Coastal Biology
BIOL 482 Coastal Biology - Syllabus
Faculty Information
Title
Instructor
Office Phone
Office Address
Office Hours
E-mail
Homepage
Course Information
Associate Professor
Iliana Baums
814.867.0491
215 Mueller Laboratory
Tues 12:30 pm - 13:30 am by appointment baums@psu.edu
http://www.personal.psu.edu/ibb3/
Credits
Course
Section
Location
Times
Start Date
Homepage
Variable (3 for lecture, 1 for trip)
482
001, 002
210 Ferguson
Tues and Thurs, 11:15 pm - 12:30 pm
14 Jan 2013 http://www.personal.psu.edu/ibb3/
Required Text
Jeffrey S Levinton, Marine Biology: Function, Biodiversity, Ecology.3rd Edition. Oxford University Press.
ISBN 978-0-19-532694-9
Reference Texts (not required)
Bertness, Gaines and Hay: Marine Community Ecology. Sinauer Associates, Inc. ISBN 0-87893-057-4 .
Library call number: QH541.5.S3M256 2001
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Coastal Biology
Morrissey and Sumich: Biology of Marine Life. 9th edition. Jones and Bartlett Publishers.
Kaplan: Coral Reefs. Peterson Field Guide. Houghton Mifflin Company. ISBN 0-618-00211-1
Kaplan: Southeastern and Caribbean Seashores. Peterson Field Guide. Houghton Mifflin Company. ISBN-
13 978-0-395-97516-9
Human: The Reef Set: Reef Fish, Reef Creature and Reef Coral (3 Volumes). New World Publications, Inc.
ISBN 1-878348-32-9
Wisehart: A Photographic Atlas of Marine Biology. Morton Publishing Company. ISBN: 9780895827852.
Library call number QH91.17.W57 2012
Trujillo and Thurman: Essentials of Oceanography, 10 edn. Prentice Hall. ISBN-13: 9780321668127.
Library call number GC11.2.T49 2011
Course Description
Biol 482 is a combination lecture and intensive field course designed to introduce participants to the
Caribbean coral reef biome and other near-shore environments such as rocky shores, mangroves and seagrass beds. Students will learn through theoretical and practical exercises how environmental and biological factors interact to sustain near-shore ecosystems. We will discover and describe the amazing diversity of coral reef systems, explore the physiological and behavioral adaptations that enable organisms to live in this environment and deduct the basic ecological principles that underlie the function of near-shore ecosystems. We will be reading primary literature throughout the course.
Students may choose to focus on current issues in marine conservation science as part of their class projects/proposal. Topics may include but are not limited to connectivity among marine populations, metapopulations-dynamics, adaptation to climate change, and conservation genetics. A (optional) field trip during spring break will take us to the beautiful island of Curacao, part of the Netherland Antilles in the southern Caribbean. Healthy coral reefs, mangroves and seagrass beds are easily accessible from shore and we will study them by snorkeling. The colonial past and economic realities in Curacao provide an instructive backdrop to understand the complexity of marine conservation issues today. This course requires strong participation and thus is most suited for highly motivated students. All participants must pass a swimming test before leaving for Curacao. Participants will be charged a fee to cover the trip costs to Curacao and have to bring their own snorkel gear. Field trip limited to 10 students. Variable credit hours (3 for lecture, 1 for field trip).
Course Objectives
1.
To introduce basic concepts of oceanography, biodiversity, ecology and evolution as they pertain to marine coastal environments.
2.
To learn through theoretical and practical exercises how environmental and biological factors interact to sustain near-shore ecosystems.
3.
To acquire field skills to study marine near-shore environments.
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Coastal Biology
4.
To improve discussion, analytical, presentation and writing skills.
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Coastal Biology
Tentative Schedule
Date Topics, Activities
Jan 14 Overview of course requirements;
Distribution and categories of coastal ecosystems
Jan 16 The ocean: topography, sea floor (Ch1,2),
Hypothesis testing
Jan 21 The ocean: topography, sea floor (Ch1,2)
Jan 23 The ocean: circulation, coastal processes (Ch
2)
Jan 28 Ecology and Evolution (Ch 3)
Jan 30 Ecology and Evolution (Ch 3)
Feb 4 Chemical and Physical Environment (Ch4)
Feb 6 Life in a fluid medium (Ch 5)
Feb 11 Benthic Life Habitats (Ch 13)
Feb 13 Midterm
Feb 18 The tidelands: Soft Sediments and Salt
Marshes (Ch 14)
Feb 20 The tidelands: Mangroves (Ch 14)
Feb
22^
Four-hour session on reef critter identification
Feb 25 The tidelands: Intertidal Communities I (Ch
14)
Feb 27 Seagrass Beds (Ch 15)
Mar 4 Ecology of Reefs (Ch 15)
Reading
Economist – Report on the sea
Darwin 1850
Dollar 1982
Kirsch et al 02
Levitan et al 04
Deadlines *
Skov and Hartnell 2002
McKillup and McKillup 2000 Homework 1
Bologna and Steneck 83
Riffel And Zimmer 07, both
All material through Feb 6 Midterm
Sillman et al 2005 One paragraph proposal
Swim test Feb
20
Research
Proposal
Field practical
Mar 6 Ecology of Reefs (Ch 15)
Mar 8- Field trip to Curacao: Seaweeds, seagrasses
