< Spring 2012 Courses
Friday Harbor Laboratories
last modified February 3, 2012

Spring 2012 Courses


FHL SPRING QUARTER: March 26 - June 1, 2012 (10 weeks)
Students arrive Sunday, March 25 after 3:00 p.m., depart Saturday, June 2 after breakfast

Applications are stlll being accepted for spring quarter until courses are filled.

Classes held Monday-Friday, 8:30 a.m. - 5:00 p.m.

Costs 2012
Student Information
Research Apprenticeship Program

Summer 2012
Autumn 2012

FHL SPRING 2012 COURSE LIST

1) THE ZOO-BOT QUARTER
Students choose a combination of courses to total 14-16 credits:

- Marine Zoology (Biol 430, 5 credits)
- Marine Botany (Biol 445, 5 credits)
- Ecology & Physiology of Nearshore Organisms Research Apprenticeship (Biol/Fish/Ocean 479, 6 credits)
- Developmental Biology Lab (Biology 412, 4 credits)
- Chemical Oceanography (Ocean 400, 4 credits)
- Ocean Acidification Research Apprenticeship (Ocean 494, 6 credits)


2) MARINE GENOMICS RESEARCH APPRENTICESHIP (Biol 479, 15 credits)

3) MARINE SEDIMENTARY PROCESSES RESEARCH APPRENTICESHIP (Ocean 492, 15 credits)

4) BEAM REACH PROGRAM
    March 26 - June 1
    (Ocean 360 + Ocean 365, 18 total credit)


5) THREE SEAS PROGRAM
    March 27 - May 18 (students arrive March 26)
    Northeastern University Program

6) ORGANISMAL BIOLOGY SEMINAR (Biol 490 D or Biol 590 A, 1 credit)

Credits for FHL coursework will be earned through the University of Washington but applicants to FHL courses do not need to be enrolled at University of Washington. Students from all over the world come to study and conduct research at Friday Harbor Labs.

UW students are encouraged to contact the Student Coordinators in their respective departments:

To apply, students should (a) follow the application procedures and (b) e-mail their preferred course choices to Stacy Markman.



The Zoo-Bot Quarter 2012

Applications are stlll being accepted for spring quarter until courses are filled.

Student choose a combination of courses to total 14 - 16 credits:

- Marine Zoology (Biol 430, 5 credits).
- Marine Botany
(Biol 445, 5 credits)
- Ecology & Physiology of Nearshore Organisms Research Apprenticeship* (Biol/Fish/Ocean 479, 6 credits)
- Developmental Biology Lab (Biology 412, 4 credits)
- Chemical Oceanography (Ocean 400, 4 credits, lecture only, no lab fee)
- Ocean Acidification Research Apprenticeship* (Ocean 494, 6 credits)

To apply for the Zoo-Bot Quarter:

1) Submit the web-based FHL application form, selecting "Zoo-Bot Quarter 2012" from the Spring Quarter course list, and then

2) Email your course preferences to Stacy Markman.

*It may be possible, with faculty permission, to enroll for a research apprenticeship for more than 6 credits, replacing one of the other course choices.

COURSE FACULTY:

- Marine Zoology (Biology 430, 5 credits)
Dr. Megan Dethier, Department of Biology, University of Washington

- Marine Botany (Biology 445, 5 credits)
Dr. Charles O'Kelly, Friday Harbor Laboratories, University of Washington

- Ecology & Physiology of Nearshore Organisms Research Apprenticeship (Biol/Fish/Ocean 479, 6 credits)
Dr. Megan Dethier, Department of Biology, University of Washington
Dr. David Duggins, Friday Harbor Laboratories, University of Washington

- Developmental Biology Lab (Biology 412, 4 credits)
Dr. Billie Swalla, Department of Biology, University of Washington

- Chemical Oceanography (Ocean 400, 4 credits)
Dr. James W. Murray, School of Oceanography, University of Washington

- Ocean Acidification Research Apprenticeship (Ocean 494, 6 credits).
Dr. James W. Murray, School of Oceanography, University of Washington

Photo: Dr. Emily Carrington

COURSE DESCRIPTIONS:


The Zoology and Botany courses survey the groups of marine invertebrates and plants represented in the San Juan Archipelago; natural history, adaptations, evolution, and taxonomy. Considerable field work and detailed laboratory study of organisms is included. All students will perform organized outreach activities with the local schools. A field trip to the outer coast will allow contrasts of the organisms and ecology there.

