Writing Research Papers
Writing is easy. All you do is stare at a blank sheet of paper until drops of blood form on your forehead. --- Gene Fowler
A major goal of this course is the development of effective technical writing skills. To help you become an accomplished writer, you will prepare several research papers based upon the studies completed in lab. Our research papers are not typical "lab reports." In a teaching lab a lab report might be nothing more than answers to a set of questions. Such an assignment hardly represents the kind of writing you might be doing in your eventual career.
Written and oral communications skills are probably the most universal qualities sought by graduate and professional schools as well as by employers. You alone are responsible for developing such skills to a high level.
Resources for learning technical writing
Before you begin your first writing assignment, please consult all of the following resources, in order to gain the most benefit from the experience.
- General form of a typical research article
- Specific guidelines (if any) for the assignment – see the writeups on individual lab studies
- McMillan, VE. "Writing Papers in the Biological Sciences, Third Ed." New York: Bedford/St. Martin's, 2001. ISBN 0-312-25857-7 (REQUIRED for Bioc 211, 311, recommended for other science courses that include writing)
- Writing portfolio examples (pdf)
As you polish up your writing skills please make use of the following resources
For Biosciences majors the general guidelines apply to future course work, as can be seen by examining the guidelines for the advanced experimental sciences research paper (Bioc 311).
General form of a research paper
An objective of organizing a research paper is to allow people to read your work selectively. When I research a topic, I may be interested in just the methods, a specific result, the interpretation, or perhaps I just want to see a summary of the paper to determine if it is relevant to my study. To this end, many journals require the following sections, submitted in the order listed, each section to start on a new page. There are variations of course. Some journals call for a combined results and discussion, for example, or include materials and methods after the body of the paper. The well known journal Science does away with separate sections altogether, except for the abstract.
Your papers are to adhere to the form and style required for the Journal of Biological Chemistry, requirements that are shared by many journals in the life sciences.
Specific editorial requirements for submission of a manuscript will always supercede instructions in these general guidelines.
To make a paper readable
- Print or type using a 12 point standard font, such as Times, Geneva, Bookman, Helvetica, etc.
- Text should be double spaced on 8 1/2" x 11" paper with 1 inch margins, single sided
- Number pages consecutively
- Start each new section on a new page
- Adhere to recommended page limits
Mistakes to avoid
- Placing a heading at the bottom of a page with the following text on the next page (insert a page break!)
- Dividing a table or figure - confine each figure/table to a single page
- Submitting a paper with pages out of order
In all sections of your paper
- Use normal prose including articles ("a", "the," etc.)
- Stay focused on the research topic of the paper
- Use paragraphs to separate each important point (except for the abstract)
- Indent the first line of each paragraph
- Present your points in logical order
- Use present tense to report well accepted facts - for example, 'the grass is green'
- Use past tense to describe specific results - for example, 'When weed killer was applied, the grass was brown'
- Avoid informal wording, don't address the reader directly, and don't use jargon, slang terms, or superlatives
- Avoid use of superfluous pictures - include only those figures necessary to presenting results
Select an informative title as illustrated in the examples in your writing portfolio example package. Include the name(s) and address(es) of all authors, and date submitted. "Biology lab #1" would not be an informative title, for example.
AbstractThe summary should be two hundred words or less. See the examples in the writing portfolio package.
An abstract is a concise single paragraph summary of completed work or work in progress. In a minute or less a reader can learn the rationale behind the study, general approach to the problem, pertinent results, and important conclusions or new questions.
Writing an abstract
Write your summary after the rest of the paper is completed. After all, how can you summarize something that is not yet written? Economy of words is important throughout any paper, but especially in an abstract. However, use complete sentences and do not sacrifice readability for brevity. You can keep it concise by wording sentences so that they serve more than one purpose. For example, "In order to learn the role of protein synthesis in early development of the sea urchin, newly fertilized embryos were pulse-labeled with tritiated leucine, to provide a time course of changes in synthetic rate, as measured by total counts per minute (cpm)." This sentence provides the overall question, methods, and type of analysis, all in one sentence. The writer can now go directly to summarizing the results.
Summarize the study, including the following elements in any abstract. Try 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 shoud be reported
- Important conclusions or questions that follow from the experiment(s)
- 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
- Corrrect 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
IntroductionYour introductions should not exceed two pages (double spaced, typed). See the examples in the writing portfolio package.
The purpose of an introduction is to aquaint the reader with the rationale behind the work, with the intention of defending it. It places your work in a theoretical context, and enables the reader to understand and appreciate your objectives.
