BIOS 3010: Ecology, Dr Stephen Malcolm
Term Paper: Information on structure and sources
I would like you to write a well-structured and conceptually significant
review paper that addresses an issue relevant to ecology. You can choose any
issue and at any scale that describes any ecological interaction from microbes to
manatees, or eubacteria to eucalypts. Please make sure you emphasize an
ecological concept and please do not simply describe the natural history of a
species or a community. These concepts can include anything from community
structure and ecosystem function to processes such as predation, herbivory,
competition and patterns such as population structure in relation to resource,
harvesting or conservation issues. This can include ecological risks of using
genetically modified crops, fisheries, forestry etc.
Please structure the paper as follows:
1. Introduction
a. Observation: Briefly describe an observation or phenomenon (for
example, describe the migration of whales to the coast of Maine each
year).
b. Concept: Describe the ecological concept that attempts to explain this
observation (for example, migration is a behavior that many animals show
in order to redistribute themselves in space according to a number of
ecological interactions – such as responses to changes in conditions or
resource availability, or interactions with natural enemies).
c. Hypotheses: Science progresses through hypothesis falsification rather
than proof and we need to be able to reject a null hypothesis of “no
effect” before we can accept a plausible alternative hypothesis to
explain our initial observation. So we use the relevant ecological
concept to erect a null hypothesis and a series of testable alternative
hypotheses.
For example, whale movement may be random and this is a plausible
null hypothesis (designated Ho = whale movement is random – there is
an equal probability of a whale occurring at any point in any ocean at
any time). If you can collect data (in your case published information)
that allows you to reject this null hypothesis then you can start testing
Dr. Stephen Malcolm
BIOS 3010: term paper
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alternative hypotheses. These could include a single possible factor,
or all possible factors that might influence whale movement. One
hypothesis could be that whales respond to the seasonal upwelling of
nutrients off the coast of Maine (=H1), another might be that they find
“enemy-free space” off the coast of Maine (they may be escaping
predators in the Caribbean)(=H2). These are just two possible
alternative hypotheses that you may be able to accept having rejected
your null hypothesis based on your review of published information.
You would accept the simplest (most parsimonious) of the alternative
hypotheses consistent with your evidence and this could include more
than one alternative hypotheses.
2. Methods and Study System
Your methods are basically a search of the literature to find sources of
information that test your hypotheses. Thus you should list databases and
perhaps information about how long you searched and where or how. In this
section you should also give a brief description of your organisms or system. So
please keep a record of how much time you spend searching each database. It
might be interesting to analyze these data in a way that shows the number of
citation hits per unit time spent searching each database and then graph these
data.
3. Results
Your main text will order your information in the same order as you
presented your hypotheses (sub-headings work well). Here you will describe the
information that will allow you to test your null hypothesis and possibly accept
one or more alternative hypotheses that can plausibly explain your initial
observation within the context of the relevant ecological concept.
4. Discussion and Conclusion
This last section can be quite short and will draw a conclusion based
on your initial observation, hypothesis presentation and hypothesis test. You
should be able to reach a conclusion about why the original observation
occurred. However, you may not have reached a conclusion because more
information is needed and so you could extend this section to discuss needed
research.
5. Sources of information/Literature Cited
Information comes in many forms and as you know it has exploded
with the advent of the web. However, the reliability of published information
varies according to the degree of scrutiny it receives before it is published or
made available. Typically, web resources are checked only by the person who
makes them available and so they are mostly not peer-reviewed – except by
default or attrition and a process of weeding out false or unreliable information.
In order of significance and degree of peer-review these sources fall into 4
categories (please note that this information reinforces Lab 1) :
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(i)
Primary Literature:
The best information is published in the “primary” literature.
These are the peer-reviewed and edited journals published by
reputable publishers around the world – but especially in North
America, Europe, Japan and Australia. These journals publish the
results of carefully designed research. Some excellent review
journals may also be included in this category and some journals
perform a multiple function in this category of publishing primary
research, reviews and news of new and preliminary results that have
great potential to be important – the best known of these are the
journals, Nature and Science.. The Proceedings of the National
Academy of Sciences of the USA and the Proceedings of the Royal
Society are also two journals that sometimes publish important
ecological work – they are publications of the premier scientific
societies in the USA and Great Britain, respectively and emphasize
prestige!
Examples of Primary Ecological Journals:
Ecology, Journal of Animal Ecology, Journal of Ecology,
Journal of Applied Ecology, Ecological Monographs, Oikos,
Oecologia, American Naturalist.
Plus more specialized journals such as: Ecological
Entomology, Molecular Ecology, Behavioural Ecology, Evolutionary
Ecology, Conservation Biology, Journal of Chemical Ecology,
Chemoecology, Freshwater Biology, Journal of Zoology, Biological
Journal of the Linnean Society, and Journal of Theoretical Biology.
