various temperatures", not "My results".) For graphs, you should also label the x and y axes. 2. Don't use a table or graph just to be "fancy". If you can summarize the information in one sentence, then a table or graph is not necessary. DISCUSSION 1. Highlight the most significant results, but don't just repeat what you've written in the Results section. How do these results relate to the original question? Do the data support your hypothesis? Are your results consistent with what other investigators have reported? 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? How do y our results fit into the big picture? 2. End with a one-sentence summary of your conclusion, emphasizing why it is relevant. ACKNOWLEDGMENTS This section is optional. You can thank those who either helped with the experiments, or made other important contributions, such as discussing the protocol, commenting on the manuscript, or buying you pizza. REFERENCES (LITERATURE CITED) There are several possible ways to organize this section. Here is one commonly used way: 1. In the text, cite the literature in the appropriate places: Scarlet (1990) thought that the gene was present only in yeast, but it has since been identified in the platypus (Indigo and Mauve, 1994) and wombat (Magenta, et al., 1995). 2. In the References section list citations in alphabetical order. Indigo, A. C., and Mauve, B. E. 1994. Queer place for qwerty: gene isolation from the platypus. Science 275, 1213-1214. Magenta, S. T., Sepia, X., and Turquoise, U. 1995. Wombat genetics. In: Widiculous Wombats, Violet, Q., ed. New York: Columbia University Press. p 123-145. Scarlet, S.L. 1990. Isolation of qwerty gene from S. cerevisae. Journal of Unusual Results 36, 26-31.   EDIT YOUR PAPER!!! "In my writing, I average about ten pages a day. Unfortunately, they're all the same page." Michael Alley, The Craft of Scientific Writing A major part of any writing assignment consists of re-writing. Write accurately Scientific writing must be accurate. Although writing instructors may tell you not to use the same word twice in a sentence, it's okay for scientific writing, which must be accurate. (A student who tried not to repeat the word "hamster" produced this confusing sentence: "When I put the hamster in a cage with the other animals, the little mammals began to play.") Make sure you say what you mean. Instead of: The rats were injected with the drug. (sounds like a syringe was filled with drug and ground-up rats and both were injected together) Write: I injected the drug into the rat.

• Be careful with commonly confused words:

Temperature has an effect on the reaction. Temperature affects the reaction.

I used solutions in various concentrations. (The solutions were 5 mg/ml, 10 mg/ml, and 15 mg/ml) I used solutions in varying concentrations. (The concentrations I used changed; sometimes they were 5 mg/ml, other times they were 15 mg/ml.)

 Less food (can't count numbers of food) Fewer animals (can count numbers of animals)

A large amount of food (can't count them) A large number of animals (can count them)

The erythrocytes, which are in the blood, contain hemoglobin. The erythrocytes that are in the blood contain hemoglobin. (Wrong. This sentence implies that there are erythrocytes elsewhere that don't contain hemoglobin.)

Write clearly

1. Write at a level that's appropriate for your audience.

"Like a pigeon, something to admire as long as it isn't over your head." Anonymous

 2. Use the active voice. It's clearer and more concise than the passive voice.

 Instead of: An increased appetite was manifested by the rats and an increase in body weight was measured. Write: The rats ate more and gained weight.

 3. Use the first person.

 Instead of: It is thought Write: I think

 Instead of: The samples were analyzed Write: I analyzed the samples

 4. Avoid dangling participles.

 "After incubating at 30 degrees C, we examined the petri plates." (You must've been pretty warm in there.)

  Write succinctly

 1. Use verbs instead of abstract nouns

 Instead of: take into consideration Write: consider

 2. Use strong verbs instead of "to be"

 Instead of: The enzyme was found to be the active agent in catalyzing... Write: The enzyme catalyzed...

 3. Use short words.

Instead of: Write: possess have sufficient enough utilize use demonstrate show assistance help terminate end

4. Use concise terms.

 Instead of: Write: prior to before due to the fact that because in a considerable number of cases often the vast majority of most during the time that when in close proximity to near it has long been known that I'm too lazy to look up the reference

5. Use short sentences. A sentence made of more than 40 words should probably be rewritten as two sentences.

 "The conjunction 'and' commonly serves to indicate that the writer's mind still functions even when no signs of the phenomenon are noticeable." Rudolf Virchow, 1928

Check your grammar, spelling and punctuation

1. Use a spellchecker, but be aware that they don't catch all mistakes.

 "When we consider the animal as a hole,..." Student's paper

 2. Your spellchecker may not recognize scientific terms. For the correct spelling, try Biotech's Life Science Dictionary or one of the technical dictionaries on the reference shelf in the Biology or Health Sciences libraries.

 3. Don't, use, unnecessary, commas.

 4. Proofread carefully to see if you any words out.

USEFUL BOOKS

Victoria E. McMillan, Writing Papers in the Biological Sciences , Bedford Books, Boston, 1997 The best. On sale for about $18 at Labyrinth Books, 112th Street. On reserve in Biology Library

Jan A. Pechenik, A Short Guide to Writing About Biology , Boston: Little, Brown, 1987

Harrison W. Ambrose, III & Katharine Peckham Ambrose, A Handbook of Biological Investigation , 4th edition, Hunter Textbooks Inc, Winston-Salem, 1987 Particularly useful if you need to use statistics to analyze your data. Copy on Reference shelf in Biology Library.

Robert S. Day, How to Write and Publish a Scientific Paper , 4th edition, Oryx Press, Phoenix, 1994. Earlier editions also good. A bit more advanced, intended for those writing papers for publication. Fun to read. Several copies available in Columbia libraries.

William Strunk, Jr. and E. B. White, The Elements of Style , 3rd ed. Macmillan, New York, 1987. Several copies available in Columbia libraries.  Strunk's first edition is available on-line.