Scholarly Research

Creating a working bibliography

The first step is to create a working bibliography or a list of sources that appear to be relevant at the initial stage of your research.  Talk to your supervisor, or the library staff, about help with techniques for locating sources.

Critically evaluating sources

As you begin to extract information from your sources, critically evaluate each for relevance, validity and accuracy. Be discriminating; if the source is not worthy of your paper then leave it out.  Think about the nature of the source; the objectivity, qualifications of the author, and level.  Ask yourself whether the source is primary or secondary.  Primary sources are basic materials with little or no annotation or editorial alteration, such as manuscripts, dairies, letters, interviews and laboratory reports.  Secondary sources derive from primary materials and include analysis and/or interpretation.  Objectivity refers to a lack of bias or prejudice but keep in mind that most sources have some sort of bias or point of view. The level of the source refers to the intended audience, so look at the sentence structure, the complexity of ideas and implied background.  

Collecting information

The essence of scholarly research is extracting from voluminous and scattered sources the facts that are relevant to your topic, and equally important, recording and arranging the facts so that they are readily usable for analysis and composition.  Find a note taking procedure that is accurate, efficient and personally comfortable.  Most style guides recommend using note cards.  It is worth your time to page through a couple of these style guides before you begin research.  You can then adopt one their systems or synthesize your own.  Remember, this small amount of work now will save you endless hours chasing after lost sources later on.  You want two things in your notes: the data and interpretation of the data. Do not forget to include all bibliographic information as you go.  Your notes may be brief as long as they are clear; remember that what seems clear when you make a note may be ambiguous several weeks later when you are writing.  The data in the source should be summarized, unless you think you may want to quote a certain passage verbatim in your essay, or unless a statement is so important that you know you will need the exact wording.  It is important to note that in scientific writing, one hardly ever quotes a source verbatim.  It is only done if the style, essence or content is particularly remarkable or innovative and cannot be paraphrased without losing effect. Do not waste time making extensive notes on a well-indexed source that will be at your elbow when you write your essay.


Outlining the paper

Start with your thesis statement or the controlling idea.  This is the answer to the question that started the research.  All ideas within the paper must be relevant to this controlling idea.  Your thesis may change during research or even during writing, so be flexible.  You may decide to widen your thesis further, or conversely, concentrate on a particular part. Talk to your advisor about the scope of the conclusions that you are expected to draw.  Your final thesis statement should cover all points.  Avoid disconcerting the reader by straying into an area of inquiry not suggested by the thesis statement.  The outline is a good place to cover your bases in this regard.  The outline puts all your ideas in one place. It should be easy to see how all the points logically apply to the thesis statement.

Writing a draft.

Most importantly, be willing to re-write. It is most likely that more than one draft will be required.  It is often hard to get the actual writing underway, especially since you may not see just how the essay is going to develop. The best solution is to just start writing, without worrying too much in your first draft about style or length.  Just get your facts and ideas down, in a logical order as indicated by your outline, and often problems will smooth themselves out. If you are having trouble with the introduction, just skip it and move on the rest of your paper. In fact, it is often easier to write the introduction after the rest of the writing is done; you know what needs to be introduced and in what order.  If the essay in its entirety overwhelms you, then try splitting it up into sections and concentrate on those one at a time. Just remember to work on integrating them into a balanced whole when you are done.  You are expected to use proper grammar and to spell correctly, but above all, strive for clarity, vigor and objectivity.  Show that you know what you are writing about. If you are confused, then your writing will sound confused, so think your points through carefully before, during, and after you make them a part of your composition. You are also writing for the average, well-informed reader, so try and define any scientific terms that may be ambiguous or particularly specialized.  Whenever possible, use direct rather then indirect statements, the active rather than the passive voice, and make every sentence or paragraph an organic whole. Do not indulge in excessive verbiage; scientific concepts are best expressed by simple and succinct words and sentences. Make your narrative move.  The emphasis, in this project, is on ideas, so strive for elegance in your logic before you do so in your prose. Finally, remain objective. Scientific convention demands that you stick to the data and your interpretation of the data. Religious doctrine can be incorporated as long as it is forms a logical part of your interpretation of the data. 

Incorporating religious aspects

Avoid tacking on a religious section at the end of your essay.  It will only look unnatural and forced.  Talk to your advisor about the applicability of doctrine to your subject and how it can be incorporated in your paper.