Plus geographically relevant journals in countries with a
strong ecological tradition such as the countries of Europe (especially
Britain and Scandinavia), Japan, Canada, Australia and New Zealand.
Many discipline-specific journals also publish important
ecological papers, such as: Evolution, Evolutionary Ecology,
Limnology & Oceanography, Animal Behaviour, and Journal of
Experimental Botany.
Although the following journals publish review articles, they are of
such high quality and offer such excellent syntheses of information
that they can also be considered primary journals:
Annual Review of Ecology & Systematics, Annual Review
of Entomology and Advances in Ecological Research.
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(ii) Secondary Literature:
The primary journals provide information that is also
digested in a “secondary” literature that reviews the primary literature
to focus trends in thought. Some popular science magazines such as
Scientific American and American Scientist also fit into this category
with a rigorous editorial review of published material. The Elsevier
Trends series of journals publish peer-reviewed articles and are a
good source of short and interesting reviews of ideas. Trends in
Ecology and Evolution is a good source of ideas in ecology.
(iii) Magazines:
Next are the purely news journals or weekly magazines that
publish commentaries and reports of new research and new ideas as
they reach the primary literature. Examples include Science News
and New Scientist. These articles are also screened by an editorial
board.
(iv) Web-based information and “gray” literature:
Lastly, web-based information is easily accessible and
widely available, along with newspaper reports. These are useful to
find out who is doing what quickly and to direct your search at
particular authors. However, they should not be the main source of
your information for a review paper. If you do use any web sources
they must be fully cited and acknowledged. Gray literature refers to
the millions of reports that exist – these are rarely reviewed before
being made available, or if they are, they are reviewed superficially.
They are usually a description of work done and often do not
constitute a reliable source of information. However, these reports
can often be a useful source of data for further analysis.
Some suggested concepts to review:
• Migration (in space or time)
• Predation (foraging behaviors/defense-offense, population dynamics)
• Herbivory (the world is green – are plants winning)
• Parasitism (the most successful organisms?)
• Disease dynamics (why do some diseases spread and others don’t)
• The ecology of infectious diseases
• Distribution and abundance of invasive organisms
• Competition (coexistence/competitive exclusion)
• Ecological effects of global warming/acid deposition/elevated
atmospheric gases etc.
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• Conservation ecology (habitat fragmentation/size of nature reserves,
species protection, community & ecosystem protection etc.).
• Ecological risk assessment (pesticides, genetically modified
organisms).
• Population structure.
• Sustainable resource harvesting (fisheries, forestry, hunting etc.)
Instructions for the term paper
The syllabus instructions state: “The term paper will be a structured,
hypothesis-based review of an ecological topic of your choice. The term paper
topic will be chosen at the start of the course and the final paper will be handed in
for assessment no later than the lecture meeting on December 7. Further
information about the paper will be handed out in class.”
In order to receive full credit for the term paper I would like you to
follow this schedule of events:
Date
Activity
September 21 Hand in paper topic with summary description
of an ecological observation
October 19 Hand in annotated bibliography on topic
October 29/30 Hand in detailed plan of your paper
November 18 Hand in complete draft of your paper
December 7 Hand in final revised paper
Total
Score
Bonus 1
(<5 points)
30 points
30 points
40 points
100 points
200 points
Please look at published papers in the journal Ecology to give yourself
an idea of the form and content of the published papers. With each yearly
volume there is a “Table of Contents” and so you can scan several issues quickly
for subjects that might interest you and you can access articles online through
JSTOR up to 2012 (http://www.jstor.org/journals/00129658.html). The most
recent 48 months are in the library print version of the journal.
Please format your paper like this journal: i.e. both left and right
justified pages (straight margins on both sides of the page - like this one! but
don’t use 2 justified columns as in the journal), title in bold, uppercase typeface,
your name in small caps, your University address below your name in italics, then
an ABSTRACT followed by key words. Please use the 12 point Times/Times
Roman font and single-spaced (although if you were submitting this paper for
publication it would be double-spaced). As a guideline, the text of the paper
should be at least 8 pages long (excluding references, tables and figures). An
example of a published paper is given with this lab handout (click the reference to
access the enclosed pdf):
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Hunter, M. D., and R. E. Forkner. 1999. Hurricane damage influences foliar polyphenolics
and subsequent herbivory on surviving trees. Ecology 80(8): 2676-2682.
The text should start with an INTRODUCTION to your review topic that
states clearly why you are reviewing the topic. Then divide your paper into
sections about the METHODS (with organisms and system described),
RESULTS and DISCUSSION. You can also give SUBHEADINGS within these
main headings that partition the topic into logical units (this also makes it easier
to write the review). If you receive any help or advice or information that you
have included in the review please give ACKNOWLEDGEMENTS to these
sources. Please also make sure that you avoid any hint of plagiarism - quotes
and their sources must be fully acknowledged and referenced (note: if plagiarism
occurs the term paper will receive a score of zero – we do check!).