The Ecology & Physiology of Nearshore Organisms Research Apprenticeship will focus on the ecology and physiology of marine organisms and their communities. The projects are guided research, under diverse local mentors, on a preselected topic, with some latitude for students to develop their own directions. Example projects involve the biomechanics of seaweeds, invertebrates, and fishes; food web ecology, including the role of seaweeds exported into deep water habitats; assessing algae as targets for the biofuels and other aquaculture-based industries; and behavioral predator-prey observations, for instance of crabs consuming clams or protozoa consuming microalgae. Skills gained include overall conduct of independent research, data analysis and interpretation, and practice in scientific writing. UW students earn “W” credits in this writing-intensive course.
Prerequisites: Appropriate background in biological sciences and permission of instructors.

Enrollment limited to 18 students.

Developmental Biology Lab (Biology 412, 4 credtis)
See the beauty of Embryology and Development in invertebrate animals, especially ascidians and echinoderms. Watch morphological changes in developing animals; Learn about the Genetic regulation of development; Do your own project on Bioinformatics and Genomics; Experimental analysis of developing systems; Students will do hands on labs with embryos, labeling with fluorescent probes and microscopy.

Chemical Oceanography (Ocean 400, 4 credits)
This course will introduce undergraduates in marine biology to some of the main interdisciplinary themes in oceanography and The Global Carbon Cycle. The Themes include: What controls the composition of seawater and are humans changing it? What are the Chemical Constraints on Biological Production in the Ocean? What is the Fate of organic matter produced by biological production and what are the impacts of this organic
matter on the ocean and underlying sediments?

Ocean Acidification Research Apprenticeship (Ocean 494, 6 credits)
Students will participate in an ocean acidification mesocosm experiment. Each student will help with design and conducting the overall sampling but will have their own specific research topic in in microbiology, phytoplankton or zooplankton. Students will also learn the chemical basics of the ocean carbonate system and how to conduct calculations of the important carbonate species. Students will learn the key analytical methods for the carbonate system (dissolved inorganic carbon and alkalinity). A final report will include the methods use, data obtained and what they mean.

Faculty contact information:

mdethier@u.washington.edu

cjokelly@u.washington.edu

bjswalla@u.washington.edu

jmurray@u.washington.edu


More information about research apprenticeships

Students from University of Washington may be eligible for funding from the Mary Gates Endowment for Students ($1200 for the 6-credit research apprenticeship portion of the ZooBot Quarter). Minimum eligibility guidelines are at least sophpmore year for a 6-credit apprenticeship, and at least junior standing for a 15-credit apprenticeship, 3.0 GPA and sufficient course background in introductory science courses; exceptions can be made for students with excellent recommendations and other specific information.

Spring 2012 Zoobot Syllabus

Costs 2012

Student Information

Research Apprenticeship Program


Marine Genomics: from Biodiversity to Evolution

Spring Quarter, Research Apprenticeship

Integration of Genomics, Development and Neuroscience into a Coordinated Training Program to explore the origin of major innovations in the evolution of signaling systems

Dr. Leonid L. Moroz
Professor of Neuroscience, Biology and Chemistry, Department of Neuroscience, College of Medicine and The Whitney Laboratory for Marine Bioscience; University of Florida
moroz@whitney.ufl.edu

Dr. Billie Swalla
Professor of Biology, Department of Biology; University of Washington
bjswalla@u.washington.edu

Biology and Medicine today is the Biology of Genomes. Advances of modern genomic sciences and technologies are just beginning to be introduced into traditional zoological and comparative disciplines including marine biology. Moreover, there is an unfortunate divide between a few so-called “genomic” model organisms and a diversity of available species with unique development or functional characteristics but which lack genomic information. This gap is even more dramatic when an experimental biologist starts to address complex evolutionary questions or mechanisms of adaptation in various ecosystems including marine habitats. It is a long-desired goal of a biologist to both use a wide diversity of species for physiological tests and to integrate these experimental tests (or evolutionary hypotheses) with sufficient genomic information for any given species (or even multiple species) within months or even weeks.

Thus, we have developed an apprenticeship that will address these emerging challenges in genomic biology and marine genomics in particular. We would like to teach students how to integrate genomics and physiology; how to use non-traditional experimental preparations from less explored invertebrate groups and make them powerful models with extensive genomic information. In fact, during the apprenticeship, we will teach students to sequence and annotate both genomes and transcriptomes. We will design crucial experiments and introduce novel experimental models for genomic biology such as basal metazoans (Ctenophores, possibly selected Cnidarians) and basal deuterostomes (such as Hemichordates, Echinoderms and Tunicates). Conceptually, we will integrate genomic and functional analysis for representatives of these two key lineages known to be crucial in our understanding of the origin and evolution of animal organization, and specifically evolution of signaling pathways.

