Writing the Scientific Article


Brilliance has an obligation not only to create but also to communicate.
J.R. Platt

The trouble with most of us is that we would rather be
ruined by praise than saved by criticism.
Norman Vincent Peale

Writing the Scientific Article

Review the Honor Code Guidelines for BIOS 311.

  • A single lab paper in the style of a journal article submitted for publication is due TWO WEEKS after the last day of laboratory class. Drafts of each stage of the paper will be evaluated during the course and must be turned in with the final paper.
    • Do not worry about “perfection” with your FIRST ROUGH DRAFTS; you need something to work with, and that is why it’s called a “rough draft.”
    • The only way to have something to revise is to write something down in the first place.
    • The two main reasons I require you to write drafts of each section are
      1) making you write something each week prevents your waiting until the night before the final paper is due to start writing
      2) turning in a draft each week lets me give you feedback on each section and allows you time to revise your work for the final paper
  • NOTE: Submit all work in its final form (i.e., NOT handwritten, on a computer disk, as an attachment, or in an e-mail message).

  • For your own protection, I will make a copy of your final paper to keep on file. When you submit your final paper, please put your work loosely in a folder with pockets (not the kind with 3-rings); do NOT use staples or paper clips.

  • Please review my grading criteria and checklist for the final paper.

The scientific paper is traditionally divided into four sections: introduction, materials and methods, results, and discussion. These sections are typically completed through an iterative process because no single section can be written without consideration of another. The introduction is compiled from reference material and reflects the thought processes or lines of reason that lead you to perform experiments in the laboratory. The remainder of the paper is constructed concurrently as the experiment is constructed and planned. In the final draft the organization of the materials and methods section is coordinated with the results section. The results section presents pertinent data in nearly chronological order and directs the reader along the same mental paths through the data that you took in solving the problem. The discussion section provides interpretation of the data and projections as to the meaning of the results. The use of good references throughout the paper gives the work credibility by demonstrating an awareness of previous works.

Writing a scientific article is not an easy task no matter how simple the actual experiment or concept. Practice, good planning, and organized record keeping are the only means to simplify the process.

Introduction

The Introduction should “introduce” the paper. The reader should be presented with enough background information to be able to understand and evaluate the purpose of your study without having to refer to other works. The rationale for the study should be presented. Provide salient references but avoid trying to make an exhaustive review of the topic.

In the introduction, define the problem clearly. If the problem is not stated in a reasonable, understandable way, the reader will have no interest in your solution. Follow with some review of the literature to allow the reader to understand why the study is necessary and how you attempted to resolve it. Talk in general terms about techniques used to solve the problem, if necessary, but do not present any specifics about the protocols here. The final portion should be the statement of the principal results.

  • Present the nature and the scope of the problem investigated.
  • Provide enough background to orient the reader and justify the study.
  • State the goal/objectives and method of the investigation.
  • Briefly state the principal results of the investigation.

Experimental Procedures (Materials and Methods)

This section should be the easiest to write if you have good notebook skills. A well written Experimental Procedures section allows a competent scientist to duplicate your results. Present specific information about your materials. The suppliers and purity of reagents can be useful bits of information. Present methods in chronological order but related methodologies can be grouped as a section. Be succinct when describing the protocols. Strive for the minimum of information that would allow another competent scientist to duplicate your results but be careful that essential information is included. The use of subheadings is recommended and should be coordinated with the results section. When a method is used that has been well described in another article, reference the specific article describing a method but outline the basic premise while stating the reference.

  • Ask yourself this question: Could someone else follow my words in this section and perform the same experiment with the same results?

