Results for BIO

Chili peppers are used worldwide. They are grown in astonishing variety even though they are used most often to flavor food. Yet the first chile peppers evolved in what Europeans call the New World (Central and South America). How do we know chilis came from the New World? How did they get to Europe, Africa, India, China? How did chilis become an integral part of so many cuisines? What forms of chili pepper do we find around the world?

Traditional ecological knowledge--the knowledge developed and maintained by local communities over many generations about their natural environment--is increasingly recognized as fundamental to solving environmental problems. In this seminar, we will explore some of the cutting-edge research on traditional ecological knowledge and its conceptual and practical role in ensuring environmental sustainability. We will address some key questions. For example, what makes traditional ecological knowledge different from Western science? What led to the recent increase in Western scientists' appreciation of traditional ecological knowledge? How can traditional ecological knowledge inform environmental sustainability in a world that is undergoing rapid climate change, land use change, and biological invasion? And how can Western science complement traditional ecological knowledge to achieve sustainability? The core of this seminar will be discussion based on reading of primary articles. We will also have field trips and learn from guest speakers.

This course provides an authentic research experience where you will study the consequences of disease-related mutations in a neuronal kinesin (KIF1A). You will evaluate scientific arguments; make discoveries by generating, testing, and revising hypotheses; communicate findings to others through oral and poster presentations; and build confidence in yourselves as scientific thinkers. To do so, you will use behavioral, genetic, and cell biological tools to assay how KIF1A mutations affect C. elegans neurons, and connect your findings to clinical severity. Completed or co-requisite in introductory courses in cell and molecular biology ( BIO 82 and 83 or HUMBIO 2A and 3A) and ( CHEM 31A and 31B or CHEM 31M).

The goal of this course is to develop an understanding of how to conduct biological research, using a topic in Ecology, Evolutionary Biology, and Plant Biology as a practical example. This includes the complete scientific process: assessing background literature, generating testable hypotheses, learning techniques for field- and lab-based data collection, analyzing data using appropriate statistical methods, and, finally, writing and sharing your results. To build these skills, this course will focus on nectar microbes at Stanford's nearby Jasper Ridge Biological Preserve. Students, working in teams, will develop novel research hypotheses and execute the necessary experiments and measurements to test these hypotheses. The capstone of the course is an oral presentation of student teams' research findings, as well as a research paper written in the style of a peer-reviewed journal article. Labs will be completed both on campus and at Jasper Ridge. Although there are no pre-requisites to enroll in the class, it will be helpful if you have already taken BIO 81 or HUMBIO 2A. IMPORTANT NOTE: Satisfies WIM requirement in Biology but must be taken for a letter grade.

This course will focus on the basic structures inside cells and how they execute cellular functions. Topics include organelles, membrane trafficking, the cytoskeleton, cell division, and signal transduction. Classic and recent primary literature will be incorporated into lectures with an emphasis on state of the art experimental approaches. Prerequisites: BIO 83 is highly recommended.

The Ecology and Natural History of the Jasper Ridge Biological Preserve is an upper-division course that aims to help students learn ecology and natural history using a 'living laboratory,' the Jasper Ridge Biological Preserve. The course's central goal is that, as a community of learning, we examine 'via introductory discussions, followed by hands-on experiences in the field' the scientific basis of ecological research, archaeology, edaphology, geology, species interactions, land management, and multidisciplinary environmental education. The first 10 sessions that compose the academic program are led by the instructors, faculty (world-experts on the themes of each session), and JRBP staff. In addition, this 20-week class (winter and spring quarters) trains students to become JRBP Docents that will join the Jasper Ridge education affiliates community. Completion of both Winter (BIO 105A) and Spring (BIO 105B) sequence training program is required to join the Ecology and Natural History of Jasper Ridge Biological Preserve course.

This course serves as a companion and continuation for the Fall and Winter sessions of bioBUDS ( BIO 114A and 114B). If demand exceeds slots available, preference will be given to students who participated in the Fall and/or Winter sessions. This program will pair participating students with a lab/research mentor based on student-ranked preferences. Students will work on a research project with their mentor for the duration of the quarter. Enrollment in BIO114C is required to participate in the internship, and class sessions will focus on tracking internship progress and evaluating mentorship relationships. For information, visit our website: https://biobuds.stanford.edu. An application link will be available on our website in early February.

