Biol 336- Integrative Animal Biology - Spring 2006
Instructor: Chris Gillen
310 Higley Hall
PBX 5399
email: GILLENC

last update - April 20, 2006 7:52 AM
please send corrections, comments to gillenc@kenyon.edu

Overview: Biology is becoming increasingly integrative. Complex biological questions are being addressed by multiple disciplines and approaches, operating across organizational levels and using a diverse array of organisms. This course takes an integrative approach towards understanding animals. We will explore fundamental questions about animals from the perspective of different organizational levels and experimental approaches. We will examine a wide diversity of animals, extending our interest beyond the well-known model organisms. A focus will be learning to think critically in an integrative way about animal biology. Careful reading and writing about important topics in animal biology will be emphasized.

It is not easy to define Integrative Biology, but this description by Marvalee H. Wake of UC Berkeley is a good starting place.

Prerequisites: Prerequisite for this course is one 200 level Biology course or permission of the instructor.

Texts: This course has three books:

• Janet Moore, Introduction to the Invertebrates, is a succinct textbook describing invertebrate animals, including their structure, physiology, and evolutionary relationships.
• Steven Vogel, Cats' Paws and Catapults: Mechanical Worlds of Nature and People, compares human technology to nature's technology. This is not a textbook, but rather an provocative exploration of the similarities and differences between the natural world and man-made objects.
• J. Scott Turner, The Extended Organism: The Physiology of Animal-Built Structures, looks at physiology at the interface of animals and their environments. Like Cats' Paws, this is not a textbook, and it contains challenging arguments about the nature of animal physiology and evolution.

Generally, we will use the Moore text to learn the basics about invertebrate animals, and use the Vogel and Turner books to generate discussion. Moore is assigned every week. Most class meetings also cover one chapter in Vogel or Turner. Four class meetings will be devoted to reading primary literature (found in the p/data/biology/biol336 folder).

Weekly reading (WR): Class meetings will primarily be discussions of the assigned readings. Therefore, it is imperative that you carefully read the assigned material for each class meeting. Once each week (Tuesday or Thursday) you will hand in a weekly reading assignment. Half the class will write these for the Tuesday reading, half for the Thursday reading. These assignments will consist of:

• Keyword list. List at least 10 key terms used in the day's reading. You need not list definitions, but you should try to learn the meaning of each word. If you can not find the meaning of a word in your list, put an "*" next to it. Check out the "sources" section at the end of this syllabus, or the books on reserve in the Biology Reading Room for help with definitions.
• Two one page essays. The intent here is to write about some interesting aspect of the reading. These essays will usually focus on the Vogel, Turner, or research article reading, though you may use Moore when appropriate. You might choose any of the following forms for your essay:
  • Controversy: Identify a controversial topic in the reading and describe it.
  • Key sentence: Choose a key sentence in the reading, one that makes an important point. State the sentence, give the page number and line number, and explain it in your own words. Explain why the sentence is important.
  • Connection: Connect some aspect of the reading to another one of the assigned texts, to something else we've discussed in the course, or to a different class you've taken.
  • Contrast: Take two examples (either animals, animal made-structures, or human-made structures) and contrast them, showing how they are different.
  • Principle: Identify a general principle in the reading and show how it relates to two or more different animals.
  • Paragraph: Find a paragraph in the reading that is trying to make an argument. Evaluate the strength of the argument. How strong is the evidence and how well is it presented?
  • Wild card: Write something interesting about the reading. No more than one wild-card per week and no more than four for the semeseter. Be careful to focus your essay into a coherent and interesting argument.
  At the top of each essay, indicate which form you are following. These essays will be due 30 hours before class. Deadline is Monday morning at 2am for Tuesday classes and Wednesday morning at 2am for Thursday classes. Ordinarily, I will read them and provide feedback before class. I will also often use the ideas in these essays as a basis for class discussions.
• There are 14 WR assignments for the semester. I will average the grades for your best 12.

Short essays (SE): Four three-page essays are assigned. The basis for each of these essays can be one of the WR essays that you have written. Alternatively, it might be an idea that arose out of class discussion or your further reading and thinking. You may incorporate what you've learned in class discussions in these essays. You must also use at least two outside (not one of the class books) sources, including at least one must be a primary research article. The idea here is to try to say something interesting, controversial, exciting, provocative, integrative, synthetic, and/or creative about animal biology. Vogel and Turner are good models in this regard.

