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2011
Writing a scientific paper
A major goal of this course is to improve your ability to analyze scientific data and write a scientific paper. Poor
writing is easy, but good writing is very difficult. Moreover, the only way to improve writing is to practice. You will
turn in two drafts of a scientific paper based on the data collected on our field trip.
What is a draft??
Writing a ‘draft’ does not mean blasting out a few pages, running a quick spell-check, and then printing it out just in
time for class. A draft is your best effort to write a good paper. All writers create many drafts before submitting
manuscripts. In scientific writing, the primary author will typically spend a great deal of time writing the first draft,
which is then submitted to co-authors, friends and colleagues for a ‘friendly review.’ The draft is then revised based
on the comments of colleagues. Depending on the condition of the first draft, the author may send it out to colleagues
a second time before submitting it to a scientific journal where it is reviewed by experts selected by the journal’s
editor. The reviewers make more suggestions, which the author must either incorporate or refute to the satisfaction of
the editor. Thus, any published paper has gone through a minimum of three or four drafts. Keep in mind that for
each draft seen by someone else, the author has probably worked up several revisions.
What is peer review??
Peer review is just that, a review of your writing by your peers. Peer review is an essential element of scientific
writing: papers appear in journals only after a careful peer review process. In the description above, the peers were
the friendly reviewers and the journal’s reviewers, who are expected to carefully read the manuscripts and judge
whether the topic, the methodology, and the interpretation of the study are worthy of publication and contribute to our
understanding of a particular subject.
For this class, your peers are your classmates. Later this semester, you will submit a draft of your river paper to be
reviewed by a classmate. At the same time, you will receive someone else’s manuscript to review. You’ll find that
reviewing other peoples’ writing will also improve your own writing. Seeing other peoples’ errors makes it easier to
see your own, while seeing someone clearly express a complicated idea may improve your ability to do the same.
Checklist for writing a scientific paper, use this before you begin writing:
Have you identified your hypotheses?
Have you collected data that test the predictions of the hypotheses?
Have you performed the appropriate statistical tests?
Have you determined whether your data support your hypotheses (conclusions)?
Have you researched literature (primary literature only) relevant to your hypothesis?
If you can answer "yes" to all of the above questions, you are ready to start writing your paper.
A scientific paper consists of eight parts:
1) Title:
The Title is very important. The Title will either compel people to read the paper or cause them to pass it by. The
Title should be short and concise, yet descriptive. Day (1994) describes a good Title as one which has "the fewest
possible words that adequately describe the contents of the paper."
Good Title: The effect of predation risk and prior experience on foraging behavior, habitat selection and aggregation
of goldfish (Carassius auratus).
Bad Title: Predation on goldfish (Carassius auratus)
2) Abstract:
In many ways, the Abstract is one of the most difficult sections to write. The Abstract should give a short but thorough
summary of the entire paper. That means it needs to state the hypothesis (and the justification for the hypothesis), brief
methods, results, and your conclusions. Most people prefer to write this section last, after the rest of the paper has
already been written.
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3) Introduction.
Think of the Introduction as having two parts. The first part is designed to bring the readers up to speed by briefly
discussing the previous research related to your study, and pointing out any knowledge gaps. This is the justification
for your hypothesis, and lets the reader know that you didn't come up with the hypothesis out of the blue. This part
should be no longer than a few paragraphs. The second part identifies your hypotheses, predictions, and the objectives
of the paper.
4) Methods
The Methods tell the readers what you did and how you did it (including field equipment, lab equipment and
chemicals, statistical methods, etc.). It is important in the Methods to give very specific information, so that a reader
could repeat your study if needed. This is a very important point: the foundation of science relies on replication.
However, you must also avoid going into gratuitous detail; conciseness is important. You may find it useful to break
this section into subsections (field sampling, data analysis, etc).