Writing an introduction
The abstract is the only text in a research paper to be written without using paragraphs in order to separate major points. Approaches vary widely, however for our studies the following approach can produce an effective introduction.
- 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 briefy describe the experimental design and how it accomplished the stated objectives.
- 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.
Materials and MethodsThere 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.
This should be the easiest section to write, but many students misunderstand the purpose. The objective 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 your work. It is not to be a step by step description of everything you did, nor is a methods section a set of instructions. In particular, it is not supposed to tell a story. By the way, your notebook should contain all of the information that you need for this section.
Writing a materials and methods section
- 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 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 it and the source should be singled out, otherwise no.
- 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.
- See the examples in the writing portfolio package
- Report the methodology (not details of each procedure that employed the same methodology)
- Describe the mehodology completely, including such specifics as 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, and that's all. For example, the Bradford assay is well known. You 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.
- 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.
ResultsThe page length of this section is set by the amount and types of data to be reported. Continue to be concise, using figures and tables, if appropriate, to present results most effectively. See recommendations for content, below.
The purpose of a results section is to present and illustrate your findings. Make this section a completely objective report of the results, and save all interpretation for the discussion.
Writing a results section
IMPORTANT: You must 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.
- Summarize your findings in text and illustrate them, if appropriate, with figures and tables.
- In text, describe each of your 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 your 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.
- 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
DiscussionJournal guidelines vary. Space is so valuable in the Journal of Biological Chemistry, that authors are asked to restrict discussions to four pages or less, double spaced, typed. That works out to one printed page. While you are learning to write effectively, the limit will be extended to five typed pages. If you 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 your data in the discussion in appropriate depth. This means that when you explain a phenomenon you must describe mechanisms that may account for the observation. If your results differ from your expectations, explain why that may have happened. If your 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.
- 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.
- When you refer to information, 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 (including yourself) 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."
The biggest mistake that students make in discussions is 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.
Please note that in the introductory laboratory course, you will not be required to properly document sources of all of your information. One reason is that your major source of information is this website, and websites are inappropriate as primary sources. Second, it is problematic to provide a hundred students with equal access to potential reference materials. You may nevertheless find outside sources, and you should cite any articles that the instructor provides or that you find for yourself.
List all literature cited in your 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). Some of your papers may not require references, and if that is the case simply state that "no references were consulted."
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The section headings (Abstract, Introduction, etc.) should be centered and the body of each section should follow immediately below the heading. Do not begin each section on a new page. If one section ends part of the way down the page, the next section heading follows immediately on the same page.
One important general rule to keep in mind is that a scientific paper is a report about something that has been done in the past. Most of the paper should be written in the PAST TENSE (was, were). The present tense (is, are) is used when stating generalizations or conclusions. The present tense is most often used in the Introduction, Discussion and Conclusion sections of papers. The paper should read as a narrative in which the author describes what was done and what results were obtained from that work.
Every scientific paper must have a self-explanatory title. By reading the title, the work being reported should be clear to the reader without having to read the paper itself. The title, "A Biology Lab Report", tells the reader nothing. An example of a good, self-explanatory title would be: "The Effects of Light and Temperature on the Growth of Populations of the Bacterium, Escherichia coli ". This title reports exactly what the researcher has done by stating three things:
If the title had been only "Effects of Light and Temperature on Escherichia coli ", the reader would have to guess which parameters were measured. (That is, were the effects on reproduction, survival, dry weight or something else?) If the title had been "Effect of Environmental Factors on Growth of Escherichia coli ", the reader would not know which environmental factors were manipulated. If the title had been "Effects of Light and Temperature on the Growth of an Organism", then the reader would not know which organism was studied. In any of the above cases, the reader would be forced to read more of the paper to understand what the researcher had done.
Exceptions do occur: If several factors were manipulated, all of them do not have to be listed. Instead, "Effects of Several Environmental Factors on Growth of Populations ofEscherichia coli " (if more than two or three factors were manipulated) would be appropriate. The same applies if more than two or three organisms were studied. For example, "Effects of Light and Temperature on the Growth of Four Species of Bacteria" would be correct. The researcher would then include the names of the bacteria in the Materials and Methods section of the paper.
The abstract section in a scientific paper is a concise digest of the content of the paper. An abstract is more than a summary. A summary is a brief restatement of preceding text that is intended to orient a reader who has studied the preceding text. An abstract is intended to be self-explanatory without reference to the paper, but is not a substitute for the paper.