Long essays (LE): Two five-page essays are assigned. I expect that these will be revisions and expansions of short essays. You must use at least four outside sources, including at least two must be primary research articles. Like the short essays, the idea here is to be interesting, controversial, exciting, provocative, integrative, synthetic, and/or creative.

How to make a strong argument in your essays.

Procedure and standards for submitted work: All work for this class should be submitted to me as an e-mail attachment with the following guidelines:

• Documents must be in Microsoft Word format (.doc).
• Assignments should be handed in as single files.
• Do not embed pictures or drawings or anything else fancy into your files. They should be simple text.
• The e-mail should contain the following subject line: Biol336 [the abbreviation of the assignment]. For example: Biol336 WR, Biol336 SE, or Biol336 LE.

Work submitted in this class must conform to the following basic standards or it will be returned for revision without a grade.

• Assignments with multiple pages must be paginated.
• Assignments must include a list of references cited in a proper format.
• Assignments must be proofread for spelling and grammatical errors.
• Assignments must conform to page limits. You must use 12 point Times New Roman, double-spaced, with one-inch margins. You may include your name and the date as a header so that it does not use precious space.

Grading criteria for essays: Excellent essays will have the following characteristics:

• The essay has a central theme or focus. The entire essay makes a coherent argument.
• The essay demonstrates critical, creative, and/or insightful thought about animals. It makes a particular point or statement about animal biology and provides supporting evidence.
• The essay is synthetic, comparative and/or integrative. It incorporates thought at more than one biological level and/or discusses different animal groups.
• The essay uses the relevant scientific literature, including primary research articles, effectively. Outside literature is used to support the main argument of the essay.
• The essay effectively incorporates material from the course texts.
• The essay demonstrates a deep understanding of the underlying biology.
• The essay is well-written and well organized. It follows the format and page limits described in the project assignment

Class attendance and participation: Class attendance is mandatory. Class participation and attendance will account for 25% of your grade. Additionally, there will be a 3 point reduction in the final average for every 3 unexcused absences (no penalty for less than 3 unexcused absences). To participate intelligently in class, it is imperative that you read the assigned material before each class, even when you are not assigned to write about it. Please feel free to ask questions, add insights, request clarifications, etc. at any time during class. Speaking in class will be a primary determinant of class participation, but I realize that there are many different styles and will consider other contributions. In order for you to receive feedback on your class participation, you are invited to schedule a feedback meeting in the 5th or 10th week of the semester.

This class begins at 8:10. Please be prepared to begin class at 8:10. This means arriving at about 8:05. Late arrivals will be counted as absences.

Academic honesty:This class will follow the official Kenyon College position on academic honesty .

Students with special needs: Students with disabilities who will be taking this course and may need disability related academic accommodations are encouraged to make an appointment to see me as soon as possible to discuss your learning needs. Also, you are required to register for support services with the Office of Disability Services in the Old Bank Building. Please contact Erin Salva at 5453 or e-mail salvae@kenyon.edu.

Grading:
You are entitled to know how you are doing at any point in the class. Please see me if you want to know your current grade in the class.
Weekly reading assignments = 25%
Short essays = 25%
Long essays = 25%
Class attendance and participation = 25%

Deadlines and conflicts:  Work in this class that is handed in late will be penalized 1/3 grade per day.  For example, a B+ will become a B.  If conflicts exist with scheduled extracurricular events, students must contact me one week before the date to discuss ways to handle the conflict.  Written assignments should be handed in before the due date if a class is to be missed because of a scheduled event.
   
Schedule:  (this is a tentative schedule, and may change as the course progresses)
 

