The article could be considered a brief manual for publication.Writing a research manuscript is an intimidating process for many novice writers in the sci­ences. One of the stumbling blocks is the beginning of the process and creating the first draft. This article presents guidelines on how to initiate the writing process and draft each section of a research manuscript. The article discusses seven rules that allow the writer to prepare a well-structured and comprehensive manuscript for a publication submission. In ad­dition, the author lists different strategies for successful revision. Each of those strategies represents a step in the revision process and should help the writer improve the quality of the manuscript. The article could be considered a brief manual for publication.

It is late at night. You have been strug­gling with your project for a year. You gen­erated an enormous amount of interesting data. Your pipette feels like an extension of your hand, and running western blots has become part of your daily routine, similar to brushing your teeth. Your colleagues think you are ready to write a paper, and your lab mates tease you about your “slow” writing progress. Yet days pass, and you cannot force yourself to sit down to write. You have not written anything for a while (lab reports do not count), and you feel you have lost your stamina. How does the writ­ing process work? How can you fit your writing into a daily schedule packed with experiments? What section should you start with? What distinguishes a good research paper from a bad one? How should you re­vise your paper? These and many other questions buzz in your head and keep you stressed. As a result, you procrastinate. In this article, I will discuss the issues related to the writing process of a scientific paper. Specifically, I will focus on the best ap­proaches to start a scientific paper, tips for writing each section, and the best revision strategies.

1.Schedule Your Writing Time In Outlook

Whether you have written 100 papers or you are struggling with your first, starting the process is the most difficult part unless you have a rigid writing schedule. Writing is hard. It is a very difficult process of in­tense concentration and brain work. As stated in Hayes’ framework for the study of writing: “It is a generative activity requiring motivation, and it is an intellectual activity requiring cognitive processes and memory” [1]. In his book How to Write a Lot: A Prac­tical Guide to Productive Academic Writing, Paul Silvia says that for some, “it’s easier to embalm the dead than to write an article about it” [2]. Just as with any type of hard work, you will not succeed unless you prac­tice regularly. If you have not done physical exercises for a year, only regular workouts can get you into good shape again. The same kind of regular exercises, or I call them “writing sessions,” are required to be a pro­ductive author. Choose from 1- to 2-hour blocks in your daily work schedule and con­sider them as non-cancellable appointments. When figuring out which blocks of time will be set for writing, you should select the time that works best for this type of work. For many people, mornings are more produc­tive. One Yale University graduate student spent a semester writing from 8 a.m. to 9

when her lab was empty. At the end of the semester, she was amazed at how much she accomplished without even interrupting her regular lab hours. In addition, doing the hardest task first thing in the morning con­tributes to the sense of accomplishment dur­ing the rest of the day. This positive feeling spills over into our work and life and has a very positive effect on our overall attitude.

Rule 1: Create regular time blocks for writing as appointments in your calendar and keep these appointments.

2. Start With An Outline

Now that you have scheduled time, you need to decide how to start writing. The best strategy is to start with an outline. This will not be an outline that you are used to, with Roman numerals for each section and neat parallel listing of topic sentences and sup­porting points. This outline will be similar to a template for your paper. Initially, the outline will form a structure for your paper; it will help generate ideas and formulate hy­potheses. Following the advice of George M. Whitesides, “. . . start with a blank piece of paper, and write down, in any order, all important ideas that occur to you concern­ing the paper” [3]. Use Table 1 as a starting point for your outline. Include your visuals (figures, tables, formulas, equations, and al­gorithms), and list your findings. These will constitute the first level of your outline, which will eventually expand as you elabo­rate.

