Course Syllabus: GGR 1216 – Advanced Biogeochemical Processes (Winter 2016) COURSE ADMINISTRATIVE INFORMATION GGR1216H: Advanced Biogeochemical Processes (cross listed as GGR406H5S) Lectures: Mondays 12:00 -­‐ 3:00 DV 1147 (UTM Campus) Course Website on Blackboard: GGR406H5S in the My Courses module at http://portal.utoronto.ca Course description: Biogeochemistry explores the intersection of biological, chemical, and geological processes that shape the environment. In an era of unprecedented human-­‐induced environmental and climate change, research in this field is advancing rapidly. This seminar course explores the processes underlying biogeochemical cycles of major elements such as carbon and nutrients, and examines how humans alter these cycles. Topics covered include biogeochemical processes in atmospheric, aquatic and terrestrial compartments, emerging techniques (e.g., stable-­‐isotopes) used in biogeochemistry, and how disruptions to these processes are at the root of many environmental issues such as eutrophication, climate change, ocean acidification and toxic metal contamination. PERSONNEL INFORMATION Instructor: Dr. Igor Lehnherr Office: DV 3281 (UTM) Office hours: Thursdays 1:30 -­‐ 3:00, or by appointment Email: [email protected] Communications: •
Always use your University of Toronto e-­‐mail address (…@mail.utoronto.ca) for all course-­‐
related communications. Other e-­‐mail addresses may be filtered as spam and we do not promise to respond to them. •
Please include the course code (e.g., ENV100Y5Y) as part of your subject line, and include your full name and student number in the body of the e-­‐mail. •
Please read the course handouts and check the course Blackboard site before e-­‐mailing a question, to make sure that it hasn’t already been answered. •
The first person that you should e-­‐mail concerning department-­‐ or program-­‐related queries or to submit documentation regarding a missed quiz or test is the Academic Counsellor for Geography/Environment, Sabrina Ferrari ([email protected]). COURSE ACADEMIC CONTENT AND REQUIREMENTS INFORMATION Course text: The course will be based primarily on the lecture material, and assigned readings from the scientific literature, which are accessible through the University of Toronto Library and/or provided on Blackboard. The following e-­‐book is also available through the University of Toronto Library, and is an excellent resource that students may wish to refer to for additional information: “Biogeochemistry: An analysis of global change” (3rd ed., 2012) by WH Schlesinger and ES Bernhardt (ISBN 978-­‐0123858740) Additional resources available through the library that students may find helpful: "Environmental Microbiology: From genomes to biogeochemistry" (2008) by EL Madsen (ISBN 9781405136471) Weekly paper discussions and reading reports: Eight times over the course of the term, you will be assigned one or two articles chosen from the recent scientific literature that will be discussed in-­‐class. Prior to each discussion period, you will be expected to thoroughly read the article and arrive at class prepared to discuss it. As this course is intended to be a seminar course, students are expected to actively engage in these discussions, with 20% of the course grade based on participation and contribution to discussions. In addition, you will write weekly reading reports (8 in total), due at the beginning of class the day the papers is being discussed, according to the following format: • Give the title, author(s), date, and source of each reading. Citation style will be as follows: Etkina, E. and D. Ehrenfeld. 2000. Helping ecology students to read: the use of reading reports. BioScience 50: 602-­‐608. (i.e., Authors. Year. Title. Journal and Volume: page numbers) • State the senior author's position and affiliation (e.g., Assistant Professor, Department of Geography, University of Toronto) • In 1-­‐3 sentences, summarize the main point(s) of the reading • In 1-­‐2 sentences EACH, describe: o The major strength of the study/reading o The major weakness of the study/reading o Your overall opinion/evaluation of the reading • In 1-­‐2 sentences, state why you think that the reading was assigned These weekly reading assignments are designed to foster critical thinking and analysis of current literature. Each report should be NO MORE than 500 words, not including the paper citation and author information (include word count at the bottom of the page). Grammar, spelling, sentence structure will count towards your grade. I will read and comment on each of your