To survive, grow, and reproduce, organisms coordinate different molecular processes so they can use available resources and cope with environmental conditions. This laboratory course explores molecular and cellular integration in bacteria. Experiments include the quantification of growth, mutational screens and mutant analysis, gene cloning, and measuring/engineering gene-expression. These "wet lab" approaches will be combined with "dry lab" approaches to analyze experimental findings and explore further the link between molecular processes, cell-physiology, and ecology. Prerequisite: MATH 51 or MATH 19, 20,21. Recommended: microbiology (e.g. BIO 62 or 162) and molecular biology/biochemistry/genetics courses (e.g. BIO 82 or 83). Enrollment via Application: https://forms.gle/etRHRhhaRJxUMyNW9

Advanced undergraduate survey of ornithology, introducing students to the biology of birds and giving them to tools to use birds as model systems for research. Topics will include avian evolution, physiology, adaptations, behavior, and ecology. Focus throughout on identification of California birds and applications to current bird conservation issues. Course will include lectures and a field component which will expose students to standard avian research techniques such as mistnetting, banding, and point count surveys. Prerequisite: BIO 81 or BIO 105A/B or instructor approval.

The ocean is impacted by overfishing, plastic pollution, climate change and acidification, which are leading to the disruption of marine ecosystem functions and services critical for human wellbeing. Ocean mining, offshore wind farming, increasing shipping, land sea interactions and carbon sequestration are all posing a whole new set of unprecedented challenges and, at the same time, opportunities to solve the pressing problem humanity has to face. By leveraging the unique location of Hopkins Marine Station as a living laboratory in Monterey Bay, this course will provide a unique opportunity for students to learn through real world examples about the multifaceted nature of problems at the very core of ocean sustainability. Course taught in-person only at Hopkins Marine Station; for information on how to spend spring quarter in residence: https://hopkinsmarinestation.stanford.edu/undergraduate-studies/spring-courses-23-24 (Individual course registration also permitted.) Depending on enrollment numbers, a weekly shuttle to Hopkins or mileage reimbursements for qualifying carpools will be provided; terms and conditions apply.

Laboratory and lectures. Advanced microscopy and imaging, emphasizing hands-on experience with state-of-the-art techniques. Students construct and operate working apparatus. Topics include microscope optics, Koehler illumination, contrast-generating mechanisms (bright/dark field, fluorescence, phase contrast, differential interference contrast), and resolution limits. Laboratory topics vary by year, but include single-molecule fluorescence, fluorescence resonance energy transfer, confocal microscopy, two-photon microscopy, microendoscopy, and optical trapping. Limited enrollment. Recommended: basic physics, basic cell biology, and consent of instructor.

(Formerly GEOLSCI 136 and 236) The course will focus on the macroevolution of animals. We will be exploring how paleobiology and developmental biology/genomics have contributed to our understanding of the origins of animals, and how patterns of evolution and extinction have shaped the diversity of animal forms we observe today. Change of Department Name: Earth and Planetary Science (Formerly Geologic Sciences).

Principles and application of the science of preserving biological diversity. Conceptually, this course is designed to explore the major components relevant to the conservation of biodiversity, as exemplified by the Latin American region. The conceptual frameworks and principles, however, should be generally applicable, and provide insights for all regions of the world. All students will be expected to conduct a literature research exercise leading to a written report, addressing a topic of their choosing, derived from any of the themes discussed in class.

Students in this course will uncover key principles of genetics and molecular biology through investigation of case studies of human disease and novel therapeutic approaches in development. This course will require close reading and discussion of primary literature and will emphasize and support the development of critical skills in scientific communication. Students will utilize a variety of mediums to convey scientific information to a range of audiences in a series of projects completed during the quarter. Prerequisites: BIO 82, 83 and 86 or equivalent.

Multidisciplinary. How to approach complex normal and abnormal behaviors through biology. How to integrate disciplines including sociobiology, ethology, neuroscience, and endocrinology to examine behaviors such as aggression, sexual behavior, language use, and mental illness.

