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Syllabus for Marine Biology - Biology 477, Fall Term, 2016 Lectures: 11-12:20 Tues/Thurs in Th297. Labs: Thurs 12:30-4:30 p.m., Fri 12-4:50 p.m. Th215 Lecturer: Joel Elliott Office: Th223J Phone: 879-8593 email: jkelliott@pugetsound.edu Office hours: Tuesday 12:30-1:30 pm, Friday 11:00 - noon, and by appointment Moodle:

x The materials for this course are available on the Moodle website. x Please refer to this site for the definitive version of the course schedule, syllabus,

reading list, lecture materials, assignments, and data sources for projects. Required texts:

x Levinton, J.S. 2014. Marine Biology: Function, Biodiversity, Ecology. 4th ed. x Harbo, R. 2011. Whelks to Whales: Coastal Marine Life of the Pacific Northwest.

Recommended additional texts:

x Your writing guide from introductory biology

Course description The marine environment encompasses 99% of the Earth's biosphere and contains an incredible diversity of microbial, algal, and animal life forms. This course will examine the biology of these organisms and the abiotic (e.g., salinity, nutrients, water currents and tides) and biotic factors (e.g., competition, predation, symbiosis) that influence their distribution and abundance. Specific topics will include primary and secondary production, rocky intertidal biodiversity, estuaries, subtidal communities, coral reefs, pelagic and deep sea communities, impacts of humans on the ocean, and conservation. Lecture periods will include discussions of primary literature and student presentations. Laboratory sessions will involve fieldwork, laboratory analyses, report writing, and multimedia presentation of project results. Prerequisites: Biology 111, 112, and 211. General objectives of the course Through lectures, laboratories, and projects you will gain experience toward some of the general curricular goals of the university: (1) the ability to think logically, analytically, and independently; (2) the ability to communicate clearly and effectively, both orally and in writing; (3) the ability to learn on one's own and as part of a group; and (4) depth of knowledge in a single field. Specific objectives of the course 1) To develop an appreciation and understanding of the marine environment, especially the waters

of Puget Sound, through readings, lectures, discussions, field studies, and laboratory analyses. 2) Learn the basic principles concerning the physical conditions of the marine environment (e.g.

temperature, salinity, DO, nutrients, water currents and tides), and be able to describe how

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marine organisms have adapted to these physical conditions. Also be able to explain how the distribution and abundance of marine organisms is influenced by changes in these physical parameters.

3) Be able to recognize many of the organisms that occur in particular marine habitats (e.g., plankton, nekton, rocky and soft-sediment intertidal and subtidal, docks and pilings), and describe major aspects of their natural history.

4) Gain an understanding of the important ecological relationships among different marine organisms (e.g., predator-prey, competition, symbiosis, indirect effects), and their influence on distribution and abundance patterns and community structure.

5) Obtain practical experience in applying different sampling methods in the marine environment and then using standard techniques for analyzing samples in the laboratory. Then, analyze the data appropriately and produce a written research report.

6) Formulate hypotheses, develop a research proposal, and conduct a research study to investigate a particular problem in marine biology. Work as part of a team to design the research project, carry it out effectively, and then present the results in both oral and written formats.

Quizzes and Exams There will be 4 quizzes, one midterm exam, and a final exam (see schedule). Questions on quizzes and exams will be a combination of multiple choice, short answer, problem sets, and essays. The quizzes and exams will cover specified sections of the text and assigned reading. You should be able to utilize your knowledge of local marine species (know common or species names) to provide examples of concepts discussed in lecture. Each quiz will cover material from the previous lectures. They will be take-home quizzes, and I will post the questions along with problem sets on the Moodle website. The take-home quizzes are due at the start of the Tuesday lecture each week. All exams will be held in our regular lecture room (T 297). Note the dates of the exams on the Course Schedule. THERE WILL BE NO MAKE-UP EXAMS. If you have any anticipated problem with taking an exam on the specified date, see me ASAP. If you do miss an exam for a legitimate reason (e.g., documented medical problem), I will consider that in the calculation of your final grade. Reviews of primary literature You will write 4 reviews (approximately two pages in length, 1.5 spacing) of papers from the primary literature on marine biology. Everyone will write a review of the first paper, and then you can choose to write a review of 3 of the next 5 papers. A set of instructions follows in a separate handout. Group Projects Two group projects conducted in lab will be graded. 1) An examination of water quality and plankton at different sites in Commencement Bay, and 2) An investigation of organismal diversity in the rocky intertidal.