weekly assignments, and you will receive a grade between 0 and 5, corresponding to the following categories: • 0 (report not handed in) • 1 (inadequate) • 3 (acceptable) • 4 (very good) • 5 (exceptional) Your best 7 out of 8 grades (your worst grade will be discarded) will each contribute 5% towards your overall grade, totalling 35% of your final grade. Due dates for these assignments are Jan. 18 and 25; Feb. 1, 8, 22, and 29; and Mar. 7, and 14. LATE READING REPORT ASSIGNMENTS WILL NOT BE ACCEPTED (Grade will be zero) In addition, graduate students will each have the opportunity to lead the group discussion for one of the assigned readings, and this exercise will be evaluated as a component of your participation grade. Presentation: The presentation will address an interesting aspect of biogeochemistry, as chosen by each student. Students will be expected to develop a brief proposal and outline in early February. The choice of topic for your presentation is up to you (but must be approved by the course instructor). Presentations will be 20-­‐25 minute in duration and given during the last scheduled class at the end of term (April 4). Term Paper: Each student will be expected to write a term paper, due March 21. The topic of the paper may be related to your thesis, but must be grounded in Biogeochemistry. More details will be provided in class near the beginning of the term. Normally, students will be required to submit their course essays to Turnitin.com for a review of textual similarity and detection of possible plagiarism. In doing so, students will allow their essays to be included as source documents in the Turnitin.com reference database, where they will be used solely for the purpose of detecting plagiarism. The terms that apply to the University's use of the Turnitin.com service are described on the Turnitin.com web site”. Students may opt out of submitting their paper through Turnitin.com, in which case the course instructor may require submission using other methods or with alternative demonstrations of originality such as an interview, draft versions of essays, or copies of background notes. Grading scheme: Reading reports 35% Participation (including leading class discussion of one of the assigned readings) 20% Presentation 15% Term Paper 30% Academic support available: 1) Contact information stated above for specific questions and concerns. 2) Course Blackboard site for lecture topics, review questions, articles, diagrams that are not otherwise accessible, discussion board for general questions and answers. 3) Your ability to write an effective term paper is a significant aspect of your grade assessment, so it is important to write well. A good way to prepare is to consult Specific Types of Academic Writing listed at University of Toronto Advice on Academic Writing, where there is guidance on this and other aspects of academic writing. 4) For access to reading material try the UTM Library http://library.utm.utoronto.ca. Material that cannot be accessed in this way will be placed on reserve. 5) To address weaknesses in the skills noted in the course description above contact the Robert Gillespie Academic Skills Centre www.utm.utoronto.ca/asc. 6) Just before the end of term be sure to check the UTM Exam Schedule at https://registrar.utm.utoronto.ca/student/examschedule/finalexams.php. WEB LINKS Required Links: •
Code of Behaviour on Academic Matters from the most recent Academic Calendar •
UTM AccessAbility Resource Centre Other Useful Links: •
University of Toronto Advice on Academic Writing •
UTM Library http://library.utm.utoronto.ca •
Robert Gillespie Academic Skills Centre www.utm.utoronto.ca/asc •
UTM Exam Schedule https://registrar.utm.utoronto.ca/student/examschedule/finalexams.php POLICIES Accessibility Needs: The University of Toronto is committed to accessibility. If you require accommodations for a disability, or have any accessibility concerns about the course, the classroom or course materials, please contact Accessibility Services as soon as possible: http://www.accessibility.utoronto.ca/Home/About-­‐Us.htm Students may also want to contact Accessibility Services Office if they have problems arising from chronic issues or injuries sustained during the term that affect their ability to do tests. For more information, see http://www.accessibility.utoronto.ca/Faculty-­‐and-­‐Staff.htm Missed Term Work (Assignment/Lab – as per Department of Geography policy): Late assignments, with the exception of the reading reports which will not be accepted after the due date, will be subject to a late penalty