Bio Research Paper Example

WRITING A SCIENTIFIC RESEARCH ARTICLE

| Format for the paper | Edit your paper! | Useful books |

FORMAT FOR THE PAPER

Scientific research articles provide a method for scientists to communicate with other scientists about the results of their research. A standard format is used for these articles, in which the author presents the research in an orderly, logical manner. This doesn't necessarily reflect the order in which you did or thought about the work.  This format is:

| Title | Authors | Introduction | Materials and Methods | Results (with Tables and Figures) | Discussion | Acknowledgments | Literature Cited |

TITLE

  1. Make your title specific enough to describe the contents of the paper, but not so technical that only specialists will understand. The title should be appropriate for the intended audience.
  2. The title usually describes the subject matter of the article: Effect of Smoking on Academic Performance"
  3. Sometimes a title that summarizes the results is more effective: Students Who Smoke Get Lower Grades"

AUTHORS

1. The person who did the work and wrote the paper is generally listed as the first author of a research paper.

2. For published articles, other people who made substantial contributions to the work are also listed as authors. Ask your mentor's permission before including his/her name as co-author.

ABSTRACT

1. An abstract, or summary, is published together with a research article, giving the reader a "preview" of what's to come. Such abstracts may also be published separately in bibliographical sources, such as Biologic al Abstracts. They allow other scientists to quickly scan the large scientific literature, and decide which articles they want to read in depth. The abstract should be a little less technical than the article itself; you don't want to dissuade your potent ial audience from reading your paper.

2. Your abstract should be one paragraph, of 100-250 words, which summarizes the purpose, methods, results and conclusions of the paper.

3. It is not easy to include all this information in just a few words. Start by writing a summary that includes whatever you think is important, and then gradually prune it down to size by removing unnecessary words, while still retaini ng the necessary concepts.

3. Don't use abbreviations or citations in the abstract. It should be able to stand alone without any footnotes.

INTRODUCTION

What question did you ask in your experiment? Why is it interesting? The introduction summarizes the relevant literature so that the reader will understand why you were interested in the question you asked. One to fo ur paragraphs should be enough. End with a sentence explaining the specific question you asked in this experiment.

MATERIALS AND METHODS

1. How did you answer this question? There should be enough information here to allow another scientist to repeat your experiment. Look at other papers that have been published in your field to get some idea of what is included in this section.

2. If you had a complicated protocol, it may helpful to include a diagram, table or flowchart to explain the methods you used.

3. Do not put results in this section. You may, however, include preliminary results that were used to design the main experiment that you are reporting on. ("In a preliminary study, I observed the owls for one week, and found that 73 % of their locomotor activity occurred during the night, and so I conducted all subsequent experiments between 11 pm and 6 am.")

4. Mention relevant ethical considerations. If you used human subjects, did they consent to participate. If you used animals, what measures did you take to minimize pain?

RESULTS

1. This is where you present the results you've gotten. Use graphs and tables if appropriate, but also summarize your main findings in the text. Do NOT discuss the results or speculate as to why something happened; t hat goes in th e Discussion.

2. You don't necessarily have to include all the data you've gotten during the semester. This isn't a diary.

3. Use appropriate methods of showing data. Don't try to manipulate the data to make it look like you did more than you actually did.

"The drug cured 1/3 of the infected mice, another 1/3 were not affected, and the third mouse got away."

TABLES AND GRAPHS

1. If you present your data in a table or graph, include a title describing what's in the table ("Enzyme activity at various temperatures", not "My results".) For graphs, you should also label the x and y axes.

2. Don't use a table or graph just to be "fancy". If you can summarize the information in one sentence, then a table or graph is not necessary.

DISCUSSION

1. Highlight the most significant results, but don't just repeat what you've written in the Results section. How do these results relate to the original question? Do the data support your hypothesis? Are your results consistent with what other investigators have reported? If your results were unexpected, try to explain why. Is there another way to interpret your results? What further research would be necessary to answer the questions raised by your results? How do y our results fit into the big picture?

2. End with a one-sentence summary of your conclusion, emphasizing why it is relevant.

ACKNOWLEDGMENTS

This section is optional. You can thank those who either helped with the experiments, or made other important contributions, such as discussing the protocol, commenting on the manuscript, or buying you pizza.

REFERENCES (LITERATURE CITED)

There are several possible ways to organize this section. Here is one commonly used way:

1. In the text, cite the literature in the appropriate places:

Scarlet (1990) thought that the gene was present only in yeast, but it has since been identified in the platypus (Indigo and Mauve, 1994) and wombat (Magenta, et al., 1995).

2. In the References section list citations in alphabetical order.

Indigo, A. C., and Mauve, B. E. 1994. Queer place for qwerty: gene isolation from the platypus. Science 275, 1213-1214.

Magenta, S. T., Sepia, X., and Turquoise, U. 1995. Wombat genetics. In: Widiculous Wombats, Violet, Q., ed. New York: Columbia University Press. p 123-145.

Scarlet, S.L. 1990. Isolation of qwerty gene from S. cerevisae. Journal of Unusual Results 36, 26-31.

