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Writing a Scientific Paper
Author: ADMIN (ukstudent at gmail dot com)
Published: Mon, 28-Mar-2005
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Writing a Scientific Paper. Article by Louise Wootton, Ph.D. Georgian Court University, Lakewood NJ 08723

There are two main types of scientific paper: a research paper which will become part of the primary literature and a review paper which will become part of the secondary literature.

A research paper describes a new experiment, or series of experiments, conducted by the author(s). It focuses upon the outcome (results) of the experiments but will also describe the methods used and describes the implications of this experiment.

A review paper does not describe the author's own work, but rather synthesizes ideas and results from other research papers that have been published in a certain subject area. This requires a different sort of research... a complete review of the literature in your chosen area. Moreover, a good research paper is more than a descriptive "listing" of the findings of various scientific studies.. more than a glorified annotated bibliography. Instead this paper should be a thoughtful integration of the results and ideas coming from a number of studies in order to provide a new perspective or understanding or to provoke discussion within that field. The conclusions of a number of studies need to be placed in perspective with one another... do they agree? If not, how might the apparent conflicts be solved? What might be productive areas to research in the future? A useful resource for a student writing a review paper are the "Annual Reviews" that are available for a number of fields "Annual Review of Ecology and Systematics", "Annual Review of Cell and Developmental Biology" "Annual Review of Immunology" etc.

Picking a research topic

A. Start by formulating some questions. Don't worry if they're still vague... that's what the next steps are for!

B. Review the Literature. Start by hitting the stacks and read up on the background for your area so that you are well versed in the language and ideas of the field. Only then should you hit the CD-ROM and on-line search to find recent primary and secondary research articles on the topic you've chosen. At this point you're best find will be a good review article as that will provide you with an overview of the current state of research in your field, as well as (hopefully) pointing toward some productive avenues for further research... and of course providing you with a huge resource of reference materials in terms of its literature cited section!

As you read the papers in your literature review take notes about the findings of the article, and any implications for your question. Include a complete citation so that you can refer to the paper again easily when you're writing up. Take note of who the experts in the field seem to be (so that you can search for more papers by them later), and what types of methods seem to be popular for answering the types of question you're asking. As you are reading you will start to get a feeling for whether your question is a good one, (i.e. important, not done already etc).

C. Talk to your advisor and other students or faculty members in your field. Bounce ideas around. Then go back and read some more!

D. Draft your (modified) question in the form of a testable hypothesis. Consider here any limitations of time, space and money. Make sure your study is do-able (again it may be good to bounce your hypothesis off your advisor at this point)

E. Decide how you will test your hypothesis. What experiments will you do? What variable(s) will you measure? What variable(s) will you manipulate, control or ignore? How will you analyze your data?

F. Do the experiment! Keep careful records including observations and "thoughts to self"... you will thank yourself later!

G. Analyze the data using appropriate statistical tests.

H. Make conclusions.

I. Continue Your Literature Review.

J. Write the Report. (See below)

Writing a research paper

General points:

Give yourself enough time to work. Remember that writing is a process. A good paper doesn't come out perfect first time for anyone. Even the best scientists have to struggle to organize their papers and everyone, including you, needs to go through several revisions before they reach the final product... so don't feel bad, and don't skimp on revisions!

The quality of the writing reflects the quality of the research! Use clear, direct prose. Make every word count. Don't use extra words, or excessively long words when shorter ones will do. Write as you would speak.

Find a good paper from a respected journal and use it as a model for your own writing.

Start with an outline of the paper sketching out what's going to go in the introduction etc. Use subtopics and subject sentences to build your outline.

Then write a rough draft that includes the main ideas and fleshes out your topic sentences into paragraphs in rough form (don't worry about details like exact references, full sentences etc at this point).

Use the active voice when possible. There is a trend in scientific publishing toward writing "I measured 50ml..." rather than "50ml was measured". The active voice is usually less wordy and more interesting to read. However, there is such a strong history of writing in the passive voice in biology that it is hard to resist and some professors and editors are still very attached to it. Moreover, there is a problem when writing in the active voice as a single author in that the incessant "I" in the materials and methods can become a distraction, and should be minimized. Multiple authored papers can duck this problem with the more acceptable "we".