The abstract should present, in about 250 words, the purpose of the paper, general materials and methods (including, if any, the scientific and common names of organisms), summarized results, and the major conclusions. Do not include any information that is not contained in the body of the paper. Exclude detailed descriptions of organisms, materials and methods. Tables or figures, references to tables or figures, or references to literature cited usually are not included in this section. The abstract is usually written last. An easy way to write the abstract is to extract the most important points from each section of the paper and then use those points to construct a brief description of your study.
The Introduction is the statement of the problem that you investigated. It should give readers enough information to appreciate your specific objectives within a larger theoretical framework. After placing your work in a broader context, you should state the specific question(s) to be answered. This section may also include background information about the problem such as a summary of any research that has been done on the problem in the past and how the present experiment will help to clarify or expand the knowledge in this general area. All background information gathered from other sources must, of course, be appropriately cited. (Proper citation of references will be described later.)
A helpful strategy in this section is to go from the general, theoretical framework to your specific question. However, do not make the Introduction too broad. Remember that you are writing for classmates who have knowledge similar to yours. Present only the most relevant ideas and get quickly to the point of the paper. For examples, see the Appendix.
MATERIALS AND METHODS
This section explains how and, where relevant, when the experiment was done. The researcher describes the experimental design, the apparatus, methods of gathering data and type of control. If any work was done in a natural habitat, the worker describes the study area, states its location and explains when the work was done. If specimens were collected for study, where and when that material was collected are stated. The general rule to remember is that the Materials and Methods section should be detailed and clear enough so that any reader knowledgeable in basic scientific techniques could duplicate the study if she/he wished to do so. For examples, see the Appendix.
DO NOT write this section as though it were directions in a laboratory exercise book. Instead of writing:
Simply describe how the experiment was done:
Also, DO NOT LIST the equipment used in the experiment. The materials that were used in the research are simply mentioned in the narrative as the experimental procedure is described in detail. If well-known methods were used without changes, simply name the methods (e.g., standard microscopic techniques; standard spectrophotometric techniques). If modified standard techniques were used, describe the changes.
Here the researcher presents summarized data for inspection using narrative text and, where appropriate, tables and figures to display summarized data. Only the results are presented. No interpretation of the data or conclusions about what the data might mean are given in this section. Data assembled in tables and/or figures should supplement the text and present the data in an easily understandable form. Do not present raw data! If tables and/or figures are used, they must be accompanied by narrative text. Do not repeat extensively in the text the data you have presented in tables and figures. But, do not restrict yourself to passing comments either. (For example, only stating that "Results are shown in Table 1." is not appropriate.) The text describes the data presented in the tables and figures and calls attention to the important data that the researcher will discuss in the Discussion section and will use to support Conclusions. (Rules to follow when constructing and presenting figures and tables are presented in a later section of this guide.)
Here, the researcher interprets the data in terms of any patterns that were observed, any relationships among experimental variables that are important and any correlations between variables that are discernible. The author should include any explanations of how the results differed from those hypothesized, or how the results were either different from or similar to those of any related experiments performed by other researchers. Remember that experiments do not always need to show major differences or trends to be important. "Negative" results also need to be explained and may represent something important--perhaps a new or changed focus for your research.
A useful strategy in discussing your experiment is to relate your specific results back to the broad theoretical context presented in the Introduction. Since your Introduction went from the general to a specific question, going from the specific back to the general will help to tie your ideas and arguments together.
This section simply states what the researcher thinks the data mean, and, as such, should relate directly back to the problem/question stated in the introduction. This section should not offer any reasons for those particular conclusions--these should have been presented in the Discussion section. By looking at only the Introduction and Conclusions sections, a reader should have a good idea of what the researcher has investigated and discovered even though the specific details of how the work was done would not be known.
In this section you should give credit to people who have helped you with the research or with writing the paper. If your work has been supported by a grant, you would also give credit for that in this section.
This section lists, in alphabetical order by author, all published information that was referred to anywhere in the text of the paper. It provides the readers with the information needed should they want to refer to the original literature on the general problem. Note that the Literature Cited section includes only those references that were actually mentioned (cited) in the paper. Any other information that the researcher may have read about the problem but did not mention in the paper is not included in this section. This is why the section is called "Literature Cited" instead of "References" or "Bibliography".
The system of citing reference material in scientific journals varies with the particular journal. The method that you will follow is the "author-date" system. Listed below are several examples of how citations should be presented in the text of your paper. The name(s) of the author(s) and year of publication are included in the body of the text. Sentence structure determines the placement of the parentheses.