16 and benthic microorganisms (Ch 12),
Diversity of benthic marine invertebrates (Ch
11)
Mumby et al 2007
Mar 18 Reproduction, Dispersal and Migration (Ch 6) Johnston and Miller 06
Mar 20 Reproduction, Dispersal and Migration (Ch 6) Hazen et al. 2013
Mar 25 Midterm (material up to Mar 20)
Mar 27 Plankton (Ch 9)
Ware and Thomson 2005
Midterm
Experiential
Paper
Apr 1 Productivity, food webs and global climate change (Ch 10)
Apr 3 Panel discussion
Apr 8 Panel discussion
Apr 10 Estuaries I (14)
Apr 15 Estuaries II (Ch 14)
Apr 17 Biodiversity and Conservation (Ch17)
Apr 22 Fisheries (Ch 18)
Apr 24 Environmental Impacts (CH 19)
Assigned proposals
Orth and Moore 1983
Ellis and Elphick 2007
Budd et al. 2010
Naylor et al 2000
Costello et al 2008
Read proposals
Final draft of
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Coastal Biology
Date Topics, Activities Reading Deadlines *
Research paper due
Apr 29 Student Presentations
May 1 Student Presentations
May 5 - Final Exam (material from Mar 27 – Apr 24)
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*homework will be due at various stages throughout the course.
^We will have to schedule one four-hour weekend session prior to the field trip for lectures on the plants and animals you will encounter in Curacao. This will help you identify your study objects.
Course Prerequisites
BIOL 220 (or equivalent). The field trip is optional but requires a course fee. Failure to pay the fees on time will result in the student having to drop the class. In addition, students should be reading and writing at the college junior level, have a genuine interest in the biological sciences, a willingness to learn about other cultures and biomes, an acceptable level of physical fitness (including swimming ability), and permission of the instructor.
Grading Policy
The grading scale is as follows:
F
Grading Scale %
A 100 - 95
A-
B+
B
B-
C+
C
D
94.9 - 90
87.9 - 89.9
83.33 - 87.8
80 - 83.32
75 - 79.9
70 - 74.9
60 - 69/9
59.9 and below
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Coastal Biology
The Class grade will be assigned based on the following items:
Date Grade components
Homework
Classroom participation
Grade (%)
5
15
13 Feb
4 Mar
Midterm Exam
Prelim Research proposal
14
15
25 Mar Midterm Exam 14
29 Apr and 1 May Research Paper /Presentation 25
5 May - 9 May Final Exam
Total
12
100
The Field trip grade will be assigned based on the following items:
Date
8 - 16 Mar
8 - 16 Mar
27 Mar
Grade components
Field Practical
Participation
Experiential Paper
Total
Grade (%)
20
50
30
100
Attendance Policy
Students will be handing in "minute papers" either at the beginning or at the end of the class meetings.
The purpose of the minute papers is to provide me with feedback on how you are doing with the material. So, while the minute papers are not graded as a test, your attendance in class will be noted via the minute papers. They cannot, under any circumstances, be made up. Handing in thoughtful minute papers is part of your class room participation grade.
You are encouraged to attend all lectures and are responsible for all material that is missed during an absence. Please contact your fellow students for notes and announcements. At least 90% of the material on the exams will have been discussed in class, and some of this material will not be in any of the assigned readings. This means that ATTENDANCE IN CLASS IS HIGHLY CORRELATED WITH FINAL
GRADES!!
Handing in items late
If you are submitting items to their drop-boxes on Angel after the deadline (midnight on the due date), you will lose 10% of your points per day you are late (unless you have a legitimate excuse, see below).
Research proposal, Panel and Final paper
All students, including those only taking the lecture are going to write a short research proposal. This will be the basis for the research projects we will be doing in Curacao (field participants) and provides the basis for the full research paper due at the end of class (all students). Writing research proposals is a
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Coastal Biology skill you will be able to use no matter what profession you choose after college. Your goal is to persuade others that your idea (in this case science) is worthy of committing resources to. There will be a peer review panel made up of students that will discuss each proposal (though the name of the student who wrote the proposal will not be known to the class). The panel will take place in Curacao for the field participants (Mar 8) and in class (Apr 3 and Apr 8) for lecture participants. The purpose of the panel is to choose the field projects we will carry out while in Curacao (field participants) and to give you feed-back on how well you were able to convey your ideas (all participants). Based on this feed-back you will then improve on your short proposal to submit a longer and more complete one as your final project
(everybody). Field participants have the option to write up their experimental results from Curacao into a research paper in the style of a short journal article rather than submitting a longer proposal. There are detailed instructions on how to come up with a proposal idea, what resources are available to carry out the projects, how to format the proposal and final papers and how to evaluate them in panel on the
