A DVANCED E COLOGY , BIO 411
Spring 2016
Instructor: Dr. Carrie L. Woods cwoods@pugetsound.edu
Thompson 223B
253-879-3301
Office hours: M: 11-1 pm, Th: 1-2 pm; or email for appointment
Lecture: MWF 10:00 am – 10:50 am (TH381)
Textbook: Elements of Ecology, 9 th
edition. 2015. Smith & Smith, Pearson
Readings and Website: I will assign many readings from the primary literature as we go through the course and you will also contribute papers to our discussions. Moodle will be used as the course website. I will post presentations, assignments, readings, news, etc. Please visit the site regularly.
C OURSE D ESCRIPTION AND O BJECTIVES :
This course provides an in-depth examination of major ecological fields, including ecophysiology, island biogeography, community ecology and ecosystem ecology. Current ecological research is used to introduce major concepts and methods, foster critical thinking and discussion, and to introduce issues of experimental design and analysis and different approaches to ecology. This course will enhance skills that are critical for ecologists including written and oral communication skills, quantitative and programming skills.
The overarching goals of this course are to 1) broaden and deepen your understanding of the field of ecology, 2) develop skills needed to be an independent scientist. These skills include:

Understanding the process of scientific research and discovery;

Developing your critical thinking and hypothesis testing skills;

Learning to read and critically evaluate scientific papers;

Advancing your statistical analysis skills to analyze scientific data;