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Now that you have expanded your out­line, you are ready for the next step: dis­cussing the ideas for your paper with your colleagues and mentor. Many universities have a writing center where graduate stu­dents can schedule individual consultations and receive assistance with their paper drafts. Getting feedback during early stages of your draft can save a lot of time. Talking through ideas allows people to conceptualize and organize thoughts to find their direction without wasting time on unnecessary writ­ing. Outlining is the most effective way of communicating your ideas and exchanging thoughts. Moreover, it is also the best stage to decide to which publication you will sub­mit the paper. Many people come up with three choices and discuss them with their mentors and colleagues. Having a list of journal priorities can help you quickly re­submit your paper if your paper is rejected.

Rule 2: Create a detailed outline and discuss it with your mentor and peers.

3. Continue With Drafts

After you get enough feedback and de­cide on the journal you will submit to, the process of real writing begins. Copy your outline into a separate file and expand on each of the points, adding data and elaborat­ing on the details. When you create the first draft, do not succumb to the temptation of editing. Do not slow down to choose a bet­ter word or better phrase; do not halt to im­prove your sentence structure. Pour your ideas into the paper and leave revision and editing for later. As Paul Silvia explains, “Revising while you generate text is like drinking decaffeinated coffee in the early morning: noble idea, wrong time” [2].

Many students complain that they are not productive writers because they experi­ence writer’s block. Staring at an empty screen is frustrating, but your screen is not really empty: You have a template of your article, and all you need to do is fill in the blanks. Indeed, writer’s block is a logical fallacy for a scientist — it is just an excuse to procrastinate. When scientists start writ­ing a research paper, they already have their files with data, lab notes with materials and experimental designs, some visuals, and ta­bles with results. All they need to do is scru­tinize these pieces and put them together into a comprehensive paper.

• Starting With Materials And Methods

If you still struggle with starting a paper, then write the Materials and Methods section first. Since you have all your notes, it should not be problematic for you to de­scribe the experimental design and proce­dures. Your most important goal in this section is to be as explicit as possible by pro­viding enough detail and references. In the end, the purpose of this section is to allow other researchers to evaluate and repeat your work. So do not run into the same problems as the writers of the sentences in (1):

1a. Bacteria were pelleted by centrifugation.

1b. To isolate T cells, lymph nodes were collected.

As you can see, crucial pieces of infor­mation are missing: the speed of centrifug­ing your bacteria, the time, and the temperature in (1a); the source of lymph nodes for collection in (b). The sentences can be improved when information is added, as in (2a) and (2b), respectfully:

2a. Bacteria were pelleted by centrifugation at 3000g for 15 min at25°C.

2b. To isolate T cells, medi­astinal and mesenteric lymph nodes from Balb/c mice were col­lected at day 7 after immunization with ovabumin.

If your method has previously been published and is well-known, then you should provide only the literature reference, as in (3 a). If your method is unpublished, then you need to make sure you provide all essential details, as in (3b).

3a. Stem cells were isolated, according to Johnson [23].

3b. Stem cells were isolated using biotinylated carbon nan­otubes coated with anti-CD34 an­tibodies.

Furthermore, cohesion and fluency are crucial in this section. One of the malprac­tices resulting in disrupted fluency is switch­ing from passive voice to active and vice versa within the same paragraph, as shown in (4). This switching misleads and distracts the reader.

4. Behavioral computer-based experiments of Study 1 were pro­grammed by using E-Prime. We took ratings of enjoyment, mood, and arousal as the patients listened to preferred pleasant music and un­preferred music by using Visual Analogue Scales (SI Methods). The preferred and unpreferred status of the music was operationalized along a continuum of pleasantness [4].

The problem with (4) is that the reader has to switch from the point of view of the experiment (passive voice) to the point of view of the experimenter (active voice). This switch causes confusion about the per­former of the actions in the first and the third sentences. To improve the coherence and fluency of the paragraph above, you should be consistent in choosing the point of view: first person “we” or passive voice [5]. Let’s consider two revised examples in (5).

5a. We programmed behavioral computer-based experiments of Study 1 by using E-Prime. We took ratings of enjoyment, mood, and arousal by using Visual Analogue Scales (SI Methods) as the patients listened to preferred pleasant music and unpreferred music.