Angel website in the Homework folder. It is challenging to think of a topic for research that can be done in a short amount of time with limited resources in a place you have not been to before. Therefore, I will meet with you each individually to discuss your proposal idea, tell you whether it is feasible and help you with resources. To initiate this discussion, you will hand in a one-paragraph research idea on Feb 18.
Examination Policy
Lecture exams:
There will be two midterm exam and one final exam. The exams will include short answer, fill in the blank, true or false, multiple-choice, and short essay questions.
Exam attendance: Attendance at exams is mandatory and absence during the scheduled exam time will result in a grade of zero unless prior arrangements have been made or a legitimate and verifiable excuse is provided within 48 hours of the exam. The following are the only legitimate excuses accepted:
A.
An illness that is documented by a doctor's letter or note and receipt (an appointment card from
Ritenour is not acceptable). In addition, the student must provide her/his doctor with written authorization to disclose information to the Instructor should the Instructor require additional information in order to verify that the illness was significant enough to miss the exam.
B.
A religious holiday, that is celebrated by the student AND that is officially recognized by the
University.
C.
A University-sponsored event (which must be documented by a letter from the sponsor or coach and given to the Instructor prior to the date of the exam that will be missed).
D.
A death in the immediate family (which must be documented according to the Instructor's request).
Oversleeping is not an acceptable excuse for missing an exam.
Documentation of a legitimate excuse for missing an exam is required before the make-up exam will be administered. The Instructor may seek to verify the submitted documentation by talking to the person who signed or wrote the documentation. All requests for make-up exams must be submitted to the
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Coastal Biology
Instructor within 48 hours after the exam, written on paper (not sent via e-mail), and signed and dated by you.
Course Links
Using your student access account you can log onto the course web site on Angel and will find the syllabus, lecture and presentation schedules, assigned readings, assorted extra material, and announcements. You will also find the lectures in pdf format, the day before lecture. These will provide a framework for taking notes, and you will need to fill in details in class. All material is in folders under
“Lessons”. This web page is intended for you and we are open to any suggestions that you might have for improving the site. Please contact me if you have any difficulties with the website or available files.
Academic Integrity
All Penn State policies regarding ethics and honorable behavior apply to this course (see links below for policy statements). Academic integrity is the pursuit of scholarly activity free from fraud and deception and is an educational objective of this institution. All University policies regarding academic integrity apply to this course. Academic dishonesty includes, but is not limited to, cheating, plagiarizing, fabricating of information or citations, facilitating acts of academic dishonesty by others, having unauthorized possession of examinations, submitting work of another person or work previously used without informing the instructor, or tampering with the academic work of other students. For any material or ideas obtained from other sources, such as the text or things you see on the web, in the library, etc., a source reference must be given. Direct quotes from any source must be identified as such.
All exam answers must be your own, and you must not provide any assistance to other students during exams. Any instances of academic dishonesty WILL be pursued under the University and Eberly College of Science regulations concerning academic integrity.
Disability Access Statement
The Pennsylvania State University encourages qualified people with disabilities to participate in its programs and activities and is committed to the policy that all people shall have equal access to programs, facilities, and admissions without regard to personal characteristics not related to ability, performance, or qualifications as determined by University policy or by state or federal authorities. If you anticipate needing any type of accommodation in this course or have questions about physical access, please tell the instructor as soon as possible (the first week of class). The field trip component of this class is being held in a third world country with very limited accommodation for physical disabilities.
Use of e-mail:
E-mail is an effective way to handle brief communications, but is not effective to communicate concepts, major ideas, or to discuss a student's performance in the course. Thus:
E-mail should be used to:

