Writing a Scientific Research Article

Prepared by Endang Fauziati
efauziati@yahoo.com


Introduction
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 does not necessarily reflect the order in which you did or thought about the work.  Written and oral communications skills are probably the most universal qualities sought by graduate and professional schools as well as by employers. They themselves are responsible for developing such skills to a high level.
The format of a scientific research article has been defined by centuries of developing tradition, editorial practice, scientific ethics and the interplay with printing and publishing services. A scientific research article should have, in proper order, a Title, Abstract, Introduction, Materials and Methods, Results, and Discussion.

General Format of a Scientific Research Article
1. Title
A title should be the fewest possible words that accurately describe the content of the paper. Omit all waste words such as "A study of ...", "Investigations of ..." "Observations on ...", etc. Indexing and abstracting services depend on the accuracy of the title, extracting from it keywords useful in cross-referencing and computer searching. An improperly titled paper may never reach the audience for which it was intended, so be specific. If the study is of a particular field, name it in the title. If the inferences made in the paper are limited to a particular region, then name the region in the title.

2. Abstract
A well prepared abstract should enable the reader to identify the basic content of a document quickly and accurately, to determine its relevance to the reader's interests, and thus to decide whether to read the document in its entirety. The abstract should succinctly state the principal objectives and scope of the investigation where these are not obvious from the title. More importantly, the abstract should concisely summarize the results and principal conclusions. The abstract should not include details of the methods employed unless the study is methodological, i.e. primarily concerned with methods. The abstract must be brief, not exceeding 250 words or as otherwise defined by the journal. If the essential details of the paper can be conveyed in 100 words, do not use 200. Do not repeat information contained in the title. The abstract, together with the title, must be self-contained as it is often published separately from the paper in abstracting services. Omit all references to the literature and to tables or figures, and omit obscure abbreviations and acronyms even though they may be defined in main body of the paper. The abstract is the only text in a research paper to be written without using paragraphs in order to separate major points.

An abstract usually includes the following elements. Be sure to keep the first two items to no more than one sentence each.
- Purpose of the study - hypothesis, overall question, objective
- Model organism or system and brief description of the experiment
- Results, including specific data - if the results are quantitative in nature, report quantitative data; results of any statistical analysis should be reported
- Important conclusions or questions that follow from the experiment(s)

Writing Style:
- Single paragraph, and concise
- As a summary of work done, it is always written in past tense
- An abstract should stand on its own, and not refer to any other part of the paper such as a figure or table
- Focus on summarizing results - limit background information to a sentence or two, if absolutely necessary
- What you report in an abstract must be consistent with what you reported in the paper
- Correct spelling, clarity of sentences and phrases, and proper reporting of quantities (proper units, significant figures) are just as important in an abstract as they are anywhere else.
3. Introduction
An introduction should not exceed two pages (double spaced, typed). The purpose of an introduction is to acquaint the reader with the rationale behind the work, with the intention of defending it. This is the place where we discuss the theoretical context, and this enables the reader to understand and appreciate our writing objectives.
There are various approaches used to write an introduction, however, in general, the following approach can produce an effective introduction. An introduction may include the following components:
- Describe the importance (significance) of the study - why was this worth doing in the first place? Provide a broad context.
- Defend the model - why did you use this particular organism or system? What are its advantages? You might comment on its suitability from a theoretical point of view as well as indicate practical reasons for using it.
- Provide a rationale. State your specific hypothesis(es) or objective(s), and describe the reasoning that led you to select them.
- Very briefly describe the experimental design and how it accomplished the stated objectives.

Writing Style:
- Use past tense except when referring to established facts. After all, the paper will be submitted after all of the work is completed.
- Organize your ideas, making one major point with each paragraph. If you make the four points listed above, you will need a minimum of four paragraphs.
- Present background information only as needed in order support a position. The reader does not want to read everything you know about a subject.
- State the hypothesis/objective precisely - do not oversimplify.
- As always, pay attention to spelling, clarity and appropriateness of sentences and phrases.

4. (Materials) and Methods
There is no specific page limit, but a key concept is to keep this section as concise as you possibly can. People will want to read this material selectively. The reader may only be interested in one formula or part of a procedure. Materials and methods may be reported under separate subheadings within this section or can be incorporated together.
The objective of this section is to document all specialized materials and general procedures, so that another individual may use some or all of the methods in another study or judge the scientific merit of our work. It is not to be a step by step description of everything we did, nor is a method section or a set of instructions. In particular, it is not supposed to tell a story. By the way, we notebook should contain all of the information that we need for this section.

