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Research Paper Design Methodology

Summary
The methods section of a research paper provides the information by which a study’s validity is judged.Therefore, it requires a clear and precise description of how an experiment was done, and the rationale for why specific experimental procedures were chosen. The methods section should describe what was done to answer the research question, describe how it was done, justify the experimental design, and explain how the results were analyzed. Scientific writing is direct and orderly. Therefore, the methods section structure should: describe the materials used in the study, explain how the materials were prepared for the study, describe the research protocol, explain how measurements were made and what calculations were performed, and state which statistical tests were done to analyze the data. Once all elements of the methods section are written, subsequent
drafts should focus on how to present those elements as clearly and logically as possibly. The
description of preparations, measurements, and the protocol should be organized chronologically.
For clarity, when a large amount of detail must be presented, information should be presented in sub-sections according to topic. Material in each section should be organized by topic from most to least important.

Introduction

The methods section is the most important aspect of a research paper because it provides the information by which the validity of a study is ultimately judged. Therefore, the author must provide a clear and precise description of how an experiment was done, and the rationale for the specific
experimental procedures chosen. It must be written with enough information so that: 

(1) the experiment could be repeated by others to evaluate whether the results are reproducible,

and

(2) the audience can judge whether the results and conclusions are valid. 
 

Basic Research Concepts

The scientific method attempts to discover cause-and effect relationships between objects (ie, physical matter or processes). In the physical sciences objects are regarded as variables, and a variable is anything that can assume different values. Elucidating a cause-and-effect relationship
between objects requires that variables are classified as independent, dependent, or confounding. An independent variable is one that, when manipulated, causes a change in another variable. The variable that changes in response to that manipulation is referred to as a dependent variable.
For example, intraocular pressure is a dependent variable that responds to manipulations in independent variables such as blood pressure and pupil size. A confounding or extraneous variable is anything other than the independent variable of interest that may affect the dependent variable. Therefore, a change in a dependent variable may be due wholly or in part to a change in a confounding variable. For example, a change in vena cava pressure can alter intraocular pressure by its effect upon ocular blood drainage.

Evaluation of a potential cause-effect relationship between 2 objects is accomplished through the development of the study design. A study design is simply a strategy to control and manipulate variables that provide an answer to the research question regarding potential cause-and-effect
relationships.

Validity refers to the credibility of experimental results and the degree to which the results can be applied to the general population of interest. Internal validity refers to the credibility of a study and is determined by the degree to which conclusions drawn from an experiment correctly describe what actually transpired during the study.1 External validity refers to whether (and to what degree) the results of a study can be generalized to a larger population. 1 Unfortunately, all biological systems are profoundly complex, so simple, unambiguous, direct relationships between objects can be difficult to ascertain. The internal 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. Therefore, the study protocol must be designed to control (eg, to keep constant) as many extraneous factors as possible so that any potential cause-and-effect relationship between 2 objects can be judged accurately. It is importantto emphasize that confounding variables can never be fully controlled. Furthermore, the influence of these variables may not be fully appreciated by those conducting the research. External validity is primarily determined by how subjects are selected to participate in a study and by the use of randomization procedures that limit potential bias in how subjects are assigned to treatment groups.
 

Content and Writing Style of the Methods Section

Historically, the methods section was referred to as the “materials and methods” to emphasize the 2 distinct areas that must be addressed. “Materials” referred to what was examined (eg, humans, animals, tissue preparations) and also to the various treatments (eg, drugs, gases) and instruments
(eg, ventilators) used in the study. “Methods” referred to how subjects or objects were manipulated to answer the experimental question, how measurements and calculations were made, and how the data were analyzed.