5) Results
In the Results, you report the findings of the study, including relevant statistics and citing any tables or figures that you
want to include. Make biology the subject of your sentence, not statistics! One note about citing tables and figures: it
is a waste of ink to write a sentence like, “The results of the proximity data are presented in Figure 2.” Anyone who
looks at Figure 2 knows what the data are. Instead, give some interpretation of the figure: “Fish tended to aggregate
when in the presence of a predator, and experienced fish showed the greatest propensity to aggregate (Figure 2).” This
way, when readers look at the figure, they have an idea of what to look for.
6) Discussion
In the discussion you interpret your data and give the reader the take home messages. Were your hypotheses
confirmed? Why or why not? What further experiments should be performed? How do your results compare with
published works? Make sure that you don’t present any new data in the discussion, and don’t discuss data that weren’t
included in the results.
7) Literature Cited.
You must give credit to ALL external sources of information that you used; plagiarism is unethical at all levels. If the
citation is from a journal, use the following format (you will lose points for not following this format):
Harvey, C.J., and J.T. Hinke. 1996. Habitat preferences of three species of aquarium fishes: fake plants vs. little
bubbling treasure chests. Journal of Banality 14: 105-114.
If the citation came from a book (e.g., a chapter of a book), then use the following format:
Hinke, J.T., C.J. Harvey, and J.F. Kitchell. 1996. Fins: they sure are useful for swimming. Pages 156-211 In D.R.
Seuss [Editor]. Fish biomechanics. Prentice Hall. Upper Saddle River, New Jersey.
8) Tables and Figures.
Tables and figures are extremely helpful for presenting results. Tables are best used when you want to display
information that easily breaks down into a few small categories. Tables are also best when you want to show exact
numbers. Figures are best when you want to show a trend (it is more easy to compare numbers in a figure because
it is visual). Each table needs to have a descriptive title. Each figure needs a title, and a figure legend. The figure
legend should be designed so that a reader who has barely skimmed the paper can look at the figure and be able to
interpret it.
General Guidelines for Badger Mill Creek Paper
1) Identify Question. What is the general question that you are trying to address?
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2) Research Literature. Most likely, other people have been interested in the same question as you. What were
their findings? An important part of this component is the ability to synthesize a lot of independent studies into a few
key ideas.
Make use of the excellent databases on campus to search for relevant literature. Key word searches will be especially
useful: Try looking at ‘stream habitat’ or ‘stream fish habitat’. Then, maybe get more specific: ‘trout habitat’,
‘sculpin habitat’, etc.
3) Clearly identify your hypothesis. This is a more specific statement than your question (see #1 above). Your
hypothesis should be justified via your literature review.
4) Data analysis: This should be a hypothesis-driven process. There is no generic way to analyze the data. The
correct way depends on the question that you are trying to answer.
5) Interpret. Do the data support the hypothesis? If not, what might be the reasons? What are the limitations of the
data? What parts of your hypotheses were supported by the data? This may require more literature review.
6) Write!!!
Outlines and topic sentences:
Due to time constraints, we will not have an outline due in this course. However, this does not mean that you
shouldn’t create an outline – you should! Creating an outline before you start writing will greatly reduce the time you
spend on your first draft, and greatly increase the quality of that draft. Sections 1-8 above can serve as a starting point
for your outline – you know that you need to include each of these sections. For each section you could add
subsections (especially for methods and results). After adding subsections, add some topic sentences to each section.
A good outline will have a topic sentence for every paragraph of your paper. Once you have done this, writing the
paper should be easy – just expand on each topic sentence! If a statement doesn’t apply to your topic sentence, move it
elsewhere, create a new paragraph (with a new topic sentence), or take it out.
ONE LAST BIT OF ADVICE: Reading papers from the literature is extremely important, and not just for acquiring
information, as in #2 above. Reading also familiarizes you with the style of scientific writing, which is distinct from
casual or popular writing. Adapting this style is very important; it involves being concise, avoiding vague words, and
avoiding gross subjectivity. Unfortunately, this writing style is not very flowery, but that’s not your goal as a scientific
writer. The bottom line is getting your information across in a clear, interesting way. So, take a good look at lots of
papers and see how other people share their findings.