Advancing your scientific communication skills by way of presentations and written assignments.
Lectures, Discussions and Workshops: The course is designed so that you get an introduction to the topic on Mondays and then we will discuss it as a class using an example from the scientific literature on Wednesdays. For paper discussions, I will lead the first one and then will randomly pick someone to lead the discussion. We will follow a jigsaw, fishbowl, or journal club format.
These discussions will help with understanding the ecological material and developing critical thinking skills. On Fridays we will have workshops that develop your skills that are essential for ecologists: written and oral communication skills, quantitative and analytical skills. For workshop days that we are working in R, you must bring a laptop to class.
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G RADING
Item
Exams
Exam I
Exam II
Final Exam
Research Proposal
Research Paper Topic
Annotated Bibliography
Proposal Summary
First Draft of Proposal
Peer Review
Research Proposal
Oral Presentation of Proposal
Projects
Date
3/4
4/13
5/9
2/5
2/22
3/21
4/4
4/18
5/4
4/25-5/4
Points
290
340
140
80
80
130
40
25
80
20
150
25
% of grade
36%
42%
18%
Project I
Project II
Project III
Class Participation
Paper summaries (3 x 5 pts)
Participating in class discussions
TOTAL
2/17
3/11
4/1
30
40
40
60
15
15
4%
800 100%
Exams
Exams are scheduled during lecture (see Course Schedule). Each of the first two exams will be non-cumulative . The final exam will be cumulative but will focus more on the final course section. Exams will be primarily essay format with synthetic discussion questions and data interpretation questions that will require you to incorporate knowledge from lecture, text, and scientific readings. If lectures shift, then I will inform you of what will be on the exams.
Research Proposal
You will write a research proposal on ecology that will consist of a literature review of your topic (Background) followed by a proposal of a new area of your topic (Proposal). You will choose your topic early so that you have ample time to gather your references and write your annotated bibliography. Your primary references for this paper will be the scientific literature.
You could search journals such as Ecology, Journal of Ecology, Plant Ecology, Animal Ecology or any other ecology journal. Your paper should include at least 15 scientific articles . See the
‘Research Proposal Guidelines’ on Moodle for more information on all aspects of the proposal.
Annotated Bibliography
An annotated bibliography is a list of citations to books, articles, and documents. Each citation is followed by a brief (~150 words) descriptive and evaluative paragraph, the annotation. The purpose of the annotation is to inform the reader of the relevance, accuracy, and quality of the sources cited. For this assignment, you will need to choose some area of ecology that interests you. Compile a list of references and choose the 15 most important
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papers associated with the topic. Then construct your bibliography! A great way to get greater exposure to the literature!
Proposal Summary
You will submit a one-two page double-spaced summary of your proposal. This will be written like an abstract and include a succinct overview of the background, a summary of your questions and what you propose to do, how you will answer your questions, and why the study is important.
Peer Review
The first draft of your research proposals will be read and reviewed by one of your peers and myself. Use the comments and suggestions to better the final draft of your proposal.
Oral Presentations
You will present your research proposal in a 12 min oral presentation to the class. The presentation should be done using Powerpoint. It should be 8-10 min in length with 2-4 min for questions. The presentation should introduce the topic, state the research question, summarize your proposal, and conclude with a statement on why your proposal is important.
Projects
There are 3 projects in this class that stem from the work you do in the workshops. You will have an opportunity to work on a dataset that I collected on epiphytes on the island of Dominica in the lesser Antilles in 2008. These data are not yet published. You will use this dataset to learn statistical analyses, data interpretation, data presentation, and scientific writing. BONUS: at the end of the semester, I may offer one student the opportunity to be a co-author on the manuscript for these data depending on the quality of their analyses and scientific writing.
Class Participation
There are two ways in which I will assess class participation. The first is through your paper summaries, which will highlight your involvement and understanding of our paper discussions, and the second is through class participation and how much you contribute to in-class discussions.
Paper Summaries
At three times in the semester you must submit a summary of a paper that we have discussed in class. This will include a summary of the paper (similar to an abstract), a critique of the paper, and a proposal for where the research should go next. See the ‘Guidelines for Paper
Summaries’ handout on Moodle for more information and for a grading key.
C
OURSE
P
OLICIES
You are responsible for all material covered in lectures, portions of the text assigned during lectures, and readings listed on the syllabus. In lecture periods, you will be given information that is not in the textbook and you may not make audio recordings of my lectures. Therefore you must attend lectures and take detailed notes if you want to do well in the course. The list of readings from the required book, Elements of Ecology, will be in the schedule. I will give ample notice for readings. I will add other reading material that we will discuss directly into
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Moodle as pdf files. You are responsible for printing, reading, and either bringing them to class or critically evaluating them before coming to class. I would also suggest reading the material again after class to solidify the findings.
Diversity: Lack of respect for diversity will not be tolerated in the class. Diversity encompasses age, life experiences, profession, race, religion, gender, nation, lifestyle, social class, learning style, philosophy of life, sexual orientation, personality, mental and physical challenges, customs, values, among other.
Cell phones & Laptops: cell phones should be turned OFF during lecture and lab. You should
NOT use a laptop to take notes. I have provided a link in Moodle to explain why.
There are no make-up quizzes or exams. See the course schedule for the dates of your quizzes and exams and mark them on your calendar today. If you anticipate a problem, see me immediately. If you miss an exam due to an unforeseen emergency and can provide appropriate documentation, I may take this into consideration when assigning final grades. In keeping with
University policy, the final exam will be given ONLY at the time indicated in the course schedule.
Turning in Assignments: All assignments will be turned in through Moodle (unless stated otherwise). There will be Assignment icons in Moodle that allow you to upload your assignments. This saves paper, allows me to send comments back to you outside of class, prevents lost assignments and time-stamps your submission. Feedback will be done using Track
Changes in Word and uploaded directly to Moodle. You will receive an email when I upload my edits. Assignments should be uploaded to Moodle at the start of lecture as indicated on the individual assignment and lecture schedule. Please ONLY send a WORD DOCUMENT file and use the file naming format: your last name-assignment (e.g., Woods-Assignment 1).
Late Policy: Any assignments turned in late will lose 10% a day (including weekends), down to
0%. I cannot accept any written assignments after the start of our final exam. Work turned in late on the same day that it is due will be considered ½ a day late and be assessed a penalty of 2.5% of the original point value. TO BE FAIR TO ALL STUDENTS, I MUST STRICTLY
ENFORCE THIS LATE POLICY. I will consider waiving the penalty only in a case of a medical or family emergency. Written documentation of the nature of the emergency may be required. An extra-curricular activity, travel, or work in another course is not a valid reason for late work. If you must miss class for one of these reasons, it is your responsibility to check the lecture schedule and assignment guidelines to determine if anything will be due in your absence.
Please check with me if you are unsure.
Group Work : There will be times over this course where you will work on group assignments and/or utilize data collected while working in groups. Each and every graded assignment based on such effort must be your own work. For the tables or figures, you each must make your own, even if you work together and help each other. A nyone handing in someone else’s work or printing multiple copies of the same work to be handed in separately will be treated as plagiarism.
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Office of Accessibility and Accommodation: If you have a physical, psychological, medical or learning disability that may impact your course work, please contact Peggy Perno, Director of the Office of Student Accessibility and Accommodations, Howarth 105, pperno@pugetsound.edu, 253.879.3395. She will determine with you what accommodations are necessary and appropriate. All information and documentation is confidential.
If you are enabled extra time on an exam, you must give me the form from the Office of Student
Accessibility and Accommodations ONE WEEK before any exam (at the start of class is best so I can provide adequate accommodations) . Generally, extra time is not given for inclass quizzes but if you absolutely need extra time for the quizzes, please come and talk to me the first week of class.
Student Bereavement Policy: Upon approval from the Dean of Students’ Office, students who experience a death in the family, including parent, grandparent, sibling, or persons living in the same household, are allowed three consecutive weekdays of excused absences, as negotiated with the Dean of Students. For more information, please see the Academic Handbook.
Classroom Emergency Response Guidance:
Please review university emergency preparedness, response procedures and a training video posted at www.pugetsound.edu/emergency/ . There is a link on the university home page. Familiarize yourself with hall exit doors and the designated gathering area for your class and laboratory buildings.
If building evacuation becomes necessary (e.g. earthquake), meet your instructor at the designated gathering area so she/he can account for your presence. Then wait for further instructions. Do not return to the building or classroom until advised by a university emergency response representative.
If confronted by an act of violence, be prepared to make quick decisions to protect your safety. Flee the area by running away from the source of danger if you can safely do so. If this is not possible, shelter in place by securing classroom or lab doors and windows, closing blinds, and turning off room lights. Lie on the floor out of sight and away from windows and doors. Place cell phones or pagers on vibrate so that you can receive messages quietly. Wait for further instructions.
Academic and Scientific Integrity: Academic honesty is a fundamental principle of intellectual endeavor. Scientific integrity is an integral part of the scientific process. It is your responsibility to make sure that you know and completely understand what constitutes academic dishonesty and plagiarism. It is your responsibility to read and understand the UPS policies on Academic
Integrity. If you haven’t already been through the new Academic Integrity tutorial on the library’s website, you should familiarize yourself with it: http://alacarte.pugetsound.edu/subjectguide/6-Academic-Integrity-Puget-Sound .
By becoming a part of the UPS community and taking this course, you are stating that you have read the information on the UPS web page and that you fully understand what constitutes plagiarism and the penalties for academic dishonesty.
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