The complexity of scientific inquiry necessitates that the writing of the methods be clear and orderly to avoid confusion and ambiguity. First, it is usually helpful to structure the methods section by:

1. Describing the materials used in the study

2. Explaining how the materials were prepared

3. Describing the research protocol

4. Explaining how measurements were made and what calculations were performed

5. Stating which statistical tests were done to analyze the data2

Second, the writing should be direct and precise and in the past tense. Compound sentence structures should be avoided, as well as descriptions of unimportant details. Once all elements of the methods section are written down during the initial draft, subsequent drafts should focus on
how to present those elements as clearly and logically as possibly. In general, the description of preparations, measurements, and the protocol should be organized chronologically. For clarity, when a large amount of detail must be presented, information should be presented in subsections according to topic. Within each section and subsection, material should always be organized by topic from most to least important.
 

Subjects

Judging the external validity of a study involving human subjects (ie, to whom the study results may be applied) requires that descriptive data be provided regarding the basic demographic profile of the sample population, including age, gender, and possibly the racial composition of the sample. When animals are the subjects of a study, it is important to list species, weight, strain, sex, and age. 

Who is chosen for inclusion in a study (as well as how treatments are assigned) in large measure determines what limits are placed on the generalizations that can be made regarding the study results. Thus, when writing the methods section, it is important to describe who the subjects were in the context of the research question. The selection criteria and rationale for enrolling patients into the study must be stated explicitly. For example, if the study proclaims to examine whether latanoprost reduces post-phacoemulsification intraocular pressure, then one would not anticipate that patients with combined trabeculectomy and phacoemulsifcation to be included. In addition, it is important when describing patients to provide some evaluation of their health status that is relevant to the study. 
 

Ethical Considerations

When working with human or animal subjects, there must be a declaration that the medical center’s institutional review board governing research on living matter has determined that the study protocol adheres to ethical principles. Without such approval, no research project can be conducted nor can it be published in a reputable, peerreview science journal.
 

Preparations

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 studies involving animals a detailed description should be provided on the use of sedation and anesthesia, the route of administration, and how its efficacy was evaluated.2 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. When a study involves the use or evaluation of drugs, the generic drug name should be used and the manufacturer, concentration, dose, and infusion rate should be specified. Likewise, when medical gases are used, the concentration and flow rates should be specified.

It is worth noting that the introduction of any novel method for measuring a variable, or preparing /designing a model will require intense discussion. Depending on how unique (or unorthodox) the new method is, its validation probably should be established in a separate publication, published prior to submission of the main study.
 

Protocol Design

The research protocol is the sequence of manipulations and measurement procedures that make up the experiment. Its description should follow the exact sequence of how the procedures were executed.2 Typically, this first involves a description of baseline conditions and any associated
baseline measurements, followed by the sequence of manipulations of the independent variable and the subsequent measurement of changes in the dependent variable. It is also important to describe all relevant aspects of clinical management not controlled by the protocol in the peri-experimental period.

When writing the methods section, it is important to bear in mind that the rationale or assumptions on which some procedures are based may not always be obvious to the audience. This is particularly true when writing for a general medical audience, as opposed to members of a subspecialty. Therefore, the writer must always keep in mind who his/her audience is. The rationale and assumptions on which experimental procedures are based should be briefly stated in the methods section and, if necessary, described in more detail in the discussion section. Whenever it is not obvious, the purpose of a procedure should be stated in relationship either to the research question or to the entire protocol. Writing the methods section in this style is called a purpose-procedure format.2
 

Measurements and Calculations

The next step in the methods section is to describe what variables were measured and how those measurements were made. The description of measurement instruments should include the manufacturer and model, calibration procedures, and how measurements were made. It also may be necessary to justify why and how certain variables were measured. This becomes particularly important when the object of the experiment can be approached only indirectly. Tangentially, whenever a value for a variable is used to signify a state or condition, this should be stated explicitly. For example, one could state: “Adequate intraocular pressure control was indicated by a  pressure of < 21 mm Hg.” A listing of all calculations used in the study typically follows the description of measurements.
 

Data Analysis

The last step in the methods section is to describe how the data will be presented in the results section (eg, mean vs median), which statistical tests will used for the infer-ential data, and what p value is deemed to indicate a statistically significant difference.
 