Many organisms possess a remarkable ability to repair and regenerate damaged organs and tissues. This course will explore the cellular and developmental mechanisms used to achieve regeneration. Students will learn the basic developmental and cellular mechanisms underlying the original formation of organs during normal development and how these mechanisms are modified during the regenerative process. The course will also consider how our expanding knowledge of regeneration mechanisms could be used to promote medically useful regeneration in humans. The course will involve extensive reading and analysis of primary literature. Prerequisites: BIO 86 (BIO 160 or BIO 158 recommended). Enrollment by permission of professor, apply at https://forms.gle/uoGrzagSRdTGd2hU8.

Structured population models with age and phenotypic variation. Integral population models, model fitting and dynamics. Fitness and dynamic heterogeneity. Examples from natural populations (sheep, roe deer, plants, birds). Graduate students will be responsible for additional problem sets. Prerequisites: calculus and linear algebra.

Chemical biology is an integrative discipline that seeks to apply chemical tools and approaches to understand biology. This course will introduce students to various methods and approaches used in this field, with an emphasis on the use of natural products and synthetic small molecules as probes of biological function. Specific examples will be used to illustrate the ramifications of chemical biology with molecular, cell and developmental biology. The interaction between disease and drug discovery will be considered in detail. Prerequisites: BIO 83, and BIO 82 and/or BIO 84.

Class can be taken in person or via Zoom. Introduction to the key concepts of ecology and policy relevant to marine conservation issues at the population to ecosystems level. Focus on the origin and maintenance of biodiversity and conservation applications from both the biology and policy perspectives (for example, endangered species, captive breeding, reserve design, habitat fragmentation, ecosystem restoration/rehabilitation). Also includes emerging approaches such as ecosystem-based management, ocean planning, and coupled social-ecological systems. The course will include lectures, readings and discussions of primary literature, and attendance at seminars with visiting scholars. Prerequisite: introductory biology; suggested: a policy and/or introductory ecology course. Students who want to enroll only in the seminar and discussion course (2 units) should register for OCEANS/BIO 173HA. (Graduate students register for BIO/OCEANS 273H.) For information on how to spend spring quarter in residence: https://hopkinsmarinestation.stanford.edu/undergraduate-studies/spring-courses-23-24 (Individual course registration also permitted.) Depending on enrollment numbers, a weekly shuttle to Hopkins or mileage reimbursements for qualifying carpools will be provided; terms and conditions apply.

(Graduate students register for 323H.) Five weeks of marine science including oceanography, marine physiology, policy, maritime studies, conservation, and nautical science at Hopkins Marine Station, followed by five weeks at sea aboard a sailing research vessel in the Pacific Ocean. Shore component comprised of three multidisciplinary courses meeting daily and continuing aboard ship. Students develop an independent research project plan while ashore, and carry out the research at sea. In collaboration with the Sea Education Association of Woods Hole, MA. Only 6 units may count towards the Biology major.

Capstone course series for seniors. Creative, self-reflective and scientifically relevant projects conceived, produced and exhibited over the course of three quarters. Explore scientific content of personal interest through creative forms including but not limited to writing, music, fine arts, performing arts, photography, film or new media. A written essay on the creative process and scientific significance of the selected topic will accompany the creative work. Completed projects may be included in a creative portfolio. Required enrollment in 196A,B,C. May be repeat for credit. More information can be found at visit https://web.stanford.edu/~suemcc/TSR/.

Individually arranged under the supervision of members of the faculty.

Individually arranged under the supervision of members of the faculty. Credit for work arranged with out-of-department faculty is restricted to Biology majors and requires department approval. See https://biology.stanford.edu/academics/undergraduate-research/directed-reading for information and petitions. May be repeated for credit.

Individual research taken by arrangement with in-department instructors. See http://biohonors.stanford.edu for information on research sponsors, units, and credit for summer research. May be repeated for credit.

Seniors in Biology may undertake an independent capstone project through the Independent Capstone in Biology course series, BIO 199 A, B, C. Such projects might involve creative works, research or business internships, travel-based study, teaching, or community service. Examples include the production of a teaching or business plan, a film or podcast, or a public education campaign. The Independent Capstone in Biology is best suited for those students who wish to complete their projects independently, without close peer support and collaboration, while continuing to benefit from project mentorship. Satisfies WIM in Biology.