Results

  • Open the Results section by presenting the “big picture” or overview of the experiments.
    Focus on the theoretical question at hand and do not repeat the experimental details described in the Experimental Procedures. Orient and prepare the reader for the data that follows.
  • The data must direct the reader toward the solution to the problem.
    Organize the data in logical steps that describe the trail of investigation you followed in order to reach your conclusions. If your logic is sound, the reader will easily understand why you performed certain measurements and will be interested in the actual data obtained.
  • Data is presented in text, tables or graphs depending on the material and the emphasis that you desire.
    Look at published examples of graph and table presentation and mimic that style. Each figure or graph must be able to “stand alone” with its figure legend. A descriptive title includes why the figure is important (NOT merely “SDS Gel”). Present information in the figure and legend as if this were all the reader would see for this point.Discriminate what data you present by using only the data relevant to the conclusions drawn from the study. (The preceding statement is made to keep the study focused NOT to intentionally disregard conflicting data. Please maintain high ethical standards in your scientific endeavors.) Present only representative data not endless repetitions of the same data. Keep the presentations concise and make the reading of your data as pleasant as possible. Interest fades quickly if the reader has to work hard to figure out what is being presented or why.
  • Choosing a method for clear presentation of your data depends on the type of information.
    If one or only a few determinations or differences are presented it is best to use only text. Repetitive measurements may be presented in tables or graphs. Always consider describing the results in text and ifthe text version is too complex or cumbersome then a table or graph may be warranted. Avoid redundancy when stating summary of data in text that is presented in tabular form.

    Be certain that any numbers that you present are statistically valid. Specifically, pay close attention to significant figures.

  • Clarity in the Results is paramount.
    This is the new information that you are presenting to the scientific community. All the other components of the paper are judged by the Results. The Introduction and the Materials and Methods section tell why and how you got the results and the Discussion tells what the results mean.

Discussion

The Discussion is likely the most difficult section to write and define. Many papers submitted for publication are rejected based on problems with the Discussion. There is no ruler for how long a discussion should be. State your interpretation of the results clearly to lead the reader through your conclusions, then end the paper with a summary of the significance of the study.

  • Do NOT simply restate the Results.
  • Compare your results and conclusions with published materials. Clearly contrast and compare your interpretations with previous studies and findings.
  • Discuss the theoretical implications of your work and practical applications that you foresee. Be careful to keep your theoretical projections in proportion to the scope of your experiment.
    Leave most of the speculation to the readers.
  • Present the interpretation of your findings as clearly as possible. Present a summary of evidence for each major finding.
  • Make succinct concluding statements at the end of the discussion.
    These conclusions may be what people remember most about your study.

Special note for the writing assignment for Bios 311: Be aware of flaws or weaknesses in your data but do not belabor them with infinite analysis. Exceptions and inconsistency in your data should be mentioned and unsettled points described briefly.
If the data are substantially flawed you will not include them in the paper.
Remember that this writing assignment is to emulate a paper for publication which is significantly different from a laboratory report.
While you are compiling your introduction information, judge the papers for style and try to emulate these professional papers.

Summary (Abstract)

The Summary/Abstract is a concise, complete report of a scientific investigation that “stands alone” without further explanation. The summary/abstract is typically ONE paragraph with 200 to 250 words. Lengthy discussions and references to the literature are omitted from the summary/abstract.

    The summary/abstract must include

  • basic justification for conducting the study
  • research objectives
  • basic methods used
  • specific results
  • major conclusions

References

  • Davis, M. (1997) Scientific Papers and Presentations, Academic Press, San Diego, CA
  • Day, R.A. (1994) How to Write and Publish a Scientific Paper, Fourth Edition, Oryx Press, Phoenix, AZ
  • McMillan, V.E. (2001) Writing Papers in the Biological Sciences, Third Edition, Bedford/St. Martin’s, Boston, MA

  • Review the reading assignments in McMillan, 3rd edition.
  • For additional information and examples, read Writing Research Papers on Dr. Caprette’s Bios 211 web page.

Style Guidelines for the Final Paper

**Adapted for BIOS 311 from The Journal of Biological Chemistry:
Instructions to AuthorsandEditorial Policies and Practices

Organization

  • Text MUST be typed in a font size of 12 points; use either Times or Times New Roman.
  • Print on 8.5 x 11 paper; do NOT submit electronically in PDF format and do NOT use the two column layout as shown on the JBC website.
  • Use double spacing throughout.
  • Use one-inch margins.
  • Arrange in the following order:
    1. title page with title, author(s), and complete name(s) of institution(s)
    2. summary
    3. introduction
    4. experimental procedures
    5. results
    6. discussion
    7. references
    8. footnotes
    9. figure legends
    10. tables
    11. figures
  • Number ALL pages, including figures; the title page is page 1.
  • You may put legends, tables, and figures after the references OR insert the tables and figures into the appropriate place in the body of the paper. 

