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the Fall 2011 course syllabus. - Bucknell University

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Amphibian Biology: <strong>Fall</strong> <strong>2011</strong>, Page 1 of 3<br />

Course Syllabus: Amphibian Biology – BIOL314/614-01<br />

<strong>Fall</strong> <strong>2011</strong> (Aug 24 – Dec 06)<br />

Lecture: Tue and Thur: 2:30 pm – 3:52pm @ Biology Bldg 104<br />

Lab: Thur: 9:00 am – 12:00pm @ Biology Bldg 318<br />

Instructor:<br />

Dr. Mizuki Takahashi<br />

Office location: Biology Bldg 307<br />

Office phone: 577-1142<br />

mt027@bucknell.edu<br />

How to reach me:<br />

- Office hours: Tues & Thurs 9-11AM<br />

- Appointments via emails (Title: BIOL314/614)<br />

- Stop by anytime <strong>the</strong> door is open!<br />

Textbook:<br />

1. Vitt, L. J. and J. P. Caldwell. 2009. Herpetology. 3rd edition. Elsevier / Academic Press.<br />

Optional:<br />

2. Conant, R. and J. T. Collins. 1998. A Field Guide to Reptiles and Amphibians: Eastern and<br />

Central North America. Houghton Mifflin Company. ~$14 from Amazon<br />

3. Hulse, A. C., E. Censky and C. J. McCoy. 2001. Amphibians and Reptiles of<br />

Pennsylvania and <strong>the</strong> Nor<strong>the</strong>ast. Comstock Publishing Associates. ~$40 from Cornell<br />

<strong>University</strong> Press or Amazon<br />

Laboratory/Field Equipment:<br />

A waterproof notebook (Required: you can purchase this at <strong>the</strong> <strong>Bucknell</strong> bookstore) and pencil<br />

(or waterproof pen). Clothing and footwear that can get wet and dirty in <strong>the</strong> field.<br />

Course Description/Objectives:<br />

On-going global amphibian decline has received increasing media attention, but current research<br />

and conservation efforts are insufficient to safeguard <strong>the</strong>se fascinating animals. As a result,<br />

amphibians are <strong>the</strong> most threatened group of vertebrates in <strong>the</strong> world. The lecture section of this<br />

<strong>course</strong> broadly explores <strong>the</strong> biology of amphibians as well as environmental issues that are<br />

driving <strong>the</strong> extinction of frog and salamander populations. The laboratory section will include<br />

lab- and field- identification of amphibians and <strong>the</strong> survey of amphibian killing fungi<br />

(Batrachochytrium dendrobatidis) among local amphibian populations. Through lectures and lab<br />

activities, students will develop <strong>the</strong> ability to (1) read, critique, and interpret scientific papers, (2)<br />

syn<strong>the</strong>size information, ideas, and data to draw reasonable inferences, and (3) scientifically write<br />

and orally present <strong>the</strong>ir work.<br />

Class Participation:<br />

You are expected to attend every class and to participate in discussion, which will be evaluated as<br />

“Class Participation”. To contribute to class discussions, you are expected to do reading<br />

assignments before attending lectures. The reading assignments consist of specific chapters of <strong>the</strong><br />

textbook as well as scientific papers that will be provided to <strong>the</strong> class. Please turn off your cell<br />

phone during <strong>the</strong> class. Participation points will be taken off for each cell phone use.<br />

Plagiarism:<br />

It is academically dishonest to steal ideas, paragraphs, or sentences from existing sources and use<br />

<strong>the</strong>m in your works. <strong>Bucknell</strong> <strong>University</strong> as an academic institute takes plagiarism seriously and<br />

all paper submissions for this class have to go through “SafeAssignments” within Blackboard,<br />

which detects possible plagiarism. If you have any questions about plagiarism, please contact me<br />

before you submit papers.


ASSIGNMENTS<br />

Please see “Assignment Guidelines” for more information<br />

Amphibian Biology: <strong>Fall</strong> <strong>2011</strong>, Page 2 of 3<br />

Examinations (individual):<br />

Following <strong>the</strong> <strong>syllabus</strong> schedule, <strong>the</strong>re will be two mid-term exams and a final comprehensive<br />

exam. Exam material will cover lecture, textbook information and in-class discussion. Students<br />

who arrive late will not have an extended exam period. Exams will not be given out after <strong>the</strong> first<br />

student leaves <strong>the</strong> room.<br />

Laboratory Research Paper and Presentations (group):<br />

The class will be divided into 4 groups of 3-4 students and each group will conduct an<br />

independent research project to test <strong>the</strong> prevalence of an amphibian killing fungus,<br />