Writing a (Material) and Method Section
Materials (Natural Science):
- Describe materials separately only if the study is so complicated that it saves space this way.
- Include specialized chemicals, biological materials, and any equipment or supplies that are not commonly found in laboratories.
- Do not include commonly found supplies such as test tubes, pipet tips, beakers, etc., or standard lab equipment such as centrifuges, spectrophotometers, pipettors, etc.
- If we use of a specific type of equipment, a specific enzyme, or a culture from a particular supplier is critical to the success of the experiment, then this equipment and the source should be singled out, otherwise not necessary.
- Materials may be reported in a separate paragraph or else they may be identified along with your procedures.
- In biosciences we frequently work with solutions - refer to them by name and describe completely, including concentrations of all reagents, and pH of aqueous solutions, solvent if non-aqueous.

Methods:
- Report the methodology (not details of each procedure which employed the same methodology)
- Describe the methodology completely (i.e. temperatures, incubation times, etc.)
- To be concise, present methods under headings devoted to specific procedures or groups of procedures
- Generalize, report how procedures were done, not how they were specifically performed on a particular day. (For example, report "samples were diluted to a final concentration of 2 mg/ml protein;" don't report that "135 microliters of sample one was diluted with 330 microliters of buffer to make the protein concentration 2 mg/ml.") Always think about what would be relevant to an investigator at another institution, working on his/her own project.
- If well documented procedures were used, report the procedure by name, perhaps with reference. (For example, the Bradford assay is well known. We need not report the procedure in full - just that you used a Bradford assay to estimate protein concentration, and identify what you used as a standard. The same is true for the SDS-PAGE method, and many other well known procedures in biology and biochemistry)

Writing Style:
- It is awkward or impossible to use active voice when documenting methods without using first person, which would focus the reader's attention on the investigator rather than the work. Therefore, when writing up the methods most authors use third person passive voice.
- Use normal prose in this and in every other section of the paper; avoid informal lists, and use complete sentences.

What to avoid
- Materials and methods are not a set of instructions.
- Omit all explanatory information and background - save it for the discussion.
- Omit information that is irrelevant to a third party, such as what color ice bucket you used, or which individual logged in the data.

5. Results
The page length of this section is set by the amount and types of data to be reported. However, it is better to continue to be concise, using figures and tables, if appropriate, to present results most effectively. The purpose of a result section is to present and illustrate the research findings. Make this section a completely objective report of the results, and save all interpretation for the discussion.

Writing a Result Section
It is important to clearly distinguish material that would normally be included in a research article from any raw data or other appendix material that would not be published. In fact, such material should not be submitted at all unless requested by the instructor.

Result section commonly includes the following components:
- Summarize the findings in text and illustrate them, if appropriate, with figures and tables.
- In text, describe each of the results, pointing the reader to observations that are most relevant.
- Provide a context, such as by describing the question that was addressed by making a particular observation.
- Describe results of control experiments and include observations that are not presented in a formal figure or table, if appropriate.
- Analyze your data, then prepare the analyzed (converted) data in the form of a figure (graph), table, or in text form.

What to avoid
- Do not discuss or interpret the results, report background information, or attempt to explain anything.
- Never include raw data or intermediate calculations in a research paper.
- Do not present the same data more than once.
- Text should complement any figures or tables, not repeat the same information.
- Please do not confuse figures with tables - there is a difference.

Writing Style
- As always, use past tense when you refer to your results, and put everything in a logical order.
- In text, refer to each figure as "figure 1," "figure 2," etc. ; number your tables as well (see the reference text for details)
- Place figures and tables, properly numbered, in order at the end of the report (clearly distinguish them from any other material such as raw data, standard curves, etc.)
- If you prefer, you may place your figures and tables appropriately within the text of your results section.

Figures and Tables
- Either place figures and tables within the text of the result, or include them in the back of the report (following Literature Cited) - do one or the other.
- If you place figures and tables at the end of the report, make sure they are clearly distinguished from any attached appendix materials, such as raw data
- Regardless of placement, each figure must be numbered consecutively and complete with caption (caption goes under the figure)
- Regardless of placement, each table must be titled, numbered consecutively and complete with heading (title with description goes above the table)
- Each figure and table must be sufficiently complete that it could stand on its own, separate from text .