Individual research by arrangement with out-of-department instructors. Credit for 199X is restricted to declared Biology majors and requires department approval. See https://biology.stanford.edu/academics/undergraduate-research/research for information on research sponsors, units, petitions, deadlines, credit for summer research, and out-of-Stanford research. May be repeated for credit.

To survive, grow, and reproduce, organisms coordinate different molecular processes so they can use available resources and cope with environmental conditions. This laboratory course explores molecular and cellular integration in bacteria. Experiments include the quantification of growth, mutational screens and mutant analysis, gene cloning, and measuring/engineering gene-expression. These "wet lab" approaches will be combined with "dry lab" approaches to analyze experimental findings and explore further the link between molecular processes, cell-physiology, and ecology. Prerequisite: MATH 51 or MATH 19, 20,21. Recommended: microbiology (e.g. BIO 62 or 162) and molecular biology/biochemistry/genetics courses (e.g. BIO 82 or 83). Enrollment via Application: https://forms.gle/etRHRhhaRJxUMyNW9

Advanced undergraduate survey of ornithology, introducing students to the biology of birds and giving them to tools to use birds as model systems for research. Topics will include avian evolution, physiology, adaptations, behavior, and ecology. Focus throughout on identification of California birds and applications to current bird conservation issues. Course will include lectures and a field component which will expose students to standard avian research techniques such as mistnetting, banding, and point count surveys. Prerequisite: BIO 81 or BIO 105A/B or instructor approval.

Seminar. This course focuses on the logic of how neural circuits process information and control behavior, as well as how neural circuits are assembled during development and modified by experience. Emphasis is on primary literature. Topics include: neurons as information processing units; simple and complex circuits underlying sensory information processing, motor control, and cognitive function; and development and plasticity of neural circuits. Advanced undergraduates and graduate students with background in physical science, engineering, and biology may apply to enroll. Enrollment is by application only: https://luolab.stanford.edu/teaching. Please submit by the last week of the winter quarter. Recommended: background in neuroscience.

Laboratory and lectures. Advanced microscopy and imaging, emphasizing hands-on experience with state-of-the-art techniques. Students construct and operate working apparatus. Topics include microscope optics, Koehler illumination, contrast-generating mechanisms (bright/dark field, fluorescence, phase contrast, differential interference contrast), and resolution limits. Laboratory topics vary by year, but include single-molecule fluorescence, fluorescence resonance energy transfer, confocal microscopy, two-photon microscopy, microendoscopy, and optical trapping. Limited enrollment. Recommended: basic physics, basic cell biology, and consent of instructor.

Principles and application of the science of preserving biological diversity. Conceptually, this course is designed to explore the major components relevant to the conservation of biodiversity, as exemplified by the Latin American region. The conceptual frameworks and principles, however, should be generally applicable, and provide insights for all regions of the world. All students will be expected to conduct a literature research exercise leading to a written report, addressing a topic of their choosing, derived from any of the themes discussed in class.

(Formerly GEOLSCI 136 and 236) The course will focus on the macroevolution of animals. We will be exploring how paleobiology and developmental biology/genomics have contributed to our understanding of the origins of animals, and how patterns of evolution and extinction have shaped the diversity of animal forms we observe today. Change of Department Name: Earth and Planetary Science (Formerly Geologic Sciences).

The genomics revolution has fueled a renewed push to model evolutionary processes in quantitative terms. This course will provide an introduction to quantitative evolutionary modeling through the lens of statistical physics. Topics will range from the foundations of theoretical population genetics to experimental evolution of laboratory microbes. Course work will involve a mixture of pencil-and-paper math, writing basic computer simulations, and downloading and manipulating DNA sequence data from published datasets. This course is intended for upper level physics and math students with no biology background, as well as biology students who are comfortable with differential equations and probability.

Structured population models with age and phenotypic variation. Integral population models, model fitting and dynamics. Fitness and dynamic heterogeneity. Examples from natural populations (sheep, roe deer, plants, birds). Graduate students will be responsible for additional problem sets. Prerequisites: calculus and linear algebra.

