Courses 2025-26

Biological processes take place at length scales ranging from that of individual protein molecules all the way to the algal blooms or rainforests that can be seen from space and over a dizzying nearly 30 orders of magnitude in time scales. This course will start by examining the biology of processes such as how plants and animals colonize oceanic islands and the physics of how animals such as wildebeest form giant herds during their year-long migration. With these wonders of the living world revealed, we will then seek to understand biological phenomena by thinking about genes and cells. May be taken pass/fail if taken in a first-year student's first year.

Have you ever wondered how a penguin swims or why a maple seed spins to the ground? Can a flea jump as high as a kangaroo? Is spider silk really stronger than steel? This class will offer answers to these and other questions related to the mechanical design of plants and animals. The course will provide a basic introduction to how engineering principles from the fields of solid and fluid mechanics may be applied to the study of biological systems. The course emphasizes the organismal level of complexity, although topics will also connect phenomenology at the molecular, cellular, and tissue-level scales. Topics include the physical properties of biological materials, viscoelasticity, biological pumps, muscle mechanics, neural control, and animal locomotion. May be taken pass/fail if taken in the first-year student's first year. Limited enrollment.

Do biological systems compute? Can we compute with biological systems? Is computer code a meaningful metaphor for genetic code? Do neural networks in biology have much to do with neural networks in computer science? In this class we will investigate these and other questions with a view towards learning about deep connections between biology and computer science that shed light on fundamental questions in biology. May be taken pass/fail if taken in a first-year student's first year.

We are bombarded by biological threats from the outside, ranging from toxic particulates to epidemic viruses, and also by threats from within, like cancer. How do our bodies manage to be victorious against these threats for so many years, in most cases? Many people have some familiarity with aspects of the answers now, due to COVID-19. But how can these defense mechanisms actually work, and how can they coordinate their actions to be effective and safe? Why do they fail? This course will zoom between scales to introduce the cells that the body uses for immune defense and how they execute their roles, both system-wide and at the molecular level. A central theme will be how the system is controlled by cellular "software" reading the genetic code, by ultra-rapid evolutionary mechanisms, and by elegant cell-cell communication networks. Lectures and student presentations will be included. May be taken pass/fail if taken in a first-year student's first year. Limited enrollment. Given in alternate years; offered 2025-26.

Due to the development of new technologies in the 21st century, experimental and computational tools, such as the sequencing of nucleic acids, have become faster and more inexpensive. These new tools have allowed the biological sciences to use genetics and genomics to reveal the functional relationships of life forms across the biosphere as never before. The largest conceptual shift enabled by this new capacity is the discovery of the unexpected complexity of the invisible world of microbes. We have learned that their diversity dwarfs that of animals and plants, and that they underlie the health of all corners of the biosphere and its inhabitants. In addition, genomic analyses of microbes have revealed that they 'invented' almost every fundamental feature of biological systems, and that macroorganisms have primarily added nuances as they build upon these essential foundations. This course aims to provide students with a comprehensive view of the structure and function of the biosphere, from its evolutionary history to its molecular underpinnings and emergent ecological patterns. The integration of micro- and macrobiology in an introductory biology course will allow students to both focus on the fundamental principles driving life and to build a comprehensive conceptual framework for understanding biology, much as chemistry and physics did in the 20th century as they developed a long-lasting framework for their introductory courses.

This course and its sequel, Bi 9, cover biology at the molecular and cellular levels. Bi 8 emphasizes genomic structure and the mechanisms responsible for the transmission and expression of genetic information. The focus is on the ways that the information content of the genome is translated into distinctive, cell-type specific patterns of gene expression and protein function. Assignments will include critical dissections of papers from classical and current research literature and problem sets.

Continues coverage of biology at the cellular level, begun in Bi 8. Topics: cytoplasmic structure, membrane structure and function, cell motility, and cell-cell recognition. Emphasis on both the ultrastructural and biochemical approaches to these topics.

An introduction to molecular, cellular, and biochemical techniques that are commonly used in studies of biological systems at the molecular level.

Special problems involving laboratory research in biology; to be arranged with instructors before registration. Must give a public presentation reporting results of work. May be counted as advanced lab credit. May be repeated for credit.

Special problems involving laboratory research in biology; to be arranged with instructors before registration. Graded pass/fail.

