Name: _____________________________________________ SCB 265: Fundamentals of Ecology

Lab 5a: The Literature of Ecology and the Structure of a Scientific Paper

Introduction: Ecological literature

One of the main objectives of this discussion of ecological literature is that it will assist you in preparing the lab
report that you will complete this semester. You will be turning it in as if you were submitting it to the journal
The Science of Nature. A link to this journal and the instructions for authors can be found here:
https://www.springer.com/life+sciences/journal/114. Further, learning the proper format for submitting a paper
can be of huge value to you in future classes, or in a future occupation.

The majority of published research in Ecology (or any scientific discipline) winds up in either books or journals.
Scientific journals are considered primary literature/sources, whereas books are considered secondary
literature/sources. There are a number of reasons to publish research in scientific journals. One reason is that it
brings your work to exactly the types of experts who would like to read it. For example, there are journals that
are primarily devoted to the publication of ecological studies, sometimes with a specific focus or subdiscipline.
Examples of these journals include Ecology, American Naturalist, Oikos, Journal of Ecology, Functional
Ecology, Oecologia, and Behavioral Ecology. Some journals that publish ecological research have a taxonomic
focus, such as Auk and Condor (ornithology focus), Ecological Entomology and Annals of the Entomological
Society of America (entomology focus), and Herpetologia (herpetology focus). There are (of course) journals
that are geared towards a general audience (e.g. Science, Nature, The Science of Nature), and sometimes they
publish ecological research in addition to research from other disciplines.

Another major reason to publish in scientific journals is the incredibly important process of peer review. When
an article is submitted to a journal, the editors (if they see merit in the work), will send it out to other experts in
the field for them to critique it. During the review, the reviewers (AKA: referees) will determine if the study
was logical, if the experiment(s) were sound, if the analysis(es) were appropriate, if the conclusions make sense,
and if biases were avoided. They will then report to the editor whether they think that the article should be
rejected, accepted, or needs more work before acceptance (the additional work may include further experiments,
additional analyses, corrections to figures, etc.). The process of peer review helps to ensure that very little bad
science gets published.

One more note about the nature of scientific writing. It tends to be concise, especially when compared to other
disciplines. For example, if you are writing something in an English or History course, the emphasis is often on
writing in complicated, drawn-out prose. At times, verbosity is even encouraged. Papers are often given page
minimums. In science, the emphasis tends to be on writing clearly and concisely, but still with enough detail for
your readers to understand what you did. In fact, journals often have page (or word) maximums, rather than
minimums.

The structure of a scientific journal article

For the most part, all journals follow the same format: Title Page, Abstract, Introduction, Methods, Results,
Discussion, and Literature Cited. The Title Page usually contains an informative title, the author’s name and
affiliation, and a running head. Titles in scientific literature are brief and describe the content of the article.
They tend to not be flashy (although this isn’t always true). The title “Effects of simulated vibration on Polistes
fuscatus offspring development” may seem stale, but it provides the reader with exactly the information that
they need to know to determine if they want to read it. Below the title, you often find the author’s name, and
below that, their affiliation. The affiliation usually includes their academic department, their school or
university, their departmental address, and their email. Below that you usually find something known as a
Running Head. This, like the title, is a shortened version of what the paper is about, often no more than 40
characters (including spaces). This will be placed on the top of every page of the journal article. Please note that
the journal format we are using (The Science of Nature) does not employ a Running Head.
After the title page, a new page is started that will contain one major section, the Abstract. An Abstract can be
difficult to write, because essentially you are distilling the entire article into a single paragraph. Most scientists
looking for articles will peruse titles and read the Abstract if a title grabs their interest. They should be able to
tell from the Abstract if it is a paper worth reading or not. Below the Abstract, journals usually ask for the
author(s) to provide 4-6 Key Words that are used for indexing. Think of them as hashtags; they are words that
will be linked to the paper that can be used by others who are interested in particular topics to find your paper
through a search engine.

After the Abstract page, an author will move to the next free page and create the next major section, the
Introduction. This is one of the most important parts of the paper because it essentially outlines why the work
was conducted. The Introduction should provide the reader with enough background information to appreciate
the study, while citing references that put the work into context within their scientific field (i.e. What is known?
What wasn’t known that caused you to study this topic?). Usually, the author will introduce their research
question here, along with their hypothesis. Throughout the Introduction, the author should be building rationale
for why their hypothesis makes sense, based both on logic and what is already known about the topic. If you do
not, you end up with a hypothesis that basically “comes out of nowhere”, which can leave the reader confused.

After the Introduction, you have the Methods section, which for some journals will be referred to as the
Methods and Materials. If the introduction section answers the question of “why?”, the Methods will answer the
questions of “where?”, “when?”, “what?”, and “how?”. Not all of these questions will be relevant for every
study. For example, in some studies the time that a study was conducted is relevant, but if a study conducted at
a certain time of day could have been completed at any other time, it should be left out. At minimum, the
Methods should contain enough information for the reader to repeat the study. Your Methods section will also
have some description of the statistical hypotheses and statistical tests used to analyze the data. Finally, it’s
worth noting that the Methods section is always written in past tense. Think about it, you already did these
things.