The anatomy of a research paper

The paper should include in order (acknowledgements can go before TOC or at end, and appendices are optional):

  • Title Page
  • Abstract
  • Acknowledgements
  • Table of Contents
  • Separate lists of Tables and Figures

·      Introduction (Can incorporate info from literature review)

  • Results/Methods (Separate methods section only required for original laboratory research)
  • Discussion
  • Conclusions
  • References
  • Tables, in chronological order (numbered and explained above each table 1, 2, 3, etc.)
  • Figures, in chronological order (numbered and explained below each figure 1, 2, 3, etc.)
  • Appendices

The title page should include:

  1. The title of the paper
  2. Key words
  3. The student’s name
  4. The course
  5. The instructor/advisor/readers names
  6. The date

The abstract

The abstract is a brief descriptive summary.  It should include a statement of the problem or issue, a brief description of the research method and design, major findings and their significance, and your conclusions.  A reader should be able to decide, from the abstract, whether to read the entire paper.  The abstract is not part of the paper, so it is not numbered or counted as a page.

The table of contents

The table of contents precedes all sections it lists.  It should list all elements of the preliminaries, the chapter titles, the main headings and sub-headings in the text, and the reference materials.  The beginning page of each section is indicated along the right-hand margin.

The list of tables and figures (must include at least 2 tables/figures)

A list of tables and figures should follow the table of contents. Each type of illustrative matter should be shown on a separate page that follows the references (List of tables on one page, list of figures on another). Charts, maps, graphs and illustrations are usually grouped as figures but may be grouped or designated by their more descriptive names. All captions should appear in the listing exactly as they are in the text.

The Body of the Paper (the length of the rough draft needs to be 3500 words, excluding literature cited, and the length of the final draft 4000-5000 words~15-20 pages excluding literature cited)

There are generally six or seven sections:

  1. Introduction
  2. Results/Methods (simple presentation of data)
  3. Discussion (includes analysis of the data)
  4. Summary and conclusions
  5. Literature Cited (Reference section) includes all references that are cited in the text.
  6. Tables and Figures (one per page)

The Introduction (can be guided by the lit review)

This section provides the reader with three things:

  1. An introduction to the subject area, the importance and validity of the research, the potential contributions of the research and background information. 
  2. A clear and concise statement of the problem/question, with an appropriate analysis of its delimitation or scope.
  3. A treatment of the theoretical framework within which the investigation was conducted. (e.g., basic assumptions, definitions of terms etc.)

Methods and design of the investigation (for original research only-otherwise, methods are summarized in results section)

In this section you should discuss:

  1. Your method of research
  2. The nature of your sample and control groups, if any
  3. The data required to test/answer your hypothesis
  4. Your sources of data
  5. The procedures followed in gathering and analyzing the data

Results (and Methods if not your own original research)

This section should include, primarily, the results of the investigation (usually without interpretation/evaluation).  You may accompany the data with charts and tables, as supplements, if you choose.  Methods used for each study can be summarized and included with results.

Discussion and analysis of data

In this section, you should discuss:

  1. Your evaluation/interpretation of the data
  2. Implications of the findings for revising the existing body of knowledge
  3. Possible contributions to research methodology
  4. Relation of your results with previously published studies
  5. Limitations of the study
  6. Unexpected results and their ramifications
  7. Practical application of the findings
  8. Speculations about further studies.

Summary and conclusions

The summary/conclusions are generally a short paragraph or two summarizing the findings of the paper. Be sure to re-state the hypothesis and indicate how it was (or wasn’t) supported.

Literature Cited (Reference section)

See the CSE citation format handout!

The reference section of the paper must list all references cited within the text. The convention for most scientific papers is that within the text (and in figure and table legends) the reference will include the first (two) author’s last names and date of publication. If there are more than two authors, “et al.” will be added to the first author’s last name. For example, a line of text derived from a paper by Smith and Jones will be followed by (Smith and Jones, 1999). In the reference section of the paper, the references will be listed by author’s last name first in alphabetical order, followed by other authors (all must be listed in the reference section), followed by the date of the publication, the title of the article or book, then the journal (with volume and page numbers) or publisher (and number of pages). Journal titles can be abbreviated. For the same author, references are listed in order of publication (oldest to most recent). For references with multiple authors but the same first author, they will be listed according to second author’s last name (alphabetically), etc. Web references should be listed in primarily the same way: with an author’s last name first, date of article or update of site second, title of article or page, then the website address. If an author and date are not available on the website, it is probably not a reliable source for information for this type of paper.


The acknowledgments is an optional section. It includes simple and tactful expressions of appreciation for assistance and guidance.

General conventions

Page numbering

Page numbering should be in Arabic numerals, starting with the text, or the body of the paper.  All pages are numbered, including chapter and section title pages.  Position all page numbers one inch from the bottom of the page, in the center, or flush with the right margin. Use lowercase roman numerals for the front matter, placed once inch from the bottom of the page, centered.