Once you have finished with your rough draft, take a break before rereading your paper. Then start to fiddle with the details (cleaning up the prose etc)..

Let a friend or colleague read your draft. Listen to what they say.

Write your second draft.

Spell check and check the grammar carefully. Make sure the ideas are outlined clearly and flow logically within the text.

Publish!

What goes where? Sections of a research paper

Title. The title should be informative, specific and short (13 word max., usually) and should include the species studied, what was measured and the location of the study, if it is important. (i.e. the key words that someone else would use to search for your article.

e.g. "Mating disruption of Douglas-fir tussock moth (Lepidoptera: Lymantriidae) using a sprayable bead formulation of Z-6-Heneicosen-11-one" (Long! but includes all three key parameters.)

e.g. Fish predation on Notonecta (Hemiptera): relationship between prey risk and habitat utilization. (Nice length, but site has been omitted.)

Abstract. Although it should be short (100-150 words) this should outline the study's objectives, methods, results, conclusions and relevance. If published, the abstract will appear in citation sources such as Biological Abstracts and Science Citation Index. It is the first thing someone will read, and it must be descriptive and interesting! The abstract demands clear, direct writing. When readers finish the abstract, they should be so intrigued by the experiment that they decide to read t he entire paper.

Introduction. The introduction should provide the background information about your experiment. It should also outline the objectives of your study. After reading it a reader should understand why your question is significant. Try to maintain the flow from broad to specific. Don't use the introduction as an information dump to show the reader how much you found on a topic. Show the reader you understand the relevant issues in a field and know how your study complements this information. I n both this section and the discussion be careful with citations. It should be always clear which ideas are yours and which ideas (and words) are cited from other papers. Also try never to cite something someone else cited ("chain citation"). Try to go back and find the original paper, even if this means getting important foreign papers translated.

Materials and methods. This should be the easiest section to write as all you have to do is to state what you did in such a way that, after reading it, another qualified scientist should be able to repeat your experiment. This section is often a good place to start writing, as you can write it up as you are doing the experiments. It is written in the past tense as a description of the experiments you carried out. It should include your experimental design and describe the variables measured. If there is a simple well-known procedure it's OK just to name the technique. If it's new or you did something different, you should spend time describing the protocol used. You should also justify why you chose the variables to measure and the methods you used. Be sure to mention the equipment that you used (manufacturer and model number, if unusual) as you outline your technique (this should be integrated smoothly into the text not listed like a shopping list at the beginning of your paper). If relevant, you should also stipulate the conditions used when the test was performed (temp, light, etc.). Finally, you should describe which statistical tests you used to analyze the data, and any transformations performed.