of 10% per day (including weekends) of the total marks for the assignment. Assignments submitted five calendar days beyond the due date will be assigned a grade of zero. Academic accommodation can be made when an assignment is late. For accommodations on late/missed assignments please see section on “Extension of Time”. Informing Your Professor and Submitting Appropriate Documentation: The following steps must be completed in order to be considered for academic accommodation for any course work such as missed tests or late assignments: 1. Students must inform their professor in writing (e-­‐mail is acceptable) within 24 hours of a test date/assignment due date of any circumstances that prevent them from writing a test or submitting an assignment on time. 2. Original supporting documentation (e.g. Verification of Student Illness or Injury form, accident report, etc) MUST BE SUBMITTED to the instructor. Please Note: If you missed your test for a reason connected to your registered disability, please be advised that the department will accept documentation supplied by the UTM AccessAbility Resource Centre. Note: (i) ROSI declarations are not accepted as supporting documentation. (ii) If your reason for absence is due to a last minute flight due to a family emergency (illness/death etc.) you must provide your flight itinerary INCLUDING the date the flight was purchased as well as boarding passes in addition to proof of death/illness/accident. 3. Verification of Student Illness or Injury forms MUST include the statement "This Student was unable to write the test on date(s) for medical reasons". Documentation MUST show that the physician was consulted within ONE day of the test date. A statement merely confirming a report of illness made by the student is NOT acceptable (such as, “This patient tells me that he was feeling ill on that day.”). Verification of Student Illness or Injury forms can be found on the Office of the Registrar’s webpage (http://www.illnessverification.utoronto.ca/getattachment/index/Verification-­‐of-­‐Illness-­‐or-­‐
Injury-­‐form-­‐Jan-­‐22-­‐2013.pdf.aspx). Please note that the written explanation and documentation that you submit represents an appeal from you, requesting the opportunity to account for that portion of your grade in some other manner. If an appeal is not received, or if the appeal is deemed unacceptable, you will receive a grade of zero for the item you missed. If the appeal is granted – that is, your reason for missing the item is considered acceptable by the committee – then a mechanism for accounting for the grade value of the missed item will be discussed. Decisions will be communicated by email within two weeks of receipt of all completed documents. Note: It is your responsibility to ensure your email account is working and able to receive emails. Claims that a Departmental decision was not received will NOT be considered as a reason for further consideration. Contact the course instructor should you NOT receive notification of your decision within 2 weeks of submission. Note that holidays and pre-­‐purchased plane tickets, family plans, your friend’s wedding, lack of preparation, or too many other tests are not acceptable excuses for missing a quiz, a test, an assignment or any other item of term work. Extension of Time Students MUST submit a request to the course instructor for extension in ADVANCE of the deadline in order to receive a decision. Academic Integrity/Honesty or Academic Offenses: It is your responsibility as a student at the University of Toronto to familiarize yourself with, and adhere to, both the Code of Student Conduct and the Code of Behaviour on Academic Matters. This means, first and foremost, that you should read them carefully. •
The Code of Student Conduct is available from the U of T Mississauga website (Registrar > Academic Calendar > Codes and Policies) or in your print version of the Academic Calendar. •
The Code of Behaviour on Academic Matters is available from the U of T Mississauga website (Registrar > Academic Calendar > Codes and Policies) or in your print version of the Academic Calendar. •
Plagiarism is an academic offense at the University of Toronto. Plagiarism is quoting (or paraphrasing) the work of an author (including the work of fellow students) without proper use of citation (and quotations marks when using an author’s words). Students also should not be submitting any academic work for which credit has previously been obtained or is being sought, without first discussing with the instructor. Penalties for plagiarism can include grades of zero on an assignment or course, notations on transcripts, and suspension from the university. For further clarification and information, please see the Faculty of Arts & Science policy on Academic Misconduct at http://www.artsci.utoronto.ca/osai/The-­‐rules/what-­‐is-­‐academic-­‐