Week	Dates	Tuesday reading	Thursday reading	Assignments
1	Jan 17,19	This syllabus Lobster sound production - Patek, JEB 2002.	Vogel - preface, 1 Turner - preface, 1 Moore - 1 (Evolution)	WR for everyone is due Thursday morning at 2am.
2	Jan 24, 26	Vogel - 2 (Design, Evolution) Moore - 2 ( Molecular Evolution)	Choanoflagellate - King et al., Science, 2003. Moore - 20 (Invert Evol History)
3	Jan 31, Feb 2	Turner - 2 (Thermodynamics) Moore - 3 (Porifera)	Vogel - 3 (Size and Scaling) Moore - 4 (Cnidaria)	Short Essay 1
4	Feb 7, 9	Vogel - 4 (Surfaces, Curves) Moore - 5 (Worms)	Turner - 3 (Energy, Efficiency) Moore - 19 (Development)
5	Feb 14, 16	Turner - 4 (Gravitaxis) Moore - 6 (Platyhelminthes)	Vogel - 5 (Stiff, Soft)	Feedback meeting 1
6	Feb 21, 23	Vogel - 6 (Rigidity) Moore - 7 (Nemertea)	Turner - 5 (Shape, Growth) Moore - 8 (Nematoda)	Short Essay 2
7	Feb 28, Mar 2	Anenome Hox - Finnerty, et al., Science, 2004. News and Views	Vogel - 7 (Push, Pull) Moore - 9 (Annelids)
8	Mar 21, 23	Vogel - 8 (Engines) Moore - 10 (Molluscs)	Turner - 6 (Feeding, Digging) Moore - 11 (Bivalves, Cephalopods)
9	Mar 28, 30	Vogel - 9 (Batteries, Transmission) Moore - 12 (Arthropods)	Vogel - 10 (Pumps, Jets, Flying, Swimming)	Short Essay 3
10	Apr 4, 6	Turner - 7 (Water) Moore - 13 (Crustacea)	Cambrian disparity - Briggs, Fortey, Science, 1989. Moore - 14 (Chelicerate, Myriapods)	Feedback meeting 2
11	Apr 11, 13	Vogel - 11 (Growth, Repair, Development)	Turner - 8 (Respiration) Moore - 15 (Insects)	Long Essay 1
12	Apr 18, 20	Turner - 9 (Temperature, Photosynthesis) Moore - 16 (Lophophorates)	Vogel - 12,13 (Copying) Moore - 17 (Echinoderms)
13	Apr 25, 27	Swimbladder - Berenbrink et al., Science, 2005 News and Views, Supplement.	Turner - 10 (Sound) Moore - 18 (Chordata)	Short Essay 4
14	May 2, 4	Turner - 11 (Gaia, Homeostasis) Moore - 20 (Invert Evol. History)	Vogel - 14 (Contrasts, Convergences, Consequences)

Long essay 2 is due at the scheduled final exam period: May 8, 1:30 p.m. There is no additional final exam.

Sources (some of these may only be available from within the Kenyon network):

• Dictionaries, Encyclopedias
  • Online Biology Dictionary: http://www.biology-online.org/dictionary.asp
  • Cell Biology Dictionary: http://on.to/cellbiology
  • Life Sciences Dictionary: http://biotech.icmb.utexas.edu/search/dict-search.html
  • Academic Press Science and Tech Dictionary: http://www.gecdsb.on.ca/d&g/apr00/web1.htm
  • Access Science Encyclopedia: http://www.accessscience.com/server-java/Arknoid/science/AS
  • Oxford Biological Sciences Dictionaries: http://www.oxfordreference.com/views/SUBJECT_SEARCH.html?subject=s2&authstatuscode=202
• Animal Diversity and Evolution sites
  • Berkeley Introduction to the Metazoa: http://www.ucmp.berkeley.edu/phyla/phyla.html
  • Univ. Michigan Animal Diversity site: http://animaldiversity.ummz.umich.edu/site/index.html
  • The Tree of Life Project: http://tolweb.org/tree/phylogeny.html
  • The Shape of Life: http://www.pbs.org/kcet/shapeoflife/
  • Niche Construction: http://www.st-andrews.ac.uk/~seal/niche/index.html
  • The Anomalocaris page: http://www.trilobites.info/background.html
    
• University Departments, Funding Agencies, Professional Societies
  • Integrative Biology Department at UC Berkeley: http://ib.berkeley.edu/
  • Yale Department of Organismal and Integrative Biology: http://www.biology.yale.edu/oib/
    
  • Univ. Illinois Integrative Biology Department: http://www.life.uiuc.edu/sib/
  • UT Southwestern Integrative Biology: http://www8.utsouthwestern.edu/utsw/home/education/integrativebiology/
  • UT Austin Integrative Biology: http://www.biosci.utexas.edu/ib/
  • NSF Division of Integrative and Organismal Biology: http://www.nsf.gov/div/index.jsp?div=IOB
  • Society of Integrative and Comparative Biology: http://www.sicb.org
• Have a link to add to this list? E-mail me at gillenc@kenyon.edu

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