Point out any errors or oversights made by the instructor during lectures.

Set up an appointment to talk with the instructor if you cannot meet during regularly scheduled office hours.

Ask questions about lecture material that can be answered in a brief sentence.
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Coastal Biology
E-mail should NOT be used to:

Ask for explanations about concepts, ideas, theories, processes, or any other information that requires more than a very short answer. We will explain things and answer major questions much better by talking with you in person than via e-mail.

Ask about your points or grade -- if you feel that a grading mistake has been made we can discuss your concerns in person.

Provide final documentation for a missed exam or assignment.
Preparation and Participation are very important to your success in this course!
Your participation during lecture and the field trip is vitally important to your understanding the material. If you have a question or comment, please feel free to stop me during or after lecture.
The best thing that can be done to ensure success in this course is to be prepared when you come into lecture. So again, I strongly recommend reading the relevant material and reviewing the notes from previous lectures before lecture begins.
Field Trip
This is a representative itinerary. It will change without a doubt once we are in Curacao. Field work is dependent on a multitude of conditions (such as weather, boat access, health etc) and thus requires flexibility. By being on time and organized, you will maximize our chances of getting everything done.
Date
Mar 8
Mar 9
Mar 10
Mar 11
Mar 12
Activity Day
Arrival in Curacao and Orientation, proposal peer review panel
Proposal peer review panel, Introduction to
Snorkeling at Carmabi
Snorkel at coral reefs
Snorkel at mangroves
Drive to fossil reefs, snorkel at seagrasses, visit salinas
Snorkel wreck, Free afternoon
Visit Sea Aquarium, Field Practical
Departure for State College
Evening
Evening orientation lecture
Evening journaling and lecture (coral, fish
I.D.)
Evening journaling and night beach seining
Evening journaling and lecture (fossils)
Night snorkel at beach
Mar 13
Mar 14
Mar 15
Dinner in town
Packing and discussion session

We will be traveling to a foreign country. You must observe all safety rules
(http://www.international.psu.edu/studioabroad) while participating in the travel component of the course. Your safety is very important to me and I will do what I can to make the trip enjoyable and safe. However, you are ultimately responsible for your own health and safety.
Additional rules of conduct will be presented by our hosts in Curacao, including boating safety, snorkeling guidelines, and behavior at the field station and in the town of Willemstad. Students with health concerns that might impact travel, boating, sun exposure, and other activities must bring this to my attention within the first two weeks of the semester so that we can try to accommodate you.
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
Jennifer Boulay will be our teaching assistant for the field trip. You may contact her at jnb186@psu.edu.

Failure to make necessary deposits within the deadlines may result in you being withdrawn from the course. Promise of payment may not be sufficient to ensure continued enrollment. This is because the number of students going on the trip determines how many rooms and cars etc we need to organize and so a reliable headcount is imperative.

Students travelling on short-term, international studies programs led by Penn State faculty members embedded in residentially-taught courses must enroll in HTH Worldwide insurance. I will submit a “Student Roster” to Education Abroad (EA). When EA receives this form, they will submit it to HTH Worldwide. HTH will then send each student an email with a secure link to their website where the students must log in with their PSU ID and pay for the coverage with a credit card (approx. $0.75/day). These enrollment emails from HTH can sometimes end up in email junk mail boxes, so please be on the lookout for them.

You must possess a valid passport before departure for Curacao. Procedural information and forms may be obtained from the following web site: http://travel.state.gov

You will be required to pass a swimming competency exam at the Natatorium before being allowed to travel to Curacao, scheduled outside of class.

Immunization requirements and related health information is available from the CDC website
(http://www.cdc.gov/travel/). It is your responsibility to obtain the necessary vaccinations and travel medications, if necessary. Get started early, it may take several weeks to complete immunization schedules.

You must bring snorkeling equipment (e.g., mask, snorkel, fins, wet suit, gloves) to participate in the travel component of the course. You are much better off purchasing your own gear ahead of time and practicing with it to make sure that your gear fits correctly. You will be miserable if your masks leaks or your fins that cause you blisters.

SCUBA diving is not part of this course.

I will provide you with a checklist of times to bring at a later point (e.g. a notebook, pencils, etc).
Experiential Paper Guidelines
An important component of the course is the writing of an experiential paper based each student’s observations. The foundation of the paper will be based on journal entries. On most days in
Curacao, a quiet time will be scheduled for journaling during which students will have an opportunity to record their perceptions of the day’s activities and experiences. You will also be expected to engage those you encounter in extended conversations about life in Curacao. What are the educational and employment opportunities? What are the health concerns? What role does religion play in the life of the average person? Throughout our stay we will be surrounded by a diversity of people who staff the compound, pilot the boats, and live and work in Curacao. Curacao is populated by papiemento-speaking peoples, who are of mixed African and European ancestry, Creoles, who speak a Creole dialect of English and who are largely of African and African-European extraction, and Garifuna, who are descendants of
Carib Indians and Africans as well as Indians. Moreover, there is a sizeable population of colorful and opinionated expatriates from the Netherlands and other countries. You will have ample opportunity to learn about life in Curacao from these people.
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In addition to informal interviews, your journaling should include information about your experiences on the boats and in the water. What were your feelings before jumping into the water for the night snorkel? How did your perceptions change? What organisms impressed or surprised you the most? How would you rate your stamina and confidence and have they changed over the course of your stay? These and similar questions should be addressed. The format of the paper is relatively flexible and the writing style should be viewed as creative. The length of the paper is 5 to 6 pages, double-spaced.
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