The Methods is followed by the Results section. This section contains exactly what the heading says, the
Results, with no interpretation. In this section, the author will usually refer to either tables or figures, which are
used as a way to distill and represent the data. There is no need to have raw data in this section. Although this
section contains figures and tables, they are not placed within the text for this section when a manuscript is
submitted. Instead, they will be appended to the end of the manuscript. Figures and tables need a description for
the reader. This is called the Figure Legend. Figure legends are on a separate page that precedes the numbered
figures. Thus, the final pages of the manuscript are in the following order: References, Figure Legends, and
Figures (numbered in the order they are referenced in the manuscript). There are two common mistakes that
occur in the Results section. One is to provide interpretation for the results, which, as mentioned before, is not
the purpose of this section. The second is to have the impulse to add a lot of extra text to the section because it
tends to be one of the shorter sections of the manuscript. Resist this impulse. You should simply describe the
results in words (including the results from your statistical analyses: test statistics, p-values, whether or not
treatments were significantly different from one another) and refer your reader to the figures and tables.

The final major text section of the paper is the Discussion section. In many ways, this section is the inverse of
the Introduction. In this section you will summarize and interpret the results, draw conclusions, and describe
whether your results support or reject your hypothesis in the context of your research question. Usually, you
will describe general trends in the data, then put those results in the bigger context, describing why they are
important. Furthermore, if the results were not what you expected, you can describe why this might be so. Was
it due to human error? Incorrect assumptions? Flaws in the experimental design? It is important to note that
negative results are never bad. On the contrary, they can be extremely valuable because they tell you something
about what you are studying.
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After the Discussion section, you have a section known as the Literature Cited, also known as the References
section. Here you will compile a list of all of the references you cited throughout the previous sections. Usually
these are compiled in alphabetical order, but this varies by journal. Anytime you refer to previous data,
conclusions, or any information from a previous study, you must cite the author(s) of that study. If you do not, it
is considered plagiarism. Further, you should have been using references to build your rationale in the
Introduction. To build rationale, you need to bring previous findings into play, which means that you need to
cite those studies. Likewise, putting your results into the context of previous studies also happens in the
Discussion, meaning that you should cite studies there as well.

When you cite studies within the text, there are two main ways of doing so. Citations may come in the
beginning of a sentence, e.g.: Taylor (2018) found that vibrations increased when wasps were given
supplemental food. Alternatively, they may come at the end, e.g.: Vibrations increase when wasps are given
supplemental food (Taylor 2018). The form of an in-text citation changes when there are >1 authors.
One author: (Taylor 2018)
Two authors: (Taylor & Jeanne 2018). Note that depending on the journal an ampersand (&) may be
used, or the actual word “and” may be used.
Three or more authors: (Taylor et al. 2018). Here, et al. is an abbreviation for the Latin “et alia”,
meaning “and others”.
In general, direct quotes (word for word) are not taken from a previous publication in the sciences, but you may
find that this practice occurs in the humanities. In the sciences we tend to distill and paraphrase a particular
finding/result and cite it that way, rather than a word for word quote.

The Literature Cited section has a specific format, which differs from journal to journal. Please see the webpage
for the specific instructions for The Science of Nature, the journal style that you are using.

Finally, it is worth noting that I would like you to focus on primary sources (journals) when citing. It is good
practice to familiarize yourself with this type of literature. When using secondary sources, books are also
acceptable. Other secondary sources (newspapers, popular magazines, websites) should be avoided.

Hints, suggestions, guidelines

1. Your manuscript should be typed, and all figures should be made in a computer program (i.e. not hand-
written/drawn).
2. Make sure your manuscript is carefully organized and well-written. The highest standards for English
composition and grammar are expected when turning in a manuscript to a journal. Feel free to consult with me
or the writing center if you have any questions.
3. There used to be a strict rule about writing in passive voice when it came to writing a scientific manuscript
(i.e. avoid “I” and “we”). These rules have been relaxed, somewhat. A good mix of active and passive voice
tends to provide the best readability, in my opinion.
4. You may be tempted to write the manuscript in the order you will turn it in (Abstract, Introduction, Methods,
etc.). In practice, most scientists write the manuscript in the following order: Methods, Results, Introduction,
Discussion, Abstract, Literature Cited. Why? In this order, you are writing the sections you know the most
about first, working towards the sections that are more complicated. Further, once you know the results, you
may change how you write up your Introduction and Discussion sections.
5. Methods and results are written in past tense, while the rest of the manuscript may be present or past tense.
6. Proofread. Proofread. Proofread. Have another person proofread it, too.

I have included one of my manuscripts that was accepted for publication as an example. Please take a look at it.