ENVIRON 124L SOUND IN THE SEA: INTRODUCTION TO MARINE BIOACOUSTICS DUKE UNIVERSITY MARINE LABORATORY FALL 2010 INSTRUCTOR Wendy Dow Piniak Office: Lab 2, Room 2 Office Hours: Monday, 1300-1600 (or by appt.) Email: wed3@duke.edu Phone: (252) 504-7565 Lecture: T-Th 1000-1130 Lab: Th 1300-1500 COURSE DESCRIPTION This course will introduce you to the concepts of marine bioacoustics and the theories and controversies surrounding marine sound. You will gain a fundamental understanding of how sounds are generated by natural and anthropogenic sources, how sounds propagate through complex marine environments, and how marine organisms and humans receive, interpret and use sound. In laboratory exercises you will learn to use equipment, research techniques and analytical methodologies frequently used in the marine bioacoustics field. The course will culminate with case studies and individual research projects focusing on current topics in marine sound. You will use what you ve learned throughout the semester to analyze your topic and make recommendations for the conservation and management of marine organisms and their acoustic environments. COURSE MATERIALS Required Texts: Principles of Marine Bioacoustics (Au & Hastings 2008) and Marine Mammals and Noise (Richardson et al. 1995). Additional primary literature and supplementary text readings will be posted on Blackboard and can be found either as a pdf file on Blackboard (under course documents) or on reserve in the library. Software: MATLAB and Adobe Audition installed in the graduate computer cluster in Bookhout. LEARNING OBJECTIVES By the end of this course you will be able to: Describe how sound is generated by natural and anthropogenic sources and how it propagates through the ocean; Collect and analyze sound recordings and apply quantitative tools to the use of passive and active acoustic recordings; Describe and compare how marine organisms and humans receive, interpret and use sound; Explain the impacts marine sound can have on organisms; and Synthesize information from primary literature, evaluate current issues in marine sound and recommend actions for management and conservation. 1
GRADING AND EXAMINATIONS: Throughout the semester you will be evaluated in several ways including exams, problem sets, laboratory reports, a research paper and presentation, and participation. Midterm and final exams will be comprised of a combination of multiple choice, short answer and essay questions. You will be expected to complete all reading assignments BEFORE class and participate fully in all lecture and lab discussions. Midterm Exam 20% Final Exam 20% Laboratory Assignments 25% Final Paper/Presentation 25% Participation 10% LABORATORY ASSIGNMENTS A combination of problem sets and laboratory reports will be due throughout the semester. Problem sets are to be completed individually and will be due one week after the laboratory exercise. Laboratory reports will either be completed individually or as a group and will be due two weeks after the lab exercise. Laboratory reports should be 5 pages in length (double-spaced, excluding literature cited and figures) and in the style of a scientific manuscript (title, abstract, introduction, methods, discussion, literature cited and tables and figures). Example reports will be distributed at the first lab meeting. Group reports should include a short paragraph describing the contributions of each group member. RESEARCH PAPER/PRESENTATION Throughout the semester you will conduct an individual research project. Research topics will be selfselected and can include any current topic in marine bioacoustics. We will discuss potential topics at the start of the semester. A short project proposal will be due prior to the midterm exam. Project proposals should be no longer than 3 pages (double-spaced) and should include a title, short description of your proposed research, proposed methodology and a list of references. Final research papers should be 15 pages in length (double-spaced, excluding literature cited and figures) and in the style of an appropriate scientific journal manuscript. Final research papers will be due on the last day of class (I m happy to review drafts!). You will present your research to the class. Presentations will be 20 minutes in length and you may choose how to present your topic (Power Point presentation, class discussion, demonstrations etc. Be creative!). THE DUKE COMMUNITY STANDARD Duke University is a community dedicated to scholarship, leadership, and service and to the principles of honesty, fairness, respect, and accountability. Citizens of this community commit to reflect upon and uphold these principles in all academic and non-academic endeavors, and to protect and promote a culture of integrity. To uphold the Duke Community Standard: I will not lie, cheat, or steal in my academic endeavors; I will conduct myself honorably in all my endeavors; and I will act if the Standard is compromised. 2
