INTRODUCTION TO BIOPHYSICAL ECOLOGY: SYLLABUS

Biology 641

Fall 2005 TTH 11-12:15,  CLS 302

Instructor:

Dr. Brian Helmuth, Earth and Water Sciences Room 615; 

777-2100; helmuth@biol.sc.edu; office hours by appointment

Rationale and prerequisites: The primary goal of this course is to teach you the tools necessary to examine ecological and physiological processes from a quantitative, physical perspective. By understanding how individual organisms interact with their environment, we can then expand to examining the physiological effects of “abiotic factors” at the level of populations and communities.  For example, we can predict, to some extent, how climate change is likely to impact natural ecosystems by understanding how temperature affects the physiology of individual organisms.  In order to benefit most fully from this course you must feel comfortable with some level of mathematics, including some calculus, although usually only algebra will be required.  It is thus necessary that you have completed some formal coursework in calculus and general ecology prior to enrolling in this course.  It’s fine if your skills are a little rusty, but you should be familiar with the basic concepts of each of these disciplines.  The goal is not, however, to force you to memorize formulae but rather to understand what they mean and how to use them in the real world.  Emphasis in grading will accordingly be placed on synthesis and understanding rather than on rote memorization.  

Grading: The breakdown in grades will be as follows:

16% Exam 1
15% Exam 2
12% Calibrated Peer Review: drafts and reviews (3)
12% Written reviews of readings for discussion groups (3)
15% Lab reports (3)
20% Final paper
10% Final presentation

The final grades will not be curved, so you all have the potential to receive a 4.0 (or, conversely, a 1.0!).Final grades of >90% will earn an “A”, 81-90 a “B”, 71-80 a “C” and 61-70 a “D”.Cooperation between students is strongly encouraged, but creative symbioses during the exam will not be tolerated.  Plagiarism of any kind, including direct copying from any internet source, will not be tolerated and will result in an F.  Note that we now have an electronic means of automatically checking papers against internet sources, so if you have any doubt about what constitutes plagiarism, or what the consequences of plagiarism are, please check the USC Academic Rules of Responsibility.  Late papers, critiques and reports will be penalized at a rate of 10% per day.

Weekly reviews and lab reports: Six days will be devoted to the discussion of readings from the primary journal literature and to guided laboratory exercises. Readings will be available online at the class website. You should read these papers thoroughly and be prepared to discuss them with your peers in class. Bring with you to class a written critique (1-2 pp.) of the major goals, methods and findings of these papers. Active participation in discussions is required, and will be reflected as part of your grade for each critique.  Click here for further details on 2 page summaries of readings. Further details will be given prior to the first discussion section. Lab reports should be completed and turned in on the dates indicated in the syllabus (indicated by asterisks (**)).

Final paper: By the end of this course you should be able to formulate interesting, biologically-relevant questions that use the techniques that you have learned.You also should know the material well enough to explain it to someone else. At the end of the course, you will be given an opportunity to demonstrate these skills in 1 of 2 formats.  Graduate students will work alone on this project.  Undergraduates may work in groups of 2-3 people; however, the expectations of the final project will be adjusted accordingly.

Option 1 will be in the form of a 6-8 page grant proposal (double spaced), in which you will explain why your topic is important, what background information is known (including relevant primary literature), and how you propose to conduct your research.The topic of your proposal is limited only by what you can sell: convince me that your proposed project is interesting, relevant, worthwhile, and possible, and you're all set. Last year several students successfully submitted their proposals to funding agencies and have actually carried out their projects. Also note that if you are an undergraduate and are planning to submit your proposal to a funding agency, you will need to deal with issues of intellectual property.  Graduate students will be expected to produce a slightly longer (10 page) proposal that includes a budget and timetable, and is appropriate for submission to NSF, EPA or NASA.

Option 2 An alternative format for your final project will be to develop lesson plans suitable for teaching one or more of the techniques learned in class to K-12 students.This option is encouraged for those students who want to pursue a career in education and public outreach. For this option, you must identify the core concepts to be taught, why these concepts are important, the age level being targeted, and the specific SC Science standards to be addressed (more information on this will be presented in class).In addition to creating the plan itself, you must discuss how it will be implemented, and how you will test its effectiveness in the classroom. Graduate students must additionally present their lesson plans in a classroom setting, or else produce auxiliary materials designed to increase the instructor’s core understanding of the subject (more details to be given in class).

Drafts of the various sections of your proposals and lesson plans are due as indicated on the syllabus.  You will use the Calibrated Peer Review (CPR) system to provide feedback to one another on drafts of your final papers.  Students will anonymously review each others' papers and have an opportunity to revise their own papers using the review feedback.  This is designed to increase your critical thinking about each others' work and ideas.  Twleve points of your final grade will be calculated from these CPR activities.  Note that your grade will be based on the quality of the reviews you write about other students' work, not the reviews you receive, but you will be penalized if you do not turn in your reviews, or if you do not turn in your drafts by the deadlines. 

Each section will be evaluated by at least three classmates using a Calibrated Peer Review (CPR) System.  You will receive a grade on the quality of your feedback using CPR.  Grading of your final project will be based on content as well as clarity (use a spell checker, please!!), so it would be wise to play close attention to feedback provided by your classmates on the drafts of your papers.  If you are working in teams, you will need to coordinate with team-mates in order to ensure that writing assignments are completed on-time. 