Small group study and discussion in depth of special areas or problems in biology or biological engineering, involving regular tutorial sections with instructors drawn from the divisional postdoctoral staff and others. Usually given winter term. To be arranged with instructors before registration. Graded pass/fail.

This course develops principles of solution thermodynamics, chemical kinetics, and transport processes applied to living systems.

Intended to extend opportunities for research provided by Bi 22 into a coherent individual research project, carried out under the supervision of a member of the biology faculty. Normally involves three or more consecutive terms of work in the junior and senior years. The student will formulate a research problem based in part on work already carried out, evaluate previously published work in the field, and present new results in a thesis format. First two terms graded pass/fail; final term graded by letter on the basis of the completed thesis.

Introduction to the computations made by the brain during economic and social decision making and their neural substrates. Part a: Introduction to social and decision neuroscience. Neural substrates of reward and reinforcement learning. Unconscious and conscious processing. The neural basis of emotion. Goal-directed and habit learning. The neural substrates of facial processing.

This course covers tools needed to analyze quantitative data in biological systems. Students learn basic programming topics, data organization and wrangling, data display and presentation, parameter estimation, and resampling-based statistical inference. Students analyze real data in class and in homework.

This course introduces students to statistical modeling and inference, primarily taking a Bayesian approach. Topics include generative modeling, parameter estimation, model comparison, hierarchical modeling, Markov chain Monte Carlo, graphical display of inference results, and principled workflows. Other topics may also be included. All techniques are applied to real biological data sets in class and in homework.

The theory of evolution is arguably biology’s greatest idea and serves as the overarching framework for thinking about the diversity and relationships between organisms. This course will present a broad picture of evolution starting with discussions of the insights of the great naturalists, the study of the genetic basis of variation, and an introduction to the key driving forces of evolution. Following these foundations, we will then focus on a number of case studies including the following: evolution of oxygenic photosynthesis, origin of eukaryotes, multicellularity, influence of symbiosis, the emergence of life from the water (i.e. fins to limbs), the return of life to the water (i.e. limbs to fins), diversity following major extinction events, the discovery of Archaea, insights into evolution that have emerged from sequence analysis, and finally human evolution and the impact of humans on evolution (including examples such as antibiotic resistance). A specific focus for considering these issues will be the island biogeography of the Galapagos. Given in alternate years; offered 2025-26.

Lectures and recitation introducing the molecular basis of life processes. In the first term, topics will include the structure and chemical properties of biological macromolecules, molecular biology methods, and biological catalysis. The second term will cover an overview of metabolism and the biochemistry behind the transmission of genetic information.

Learn about viruses as fascinating biological machines, focusing on naturally-occurring and evolved variants, in silico viral vector engineering, and computational methods that include structure visualization and machine learning. This course will introduce the fundamentals in the chemistry and biology of viruses, emphasizing their engineerable properties for use in basic research and translational applications. Topics include: viruses by the numbers, mammalian and non-mammalian (plant, bacteria) viruses, enveloped vs. non-enveloped viruses, host-virus interactions, viral life cycles (replication vs. dormancy), immune responses to viruses, zoonosis, diverse mechanisms of entry and replication, the application of viruses as gene-delivery vehicles (with a focus on adeno-associated viruses or AAVs, lentiviruses, and rabies), and how to engineer viral properties for applications in basic research and gene therapy. The lectures will be complemented by short lab exercises in AAV preparation, bioinformatics and machine learning, and structure visualization. Given in alternate years; offered 2025-26.

A course on microbial genetics, emphasizing the history of the discipline as well as modern approaches. Students will be exposed to different ways of manipulating microbial genomes (primarily bacterial, but we will also cover archaea and microbial eukaryotes). The power of microbial genetics to shed light on diverse process will be discussed in a variety of contexts, ranging from environmental science to the mammalian microbiome. Given in alternate years; offered 2025-26.

A survey of the development of multicellular organisms. Topics will include the beginning of a new organism (fertilization), the creation of multicellularity (cellularization, cleavage), reorganization into germ layers (gastrulation), induction of the nervous system (neurulation), and creation of specific organs (organogenesis). Emphasis will be placed on the molecular mechanisms underlying morphogenetic movements, differentiation, and interactions during development, covering both classical and modern approaches to studying these processes.

Lecture and discussion course covering basic principles of genetics. Not open to first-year undergraduate students.