Results. The results section is where you 'present your case'. The logical flow is critical; you must convince your reader that your argument is sound. If the readers are confused by your results, or do not follow your interpretation, they may not accept that your conclusions are correct or recognize the relevance of your findings. Writing a good results section is harder than I looks. Before you start writing be sure you've looked at your data and that you are clear about what each result means... if you're not clear about it, you're reader can't hope to be. Once you figure out what your data means design your presentation to illustrate those ideas as clearly as possible. If a result is simple, recording it in the text is sufficient. For more complex results, tables or figures will be needed. In the case of the latter, try to figure out for each result which format (table or figure) most effectively transmits the information... is the exact number for each data point important? (tends to favor a table) or is the trend or pattern between data points that's important? (tends to favor a figure). Either way, a table or a figure should be titled and captioned in such a way that it is understandable on its own, so that a reader is not having to flip between your text and the tables in order to understand your point. In addition, both graphs and tables should include only the data that is relevant to the points you are making when referring to that table. Don't include trivial or distracting information. If its important give it its own table or figure; if it's not, no matter how much work went into getting that data... throw it out! Once you've decided on what data to present and what format best suits it, embed references your figures and tables into the portion of the text where they are relevant. Start out with the most general ideas and relationships e.g. "Concentration of phytoplankton had a significant effect on zooplankton fecundity (ANOVA p=0.01; Table 1)." Then, having described the basic relationship, you can enlarge upon the nature of the relationship e.g. "An exponential increase in egg production of Acartia tonsa was found for algal concentrations between 10 and 10,000 cells per ml r2 =0.779, p= 0.05; Figure 1)." When describing relationships within data sets, be careful not to use sentences like: The ANOVA showed that.." etc. Statistical tests don't show anything... they just crunch numbers. It is up to you to use the right test and interpret its results. Also, avoid allowing this section to turn into a long list of results with no interpretation. "Hours in sunlight significantly affected growth (Table 1). Soil moisture significantly affected growth (Table 2). Soil nitrogen also had a significant effect on plant growth (Table 3)." Develop each idea within the text: describe the effect; how did the levels of the independent variable differ? However, your results section should only include direct biological interpretation (the copepod grew, the alga e were healthy). Save indirect interpretations (blooms of algae may help promote fecundity of copepods during the spring and fall) for the discussion section. Finally, by convention the first table that is referred to in the results section is 'Table 1 ' and the first figure referred to, even if it is after table 1, is called 'Figure 1'. As a result it is often an idea to put off numbering your tables and figures until after you write your results section, so that your logical flow in writing the results, rather than the order of the experiments, dictates the order of the presentation of the data.
While using the first person is increasingly acceptable, especially in the methods section, avoid using personal perception when interpreting your results (I think...). This reduces your credibility. Write with authority (It is, they do)

Discussion. The discussion is where you explain your results and interpret them in light of other work in the field. Start by presenting the essential conclusions of your specific study. Then, apply your conclusions to the body of background information you relayed in your introduction. Discuss how your new findings relate to the background information you presented in the introduction. Are the major hypotheses in the field supported by your research, or contradicted? At the end of the discussion you may also choose to include suggestions for future research, or disclaimers and explanations of methodological errors made during the course of the experiment.

Acknowledgments. This section is used to thank people who provided significant help to you at any point in your research (e.g. helped with field work, reviewed early drafts of the paper, but (except theses) not usually your parents or the person who answers phones in your department!). This is also where you should acknowledge any agency that provided you or your study with funding support (check a few acknowledgement sections for examples).

Literature Cited. This section lists the references cited in the body of your paper. It is not a bibliography, so it should list only the references that were actually cited in the paper, not everything you read while writing. Formatting how you cite your references in the text and in this section varies in style between journals. Consequently, the only way to ensure that you cite literature in a correct format is to obtain a list of "instructions to authors" (usually included somewhere in each issue of a journal) and/or use the format used in a recent paper published in that journal.

Appendix: This section is rarely included in most biological journals, but may be used under special circumstances to describe technical details of interest mainly to a specialist that are not necessary for understanding the paper. Alternately an appendix may be used to provide raw data when such data represent an important resource for other scientists.

Writing a scientific review paper

General points:

Try to make your research paper an integrated synthesis of the literature, rather than a jumbled regurgitation of facts or a paper-by-paper summary of the findings of a list of references.

Give yourself enough time! For a 10-20 page paper it ideally takes a month just to carry out the library searches and to collect the necessary materials (interlibrary loans etc)... and much longer to write it up!

Start out with a clear idea of the question you are trying to answer in the paper. Write it somewhere and show it to an advisor to see if it makes sense, is "do-able" etc. In general a simple, specific idea is easier to research and to write about. Equally it must be interesting and inclusive enough to ensure there's enough material available to review.

Get to know the library a.s.a.p.! Make sure you are familiar with all the resources available to help you locate references. Make friends with the librarians. They know all the tricks of the library. Using the library well will save you hours of work and days of frustration!