misconduct and consult the ‘How not to plagiarize’ website at: http://www.writing.utoronto.ca/advice/using-­‐sources/how-­‐not-­‐to-­‐plagiarize. Expectations/Classroom Behaviour/Behaviour in the Academic Setting: Our expectation of you is that you will show respect to the Course Instructor, TAs, other faculty, staff, and fellow students. This includes arriving on time and staying for the entire class (so you don’t disturb others by your late entry or early departure); listening quietly (so you don’t disturb others by your chatting or online activities); approaching your course work with an open, honest spirit and enthusiasm; and otherwise adhering to the Code. In turn, you can expect the Course Instructor, staff, and TAs to show respect to you and your fellow students; to deliver the best course that they possibly can; to communicate their enthusiasm for the material; to maintain fairness in all aspects of course delivery and assessment; and otherwise to adhere to the University’s Code of Behaviour on Academic Matters. How to Query or Challenge a Mark: Please note that, according to UTM policy, you have one month from the date an item is returned to you, during which time you may query the mark or submit the item for remarking. Contact the Course Instructor for all queries about course marks, or if you wish to challenge a mark. Absolutely no item will be remarked after the one-­‐month period has passed. Material submitted for remarking must be accompanied by a brief written explanation detailing your reasons for dissatisfaction with the original mark (such as an addition error, or something you think the marker may have missed). The item may be returned first to the TA who originally marked it. If you are still dissatisfied, it may be passed on to the Course Instructor for reconsideration. TENTATIVE COURSE SCHEDULE (subject to change) DATE WEEK TOPIC Jan. 11 1 Introduction, What is Biogeochemistry, Metabolic/Redox Processes Jan. 18 2 Microbial Processes, examples from Carbon and Nitrogen cycles Jan. 25 3 Atmospheric biogeochemical processes Feb. 1 4 The Oceans – circulation, carbon pumps, productivity, acidification Feb. 8 5 The Global Water Cycle and linkages to biogeochemical processes Feb. 15 No Class Reading Week Feb. 22 6 Terrestrial Environments – soil and lithospheric processes Feb. 29 7 Freshwaters – lakes, wetlands, eutrophication Mar. 7 8 Contaminants – Endocrine disruptors, PAHs, mercury Mar. 14 9 Environmental Change – archives and proxies Mar. 21 10 Special topics – isotopes/stoichiometry/-­‐omics Mar. 28 No Class Easter Monday Apr. 4 11 Student Presentations Preliminary list of assigned readings (subject to change): Schindler, D.W. and Donahue, W.F. (2006). An impending water crisis in Canada’s Western Prairie Provinces. Proceedings of the National Academy of Science 103: 7210-­‐7216. Canfield, D.E., Glazer, A.N., & Falkowski, P.G. (2010). The evolution and future of Earth’s nitrogen cycle. Science, 330, 192-­‐196. Mahowald, N. (2011). Aerosol indirect effect on biogeochemical cycles and climate. Science, 334, 794-­‐
796. Doney, S. (2010). The Growing Human Footprint on Coastal and Open-­‐Ocean Biogeochemistry. Science, 328, 1512-­‐1516. Reich PB, Hobbie SE and Lee TD. (2014). Plant growth enhancement by elevated CO2 eliminated by joint water and nitrogen limitation. Nature Geoscience, 7, 920-­‐924. Schindler, DW (2012). The dilemma of controlling cultural eutrophication of lakes. Proceedings of the Royal Society B, 279, 4322-­‐4333. Raymond, P et al. (2013). Global carbon dioxide emissions from inland waters. Nature, 503, 355-­‐359. Kurek J, Kirk J, Muir D, Wang X, Evans M, and Smol J. Legacy of a half century of Athabasca oilsands
development recorded by lake ecosystems. 2013. Proceedings of the National Academy of Sciences of
the United States of America, 110: 1761-1766.
Wiklund J, Hall R, Wolfe B, Edwards T, Farewell A, Dixon D. 2012. Has Alberta oil sands development
increased far-field delivery of airborne contaminants to the Peace–Athabasca Delta? Science of the
Total Environment, 433: 379-­‐382. Martínez-­‐García A, Sigman DM, Ren H, Anderson RF, Straub M, Hodell DA, Jaccard SL, Eglinton TI, and Haug GH. (2014). Iron Fertilization of the Subantarctic Ocean During the Last Ice Age. Science, 343: 1347-­‐
1350.