Reviews of anatomy and histology, as well as in-depth discussion of cellular physiology. Building from cell function to tissues, the course explores human physiology in an organ-based fashion. First term topics include endocrine physiology, the autonomic nervous system, urinary physiology, and the cardiovascular system. Particular emphasis is placed on health issues and pharmaceutical therapy from both a research and a medical perspective.

Building on the foundations of Bi 145 a, Bi 145 b will continue the exploration of human physiology incorporating anatomy and cellular physiology. Topics include muscle physiology, the skeletal system, digestive and hepatic physiology, nutrition, the respiratory system and reproductive physiology. Particular emphasis is placed on health issues and pharmaceutical therapy from both a research and a medical perspective.

General principles of the function and organization of nervous systems, providing both an overview of the subject and a foundation for advanced courses. Topics include the physical and chemical bases for action potentials, synaptic transmission, and sensory transduction; anatomy; development; sensory and motor pathways; memory and learning at the molecular, cellular, and systems level; and the neuroscience of brain diseases. Letter grades only.

Physical models applied to the analysis of biological structures ranging from individual proteins and DNA to entire cells. Typical topics include the force response of proteins and DNA, models of molecular motors, DNA packing in viruses and eukaryotes, mechanics of membranes, and membrane proteins and cell motility.

A laboratory-based introduction to experimental methods used for electrophysiological studies of the central nervous system. Through the term, students investigate the physiological response properties of neurons in vertebrate and invertebrate brains, using extra- and intracellular recording techniques. Students are instructed in all aspects of experimental procedures, including proper surgical techniques, electrode fabrication, and data analysis. The class also includes a brain dissection and independent student projects that utilize modern digital neuroscience resources.

The neuroscience of psychiatric, neurological, and neurodegenerative disorders and of substance abuse, in humans and in animal models. Students master the biological principles including genetics, cell biology, biochemistry, physiology, and circuits. Topics are taught at the research level and include classical and emerging therapeutic approaches and diagnostic strategies. Given in alternate years; offered 2025-26.

Offers a broad survey of methods and approaches to understanding in modern neurobiology. The focus is on understanding the tools of the discipline, and their use will be illustrated with current research results. Topics include: molecular genetics, disease models, transgenic and knock-in technology, virus tools, tracing methods, gene profiling, light and electron microscopy, optogenetics, optical and electrical recording, neural coding, quantitative behavior, modeling and theory.

A course on growth and functions in the prokaryotic cell. Topics covered: growth, transport of small molecules, protein excretion, membrane bioenergetics, energy metabolism, motility, chemotaxis, global regulators, and metabolic integration.

One of the last great challenges to our understanding of the world concerns conscious experience. What exactly is it? How is it caused or constituted? And how does it connect with the rest of our science? This course will cover philosophy of mind, cognitive psychology, and cognitive neuroscience in a mixture of lectures and in-class discussion. There are no formal pre-requisites, but background in philosophy (equivalent to Pl 41, Pl 110) and in neuroscience (equivalent to NB/Bi/CNS 150) is strongly recommended and students with such background will be preferentially considered. Limited to 20.

Biology is becoming an increasingly data-intensive science. Many of the data challenges in the biological sciences are distinct from other scientific disciplines because of the complexity involved. This course will introduce key computational, probabilistic, and statistical methods that are common in computational biology and bioinformatics. We will integrate these theoretical aspects to discuss solutions to common challenges that reoccur throughout bioinformatics including algorithms and heuristics for tackling DNA sequence alignments, phylogenetic reconstructions, evolutionary analysis, and population and human genetics. We will discuss these topics in conjunction with common applications including the analysis of high throughput DNA sequencing data sets and analysis of gene expression from RNA-Seq data sets.

Lecture, laboratory, and project course aimed at understanding visual information processing, in both machines and the mammalian visual system. The course will emphasize an interdisciplinary approach aimed at understanding vision at several levels: computational theory, algorithms, psychophysics, and hardware (i.e., neuroanatomy and neurophysiology of the mammalian visual system). The course will focus on early vision processes, in particular motion analysis, binocular stereo, brightness, color and texture analysis, visual attention and boundary detection. Students will be required to hand in approximately three homework assignments as well as complete one project integrating aspects of mathematical analysis, modeling, physiology, psychophysics, and engineering. Given in alternate years; offered 2025-26.