Take notes, including full citations (authors' names, journal, date and page number) from each paper as you read it. Use index cards or a word processor. Index cards are nice in that you can shuffle them around, color code ideas on them, highlight etc. The advantage of using a word processor is that you will later be able to use your notes to cut and paste together the first draft, plus you'll have all your citations there already which saves time when building your citation list. Organize your notes. "Where did I read that?" is the plague of all writers. The better organized your notes, the less this is a problem.

Outline your paper before setting pen to paper for anything else! This will help you to organize your thoughts and will markedly improve the overall quality of your final product.

Don't be afraid to write your ideas down before they are perfectly formed. If you can get them down on paper, you can place them in a logical sequence and develop them into a flowing presentation later.

Use the draft system: Write a first draft. Leave it for a day or two. Come back to it and revise it as much as you can, then let someone read it. Once they have read it, revise the paper again. Respond to your reviewer's comments and also clarify any passages that seemed to confuse them. Expect that your paper will need revisions and don't feel bad when that turns out to be true.

While using the first person is increasingly acceptable, especially in the methods section, avoid using personal perception when interpreting your results (I think...). This reduces your credibility. Write with authority (It is, they do)

What goes into a review paper?

When writing a review paper your job is to present what is known about a specific topic and to synthesize all the unconnected threads of the individual studies into an integrated "State of the Science" type of review. In your paper you will outline the overall picture of your topic area it is currently understood by scientists in that field. Your paper should clearly outline any problems that are currently being addressed, and explain the basis of any conflicts that exist between experts in the field . If there are important conflicts as a reviewer you are in a position to suggest which side of the conflict has the weight of evidence supporting it and why. For conflicts which, in your opinion, do not yet have a clear resolution, you are also in a position to make suggestions as to the types of experiments need to be done to resolve those arguments.

Your review paper should have the following sections:

A. Title: As for a research paper, this should be short and inform your reader of the major ideas that will be discussed.

B. Abstract: Again this should be written last and should summarize the major points made within the body of your paper.

C. Introduction: Your introduction should be short and concise (ca. 1 page) and is not given a separate heading from the body of the paper. The purpose of the introduction is to introduce your reader to the ideas that you will be addressing in the body of your paper. In your introduction you should be trying to bring readers from different backgrounds up to speed with the "thesis" or objective of your paper and explain to them why it is that this issue is important. It is not a review of the field... that is what the body of the paper is for! It is generally written after the body of the paper is completed (so that you know where you've "gone" intellectually in the paper and thus can effectively communicate to your reader what to expect).

D. Body: In this portion of your paper you will outline the background for your idea and begin to synthesize ideas from the papers you've read in order to build a coherent "thesis". Before you write this section, figure out what your perspective is going to be (what are you trying to show?). Having done this, try to present your ideas in such a way that they build your discussion logically towards your goal. Outlines will be a big help to you at this stage. Frequently using heading s (e.g. History of the idea, Specific conflicts etc.) can help you to systematically address each important point that you wish to make, as well as helping your reader to follow your arguments. Once you've developed your headings you can then go back an d place topic sentences for each paragraphs of information you wish to convey under the appropriate heading. Each paragraph should have clear, well thought out points, and should contain only the information needed to make or support that point. Fill in each paragraph with more details until you have a coherent argument building towards your final, concluding statement.

E. Conclusion: Like the introduction, the conclusion section is not usually separated from the body of the paper, although it can be if it is really long. In this section you should restate the objective(s) of your paper and point out how you have satisfied these goals. It should also reiterate what the major conclusions (ideas) of your study are.

F. Acknowledgements: Again this should include only people who made considerable impact on your research... people with whom you had fruitful discussions, a librarian who spent hours with you trying to track down an elusive publication that was key to your research etc.

G. Literature Cited. Should follow the standard format outlined by the journal in which you will publish.

Further Reading: http://alpha.furman.edu/~worthen/writedoc.htm Wade Worthen's web site at Fuhrman University is specially aimed at students writing research papers in biology.


Copyright for this article belongs to Louise Wootton

This document was re-printed with the kind permission of Louise Wootton. Original Source of the article is located here: http://gcuonline.georgian.edu/wootton_l/



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