Class can be taken in person or via Zoom. Introduction to the key concepts of ecology and policy relevant to marine conservation issues at the population to ecosystems level. Focus on the origin and maintenance of biodiversity and conservation applications from both the biology and policy perspectives (for example, endangered species, captive breeding, reserve design, habitat fragmentation, ecosystem restoration/rehabilitation). Also includes emerging approaches such as ecosystem-based management, ocean planning, and coupled social-ecological systems. The course will include lectures, readings and discussions of primary literature, and attendance at seminars with visiting scholars. Prerequisite: introductory biology; suggested: a policy and/or introductory ecology course. Students who want to enroll only in the seminar and discussion course (2 units) should register for OCEANS/BIO 173HA. (Graduate students register for BIO/OCEANS 273H.) For information on how to spend spring quarter in residence: https://hopkinsmarinestation.stanford.edu/undergraduate-studies/spring-courses-23-24 (Individual course registration also permitted.) Depending on enrollment numbers, a weekly shuttle to Hopkins or mileage reimbursements for qualifying carpools will be provided; terms and conditions apply.

Open to upper-division undergraduates and graduate students. Practical, supervised teaching experience in a biology lab or lecture course. Training often includes attending lectures, initiating and planning discussion sections, and assisting in the preparation course materials. May be repeated for credit.nPrerequisite: consent of instructor.

This course is required for international students who are participating in professional internships in organizations (e.g. research institutes, education, medicine, business, policy) with a focus in the biological sciences. Students will be engaged in on-the-job training under the guidance of experienced, on-site supervisors. This course meets the requirements for curricular practical training (CPT) for students with F-1D/S status. Prior to the internship, students are required to submit a concise report detailing the proposed project and work activities. After the internship, students are required to submit a summary of the work completed, skills learned, and reflection of the professional growth gained as a result of the internship. This course may be repeated for credit. Prerequisite: Qualified offer of employment and consent of advisor.

This course provides students teaching in the Department of Biology with basic training, support, and professional development in their teaching roles. Topics include student engagement, assessment, feedback and more. Should be taken concurrently with the first teaching position.

Limited to first year Biology PhD students. Lab rotations with Biosciences faculty.

For graduate students only. Individual research by arrangement with in-department instructors.

Individual research by arrangement with out-of-department instructors. Master's students: credit for work arranged with out-of-department instructors is restricted to Biology students and requires approved department petition. See http://biohonors.stanford.edu for more information. May be repeated for credit.

Required of first-year PhD students in population biology, and ecology and evolution. Major conceptual issues and developing topics. This course is open only to Biology PhD students and is not open to auditors.

The course will focus on 5 themes for effectively managing your PhD: professionalism, scholarship, well-being, community-engagement and career development. We will meet every other week and have an active discussion-based class meeting for 2 hours. At the end of the quarter students and instructors will co-organize a departmental half-day workshop on a particular topic relevant to the topics covered in the class.

Required of PhD graduate students in the Cell, Molecular, and Organismal Biology training program. Selected faculty will lead discussion of topics related to responsible conduct of research and ethics, such as conflict of interest, authorship, collaborative research, and data management.

How you respond to the challenges commonly encountered in graduate school and ensuing careers impacts your motivation, productivity, health, and well-being. In this course you will learn: to recognize and rephrase negative self-talk and impostor fears; communicate more clearly and assertively with advisors; build supportive mentoring; handle (difficult) feedback; calm stress and overwhelming feelings; and boost resilience. Structure: NIH webinars and facilitated small discussion groups will provide vital individual support and help implement learned skills in daily life. This is a two-part series to be offered in both winter and spring, which progressively builds foundational well-being awareness with practical tools for sustainable impact on health and work habits.

(Graduate students register for 323H.) Five weeks of marine science including oceanography, marine physiology, policy, maritime studies, conservation, and nautical science at Hopkins Marine Station, followed by five weeks at sea aboard a sailing research vessel in the Pacific Ocean. Shore component comprised of three multidisciplinary courses meeting daily and continuing aboard ship. Students develop an independent research project plan while ashore, and carry out the research at sea. In collaboration with the Sea Education Association of Woods Hole, MA. Only 6 units may count towards the Biology major.

Enrollment limited to PhD students associated with departmental research groups in genetics or molecular biology.

Literature review, research, and current problems in the theory and practice of population genetics and molecular evolution. May be repeated for credit. Prerequisite: consent of instructor.