This course aims at a quantitative understanding of how the nervous system computes. The goal is to link phenomena across scales from membrane proteins to cells, circuits, brain systems, and behavior. We will learn how to formulate these connections in terms of mathematical models, how to test these models experimentally, and how to interpret experimental data quantitatively. The concepts will be developed with motivation from some of the fascinating phenomena of animal behavior, such as: aerobatic control of insect flight, precise localization of sounds, sensing of single photons, reliable navigation and homing, rapid decision-making during escape, one-shot learning, and large-capacity recognition memory.

The course covers the mechanisms by which eukaryotic cells control their duplication in a properly regulated manner. A large emphasis will be placed on the controls that cells employ to replicate and segregate their chromosomes with the necessary precision. In addition, the course will examine the mechanisms by which cells detect and rectify damaged DNA throughout the cell cycle. These various processes, collectively known as checkpoint-regulatory mechanisms, lie at the heart of how organisms maintain genomic integrity throughout their lifetimes. These pathways are essential for the prevention of cancer, birth defects, and other maladies. As part of the course, students will give presentations on key publications in the field, including both classic papers and newer papers that employ cutting-edge technologies.

Lectures covering how genetic and genomic analyses are used to understand biological systems. Emphasis is on genetic and genome-scale approaches used in model organisms such as yeast, flies, worms, and mice to elucidate the function of genes, genetic pathways and genetic networks. Given in alternate years; offered 2025-26.

This course investigates computation by molecular systems, emphasizing models of computation based on the underlying physics, chemistry, and organization of biological cells. We will explore programmability, complexity, simulation of, and reasoning about abstract models of chemical reaction networks, molecular folding, molecular self-assembly, and molecular motors, with an emphasis on universal architectures for computation, control, and construction within molecular systems. If time permits, we will also discuss biological example systems such as signal transduction, genetic regulatory networks, and the cytoskeleton; physical limits of computation, reversibility, reliability, and the role of noise, DNA-based computers and DNA nanotechnology. Part a develops fundamental results; part b is a reading and research course: classic and current papers will be discussed, and students will do projects on current research topics.

This course develops the mathematical methods needed for a quantitative understanding of biological phenomena, including data analysis, formulation of simple models, and the framing of quantitative questions. Topics include: probability and stochastic processes, linear algebra and transforms, dynamical systems, scientific programming.

In consultation with, and with the approval of, a faculty advisor (usually the student’s academic advisor) and the Caltech Center for Teaching, Learning, and Outreach. Students may obtain credit for engaging in volunteer efforts to promote public understanding of science; to mentor and tutor young people and underserved populations; or to otherwise contribute to the diversity, equity, and inclusiveness of the scientific enterprise. Students will be required to fill out short pre- and post-outreach activity forms to describe their proposal and to report on the results. Students may petition their option representative (graduate students) or academic advisor (undergraduate students) if they seek credits beyond the 12-unit limit. Offered pass/fail.

A course of lectures, readings, and discussions focused on the genetic, physiological, and ecological bases of behavior in mammals. A basic knowledge of neuroanatomy and neurophysiology is desirable. Given in alternate years. Offered 2025-26.

This advanced course will discuss the emerging science of neural "circuit breaking" through the application of molecular genetic tools. These include optogenetic and pharmacogenetic manipulations of neuronal activity, genetically based tracing of neuronal connectivity, and genetically based indicators of neuronal activity. Both viral and transgenic approaches will be covered, and examples will be drawn from both the invertebrate and vertebrate literature. Interested CNS or other graduate students who have little or no familiarity with molecular biology will be supplied with the necessary background information. Lectures and student presentations from the current literature.

The cytosol, and fluid spaces within the nucleus, were once envisioned as a concentrated soup of proteins, RNA, and small molecules, all diffusing, mixing freely, and interacting randomly. We now know that proteins in the cytosol frequently undergo only restricted diffusion and become concentrated in specialized portions of the cytosol to carry out particular cellular functions. This course consists of lectures, reading, student presentations, and discussion about newly recognized biochemical mechanisms that confer local structure and reaction specificity within the cytosol, including protein scaffolds and "liquid-liquid phase separations" that form "membraneless compartments".

Maximum enrollment: 12. Applications of spatial genomics technology to various biological samples. Projects will be selected to represent problems in neurobiology, developmental biology and translational medicine. Emphasis will be placed on generating experimental data and analysis of data with machine learning algorithms for segmentation and clustering cells with single cell genomics tools, and preparation for publication.