We operationalized the preferred and unpreferred status of the music along a continuum of pleasantness.

5b. Behavioral computer-based experiments of Study 1 were pro­grammed by using E-Prime. Ratings of enjoyment, mood, and arousal were taken as the patients listened to preferred pleasant music and unpre­ferred music by using Visual Ana­logue Scales (SI Methods). The preferred and unpreferred status of the music was operationalized along a continuum of pleasantness.

If you choose the point of view of the experimenter, then you may end up with repetitive “we did this” sentences. For many readers, paragraphs with sen­tences all beginning with “we” may also sound disruptive. So if you choose ac­tive sentences, you need to keep the number of “we” subjects to a minimum and vary the beginnings of the sentences [6].

Interestingly, recent studies have re­ported that the Materials and Methods sec­tion is the only section in research papers in which passive voice predominantly over­rides the use of the active voice [5,7,8,9]. For example, Martmez shows a significant drop in active voice use in the Methods sec­tions based on the corpus of 1 million words of experimental full text research ar­ticles in the biological sciences [7]. Ac­cording to the author, the active voice patterned with “we” is used only as a tool to reveal personal responsibility for the procedural decisions in designing and per­forming experimental work. This means that while all other sections of the research paper use active voice, passive voice is still the most predominant in Materials and Methods sections.

Writing Materials and Methods sec­tions is a meticulous and time consuming task requiring extreme accuracy and clar­ity. This is why when you complete your draft, you should ask for as much feed­back from your colleagues as possible. Numerous readers of this section will help you identify the missing links and improve the technical style of this sec­tion.

Rule 3: Be meticulous and accurate in describing the Materials and Methods. Do not change the point of view within one paragraph.

• Writing Results Section

For many authors, writing the Results section is more intimidating than writing the Materials and Methods section . If people are interested in your paper, they are interested in your results. That is why it is vital to use all your writing skills to objectively present your key findings in an orderly and logical sequence using illustrative materials and text.

Your Results should be organized into different segments or subsections where each one presents the purpose of the ex­periment, your experimental approach, data including text and visuals (tables, fig­ures, schematics, algorithms, and formu­las), and data commentary. For most journals, your data commentary will in­clude a meaningful summary of the data presented in the visuals and an explanation of the most significant findings. This data presentation should not repeat the data in the visuals, but rather highlight the most important points. In the “standard” re­search paper approach, your Results sec­tion should exclude data interpretation, leaving it for the Discussion section. How­ever, interpretations gradually and secretly creep into research papers: “Reducing the data, generalizing from the data, and high­lighting scientific cases are all highly in­terpretive processes. It should be clear by now that we do not let the data speak for themselves in research reports; in summa­rizing our results, we interpret them for the reader” [10]. As a result, many journals in­cluding the Journal of Experimental Med­icine and the Journal of Clinical Investigation use joint Results/Discussion sections, where results are immediately followed by interpretations.

Another important aspect of this section is to create a comprehensive and supported argument or a well-researched case. This means that you should be selective in pre­senting data and choose only those experi­mental details that are essential for your reader to understand your findings. You might have conducted an experiment 20 times and collected numerous records, but this does not mean that you should present all those records in your paper. You need to distinguish your results from your data and be able to discard excessive experimental details that could distract and confuse the reader. However, creating a picture or an ar­gument should not be confused with data manipulation or falsification, which is a willful distortion of data and results. If some of your findings contradict your ideas, you have to mention this and find a plausible ex­planation for the contradiction.

In addition, your text should not include irrelevant and peripheral information, in­cluding overview sentences, as in (6).

6. To show our results, we first introduce all components of exper­imental system and then describe the outcome of infections.