All literature sources must be referenced in a LITERATURE CITED
section exactly as in the journal Ecology (as shown above). Please cite
references in the text as shown in the attached example (Hunter and Forkner
1999) and then list cited references alphabetically in the “Literature Cited” section
at the end of the paper. Please format references in the same way as in the
journal (note: please list references in a single column across the page - as in the
main text). As a guideline you should refer to at least 10 primary literature
sources.
If you wish to include tables or figures, or both, please add these at the
end of your paper, numbered as Figure 1, Figure 2, or Table 1, Table 2, etc.
Tables and Figures should also include legends that explain fully what is shown
(table legends above each table and figure legends below each figure). The final
paper should be assembled in the order: Title, introduction, text,
acknowledgements, literature cited, tables, figures.
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Term Paper: Overall Grading Rubric
Term Paper - grade assignment (paper due December 7)
Category
Term paper topic
(Title & ecological observation for bonus points by September 21)
Annotated bibliography
(with title, hypotheses & summary of paper by October 19)
Detailed plan
(PowerPoint presentation in labs on October 29/30)
Draft paper
(by November 18)
Final paper:
(by December 7)
Content and presentation
(general overview)
Structure
(hypotheses, logic of organization, significance of argument)
Interest
(use of sources, innovative arguments, use of figures)
Relevance of topic to ecology
Score
bonus
References
20
Total score /200
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30
40
20
20
20
20
200
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Term Paper: Grading Rubric for Annotated Bibliography
The annotated bibliography is an opportunity for you to see how your
information research is shaping up for your term paper. By the annotated bibliography’s
due date you should have at least ten peer-reviewed primary information sources. The
annotations allow you to extract and express in your own words how each paper is
relevant to your hypothesis topic. You can begin to see what evidence supports your
hypothesis and what refutes it or is neutral (supplies background information). This
should help you decide if you need to continue to research for more information or if you
have enough to structure your arguments. In your paper you want to present all sides of
the issue before reaching a conclusion about where you stand based on the available
evidence. Finally the annotated bibliography ensures you can cite your references in the
required style for clarity and consistency.
Credit for the annotated bibliography is based on citation accuracy; source
quality, currency and appropriateness; relevance of the information to the paper’s
hypothesis topic; and value/usefulness of the annotations. All annotations must be
expressed in your own words. Plagiarism is inadmissible. For clarification about what
constitutes plagiarism see http://www.wmich.edu/library/searchpath/module6/index.html
Or http://library.acadiau.ca/tutorials/plagiarism/
For full credit for the annotated bibliography you need to submit the following
by the due date (October 19):
a) Your paper hypothesis topic
b) At least ten quality primary information sources, cited in the style of the
journal Ecology.
c) Annotations for each citation that includes a statement about how this
citation supports, refutes or is neutral with respect to your hypothesis. (If an
individual citation includes some evidence that supports and also some that
refutes then explain how this is the case). No more than 5 of the 10
citations should be neutral. If this is the case you need to do more research
to find information that bears directly on your hypothesis.
Annotated Bibliography (due October 19)
Score
Hypothesis topic
3
Citations in style of journal Ecology
2
Ten primary sources with copy of the first page
10
Relevance of sources to topic
5
Value/usefulness of annotations (positive, negative or neutral to hypothesis
10
Total score/30
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Term Paper: Grading Rubric for detailed plan
Your detailed plan should reflect the paper structure described above.
Due as PowerPoint presentation in lab on October 29/30.
Paper structure
Introduction: Observation
Score
8
Introduction: Ecological Concept
4
Introduction: Hypotheses
8
Main text (summary of system, methods and structure of text)
10
Discussion/Conclusion (final paper)
Sources of information (completed in bibliography)
----------------------30
Total score
Please see the attached pdf file for a plan presentation guide
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BIOS 3010: ECOLOGY – Fall 2015
Dr Stephen Malcolm
BONUS POINT OPPORTUNITY 1:
For up to 5 bonus points:
Give a suggested title and write a paragraph that describes what your
term paper topic will be and summarize what you think you will include. This
need not be your final term paper topic if you find an alternative topic.
You can write on any ecological topic - from microbial ecology in the
rhizosphere to the ecology of whale migration, or shift scales from the ecology of
individuals to global ecology.
You can also include economic and political themes, or ethical
aspects, resource harvesting etc., as long as the main emphasis is on ecology.
If there is a topic that especially interests you please feel free to
discuss this with me. Or if there is a topic that interests you but you don’t know
how to tackle it or where to start looking for references then again, please don’t
hesitate to contact me.
Due Date:
For credit, this bonus opportunity (title and summary paragraph) is
due by September 21.
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