Critical reviews and discussion of classic investigations and current research in paleoecology, evolution, and biogeochemistry.

This seminar course will explore and discuss the unique intersection of environmental racism, environmental justice, and academia. Course material will primarily feature readings and videos on a case study-like basis and focus on bringing conversations typically had in humanities, social sciences and activism to the bio and geosciences. Topics will center around two primary approaches: an "outward-facing" component that looks at environmental racism through the lens of various activisms, and an "inward-facing" component addressing the biases/malpractices broadly employed in the biological and geosciences, as well as the apparent moral dilemmas of decisions involving multiple stakeholders. Out of class work will largely be based on assigned readings, some multimedia presentations, and occasional writings and thought exercises. This course is taught concurrently with Hum 61 and can only be taken once, as Ge/ESE/Bi 248 or Hum 61.

Quantitative studies of cellular and developmental systems in biology, including the architecture of specific circuits controlling microbial behaviors and multicellular development in model organisms. Specific topics include chemotaxis, multistability and differentiation, biological oscillations, stochastic effects in circuit operation, as well as higher-level circuit properties, such as robustness. The course will also consider the organization of transcriptional and protein-protein interaction networks at the genomic scale. Topics are approached from experimental, theoretical, and computational perspectives.

The class focuses on quantitative studies of problems in systems neuroscience. Students will study classical work such as Hodgkin and Huxley's landmark papers on the ionic basis of the action potential, and will move from the study of interacting currents within neurons to the study of systems of interacting neurons. Topics will include lateral inhibition, mechanisms of motion tuning, local learning rules and their consequences for network structure and dynamics, oscillatory dynamics and synchronization across brain circuits, and formation and computational properties of topographic neural maps. The course will combine lectures and discussions, in which students and faculty will examine papers on systems neuroscience, usually combining experimental and theoretical/modeling components.

Lectures and literature-based discussions on the principles and experimental frontiers of embryonic axis organization, pattern formation, genomic mechanisms of cell type specification, stem cell biology, and evolutionary change.

This lecture and discussion course covers relevant aspects of the responsible conduct of biomedical and biological research. Topics include guidelines and regulations, ethical and moral issues, research misconduct, data management and analysis, research with animal or human subjects, publication, conflicts of interest, mentoring, and professional advancement. Undergraduate students with junior and senior standing may enroll. Graded pass/fail.

Emotions are at the forefront of most human endeavors. Emotions aid us in decision-making (gut feelings), help us remember, torment us, yet have ultimately helped us to survive. Over the past few decades, we have begun to characterize the neural systems that extend from primitive affective response such as fight or flight to the complex emotions experienced by humans including guilt, envy, empathy and social pain. This course will begin with an in-depth examination of the neurobiological systems that underlie negative and positive emotions and move onto weekly discussions, based on assigned journal articles that highlight both rudimentary and complex emotions. The final weeks will be devoted to exploring how the neurobiological systems are disrupted in affective disorders including anxiety, aggression and psychopathy. In addition to these discussions and readings, each student will be required to write a review paper or produce a short movie on a topic related to one of the emotions discussed in these seminars and its underlying neural mechanisms.

A brain-machine interface (BMI) records neural activity, decodes the intent of the participant, and generates control signals to operate assistive devices. Bi-directional BMIs can write signals back into the brain though electrical stimulation based on the recorded neural activity. These neurotechnologies have been advancing rapidly with therapeutic potential for several neurological diseases and disorders. Through lectures and reviews of the literature, the course will cover motor BMIs for robotics and communication, cognitive neural prosthetics, stimulation to restore sensation, and different invasive and non-invasive recording and stimulation technologies. Given in alternate years; offered 2025-26.

This course focuses on clear communication of scientific research in grant writing, networking, and research presentation. Practice is obtained through the following facilitated activities: 1) drafting the required statements for an NSF-GRFP proposal, 2) developing a networking pitch for use with non-scientists and scientists, and 3) presenting research to a scientific audience. First and second year graduate students, senior undergrads, and rising senior undergrads can enroll. Not offered 2025-26.

Students may register with permission of the responsible faculty member.

Students may register with permission of the responsible faculty member.

Students may register for research units after consultation with their adviser.