Indeed, wordiness convolutes your sen­tences and conceals your ideas from readers. One common source of wordiness is unnec­essary intensifiers. Adverbial intensifiers such as “clearly,” “essential,” “quite,” “ba­sically,” “rather,” “fairly,” “really,” and “vir­tually” not only add verbosity to your sentences, but also lower your results’ cred­ibility. They appeal to the reader’s emotions but lower objectivity, as in the common ex­amples in (7):

7a. Table 3 clearly shows that …

7b. It is obvious from figure 4 that .

Another source of wordiness is nomi- nalizations, i.e., nouns derived from verbs and adjectives paired with weak verbs in­cluding “be,” “have,” “do,” “make,” “cause,” “provide,” and “get” and construc­tions such as “there is/are.”

8a. We tested the hypothesis that there is a disruption of mem­brane asymmetry.

8b. In this paper we provide an argument that stem cells repop­ulate injured organs.

In the sentences above, the abstract nominalizations “disruption” and “argu­ment” do not contribute to the clarity of the sentences, but rather clutter them with use­less vocabulary that distracts from the mean­ing. To improve your sentences, avoid unnecessary nominalizations and change passive verbs and constructions into active and direct sentences.

9a. We tested the hypothesis that the membrane asymmetry is disrupted.

9b. In this paper we argue that stem cells repopulate injured or­gans.

Your Results section is the heart of your paper, representing a year or more of your daily research. So lead your reader through your story by writing direct, concise, and clear sentences.

Rule 4: Be clear, concise, and objective in describing your Results.

• Now It Is Time For Your Introduction

Now that you are almost half through drafting your research paper, it is time to up­date your outline. While describing your Methods and Results, many of you diverged from the original outline and re-focused your ideas. So before you move on to create your Introduction, re-read your Methods and Results sections and change your outline to match your research focus. The updated out­line will help you review the general picture of your paper, the topic, the main idea, and the purpose, which are all important for writing your introduction.

The best way to structure your intro­duction is to follow the three-move approach shown in Table 3.

The moves and information from your outline can help to create your Introduc­tion efficiently and without missing steps. These moves are traffic signs that lead the reader through the road of your ideas. Each move plays an important role in your paper and should be presented with deep thought and care. When you establish the territory, you place your research in con­text and highlight the importance of your research topic. By finding the niche, you outline the scope of your research problem and enter the scientific dialogue. The final move, “occupying the niche,” is where you explain your research in a nutshell and highlight your paper’s significance. The three moves allow your readers to evaluate their interest in your paper and play a significant role in the paper review process, determining your paper review­ers.

Some academic writers assume that the reader “should follow the paper” to find the answers about your methodology and your findings. As a result, many novice writers do not present their experimental approach and the major findings, wrongly believing that the reader will locate the necessary infor­mation later while reading the subsequent sections [5]. However, this “suspense” ap­proach is not appropriate for scientific writ­ing. To interest the reader, scientific authors should be direct and straightforward and present informative one-sentence summaries of the results and the approach.

Another problem is that writers un­derstate the significance of the Introduc­tion. Many new researchers mistakenly think that all their readers understand the importance of the research question and omit this part. However, this assumption is faulty because the purpose of the sec­tion is not to evaluate the importance of the research question in general. The goal is to present the importance of your re­search contribution and your findings. Therefore, you should be explicit and clear in describing the benefit of the paper.

The Introduction should not be long. In­deed, for most journals, this is a very brief section of about 250 to 600 words, but it might be the most difficult section due to its importance.

Rule 5: Interest your reader in the Intro­duction section by signalling all its ele­ments and stating the novelty of the work.

• Discussion Of The Results

For many scientists, writing a Discus­sion section is as scary as starting a paper. Most of the fear comes from the variation in the section. Since every paper has its unique results and findings, the Discussion section differs in its length, shape, and structure. However, some general principles of writ­ing this section still exist. Knowing these rules, or “moves,” can change your attitude about this section and help you create a com­prehensive interpretation of your results.