Final papers must be uploaded to blackboard on the final day of class no later than 5 PM.  You will also present a 10 minute synopsis of your proposal or lesson plan, including relevant background, rationale and methodology, to the rest of the class, on one of the last two days of class.

While we will frequently be reading papers from the research literature, the primary textbook for this course will be "Air and Water" by Mark W. Denny.  Sections of the text to be read prior to each class are listed on the syllabus (as MWD).The exams will primary test material from lectures and labs; however, I reserve the right to pose a few questions based solely on required sections of the text.

Click on highlighted links to download PDF versions of Labs and readings.  You must have Adobe Acrobat Reader on your machine to read these files.

 Click here to connect to Adobe and download a free copy.

 Click here to download lecture files (Powerpoint).  Note that you can also view them online by clicking each lecture below.

Syllabus : Biology 641: Introduction to Physiological Ecology

Aug. 18 (Th)         Lecture 1: Introduction to physiological ecology
                               Read USC Rules of Academic Responsibility        

Aug. 23 (Tu)     Lab 1: How do we measure “the environment?”

Introduction to field instrumentation and environmental biophysics

View Slide Show of Infrared Images to accompany Lab 1

Aug. 25 (Th) Lecture 2:  Effects of temperature on organismal physiology
  **Read Huey et al. 1989for next Tuesday. 
Click here for further details on 2 page summaries of readings.

Aug. 30  (Tu)      Paper discussion 1: Huey et al. 1989
**Summaries of Huey et al. due at beginning of class
                             **bring ibuttons from Lab 1 to class;  download ibuttons

Sept. 1 (Th)  Lecture 3: Boundary layers and Mechanisms of heat exchange in the environment I
Lab 1 reports due at beginning of class

Download sample Exam questions and answer Key

Sept. 6 (Tu) Lecture 4: mechanisms of heat exchange in the environment II


Sept. 8 (Th) Lab 2:  Convective cooling and fluctuating environments
**Read Lab 2 handout prior to class


Sept. 13 (Tu) EXAM 1
Click here to preview Equation sheet for exam 1
Lab 2 reports due at beginning of class

Sept. 15 (Th)   Lecture 5: Climate change and Biogeography


Sept. 20 (Tu)  Lecture 6: Global ecology and climate change: The bottom line
Click here to view more links and resources on global climate change


Sept. 22 (Th)  Lecture 7: Mechanics of gas and nutrient exchange

Sept. 27 (Tu)    Video: Silent Sentinels

Sept. 29 (Th)    Introduction to CPR (Briana Timmerman)
                          Paper discussion 2: Davis et al. 1998, Hodkinson 1999

Oct. 4 (Tu) Lab 3: Measuring coral respiration when you don't have an ocean
Lecture slides

Oct. 6 (Th) Communicating science to K-12 educators: Guest Lecture by Colette Dryden

Sample questions for Exam 2


Oct. 11 (Tu) EXAM 2 (material covered Sept. 15-Oct 6)
Lab 3 reports due at beginning of class

Oct. 13 (Th)     FALL BREAK- NO CLASSES    

Oct. 18 (Tu)      Lecture 8: Physiology of Diving and Saturation technology
                           Introduction to Final Projects:  Finalize groups and project ideas

Oct. 20 (Th)      Discussion of final projects (COME TO CLASS PREPARED TO GIVE A 5 MINUTE PRESENTATION)

Click here to view NSF Graduate Student Fellowship Website

Click here to view South Carolina Science Standards

Oct.  25 (Tu)       Discussion of final projects, continued

Oct. 27 (Th)      Lecture 8: Particle capture and Feeding in Flow

Nov. 1 (Tu)       Paper discussion 3: Lewis and Linn 1994
                         Calibrated Peer Review I: Draft of Final Paper Introductions Due; must be uploaded to CPR by 10AM . 
                                In order to preserve format, copy and paste in html format (with tags).
Log in to CPR web site

Nov. 3 (Th)       Lecture 9: Ecology of polar environments


Nov. 8 (Tu)       Lecture 10: Freeze tolerance and physiological ecology of polar environments
Reviews of CPR assignment 1 must be completed by 5PM today.
Log in to CPR web site

Nov. 10 (Th)     Lecture 11: Physiology and ecology of deep sea and hydrothermal vent communities
Calibrated Peer Review II: Draft of Final Paper Methods Due; must be uploaded to CPR by 10AM . 
                                In order to preserve format, copy and paste in html format (with tags).

Nov. 15 (Tu)     Lecture 12: Guest lecture by Dr. Zingmark

Nov. 17 (Th)     Work on group/individual projects
Reviews of Methods Due by 5PM:

Calibrated Peer Review III: Draft of Final Paper Discussions Due; must be uploaded to CPR by 10AM. 
                                In order to preserve format, copy and paste in html format (with tags).

Nov. 22 (Tu)     Communicating science to the news media
Reviews of Discussions Due by 5PM:

Nov. 24 (Th)    No classes: Thanksgiving break


Nov. 29 (Tu) Class presentations 1    (10 minutes per person/team)                         
View/Download Rubrics for presentations and final projects

Dec. 1 (Th) Class presentations 2 (10 minutes per person/team)  
                        **Final papers due, and must be uploaded to blackboard no later than 5 PM.