Summary

The methods section is the most important part of a research paper because it provides the information the reader needs to judge the study’s validity. Providing a clear and precise description of how an experiment was done, and the rationale for specific experimental procedures are crucial aspects of scientific writing.
 

REFERENCES

1. Hulley SB, Newman TB, Cummings SR. The anatomy and physiology of research. 
    In: Hulley SB, Cummings SR (editors). Designing clinical research. Baltimore: William &    
    Wilkins; 1988:1–11.

2. Zeiger M. Essentials of writing biomedical research papers. New York: McGraw-Hill; 
    1991:113–138.
 

I. Groups of Research Methods

There are two main groups of research methods in the social sciences:

  1. The empirical-analytical groupapproaches the study of social sciences in a similar manner that researchers study the natural sciences. This type of research focuses on objective knowledge, research questions that can be answered yes or no, and operational definitions of variables to be measured. The empirical-analytical group employs deductive reasoning that uses existing theory as a foundation for formulating hypotheses that need to be tested. This approach is focused on explanation.
  2. The interpretative group of methods is focused on understanding phenomenon in a comprehensive, holistic way. Interpretive methods focus on analytically disclosing the meaning-making practices of human subjects [the why, how, or by what means people do what they do], while showing how those practices arrange so that it can be used to generate observable outcomes. Interpretive methods allow you to recognize your connection to the phenomena under investigation. However, the interpretative group requires careful examination of variables because it focuses more on subjective knowledge.

II. Content

The introduction to your methodology section should begin by restating the research problem and underlying assumptions underpinning your study. This is followed by situating the methods you will use to gather, analyze, and process information within the overall “tradition” of your field of study and within the particular research design you have chosen to study the problem. If the method you choose lies outside of the tradition of your field [i.e., your review of the literature demonstrates that it is not commonly used], provide a justification for how your choice of methods specifically addresses the research problem in ways that have not been utilized in prior studies.

The remainder of your methodology section should describe the following:

  • Decisions made in selecting the data you have analyzed or, in the case of qualitative research, the subjects and research setting you have examined,
  • Tools and methods used to identify and collect information, and how you identified relevant variables,
  • The ways in which you processed the data and the procedures you used to analyze that data, and
  • The specific research tools or strategies that you utilized to study the underlying hypothesis and research questions.

In addition, an effectively written methodology section should:

  • Introduce the overall methodological approach for investigating your research problem. Is your study qualitative or quantitative or a combination of both (mixed method)? Are you going to take a special approach, such as action research, or a more neutral stance?
  • Indicate how the approach fits the overall research design. Your methods for gathering data should have a clear connection to your research problem. In other words, make sure that your methods will actually address the problem. One of the most common deficiencies found in research papers is that the proposed methodology is not suitable to achieving the stated objective of your paper.
  • Describe the specific methods of data collection you are going to use, such as, surveys, interviews, questionnaires, observation, archival research. If you are analyzing existing data, such as a data set or archival documents, describe how it was originally created or gathered and by whom. Also be sure to explain how older data is still relevant to investigating the current research problem.
  • Explain how you intend to analyze your results. Will you use statistical analysis? Will you use specific theoretical perspectives to help you analyze a text or explain observed behaviors? Describe how you plan to obtain an accurate assessment of relationships, patterns, trends, distributions, and possible contradictions found in the data.
  • Provide background and a rationale for methodologies that are unfamiliar for your readers. Very often in the social sciences, research problems and the methods for investigating them require more explanation/rationale than widely accepted rules governing the natural and physical sciences. Be clear and concise in your explanation.
  • Provide a justification for subject selection and sampling procedure. For instance, if you propose to conduct interviews, how do you intend to select the sample population? If you are analyzing texts, which texts have you chosen, and why? If you are using statistics, why is this set of data being used? If other data sources exist, explain why the data you chose is most appropriate to addressing the research problem.
  • Describe potential limitations. Are there any practical limitations that could affect your data collection? How will you attempt to control for potential confounding variables and errors? If your methodology may lead to problems you can anticipate, state this openly and show why pursuing this methodology outweighs the risk of these problems cropping up.