 

EDIT YOUR PAPER!!!

"In my writing, I average about ten pages a day. Unfortunately, they're all the same page."

A major part of any writing assignment consists of re-writing.

Write accurately

  1. Scientific writing must be accurate. Although writing instructors may tell you not to use the same word twice in a sentence, it's okay for scientific writing, which must be accurate. (A student who tried not to repeat the word "hamster" produced this confusing sentence: "When I put the hamster in a cage with the other animals, the little mammals began to play.")
  2. Make sure you say what you mean.
  3. Instead of: The rats were injected with the drug. (sounds like a syringe was filled with drug and ground-up rats and both were injected together)
    Write: I injected the drug into the rat.

  4. Be careful with commonly confused words:

Temperature has an effect on the reaction.
Temperature affects the reaction.

I used solutions in various concentrations. (The solutions were 5 mg/ml, 10 mg/ml, and 15 mg/ml)
I used solutions in varying concentrations. (The concentrations I used changed; sometimes they were 5 mg/ml, other times they were 15 mg/ml.)

 Less food (can't count numbers of food)
Fewer animals (can count numbers of animals)

A large amount of food (can't count them)
A large number of animals (can count them)

The erythrocytes, which are in the blood, contain hemoglobin.
The erythrocytes that are in the blood contain hemoglobin. (Wrong. This sentence implies that there are erythrocytes elsewhere that don't contain hemoglobin.)

Write clearly

1. Write at a level that's appropriate for your audience.

"Like a pigeon, something to admire as long as it isn't over your head." Anonymous

 2. Use the active voice. It's clearer and more concise than the passive voice.

 Instead of: An increased appetite was manifested by the rats and an increase in body weight was measured.
Write: The rats ate more and gained weight.

 3. Use the first person.

 Instead of: It is thought
Write: I think

 Instead of: The samples were analyzed
Write: I analyzed the samples

 4. Avoid dangling participles.

 "After incubating at 30 degrees C, we examined the petri plates." (You must've been pretty warm in there.)

 Write succinctly

 1. Use verbs instead of abstract nouns

 Instead of: take into consideration
Write: consider

 2. Use strong verbs instead of "to be"

 Instead of: The enzyme was found to be the active agent in catalyzing...
Write: The enzyme catalyzed...

 3. Use short words.

"I would never use a long word where a short one would answer the purpose. I know there are professors in this country who 'ligate' arteries. Other surgeons tie them, and it stops the bleeding just as well."
Oliver Wendell Holmes, Sr .

have
sufficientenough
utilizeuse
demonstrateshow
assistancehelp
terminateend

4. Use concise terms.

 Instead of:Write:
prior to before
due to the fact thatbecause
in a considerable number of casesoften
the vast majority ofmost
during the time thatwhen
in close proximity tonear
it has long been known thatI'm too lazy to look up the reference

5. Use short sentences. A sentence made of more than 40 words should probably be rewritten as two sentences.

 "The conjunction 'and' commonly serves to indicate that the writer's mind still functions even when no signs of the phenomenon are noticeable." Rudolf Virchow, 1928

  

Check your grammar, spelling and punctuation

1. Use a spellchecker, but be aware that they don't catch all mistakes.

 "When we consider the animal as a hole,..." Student's paper

 2. Your spellchecker may not recognize scientific terms. For the correct spelling, try Biotech's Life Science Dictionary or one of the technical dictionaries on the reference shelf in the Biology or Health Sciences libraries.

 3. Don't, use, unnecessary, commas.

 4. Proofread carefully to see if you any words out.

USEFUL BOOKS

Victoria E. McMillan, Writing Papers in the Biological Sciences, Bedford Books, Boston, 1997
The best. On sale for about $18 at Labyrinth Books, 112th Street. On reserve in Biology Library

Jan A. Pechenik, A Short Guide to Writing About Biology, Boston: Little, Brown, 1987

Harrison W. Ambrose, III & Katharine Peckham Ambrose, A Handbook of Biological Investigation, 4th edition, Hunter Textbooks Inc, Winston-Salem, 1987
Particularly useful if you need to use statistics to analyze your data. Copy on Reference shelf in Biology Library.

Robert S. Day, How to Write and Publish a Scientific Paper, 4th edition, Oryx Press, Phoenix, 1994.
Earlier editions also good. A bit more advanced, intended for those writing papers for publication. Fun to read. Several copies available in Columbia libraries.

William Strunk, Jr. and E. B. White, The Elements of Style, 3rd ed. Macmillan, New York, 1987.
Several copies available in Columbia libraries.  Strunk's first edition is available on-line.

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.

General style

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

Title Page

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.

Abstract

The summary should be two hundred words or less. See the examples in the writing portfolio package.

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 - 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)

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

Your introductions should not exceed two pages (double spaced, typed). See the examples in the writing portfolio package.

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. 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.

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 appropriateness of sentences and phrases.

Materials and Methods

There 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.

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 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

Materials:

  • 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.
Methods:
  • 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.
Style:
  • 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

The 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.

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.
  • 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.

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 (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

Discussion

Journal 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.

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. 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.
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 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.

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 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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