The purpose of the Discussion section is to place your findings in the research con­text and “to explain the meaning of the find­ings and why they are important, without appearing arrogant, condescending, or pa­tronizing” [11]. The structure of the first two moves is almost a mirror reflection of the one in the Introduction. In the Introduction, you zoom in from general to specific and from the background to your research ques­tion; in the Discussion section, you zoom out from the summary of your findings to the research context, as shown in Table 4.

The biggest challenge for many writers is the opening paragraph of the Discussion section. Following the moves in Table 1, the best choice is to start with the study’s major findings that provide the answer to the re­search question in your Introduction. The most common starting phrases are “Our findings demonstrate . . .,” or “In this study, we have shown that . . .,” or “Our results suggest . . .” In some cases, however, re­minding the reader about the research ques­tion or even providing a brief context and then stating the answer would make more sense. This is important in those cases where the researcher presents a number of findings or where more than one research question was presented. Your summary of the study’s major findings should be followed by your presentation of the importance of these find­ings. One of the most frequent mistakes of the novice writer is to assume the impor­tance of his findings. Even if the importance is clear to you, it may not be obvious to your reader. Digesting the findings and their im­portance to your reader is as crucial as stat­ing your research question.

Another useful strategy is to be proac­tive in the first move by predicting and com­menting on the alternative explanations of the results. Addressing potential doubts will save you from painful comments about the wrong interpretation of your results and will present you as a thoughtful and considerate researcher. Moreover, the evaluation of the alternative explanations might help you cre­ate a logical step to the next move of the dis­cussion section: the research context.

The goal of the research context move is to show how your findings fit into the gen­eral picture of the current research and how you contribute to the existing knowledge on the topic. This is also the place to discuss any discrepancies and unexpected findings that may otherwise distort the general pic­ture of your paper. Moreover, outlining the scope of your research by showing the lim­itations, weaknesses, and assumptions is es­sential and adds modesty to your image as a scientist. However, make sure that you do not end your paper with the problems that override your findings. Try to suggest feasi­ble explanations and solutions.

If your submission does not require a separate Conclusion section, then adding an­other paragraph about the “take-home mes­sage” is a must. This should be a general statement reiterating your answer to the re­search question and adding its scientific im­plications, practical application, or advice.

Just as in all other sections of your paper, the clear and precise language and concise comprehensive sentences are vital. However, in addition to that, your writing should convey confidence and authority. The easiest way to illustrate your tone is to use the active voice and the first person pro­nouns. Accompanied by clarity and suc­cinctness, these tools are the best to convince your readers of your point and your ideas.

Rule 6: Present the principles, relation­ships, and generalizations in a concise and convincing tone.

4. Choosing The Best Working Revision Strategies

Now that you have created the first draft, your attitude toward your writing should have improved. Moreover, you should feel more confident that you are able to accomplish your project and submit your paper within a reasonable timeframe. You also have worked out your writing schedule and followed it precisely. Do not stop — you are only at the midpoint from your destina­tion. Just as the best and most precious dia­mond is no more than an unattractive stone recognized only by trained professionals, your ideas and your results may go unno­ticed if they are not polished and brushed. Despite your attempts to present your ideas in a logical and comprehensive way, first drafts are frequently a mess. Use the advice of Paul Silvia: “Your first drafts should sound like they were hastily translated from Icelandic by a non-native speaker” [2]. The degree of your success will depend on how you are able to revise and edit your paper.

The revision can be done at the macrostructure and the microstructure lev­els [13]. The macrostructure revision in­cludes the revision of the organization, content, and flow. The microstructure level includes individual words, sentence struc­ture, grammar, punctuation, and spelling.

The best way to approach the macrostructure revision is through the out­line of the ideas in your paper. The last time you updated your outline was before writing the Introduction and the Discussion. Now that you have the beginning and the conclu­sion, you can take a bird’s-eye view of the whole paper. The outline will allow you to see if the ideas of your paper are coherently structured, if your results are logically built, and if the discussion is linked to the research question in the Introduction. You will be able to see if something is missing in any of the sections or if you need to rearrange your information to make your point.