RESEARCH FOCUS:


The primary focus of the research program and individual projects will allow students to address a series of novel but critical questions: how to integrate genomic information about a given species to understand the biology of an organism and how to design functional/physiological tests to understand gene functions in non-traditional experimental models. Proposed training and experimental projects will ultimately provide insight into how animals and signal systems have evolved. These major questions include:
i. How has independent evolution (different lineages) and the modular organization of signaling systems in animals led to the formation of different types of hormonal control, nervous systems and behaviors?
ii. How are multiple signaling pathways and the activity of more than 20,000 genes integrated into the activities of specific neurons, neural circuits and developmental programs?
iii. How have developmental mechanisms, signaling transduction pathways, nervous systems and complex behaviors evolved?
iv. How have hormonal/secretory and other cell types been integrated into developmental and nervous system functions?
v. How have learning and memory mechanisms evolved? Do Ctenophores and Hemichordates learn and remember?
vi. How has the genome-scale organization of hormonal, developmental, and neuronal systems and behavior participated in speciation and evolutionary events?
It is ancicipated that a diversity of types of signaling mechanisms in both basal deuterostomes and basal metazoans will form an ideal training and research foundation to address these questions both conceptually and experimentally.

In summary, the ultimate research goal of this initiative is to enable students to identify and characterize evolutionarily conserved set(s) of genes by direct genome-wide sequencing and comparisons across phyla. Second, students will learn how to identity and functionally explore novel signal molecules and test their unique expression in specific cells, including neurons and stem cells. We will be able to determine novel homologous cell lineages leading to formation of complex phenotypes and organ systems. The students will be exposed to a variety of organisms, with particular focus on groups that occupy salient points in animal evolution. The latter will include basal animals such as sponges, ctenophores, and cnidarians, and basal deuterostomes, such as echinoderms and selected lophotrochozoans (e.g. brachiopods, phoronids, chaetognaths). The program will explore examples of modular organization of nervous and other signaling systems across phyla. We will also discuss hypotheses and identify trends and possible selective factors leading to independent origins of motor or sensory components, as well as central nervous systems, during evolution in several animal lineages including ctenophores, cnidarians, molluscs and chordates.

We propose to take advantage of the marine resources at Friday Harbor Laboratories during the spring of 2012 with the objective to introduce participants to both larval and adult organization of basal animal lineages. Moreover we will encourage individual student projects that address more functionally oriented questions and help place the question of specific cell signaling pathways in an appropriate ecological context of life history transitions and their evolutionary implications. Finally, we are confident that some organisms used in this apprenticeship will be further promoted and developed as novel model systems in neuroscience and genomic sciences.

 Students from University of Washington may be eligible for funding from the Mary Gates Endowment for Students ($3000 for a 15-credit research apprenticeship). Minimum eligibility guidelines are at least sophpmore year for a 6-credit apprenticeship, and at least junior standing for a 15-credit apprenticeship, 3.0 GPA and sufficient course background in introductory science courses; exceptions can be made for students with excellent recommendations and other specific information.

Spring 2012 Marine Genomics Syllabus

Costs 2012

Student Information

Research Apprenticeship Program


Marine Sedimentary Processes: Elwa River Dam Removal Impacts

Spring Quarter, Research Apprenticeship
Oceanography 492 (15 credits)

Dr. Andrea Ogston
University of Washington - School of Oceanography

Dr. Charles Nittrouer
University of Washington - School of Oceanography

This research apprenticeship focuses on designing and performing studies that will allow students to evaluate the impacts of the existing dams on the marine sedimentary system and the impacts during deconstruction of the release of reservoir-trapped sediment into the marine environment. Many rivers enter into the Puget Sound area, and the sediment brought to the marine environment creates a wide variety of seabed morphologies, which form the habitat for benthic biology. Dam removal projects are becoming increasingly popular to restore habitat of depleted fisheries and river ecosystems, and to add to the recreational opportunities on the nation's rivers. But we do not yet understand the full range of effects our “restoration” will have. One of these effects is the increased sediment discharge to the coastal ocean during dam removal. In many areas, this sediment can be considered a benefit, as it is projected to mitigate on-going shoreline erosion. Yet we need to understand the processes in the nearshore sedimentary system near the mouths of rivers to evaluate the overall impacts of dam removal and to inform over-seeing agencies as they make policies and recommendations.