Chapter Titles and Headings

The way that a thesis is divided is determined by its length and complexity.  Longer papers definitely benefit from division. However, remember that it should be used to clarify organization, not to substitute for the lack of it.  Titles should indicate clearly and concisely the contents of a section or chapter and its relationship to the whole.  Headings fall into five generally accepted levels.


Centered Uppercase and Lowercase

Centered, Underlined Uppercase and Lowercase

Flush left, Underlined Uppercase and Lowercase

     Indented five spaces, underlined or italics lowercase ending with a period. The paragraph begins are the end of the heading.

If you intend to follow your own hierarchy, be consistent.  See a style guide for more information.


The purpose of the appendix is to prevent the text from becoming unduly bulky and should be used for materials that supplement the text but are not appropriate for inclusion in it.  The appendix may include: original data, summary tabulations, tables containing data of lesser importance (as distinguished from those presenting major data in the text), computer printouts, pertinent documents not available to the reader, questionnaires and verbatim comments of respondents. List each appendix by letter and title in the table of contents. e.g., Appendix A…title.


Depending on the level of your research, a glossary may be a good idea to help the reader become familiar with the appropriate terminology. A glossary is simply a list of terms and abbreviations with definitions.


The data that you collect constitutes the evidence on which your inferences and conclusions are based.  Large quantities of statistic and numerical data should be tabulated in the interest of both brevity and clarity. Simple mention of data can be presented informally in the text, as can any statistics that fit smoothly. The object of tabulation (tables) is to keep numerical data from interfering with the development of the argument. Tables are referred to in the text and should only contain quantified information and summaries; complete and original data belong in the appendix. A table should have a unified and clearly stated purpose, and not show too many kinds of data or relationships at once. Do not just place your tables in the paper and expect the reader to appreciate their significance. Remember to introduce and discuss them in the text and explain how the data supports your thesis. Tables should be organized logically and explained fully with a caption. But remember, the text should be so complete that the reader can follow the argument without referring to the tables.


Tables should be numbered with Arabic (not Roman) numerals, numbered consecutively throughout the paper, including the appendices. In other words, the first table referenced in the text should be Table 1, etc. Consult a style guide for a complete treatment of the conventions regarding the set-up of tables.

Footnotes for tables

Each table should have a self-explanatory legend and can have independent, self-contained series of footnotes. References specific to tables or figures should be included in the legend or footnotes (as well as the reference section of the paper).


The term figure usually refers to any kind of graphic representation or illustration, whether in the text or an appendix. Pages containing only photographs may be designated as either plates or figures.  Every figure must have a self-explanatory legend. Remember to include any appropriate reference to each figure in the text, detailing how it contributes to your argument.

Placement for tables and figures

Place tables and figures each on one page if possible and leave the usual margins. These should be included at the end of the paper (following the reference section) in chronological order: tables first followed by figures.

Style and Mechanics

Style: Your choices regarding sentence structure, diction and tone create the style of your writing.  The audience for the research paper is usually the academic community, so your writing should be formal in tone.

Diction (word choice): Your choices of words should be formal rather than colloquial.  Contractions and abbreviations should be avoided and, in most cases, numbers should be spelled out (especially one through ten).

Tone: Your tone conveys your attitude toward your subject.  In a scientific paper, your tone should be serious, not ironic or flippant.  Humorous, casual and conversational approaches are usually inappropriate for research papers.  The purpose of a research paper is to promote understanding and you do not want to be misinterpreted.

Personal Pronouns: Most research papers should be written in the third person – that is, with nouns or third-person pronouns (he, she, they or it) as subjects of the sentences.  Using first-person pronouns (I, we) weakens your statements by calling attention to the fact that they are opinion.  By virtue of the fact that it is your paper, the reader already assumes that it is your point of view.  Science is not usually interested in personal experiences, even such as relating to a process of research, and thus, first-person pronouns are rarely appropriate.  The same goes for second-person pronouns (you, your). Again, the reader will assume that you are addressing him/her.  Commands that imply the second-person (i.e. “Observe that…”) should also be avoided.

Tense: Use the past tense to describe the results of a particular experiment (the experiment should be completed), or to present others results.  Use the present tense for generalizations and conclusions.

Sentence Structure

  1. In general, use the active rather than the passive voice, although this is sometimes difficult when writing in the third person. (ex. active=The dog bit the man. vs. passive=The man was bitten by the dog.)
  2. Avoid expletive constructions (i.e. “there are…” or “there is…”).  It will result in weak sentences.
  3. Use the same grammatical form for all headings and titles.
  4. Make sure that you have a logical consistency between headings of the same level or equivalent importance.
  5. Present ideas in a logical and consistent sequence.  Use transitional expressions to help the reader see relationships among sentences and paragraphs.
  6. Use unbiased language.  Use plural pronouns instead of the singular masculine pronouns and use gender-neutral designations.