The next step is to revise each of the sec­tions starting from the beginning. Ideally, you should limit yourself to working on small sec­tions of about five pages at a time [14]. After these short sections, your eyes get used to your writing and your efficiency in spotting problems decreases. When reading for con­tent and organization, you should control your urge to edit your paper for sentence structure and grammar and focus only on the flow of your ideas and logic of your presen­tation. Experienced researchers tend to make almost three times the number of changes to meaning than novice writers [15,16]. Revis­ing is a difficult but useful skill, which aca­demic writers obtain with years of practice.

In contrast to the macrostructure revi­sion, which is a linear process and is done usually through a detailed outline and by sections, microstructure revision is a non­linear process. While the goal of the macrostructure revision is to analyze your ideas and their logic, the goal of the mi­crostructure editing is to scrutinize the form of your ideas: your paragraphs, sentences, and words. You do not need and are not rec­ommended to follow the order of the paper to perform this type of revision. You can start from the end or from different sections. You can even revise by reading sentences backward, sentence by sentence and word by word.

One of the microstructure revision strategies frequently used during writing center consultations is to read the paper aloud [17]. You may read aloud to yourself, to a tape recorder, or to a colleague or friend. When reading and listening to your paper, you are more likely to notice the places where the fluency is disrupted and where you stumble because of a very long and un­clear sentence or a wrong connector.

Another revision strategy is to learn your common errors and to do a targeted search for them [13]. All writers have a set of problems that are specific to them, i.e., their writing idiosyncrasies. Remembering these problems is as important for an aca­demic writer as remembering your friends’ birthdays. Create a list of these idiosyn­crasies and run a search for these problems using your word processor. If your problem is demonstrative pronouns without summary words, then search for “this/these/those” in your text and check if you used the word ap­propriately. If you have a problem with in- tensifiers, then search for “really” or “very” and delete them from the text. The same tar­geted search can be done to eliminate wordi­ness. Searching for “there is/are” or “and” can help you avoid the bulky sentences.

The final strategy is working with a hard copy and a pencil. Print a double space copy with font size 14 and re-read your paper in several steps. Try reading your paper line by line with the rest of the text covered with a piece of paper. When you are forced to see only a small portion of your writing, you are less likely to get distracted and are more likely to notice problems. You will end up spotting more unnecessary words, wrongly worded phrases, or unparal­lel constructions.

After you apply all these strategies, you are ready to share your writing with your friends, colleagues, and a writing advisor in the writing center. Get as much feedback as you can, especially from non-specialists in your field. Patiently listen to what others say to you — you are not expected to defend your writing or explain what you wanted to say. You may decide what you want to change and how after you receive the feed­back and sort it in your head. Even though some researchers make the revision an end­less process and can hardly stop after a 14th draft; having from five to seven drafts of your paper is a norm in the sciences. If you can’t stop revising, then set a deadline for yourself and stick to it. Deadlines always help.

Rule 7: Revise your paper at the macrostructure and the microstructure level using different strategies and tech­niques. Receive feedback and revise again.

5. It Is Time To Submit

It is late at night again. You are still in your lab finishing revisions and getting ready to submit your paper. You feel happy — you have finally finished a year’s worth of work. You will submit your paper tomor­row, and regardless of the outcome, you know that you can do it. If one journal does not take your paper, you will take advantage of the feedback and resubmit again. You will have a publication, and this is the most im­portant achievement.

What is even more important is that you have your scheduled writing time that you are going to keep for your future publi­cations, for reading and taking notes, for writing grants, and for reviewing papers. You are not going to lose stamina this time, and you will become a productive scientist. But for now, let’s celebrate the end of the paper.

References

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