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Research project The objective of this project is to have you study living marine organisms in the field or lab and examine some aspect of their behavior, ecology, morphology, biochemistry, etc. that interests you. This project will involve all of the components of the scientific process: making critical observations, recognizing patterns, asking questions and formulating hypotheses, testing hypotheses, then attempting to explain the patterns from a functional or evolutionary perspective. You will then present your results in a multimedia presentation and produce a written scientific report. A more detailed description of this project will be provided in a separate handout. Late work All assignments must be turned in on Moodle. Do not put any printed assignments under my door. Late assignments will be penalized 10% of a grade per day. Class participation Since this course will be interactive and will require you to work closely with others, part of your grade will be dependent on your ability and willingness to participate in class discussions and laboratory investigations, as well as interact positively with other members of the class. Grading Lecture Points Quizzes – 4 @ 30 pts each 120 Midterm lecture exam 100 Final lecture exam 150 Reviews of papers – 4 @ 10 pts each 40 Laboratory Group projects – 2 @ 60 pts each 120

Research project Project proposal 5 Project progress reports 10 Oral presentation 40 Written report 75

Participation 40 Total 700

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Classroom Emergency Response Guidance Please review university emergency preparedness, response procedures and a training video posted at www.pugetsound.edu/emergency/. There is a link on the university home page. Familiarize yourself with hall exit doors and the designated gathering area for your class and laboratory buildings. If building evacuation becomes necessary (e.g. earthquake), meet your instructor at the designated gathering area so she/he can account for your presence. Then wait for further instructions. Do not return to the building or classroom until advised by a university emergency response representative. If confronted by an act of violence, be prepared to make quick decisions to protect your safety. Flee the area by running away from the source of danger if you can safely do so. If this is not possible, shelter in place by securing classroom or lab doors and windows, closing blinds, and turning off room lights. Lie on the floor out of sight and away from windows and doors. Place cell phones or pagers on vibrate so that you can receive messages quietly. Wait for further instructions.

Office of Accessibility and Accommodations

If you have a physical, psychological, medical or learning disability that may impact your course work, please contact Peggy Perno, Director of the Office of Accessibility and Accommodations, 105 Howarth, 253.879.3395. She will determine with you what accommodations are necessary and appropriate. All information and documentation is confidential.

Copyright and Fair Use

Course materials are for educational purposes only and limited to students enrolled in the course. They are protected by copyright law and may not be copied, downloaded, stored, transmitted, shared or changed in any way outside of the course.

Bereavement Policy

Upon approval from the Dean of Students’ Office, students who experience a death in the family, including parent, grandparent, sibling, or persons living in the same household, are allowed three consecutive weekdays of excused absences, as negotiated with the Dean of Students. For more information, please see the Academic Handbook.

Course Schedule for Biology 477: Marine Biology – Fall 2016 Dr. Joel Elliott - Lecture: T, Th 11:00-12:20, Room Th297, Lab: Thurs. 12:30-4:30, Fri. 12:00 – 4:50, Room Th215

Month Day Lecture Topic Readings and quizzes Lab Topic Assignments due -all quizzes and paper reviews

due at start of class -all assignments due at

start of lab Aug. 28 Field trip: Intertidal diversity x Review species list 30 Introduction Ch. 1, 3 Sept. 1 Physical/chemical prop. of SW Ch. 2, 4 Field: Water sampling 2 Field: Water sampling 6 Plankton biology Ch. 7 8 Plankton and primary production Ch. 9,10 Plankton biology Water sampling data 9 Plankton biology Plankton data 11 Field trip: North Puget Sound x Review species list 13 Plankton and food webs Paper 1 15 Intertidal ecology Ch. 14; Quiz 1 Data analysis 16 Data analysis 17/18 Field trip: Subtidal survey I x Review species list 20 Intertidal ecology Ch. 14 22 Intertidal ecology Paper 2 Field: Subtidal survey II Water sampling/ 23 Field: Subtidal survey II Plankton report 27 Subtidal ecology Ch.15 29 Subtidal ecology Quiz 2 Data analysis 30 Data analysis Oct. 4 Oceanic nekton Ch.8 6 Oceanic nekton Paper 3 Research Conferences Research project 7 Research Conferences Proposal- 1st draft 11 Midterm exam 13 Deep sea biology Ch. 16 Independent Research Research project 14 Independent Research Proposal- revised

Month Day Lecture Topic Readings Lab Topic Assignments due 18 Mid-term break 20 Independent Research Independent Research 21 Independent Research 25 Deep sea biology Paper 4 27 Tropical communities Ch. 15: 378-403 Independent Research Intertidal lab report 28 Independent Research Nov. 1 Tropical communities Paper 5 3 Human impacts: fisheries Ch.18 Independent Research Research project 4 Independent Research progress report 1 8 Human impacts: fisheries Quiz 3 10 Human impacts: fisheries Paper 6 Independent Research 11 Independent Research 15 Human impacts: pollution Ch.19 17 Biodiversity and conservation Ch. 17 Independent Research Research project 18 Independent Research progress report 2 22 Conservation Quiz 4 24 Thanksgiving No lab 30 Research presentations Dec. 1 Research presentations Independent Research 2 Independent Research 6 Review Research project paper Due last day of classes

(Dec. 7) by 4 pm 15 Final exam - 12:00 - 2:00 pm x This printed schedule is tentative and is subject to change. Check the version available on Moodle for updates.