  1. References should be in CSE format. Author first, date of publication, title of article or book, (book and journal titles tend to be italicized), journal title and volume number or publisher, pages.  References within the text should be by author and date (e.g. Cooper 1993). You can add a page number after a comma. Most scientific articles or books can be used as examples.
  2. Make all margins 1.5 inches on the left and 1 inch of the right, top and bottom.  The right-hand margins should not be justified.
  3. Indent the first line of each paragraph 5 spaces.  Bring all subsequent lines to the left margin.
  4. When division of a word is necessary, the break should come between syllables, as a standard dictionary will indicate.  One-letter or two-letter divisions are not acceptable.  See a style guide for more information.

The finished copy

Before you begin on the finished copy, you should have an accurate, thoroughly polished final draft. Use good quality paper, 8.5 x 11 inches.  Keep the original. After grading and approval, a copy may be submitted to the college library.

Literature Cited –example section

1.         Abdel-Ghany M, Cheng H-C, Elble RC, Lin H, DiBiasio J, Pauli BU. The interacting binding domains of the beta (4) integrin and calcium-activated chloride channels (CLCAs) in metastasis. J Biol Chem 278: 49406–49416, 2003.

2.         Abdel-Ghany M, Cheng HC, Elble RC, Pauli BU. The breast cancer beta 4 integrin and endothelial human CLCA2 mediate lung metastasis. J Biol Chem 276: 25438–25446, 2001.

3.         Abdel-Ghany M, Cheng H-C, Elble RC, Pauli BU. Focal adhesion kinase activated by beta (4) integrin ligation to mCLCA1 mediates early metastatic growth. J Biol Chem 277: 34391–34400, 2002.

4.         Alevy YG, Patel AC, Romero AG, Patel DA, Tucker J, Roswit WT, Miller CA, Heier RF, Byers DE, Brett TJ, Holtzman MJ. IL-13-induced airway mucus production is attenuated by MAPK13 inhibition. J Clin Invest 122: 4555–4568, 2012.

5.         Al-Jumaily M, Kozlenkov A, Mechaly I, Fichard A, Matha V, Scamps F, Valmier J, Carroll P. Expression of three distinct families of calcium-activated chloride channel genes in the mouse dorsal root ganglion. Neurosci Bull 23: 293–299, 2007.

6.         Bothe MK, Braun J, Mundhenk L, Gruber AD. Murine mCLCA6 is an integral apical membrane protein of non-goblet cell enterocytes and co-localizes with the cystic fibrosis transmembrane conductance regulator. J Histochem Cytochem Off J Histochem Soc 56: 495–509, 2008.

7.         Bothe MK, Mundhenk L, Kaup M, Weise C, Gruber AD. The murine goblet cell protein mCLCA3 is a zinc-dependent metalloprotease with autoproteolytic activity. Mol Cells 32: 535–541, 2011.

8.         Brouillard F, Bensalem N, Hinzpeter A, Tondelier D, Trudel S, Gruber AD, Ollero M, Edelman A. Blue native/SDS-PAGE analysis reveals reduced expression of the mClCA3 protein in cystic fibrosis knock-out mice. Mol Cell Proteomics MCP 4: 1762–1775, 2005.

9.         Ching JCH, Lobanova L, Loewen ME. Secreted hCLCA1 is a signaling molecule that activates airway macrophages. PloS One 8: e83130, 2013.

10.       Connon CJ, Yamasaki K, Kawasaki S, Quantock AJ, Koizumi N, Kinoshita S. Calcium-activated chloride channel-2 in human epithelia. J Histochem Cytochem Off J Histochem Soc 52: 415–418, 2004.

11.       Davson H. The hydration of the cornea. Biochem J 59: 24–28, 1955.

12.       Elble RC, Walia V, Cheng H-C, Connon CJ, Mundhenk L, Gruber AD, Pauli BU. The putative chloride channel hCLCA2 has a single C-terminal transmembrane segment. J Biol Chem 281: 29448–29454, 2006.

13.       Evans SR, Thoreson WB, Beck CL. Molecular and functional analyses of two new calcium-activated chloride channel family members from mouse eye and intestine. J Biol Chem 279: 41792–41800, 2004.

14.       Gandhi R, Elble RC, Gruber AD, Schreur KD, Ji HL, Fuller CM, Pauli BU. Molecular and functional characterization of a calcium-sensitive chloride channel from mouse lung. J Biol Chem 273: 32096–32101, 1998.

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