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. Note that research papers are not typical "lab reports." The latter tend to be informal internal reports, or in a teaching lab, answers to a set of questions.

Guidelines for writing papers

Before preparing your first paper on the flagellar regeneration study, please consult all of the following resources, in order to gain the most benefit from the experience.

• General report form
• Examples of technical writing
• Sample journal article
• Specific guidelines to the flagellar regeneration paper
• McMillan, VE. "Writing Papers in the Biological Sciences, Third Ed." New York: Bedford/St. Martin's, 2001. ISBN 0-312-25857-7 (REQUIRED for Bios 211, 311, recommended for other science courses that include writing).

Reference materials to help you polish up your writing include the following.

• Common errors in student research papers
• Grading criteria for research papers
• Selected writing rules

Make the most of instructor feedback to help you critique your own work.

Use the McMillan reference - these web pages cannot cover the specifics of good writing in as much detail as can an entire book. You alone are responsible for the effectiveness of your writing. If you notice any inconsistencies between the reference and these guidelines, please call them to my attention.

The same policies reported on this page apply to future courses, as can be seen by examining the guidelines for the protein purification lab paper (Bios 311). Instructions for authors from the Journal of Biological Chemistry editorial board may be helpful as well. Their statement of editorial policies and practices may give you an idea of how material makes its way into the scientific literature.

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.

• Title page
• Abstract
• Introduction
• Materials and Methods
• Results
• Discussion
• Literature Cited
• Figures and tables

General style

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

• Stay focused on the research topic of the paper
• Use paragraphs to separate each important point (except for the abstract)
• 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, addressing the reader directly, and jargon or slang terms
• Avoid use of superfluous pictures - include only those figures necessary to presenting results

Title Page

Select an informative title as illustrated in the examples. Include the name(s) and address(es) of all authors, and date submitted.

Abstract

General intent

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 - preferably quantitative if that is the form taken by the data; results of any statistical analysis shoud be reported
• Important conclusions or questions that follow from the experiment(s)

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
• 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

Introduction

General intent

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. Here is the minimum information that should be included in a successful 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 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 will accomplish the stated objectives.

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 appropriatness of sentences and phrases.
  

Materials and Methods

General intent

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 could use the information to plan his/her study, or determine whether or not your methods were appropriate. It is not to be a step by step description of everything you did, nor is this a set of instructions. By the way, your notebook should contain all of the information that you need for this section

Writing a materials and methods section

Materials:

• 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
• 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
  

Results

General intent

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.

Content

• 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.
• 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.
• Please do not confuse figures with tables - there is a difference.

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
• Regardless of placement, each table must be numbered consecutively and complete with heading
• Each figure and table must be sufficiently complete that it could stand on its own, separate from text

Discussion

General intent

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.

Writing a discussion

Interpret your data in the discussion in appropriate depth. This means that when you explain a phenomenon you must explain mechanisms. 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."
• Make what conclusions you can, then suggest how the experiment might be modified, if necessary, in order to properly test the hypothesis(es) or accomplish the objective(s).
• 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?
• Be creative, and don't be afraid to speculate. Individual report guidelines will provide suggestions.

Style:

• 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 doing that).
• 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.

Literature Cited

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 report, in alphabetical order, by first author. In a proper research paper, only primary literature is used (original research articles authored by the original investigators). Never include a web site as a reference - anyone can put just about anything on a web site, and you have no 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 reports may not require references, and if that is the case simply state that "no references were consulted."