Skip to content Skip to navigation

New in Spring 2020

Agassiz Beach, Hopkins Marine Station

Marine Biology and Conservation in a Changing World


BIOHOPK 175H, 16 units

Our understanding of the oceans and its inhabitants is increasing rapidly and has opened exciting new avenues of exploration. In this course we address the latest oceans-related science, and explore emerging opportunities for innovative study of life in the sea. It is an immersion course, taught at Stanford’s Hopkins Marine Station on Monterey Bay. Students are in residence for the quarter, housed in Stanford’s nearby communal apartments.  The diverse organisms and environments of the Bay are our laboratory, and we treat the Bay as an integrated system that provides the focus for the course. Class meets daily with lectures, discussion, or lab and field work throughout the day. It consists of three sequential, linked concentrations, each three weeks in length, taught by teams of faculty experts. The subject matter is chosen to provide a coherent learning experience throughout the quarter. This design permits deep concentration on the topic at hand, and places emphasis on field and laboratory work, group discussion, individual exploration, and experiential learning.

The course includes a weekly seminar program that invites world renowned marine biologists to share their research on a variety of topics related to both the course work and to topics in marine conservation.

Because everyone enrolls in the same class, there is ample opportunity to develop working relationships and teamwork with other students and with the faculty, resulting in a vibrant learning community.

During the quarter, students are required to complete an individual capstone project of their choosing.  It can involve writing a paper in either narrative or scientific style, an analysis of published data, or the results from experiments carried out during the course, and will be mentored by one of the course instructors. The last week of the quarter is set aside to complete the capstone (which fulfills the Writing in the Major requirement for Biology and Earth Systems).

Application: Applications will be accepted beginning November 15, 2019 and continuing through February 15, 2020. Students will be notified regarding their acceptance shortly after they apply.


Course Content:


Biodiversity and Biomechanics of Monterey Bay

Robin Elahi and Mark Denny

In this 3-week concentration we explore the biodiversity of coastal ecosystems in Monterey Bay, with particular emphasis on the organisms found on local intertidal shores and in nearshore waters. Frequent field trips to a variety of habitats allow students to study organisms in nature, including rocky shores, kelp forests, seagrass beds, sandy beaches, dock communities, and mudflats. We will couch biological observations in the context of the physical environment.  Lectures are combined with laboratory studies focused on taxonomy, natural history, and the biomechanical adaptations of live organisms. 


Cells, Systems & Behavior: Neurobiology of Marine Animals

Bill Gilly and Stuart Thompson

We will examine the structure and physiology of neurons, muscle cells, and synapses - as well as the diversity of nervous systems - using examples drawn from local marine organisms. We will also cover topics in ethology including reflex behaviors, fixed action patterns, rhythm generators and learning - from simple to complex. We will address molecular mechanisms when desirable, but our primary focus will connect features of neuronal and muscular systems to the behavior of animals in the wild. Emphasis is placed on the unique sensory ecology of marine animals, social communication, and the systems informing migration behavior.  Lecture topics and discussions are coupled with work in the lab; for example, behavioral observations on octopus will explore habituation, object recognition memory, and attack behavior, as well as effects of environmental factors such as low oxygen, low temperature and pH, on these behaviors. Other lab work will use physiological recording methods to study the properties of sensory and motor systems in a variety of organisms.


Foundations of Ecology for a Changing World

Fio Micheli, Giulio De Leo and Jeremy Goldbogen

In this concentration, we will acquire a comprehensive understanding of foundational concepts in ecology - from individuals to populations, communities and ecosystems - taking advantage of the easy access to local marine and coastal ecosystems in the Monterey Bay and beyond. Through lectures, hands-on laboratory activities, group discussions and presentations, this concentration will further build students’ skills in critical scientific thinking (applied quantitative reasoning and scientific methods and analysis), reading the literature, and scientific communication. Emphasis will be placed on field observations, the development and use of mathematical and computer models in ecological theory, and the analysis, interpretation and presentation of ecological data. We will organize a series of field trips in the intertidal zone and in the pelagic environment on research vessels to monitor the abundance and distribution of zooplankton and forage fish in relation to predator foraging behavior. Written assignments, presentations and discussions are designed to provide experience in organizing and presenting information and to expose students to multiple perspectives on ecological processes and important conservation issues in the marine environment and our coastal ecosystems. Each week will include exciting opportunities for community engagement, through learning and participating in the efforts of local businesses, agencies and organizations to manage, restore and protect local natural resources and environments.


Seminar in Marine Science & Conservation

Larry Crowder

This seminar series provides an introduction to the key concepts of ecology and policy relevant to marine conservation issues at the population to ecosystems level. We will focus on the origin and maintenance of biodiversity and conservation applications from both the biology and policy perspectives (for example, overfishing, pollution, invasive species, protected species, climate change). Topics will also include emerging approaches such as ecosystem-based management, ocean planning, and coupled social-ecological systems. In addition to the weekly seminars, the course will include readings and discussions of primary literature, and opportunities to interact with visiting scholars



Supporting course offering

Experimental Design and Probability

BIOHOPK 174H, 3 units

Variability is an intrinsic feature of biological systems. This course provides an introduction to probability theory and its application to the design of experiments to address biological problems. Focus is on the use of linear models to explore and analyze biological datasets relevant to Monterey Bay and to test hypotheses (e.g., analysis of variance, regression). The R programming environment is emphasized but no prior programming or statistical background is assumed or required.