Biology 470: Senior Seminar - Size and Scaling in Biological Systems

Fall Semester

Mondays 1:10 - 4:00pm

Instructors

Siobhan Fennessy 205 Higley PBX 5455 Email: fennessym@kenyon.edu

Harry Itagaki 107 Higley PBX 5394 Email: itagaki@kenyon.edu

Overview:  Although we often look at biological phenomena as if they are distinct and separate from other processes, fundamentally, they are limited by the same physical constraints of non-living processes. More specifically, organisms and biological phenomena are constrained by physical limits to size and shape, and over time, evolution led to different solutions to specific problems imposed by physical constraints. The aim of this seminar is to investigate how physical limits affect the function of biological systems at all levels, from that of the ecosystem to that of the organelle, and to see common threads and disparities in how biological systems deal with similar problems imposed by physical limits.

This senior-level seminar class will rely heavily on the primary literature.  Students will orally present and critique relevant papers.   A synthetic paper (12-15 pages) will be the major course assignment.  Some class time will be devoted to "workshop" sessions where students will provide peer review on each other's work.

Topics: Students will contribute to the selection of topics to be addressed in this course. Some general areas to be considered include: Materials flow in biological systems; energy flow in biological systems; physical constraints of biological structure; and physical constraints on locomotion.

Text and reading: In addition to primary literature, we will use three texts for this class:

• O'Neill, R.V; D.L. DeAngelis; J.B. Waide; and T.F.H. Allen (1986) A Heirarchical Concept of Ecosystems. Princeton Univ. Press, Princeton, NJ. 253pp. (ODWA)
  
  
• Pennycuick, C.J. (1992) Newton Rules Biology. Oxford Univ. Pres, New York. 111pp. (P)
  
  
• Schmidt-Nielsen, K. (1984) Scaling: Why Is Animal Size So Important? Cambridge Univ. Press., New York. 241pp. (SN)
  
  
• The above books are not "textbooks," but are well-written explorations of their respective topics for the interested scientist; they explore the role that physical constraints play in biological processes at different levels of organization, and they will serve as foundations for the readings from the primary literature. The ideas presented in these books may not be in agreement with those of the instructors or with your ideas; what we do expect is that the class read these books critically and explore the issues as they are presented in each book.
  
  
• Each week, small student groups will be responsible for selecting and presenting articles from the primary literature and related background reading (from the texts above, reserve reading in the library, or review articles). In addition, each group will formulate a question pertaining to this reading. Students outside of the groups will write short (no more than one page) responses addressing these questions.
  
  
• Additional readings will be available on course reserve. These readings may be especially useful as background reading, and may be assigned by student discussion leaders as background reading for class discussion.
  
  
• For other resources, check the syllabus on the web for updated links.
  
  

Leading class discussions: Each student will be responsible for leading seminar 2-3 times during the semester, as part of a small group (to be assigned randomly). The group will choose articles to be assigned as reading; these articles must be approved by the instructors 10 days prior to the seminar date. This reading assignment will be provided to the entire class one week prior to the seminar date.  The group will meet with the instructors before the seminar, preferably on Thursday afternoon. The group should compose two discussion questions prior to this meeting, and these discussion questions will be distributed by e-mail on the Friday preceding seminar (see weekly response papers). The group should briefly present the articles (no more than 20 minutes total), and then facilitate class discussion. Class activities that help to demonstrate concepts and provoke discussion are encouraged.

Weekly response papers: Each week you will be provided with TWO questions related to the assigned reading, to be distributed by e-mail on Friday afternoon. Write no more than a ONE PAGE response to ONE of these questions. Weekly response papers are due at the start of seminar, and will be graded for effort and thoughtfulness. Weekly response papers are not required of students who are leading discussion for the week in question.

Paper: One 12-15 page paper will be assigned, with several drafts due throughout the semester. In addition, some class time will be devoted to "workshop" sessions where students will provide peer review on each other's work (see schedule). Students will give a brief (no more than 10 minute) PowerPoint presentation on their papers during the final week of the semester.

Participation: Class attendance and participation are a critical part of your responsibility in this seminar course, and will be included in determining your grade (see below). To participate intelligently in class, it is essential that you read and thoughtfully consider the assigned material before each class. We do not expect class participation to necessarily reflect "polished" or fully formed arguments. You are encouraged to explore an idea, suggest a possibility, or point out an area of confusion. You will not be graded on how "correct" your class participation is, but rather on how engaged you are with the material. Peer-review in the context of scheduled writing workshops is an integral part of course participation.

Grading: You are entitled to know how you are doing at any point in the class. Please see us if you are concerned about where you currently stand in this class.

Leading class discussions = 20% , Weekly response papers = 20%, Participation = 25%, Paper = 30%, Oral presentation of paper = 5%

Academic honesty: This class will follow the official Kenyon College position on academic honesty. It is your responsibility to understand and adhere to Kenyon's policies on academic honesty. For a print version, read pages 26-29 in the 2002-2003 Course of Study.

Students with special needs: If you have a hidden or visible disability which may require classroom or other accommodations please see us as soon as possible. If you have not already done so, you must register with the Coordinator of Disability Services (Erin Salva, salvae@kenyon.edu, x5145), who is the individual responsible for coordinating accommodations and services for students with disabilities. All information and documentation of disability are strictly confidential. No accommodations will be granted in this course without notification from the Office of Disability Services.

Schedule: This schedule may be adjusted during the semester. Additional reading assignments will likely be assigned for later class dates as we choose topics for discussion.

Date		Topic		Leaders		Reading		Assignment
8/26		Overview: Size and Scaling		SF, HI		ODWA-Ch. 1; SN-Ch. 1,2		Brainstorming for topics
9/2		Dimensional Analysis; Units of Measurement		SF, HI		P-Ch. 1,2; T. rex paper		Brainstorming for topics; Scaling Tutorial
9/9		Fractals		SF, HI		P-Ch. 5; Ch. 6 (to p. 86); handouts		Refinement of topics; topic due; Fractal Link 1; Fractal Link 2; Fractal Link 3
9/16		Communication At Different Levels		Brad, Dan		P - Ch. 3,4; Copepods; Birds; Animal Signals; handout		Outline due
9/23		Metabolism and Body Size		Kari, Diego, Yolande		SN-Ch. 6; Handout; Cell Metabolism; Dinosaurs; Size& Temperature; Size and Longevity; Gaia and Darwin		Outline workshop
9/30		Succession at Different Scales		Eric, Matt		arable-land; forensic; paleovegetation; post fire succession		Outline workshop redux
10/7		October Break
10/14		Materials Flow		SF, HI		SN- Ch. 7,8; chloroplast membrane; insect surface area; Landscapes; nutrient flux		Rough draft due
10/21		Scaling Up/Down in Experiments		Kari, Dan		ODWA Ch 4;space bacteria; mesocosms:		Rough draft workshop
10/28		Gap Dynamics Across Different Scales		Matt, Eric, Yolande		ODWA Ch 5; bryophytes; treefall; microbial biomass; windthrow		Discussion leading workshop
11/4		Reproductive Strategies for Different Sized Organisms (r/K)		Diego, Brad				Manuscript due
11/11		Chaotic/Non-Linear Processes		SF, HI		Gleick, additional readings to be handed out.
11/18		Immune Responses				Insect Immunity;		Manuscript workshop
11/25		Thanksgiving Break
12/2		Bio Indicators				biol. integrity; rotifers, global patterns; mfo in fish		Revised manuscript due, Oral presentation workshop
12/9		Class Presentations						All oral presentations