Batrachocytrium dendrobatidis (Bd), in central Pennsylvania. Each group will focus on<br />

amphibians that occur in one of three habitat types: ponds, streams, and forests. Four field trips<br />

are scheduled to collect amphibian skin swabs. Students will extract Bd DNA, run PCR, and<br />

detect <strong>the</strong> presence or absence of Bd via electrophoreses. This project not only provides an<br />

excellent in-class research opportunity but also <strong>the</strong> possibility of a scientific publication if each<br />

group achives high-quality science. Detailed note-taking, careful practice of molecular techniques,<br />

appropriate data analyses and interpretation, and collaborations within and among groups are<br />

critical. Each group will present <strong>the</strong> final product both in an oral and written format (i.e., journal<br />

format) at <strong>the</strong> end of <strong>the</strong> semester.<br />

Laboratory Practical (individual):<br />

There is only one lab practical scheduled on November 17. Students will be evaluated on species<br />

identification and knowledge of habitats of amphibians that can be found in Pennsylvania.<br />

Local Pet Shop Assessment (group):<br />

Pet trade is one of <strong>the</strong> serious threats to <strong>the</strong> declining amphibian populations. The goal of this<br />

exercise is to understand <strong>the</strong> “legal” pet trade trend in this area of <strong>the</strong> United States. A group of<br />

students (3 or 4) will find, via phone or internet, a local pet store in central PA that sell ei<strong>the</strong>r<br />

amphibians or reptiles, visit <strong>the</strong> store, and collect data such as species, price, where <strong>the</strong>y come<br />

from, and staff’s knowledge about <strong>the</strong> amphibians and reptiles for sale. Each group ga<strong>the</strong>rs <strong>the</strong><br />

data into a 3-4 page report (single space). Each group will also present <strong>the</strong> data to <strong>the</strong> class.<br />

Guest Speaker Reports (individual):<br />

We are planning to have two guest speakers. In each visit, students will turn in 1-2 page<br />

reports (single space) summarizing <strong>the</strong> presentation and developing your discussion on <strong>the</strong><br />

presented issues (Due: <strong>the</strong> week following <strong>the</strong> guest speech).<br />

Student-led Discussions (individual):<br />

In-class discussion is an important element of this <strong>course</strong>, in which students will learn how to<br />

read, critique, and interpret scientific papers. Each student will pick a specific date at <strong>the</strong><br />

beginning of <strong>the</strong> semester. A student will find a scientific paper related to <strong>the</strong> topics covered by<br />

<strong>the</strong> lectures during <strong>the</strong> week of his/her presentation. The assigned student has to contact me about<br />

<strong>the</strong> paper at least a week before his/her discussion date. When <strong>the</strong> paper is approved by me, (s)he<br />

will send a PDF copy of <strong>the</strong> selected paper to <strong>the</strong> class at least three days before his/her<br />

discussion date. The discussion leader prepares at least three critical questions, and moderates and<br />

stimulates discussion. We will start discussion in a small group followed by a class discussion.


Amphibian Biology: <strong>Fall</strong> <strong>2011</strong>, Page 3 of 3<br />

Laboratory Notebooks (individual):<br />

Students are expected to record in detail all field and laboratory activities in a waterproof<br />

Rite in Rain notebook. This exercise is especially important for <strong>the</strong> development of a detailed<br />

method section of your manuscript. Instruction for proper journal entry format will be<br />

provided in <strong>the</strong> first laboratory session.<br />

Extra Points (individual):<br />

Although identification of frog calls is not a part of laboratory exercises, knowing frog calls<br />

makes spring much more enjoyable. Several frog calls will be played during <strong>the</strong> final<br />

laboratory practical. 0.5 extra point will be given to each correct answer.<br />

Grading:<br />

Final Exam (comprehensive) 80 pts (20%)<br />

Lab Research Paper and Oral Presentation 80 pts (20%)<br />

Lab practical 60 pts (15%)<br />

Exam I 40 pts (10%)<br />

Exam II 40 pts (10%)<br />

Local Pet Shop Assessment Paper and Oral Presentation 30 pts (7.5%)<br />

Class Participation 20 pts ( 5%)<br />

Guest Speaker report I 15 pts (3.75%)<br />

Guest Speaker report II 15 pts (3.75%)<br />

Discussion leading 10 pts (2.5%)<br />

Laboratory notebook 10 pts (2.5%)<br />

Total 400 pts (100%)<br />

A = 400 – 368 pts (100 – 92%)<br />

A- = 368 – 360 pts (92 – 90%)<br />

B+ = 360 – 352 pts (90 – 88%)<br />

B = 352 – 328 pts (88 – 82%)<br />

B- = 328 – 320 pts (82 – 80%)<br />

C+ = 320 – 312 pts (80 – 78%)<br />

C = 312 – 288 pts (78 – 72%)<br />

C- = 288 – 280 pts (72 – 70%)<br />

D = 280 – 240 pts (70 – 60%)<br />

*Grades may be curved depending on <strong>the</strong> class performance.

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