6. Discussion
Journal guidelines vary. Space is so valuable in International Journal that authors are asked to restrict discussions to four or five pages, double spaced, typed. While learning to write effectively, the limit will be extended to six typed pages. If we practice economy of words that should be plenty of space within which to say all that you need to say. The objective here is to provide an interpretation of your results and support for all of your conclusions, using evidence from your experiment and generally accepted knowledge, if appropriate. The significance of findings should be clearly described.

Writing a discussion
Interpret the data in the discussion in appropriate depth. This means that when we explain a phenomenon we must describe mechanisms that may account for the observation. If your results differ from your expectations, explain why that may have happened. If the results agree, then describe the theory that the evidence supported. It is never appropriate to simply state that the data agreed with expectations, and let it drop at that. Consider the following recommendations:
- Decide if each hypothesis is supported, rejected, or if you cannot make a decision with confidence. Do not simply dismiss a study or part of a study as "inconclusive."
- Research papers are not accepted if the work is incomplete. Draw what conclusions you can based upon the results that you have, and treat the study as a finished work
- You may suggest future directions, such as how the experiment might be modified to accomplish another objective.
- Explain all of your observations as much as possible, focusing on mechanisms.
- Decide if the experimental design adequately addressed the hypothesis, and whether or not it was properly controlled.
- Try to offer alternative explanations if reasonable alternatives exist.
- One experiment will not answer an overall question, so keeping the big picture in mind, where do you go next? The best studies open up new avenues of research. What questions remain?
- Recommendations for specific papers will provide additional suggestions.

Writing Style:
- When referring to information, try to distinguish data generated by your own studies from published information or from information obtained from other students (verb tense is an important tool for accomplishing that purpose).
- Refer to work done by specific individuals in past tense.
- Refer to generally accepted facts and principles in present tense. For example, "Doofus, in a 1989 survey, found that anemia in basset hounds was correlated with advanced age. Anemia is a condition in which there is insufficient hemoglobin in the blood."
It is not the correct idea to present a superficial interpretation that more or less re-states the results. It is necessary to suggest why results came out as they did, focusing on the mechanisms behind the observations.

7. Literature Cited
List all literature cited in the paper, in alphabetical order, by first author. In a proper research paper, only primary literature is used (original research articles authored by the original investigators). Be cautious about using web sites as references - anyone can put just about anything on a web site, and you have no sure way of knowing if it is truth or fiction. If you are citing an on line journal, use the journal citation (name, volume, year, page numbers).
In fact, there are a variety of styles used by journals for referencing information. Citations in the text may be referred to by number or by author name. In the reference section the citations are then arranged numerically or alphabetically. Some journals have the submitters first alphabetize the authors and then number each. This is a complicated system and one which we will not use. We may choose to either number in sequence each new reference as it is cited or may alphabetize the first authors of each reference. The easiest system is the former because as we add a new reference to the text it is provided with a number. This saves you from interpreting the nuances of how to order the alphabetized authors in the latter system - it may seem trivial but, for instance, how do you alphabetize when the list of authors for two papers is identical and in the same year! When reading references, you should look at how each journal handles its references as well as articles published.

Conclusion
Writing a scientific research article is really a critical business. Some the fundamental premises include are technological obsolesce can occur in as little as 5-10 years, excellence in research is one of the ultimate roots of all academic excellence, in both undergraduate and postgraduate educations, and in science, no matter how spectacular the results are, the work is not completed until the results are published. Thus, in order to be a good scientist one should be creative, logical, intuitive, imaginative, observant, persistent, and able to learn from their mistakes. More importantly a good scientist should publish, as the motto says “publish or perished”.
The format of a publication usually varies from discipline to discipline, with different disciplines having different conventions that everyone in the discipline comes to know and follow. Also, specific formats are usually specified by different publishing agency. Scientific journals, for example, typically have a "Guide to Authors" which specifies exactly how the journal wants its manuscripts organized and presented. In the scientific community, however, there exist general conventions for publications. Scientific article generally contains some components described in this paper.

References
Day, R.A. 1979. How to Write and Publish a Scientific Paper: Philadelphia, PA, Institute for Scientific Information Press.
Said, Ismail. 2009. “Getting Published: Materials of Creativity and Skepticism”, paper presented at Research Center of Muhammadiyah University of Surakarta (1 June 2009).
Tischler, Marc E. 2008. Scientific Writing Booklet. Department of Biochemistry & Molecular Biophysics University of Arizona