COURSE SCHEDULE (SUBJECT TO CHANGE) Date Topic Readings 31Aug Introduction to marine bioacoustics NAS 1999; Ch. 2 MMN 2Sept Fundamentals of acoustics Ch. 1 Bradley & Stern 2008 Lab 1 Introduction to MATLAB 7Sept Acoustic units of measurement Brandt & Hansen 2006 9Sept Sound Propagation Ch. 4 MMN; Ch. 4 PMB Lab 2 Applying acoustic units of measurement 14Sept Signal Analysis Ch. 3.4 MMN, R Ch. 6 PMB 16Sept Measuring and recording marine sound Ch. 3 MMN; Ch. 5 PMB Lab 3 Instrumentation and recording in the field 21Sept Natural & anthropogenic sources of marine sound Ch. 2 IR; Hildebrand 2010 23Sept Data collection for hearing and ADD labs (outside class time) Lab 4 Data collection for hearing and ADD labs (outside lab time) 28Sept Passive & Active Acoustics Ch. 15 SS; Ch. 9 FB 30Sept Fisheries Acoustics - Dr. Chris Taylor Ch. 7 SS Lab 5 Field Target detection using sonar - Dr. Chris Taylor 5Oct Fundamentals of hearing Ch. 7.1 PMB 7Oct Midterm Exam (**Research Project Proposals Due 18Oct**) Lab 6 Field recording of dolphin vocalizations (weather dependent) 19Oct Psychoacoustics & electrophysiological methods Ch. 8 PMB 21Oct Fish hearing Ch. 7.5 & 9.6 PMB Lab 7 Psychoacoustic methodologies *27Oct* Dr. Doug Nowacek Seminar (Wed - 12:30-1:30pm) 28Oct Turtle and invertebrate hearing Bartol & Musick 2003, 3.3 Lab 8 Auditory evoked potentials in fish/turtles data analysis 2Nov Marine mammal hearing Ch. 7.2-4 & 9.5-5 PMB 4Nov Fundamentals of animal communication Ch. 3 AC Lab 9 Passive acoustic monitoring - Lynne Williams 9Nov Fish & marine mammal sound production & communication Ch. 10 PMB 11Nov Marine Mammal Acoustic Ecology - Dr. Doug Nowacek Ch. 7 MMN Lab 10 Species ID using digital recordings - Dr. Melissa Soldevilla 16Nov Echolocation and target detection Ch. 11 PMB 18Nov Impacts of marine sound Part I: Physiology Ch. 10&11 MMN; P&H 2009 Lab 11 Behavioral response of sea turtles to ADDs data analysis 23Nov Impacts of marine sound Part II: Behavior Ch. 9 MMN; Nowacek 2007 30Nov Methodologies for studying the impact of marine sound Tyack 2009 2Dec Regulation & Mitigation of marine sound McCarthy 2000 Lab 12 Final Exam Review/Research Project Papers Due 7Dec Research Project Presentations 9Dec Research Project Presentations & Course Wrap Up 14Dec Final Exam * Principles of Marine Bioacoustics (PMB); Marine Mammals and Noise (MMN); Fisheries Acoustics (FA); Sounds in the Sea (SS); Fish Bioacoustics (FB); Acoustic Communication (AC); Int l Regulation of Underwater Sound (IR) 3
USEFUL REFERENCES AND WEBSITES Au, W. L., A. N. Popper, and R. R. Fay (eds). 2000. Hearing by Whales and Dolphins. Springer. New York, USA. Au, W. L. 1993. The Sonar of Dolphins. Springer-Verlag. New York, USA. Bradley, D. L. and R. Stern. 2008. Underwater sound and the marine mammal acoustic environment: A guide to fundamental principles. U.S. Marine Mammal Commission. 67pp. http://mmc.gov/reports/workshop/pdf/sound_bklet.pdf Brandt, C. and C. U. J. Hansen. 2006. dbs for Dummies: A sort of introduction to the weird world of sound. Centre of Sound Communication. University of Denmark. 29pp. Laiolo, P. 2010. The emerging significance of bioacoustics in animal species conservation. Biological Conservation. 143:1635-1645. McCarthy, E. M. 2000. International regulation of underwater sound. IEEE 221-228. McCarthy, E. M. 2004. International Regulation of Underwater Sound. Kluwer Academic Publishers. Boston, MA, USA. Medwin, H. (ed). 2005. Sounds in the Sea: From Ocean Acoustics to Acoustical Oceanography. Cambridge University Press. Cambridge, UK. National Research Council. 2000. Marine Mammals and Low-Frequency Sound: Progress Since 1994. National Academy Press. Washington, D.C. USA. National Research Council. 2003. Ocean Noise and Marine Mammals. National Academies Press. Washington, D.C. USA. Nowacek, D. P., L. H. Thorne, D. W. Johnston, and P. L. Tyack. 2007. Responses of cetaceans to anthropogenic noise. Mammal Review. 37(2):81-115. Popper, A. N. and M. C. Hastings. 2009. Review Paper: The effects of anthropogenic sources of sound on fishes. Journal of Fish Biology. 75:455-489. Simmonds, J. and D. MacLennan (eds). 2005. Fisheries Acoustics: Theory and Practice (2 nd edition). Blackwell Publishing. Oxford, UK. Simmons, A. M., A. N. Popper, and R. R. Fay (eds). 2003. Acoustic Communication. Springer-Verlag. New York, USA. Southall, B. L. (ed). 2007. Marine Mammal Noise Exposure Criteria: Initial Scientific Recommendations. Aquatic Mammals 33(4). 4
Tyack, P. 2009. Acoustic playback experiments to study behavioral responses of free-ranging marine animals to anthropogenic sound. Marine Ecology Progress Series 39:187-200. Urick, R. J. 1983. Principles of Underwater Sound (3 rd edition). Peninsula Publishing. Los Altos Hills, California, USA. Webb, J. F., A. N. Popper, R. R. Fay (eds). 2008. Fish Bioacoustics. Springer-Verlag. New York, USA. Yost, W. A. 2007. Fundamentals of Hearing: An Introduction (5 th edition). Elsevier, Inc. USA. Discovery of Sound in the Sea. University of Rhode Island. http://www.dosits.org/ FishBase: A Global Information System on Fishes. http://www.fishbase.org/ MATLAB Support and tutorials. http://www.mathworks.com/academia/student_center/tutorials/launchpad.html NOAA Ocean Acoustics Program. http://www.nmfs.noaa.gov/pr/acoustics/ 5