BIOS 3010: Ecology, Dr Stephen Malcolm

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1 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. 1. Introduction Please structure the paper as follows: 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 H o = 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 page - 1

2 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 (=H 1 ), another might be that they find enemy-free space off the coast of Maine (they may be escaping predators in the Caribbean)(=H 2 ). 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) : Dr. Stephen Malcolm BIOS 3010: term paper page - 2

3 (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. Dr. Stephen Malcolm BIOS 3010: term paper page - 3

4 (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. Dr. Stephen Malcolm BIOS 3010: term paper page - 4

5 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 5. 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 and everything should be submitted electronically by to me at steve.malcolm@wmich.edu : Date Activity Score September 19 Submit your paper topic with a summary description of an ecological observation Bonus 1 (<5 points) October 10 Submit annotated bibliography on your topic 30 points October 27/28 Present a detailed plan of your paper 30 points November 16 Hand in a complete first version of your paper 40 points December 5 Hand in your final revised paper 100 points Total 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 ( 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): Dr. Stephen Malcolm BIOS 3010: term paper page - 5

6 Hunter, M. D., and R. E. Forkner Hurricane damage influences foliar polyphenolics and subsequent herbivory on surviving trees. Ecology 80(8): 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. Dr. Stephen Malcolm BIOS 3010: term paper page - 6

7 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 19) Annotated bibliography (with title, hypotheses & summary of paper by October 10) Detailed plan (PowerPoint presentation in labs on October 27/28) First version of completed paper (by November 16) Final paper: (by December 5) Content and presentation (general overview) Structure (hypotheses, logic of organization, significance of argument) Interest (use of sources, innovative arguments, use of figures) Score Bonus <5 30 Relevance of topic to ecology 20 References Total score / Dr. Stephen Malcolm BIOS 3010: term paper page - 7

8 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 Or For full credit for the annotated bibliography you need to submit the following by the due date (October 10): 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 10) 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 Dr. Stephen Malcolm BIOS 3010: term paper page - 8

9 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 27/28. Paper structure Score Introduction: Observation 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) Total score Please see the attached pdf file for a plan presentation guide Dr. Stephen Malcolm BIOS 3010: term paper page - 9

10 BIOS 3010: ECOLOGY Fall 2016 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 19. Dr. Stephen Malcolm BIOS 3010: term paper page - 10