The proximity of Friday Harbor Labs to the Elwha River makes it ideal to conduct a research cruise to the marine environment near the river mouth, and the timing of this apprenticeship will allow the investigation of highly concentrated flows discharged during the spring freshet as the initial stages of dam removal are undertaken. The lab is also uniquely situated such that field trips to a variety of sedimentary environments (e.g., local tidal flats, the Skagit River delta) can be taken on a weekly basis. These environments provide an experiential learning environment in which an understanding of the range of sedimentary processes that occur near river mouths will be gained. An informed evaluation of processes in different settings and under differing environmental conditions allow scientists to predict hazardous material transport, shoreline erosion and deposition, and change in seabed habitats due to dam installation and removal. The apprentices to be recruited for this course will have the potential to become informed scientists and managers in charge of decision-making in future restoration projects.

https://catalyst.uw.edu/workspace/ogston/23399

Faculty contact information:
ogston@ocean.washington.edu
nittroue@ocean.washington.edu

 Students from University of Washington may be eligible for funding from the Mary Gates Endowment for Students ($3000 for a 15-credit research apprenticeship). Minimum eligibility guidelines are at least sophpmore year for a 6-credit apprenticeship, and at least junior standing for a 15-credit apprenticeship, 3.0 GPA and sufficient course background in introductory science courses; exceptions can be made for students with excellet recommendations and other specific information.


Spring 2012 Marine Sedimentary Processes Syllabus
Costs 2012
Student Information
Research Apprenticeship Program


Three Seas Program

Please visit the Three Seas Program website for information about the program, its admission process and costs.

This program will convene at UW-Friday Harbor Laboratories in spring quarter in 2012.


Beam Reach Program

Ocean 360: Marine Field Research
Ocean 365: Practicing Sustainability Science

Beam Reach Marine Science and Sustainability School is offering a 10-week exploration of southern resident killer whales and the Salish Sea -- from physical oceanography and phytoplankton through forage fish and salmon to the endangered orcas themselves. Conduct your own research project while studying and living at the Friday Harbor Labs and aboard a sailing research vessel. Our silent biodiesel-electric catamaran enables you to use pioneering bioacoustic techniques and immerses you in adventure, teamwork and leadership training, sustainable technology demonstrations, and increased environmental awareness.

This program will convene at UW-Friday Harbor Laboratories in spring and autumn quarters in 2012.
Spring: March 26-June 1
Autumn: August 20-October 26

Max enrollment: 14

Faculty:
Dr. Robin Kodner
rkodner@uw.edu

Dr. Scott Veirs
scott@beamreach.org


Please visit the Beam Reach website for information about the program, its admission process and costs.



Organismal Biology Seminar
Biol 490 D or Biol 590 A, 1 credit

Dr. Kenneth Sebens
University of Washington - Friday Harbor Laboratories

Dr. Richard Strathmann
University of Washington - Friday Harbor Laboratories

THIS SEMINAR CONTINUES THE WEEKLY DISCUSSIONS AT FHL OF PAPERS IN BIOLOGY, EXCEPT THAT STUDENTS CAN REGISTER FOR CREDIT. ORGANISMAL BIOLOGY IS INTERPRETED BROADLY TO INCLUDE ASPECTS OF EVOLUTIONARY, DEVELOPMENTAL, AND FUNCTIONAL BIOLOGY AND ECOLOGY. THE ORGANISMS DO NOT ORGANIZE THEMSELVES ACCORDING TO ACADEMIC SPECIALTIES. IT IS EXPECTED THAT PARTICIPANTS IN THIS SEMINAR/DISCUSSION WILL DIFFER IN FIELDS OF RESEARCH BUT BE BROADLY CURIOUS ABOUT ORGANISMS. THE DISCUSSIONS WILL LAST APPROXIMATELY AN HOUR, BE AT A TIME ON A WEEKDAY THAT FITS THE PARTICIPANTS SCHEDULES, AND BE AT THE FRIDAY HARBOR LABORATORIES.

Enrollment Limit: 15 total students (10 students for Biol 490 + 5 students for Biol 590)


Independent Study for UW Graduate Students

During all quarters, graduate students may register for research with the consent of their faculty advisors.

600 Independent Study or Research
700 Master's Thesis
800 Doctoral Dissertation