NOTEOnce you have written all of the elements of the methods section, subsequent revisions should focus on how to present those elements as clearly and as logically as possibly. The description of how you prepared to study the research problem, how you gathered the data, and the protocol for analyzing the data should be organized chronologically. For clarity, when a large amount of detail must be presented, information should be presented in sub-sections according to topic.

ANOTHER NOTE: If you are conducting a qualitative analysis of a research problem, the methodology section generally requires a more elaborate description of the methods used as well as an explanation of the processes applied to gathering and analyzing of data than is generally required for studies using quantitative methods. Because you are the primary instrument for generating the data, the process for collecting that data has a significantly greater impact on producing the findings. Therefore, qualitative research requires a more detailed description of the methods used.


III.  Problems to Avoid

Irrelevant Detail
The methodology section of your paper should be thorough but to the point. Do not provide any background information that doesn’t directly help the reader to understand why a particular method was chosen, how the data was gathered or obtained, and how it was analyzed.

Unnecessary Explanation of Basic Procedures
Remember that you are not writing a how-to guide about a particular method. You should make the assumption that readers possess a basic understanding of how to investigate the research problem on their own and, therefore, you do not have to go into great detail about specific methodological procedures. The focus should be on how you applied a method, not on the mechanics of doing a method. An exception to this rule is if you select an unconventional methodological approach; if this is the case, be sure to explain why this approach was chosen and how it enhances the overall process of discovery.

Problem Blindness
It is almost a given that you will encounter problems when collecting or generating your data, or, gaps will exist in existing data or archival materials. Do not ignore these problems or pretend they did not occur. Often, documenting how you overcame obstacles can form an interesting part of the methodology. It demonstrates to the reader that you can provide a cogent rationale for the decisions you made to minimize the impact of any problems that arose.

Literature Review
Just as the literature review section of your paper provides an overview of sources you have examined while researching a particular topic, the methodology section should cite any sources that informed your choice and application of a particular method [i.e., the choice of a survey should include any citations to the works you used to help construct the survey].

It’s More than Sources of Information!
A description of a research study's method should not be confused with a description of the sources of information. Such a list of sources is useful in and of itself, especially if it is accompanied by an explanation about the selection and use of the sources. The description of the project's methodology complements a list of sources in that it sets forth the organization and interpretation of information emanating from those sources.


Azevedo, L.F. et al. "How to Write a Scientific Paper: Writing the Methods Section." Revista Portuguesa de Pneumologia 17 (2011): 232-238; Blair Lorrie. “Choosing a Methodology.” In Writing a Graduate Thesis or Dissertation, Teaching Writing Series. (Rotterdam: Sense Publishers 2016), pp. 49-72; Butin, Dan W. The Education Dissertation A Guide for Practitioner Scholars. Thousand Oaks, CA: Corwin, 2010; Carter, Susan. Structuring Your Research Thesis. New York: Palgrave Macmillan, 2012; Kallet, Richard H. “How to Write the Methods Section of a Research Paper.” Respiratory Care 49 (October 2004):1229-1232; Lunenburg, Frederick C. Writing a Successful Thesis or Dissertation: Tips and Strategies for Students in the Social and Behavioral Sciences. Thousand Oaks, CA: Corwin Press, 2008. Methods Section. The Writer’s Handbook. Writing Center. University of Wisconsin, Madison; Rudestam, Kjell Erik and Rae R. Newton. “The Method Chapter: Describing Your Research Plan.” In Surviving Your Dissertation: A Comprehensive Guide to Content and Process. (Thousand Oaks, Sage Publications, 2015), pp. 87-115; What is Interpretive Research. Institute of Public and International Affairs, University of Utah; Writing the Experimental Report: Methods, Results, and Discussion. The Writing Lab and The OWL. Purdue University; Methods and Materials. The Structure, Format, Content, and Style of a Journal-Style Scientific Paper. Department of Biology. Bates College.

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