Section Details

  • Title
    *should be short and as informative as possible
    *should NOT contain non-standard acronyms or abbreviations
    *should NOT exceed two printed lines
  • Summary
    *is a SINGLE PARAGRAPH
    *should succinctly and clearly describe the major findings reported in the manuscript–MUST contain SPECIFIC data
    *must NOT exceed 200 words
    *should NOT contain non-standard acronyms or abbreviations
    *should be understandable in itself (the Summary is equivalent to an Abstract)
    *avoid citing references here
  • Introduction
    *presents the purpose of the studies reported and their relationship to earlier work in the field
    *should NOT be an exhaustive REVIEW of the literature
    *generally, should NOT exceed TWO typed pages
  • Experimental Procedures
    *brief description but in sufficient detail to permit a reader to repeat the experiments
    *truly new procedures should be described in detail
    *cite previously published procedures in References
    *modifications of previously published procedures do not need to be given in detail except when necessary to repeat the work
  • Results
    *presented in figures and tables–use ( ) when referring to them in the text
    *some results not requiring documentation can be given solely in the text
    *do NOT give an extensive discussion of the Results here
  • Discussion
    *concise (usually LESS than FOUR typed pages)
    *focuses on the interpretationof the results rather than a repetition of the Results section
  • References
    *cited in text by number rather than author and date
    *References for journals and books should be in the following styles:

    1. MacDonald, G. M., Steenhuis, J. J., and Barry, B. A. (1995) J. Biol. Chem.270, 8420-8428
    2. Sambrook, J., Fritsch, E. F., and Maniatis, T. (1989) Molecular Cloning: A Laboratory Manual,2nd Ed., Cold Spring Harbor Laboratory, Cold Spring Harbor, NY

    *Journal names are abbreviated according to Chemical Abstracts.

  • Additional Notes
    *Footnotes are used to cite personal communications (i.e., the source of data)
    *Abbreviations must be given in ( ) immediately after the complete citation of the term within the text. The abbreviations of some important biochemical compounds, e.g., ATP, NADH, DNA, and amino acids in proteins, need not be defined.
    *The trivial and systematic names of enzymes should be those recommended by the Nomenclature Committe of the International Union of Biochemistry and Molecular Biology (IUBMB).

Tables

  • should have a title
  • a legend, immediately following the title, should give enough experimental detail to be understandable without the text
  • each column MUST have a heading
  • necessary abbreviations should be defined in the legend

Figures

  • should have a title
  • the legend must contain sufficient detail to make the figure easily understood
    **identify symbols and curves in the legend, not on the figure
  • appropriately sized numbers, letters, and symbols should be used so they are no smaller than 2 mm in size after reduction to a single column width (87 mm), a 1.5-column width (120 mm), or a full 2-column width (178 mm)
    **a figure may be estimated by using a reducing photocopier to see if it can fit into a single column; be sure to look at the smallest letter or symbol to decide what will be legible in print
  • numbers, letters, and symbols used in multi-paneled figures must be consistent
  • the abscissa and ordinate must be clearly labeled with appropriately sized type, and units of measurement must be given

Chemical and Mathematical Usage

  • The J. Biol. Chem.lists the abbreviations for units of measurement and certain physical and chemical quantities in TABLE 1. These abbreviations may be used without definition, are not followed by periods, and use the SAME form in the plural.
  • In general, the rules and recommendations of the IUBMB and the International Union of Pure and Applied Chemistry (IUPAC) will be used for abbreviation of chemical names, nomenclature of chemical compounds, enzyme nomenclature, isotopic compounds, optically active isomers, and spectroscopic data. The J. Biol. Chem.lists references to publications of rules and recommendations of the International Scientific Unions in TABLE II.

    Copyright, Acknowledgements, and Intended Use
    Created by B. Beason (bbeason@rice.edu), Rice University, 10 June 1999
    Updated 21 December 2005

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