Courses 2024-25

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.

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 b: History and mechanisms of reinforcement. Memory and valuation. Neural repurposing. Mentalizing and strategic thinking. Neural bases of prosociality, risky choice and delay discounting. Mathematical economic-style theories of neural circuits.

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.

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.

Lectures and recitation on the molecular basis of biological structure and function. Emphasizes the storage, transmission, and expression of genetic information in cells. Specific topics include DNA replication, recombination, repair and mutagenesis, transcription, RNA processing, and chromatin structure.

The course will cover the molecular and cellular mechanisms that mediate recognition and response in the mammalian immune system. Topics include cellular and humoral immunity, the structural basis of immune recognition, antigen presentation and processing, gene rearrangement of lymphocyte receptors, cytokines and the regulation of cellular responses, T and B cell development, and mechanisms of tolerance. The course will present an integrated view of how the immune system interacts with viral and bacterial pathogens and commensal bacteria. Given in alternate years; offered 2024-25.

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.

An advanced course of lectures, readings, and student presentations focusing on neural basis of innate body functions such as appetite, sleep, temperature, and osmolality regulation. This course will also cover the gut-to-brain interactions focusing on homeostatic functions. These include genetics, neural manipulation, and viral tracing tools with particular emphasis on data interpretation and limitation of available neuroscience tools. Given in alternate years; offered 2024-25.

The neuroscience of drugs for therapy, for prevention, and for recreation. Students learn the prospects for new generations of medications in neurology, psychiatry, aging, and treatment of substance abuse. Topics: Types of drug molecules, Drug receptors, Electrophysiology, Drugs activate ion channels, Drugs block ion channels, Drugs activate and block G protein pathways, Drugs block neurotransmitter transporters, Pharmacokinetics, Recreational drugs, Nicotine Addiction, Opiate Addiction, Drugs for neurodegenerative diseases: Alzheimer's disease, Parkinson's disease, Drugs for epilepsy and migraine, and Psychiatric diseases: Nosology and drugs. The course is taught at the research level. Given in alternate years; offered 2024-25.

An integrative approach to the study of vertebrate evolution combining comparative anatomical, behavioral, embryological, genetic, paleontological, and physiological findings. Special emphasis will be given to: (1) the modification of developmental programs in evolution; (2) homeostatic systems for temperature regulation; (3) changes in the life cycle governing longevity and death; (4) the evolution of brain and behavior. Letter grades only. Given in alternate years; offered 2024-25.

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.

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.

A course on the metabolic diversity of microorganisms. Basic thermodynamic principles governing energy conservation will be discussed, with emphasis placed on photosynthesis and respiration. Students will be exposed to genetic, genomic, and biochemical techniques that can be used to elucidate the mechanisms of cellular electron transfer underlying these metabolisms. Given in alternate years; offered 2024-25.

The cornerstone of current progress in understanding the mind, the brain, and the relationship between the two is the study of human and animal cognition. This course will provide an in-depth survey and analysis of behavioral observations, theoretical accounts, computational models, patient data, electrophysiological studies, and brain-imaging results on mental capacities such as attention, memory, emotion, object representation, language, and cognitive development. Given in alternate years; offered 2024-25.

Lectures and discussions on the underlying principles behind digital, video, differential interference contrast, phase contrast, confocal, and two-photon microscopy. The course will begin with basic geometric optics and characteristics of lenses and microscopes. Specific attention will be given to how different imaging elements such as filters, detectors, and objective lenses contribute to the final image. Course work will include critical evaluation of published images and design strategies for simple optical systems and the analysis and presentation of two- and three-dimensional images. The role of light microscopy in the history of science will be an underlying theme. No prior knowledge of microscopy will be assumed. Given in alternate years; offered 2024-25.

Structural, phylogenetic, and metabolic diversity of microorganisms in nature. The course explores microbial interactions, relationships between diversity and physiology in modern and ancient environments, and influence of microbial community structure on biogeochemical cycles. Introduction to ecological principles and molecular approaches used in microbial ecology and geobiological investigations. Given in alternate years; offered 2024-25.

Plants comprise most of the mass of living things on land, serve as the ultimate source of almost all human food and energy, and are a dominating force in the carbon and oxygen cycles. This lecture, reading and lab course will introduce topics in plant systematics, evolution, genetics, genomics, development, and ecology, with emphasis on plant interactions with soil and the bacteria, fungi, and animals that inhabit it. Students from all options are welcome.

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.

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.

This course provides an intensive, hands-on, pragmatic introduction to computer programming aimed at biologists and bioengineers. No previous programming experience is assumed. Python is the language of instruction. Students will learn basic concepts such as data types, control structures, string processing, functions, input/output, etc., while writing code applied to biological problems. At the end of the course, students will be able to perform simple simulations, write scripts to run software packages and parse output, and analyze and plot data. This class is offered as a week-long summer "boot camp" the week after Commencement, in which students spend all day working on the course. Students who do not have a strong need for the condensed boot camp schedule are encouraged to take BE/Bi 103 a instead. Graded pass/fail.

This course is a practical introduction to machine learning methods for biological data, focusing on three common data types in biology-images, sequences, and structures. This course will cover how to represent biological data in a manner amenable to machine learning approaches, survey tasks that can be solved with modern deep learning algorithms (e.g. image segmentation, object tracking, sequence classification, protein folding, etc.), explore architectures of deep learning models for each data type, and provide practical guidance for model development. Students will have the opportunity to apply these methods to their own datasets.

An advanced course with classes based on active discussion, lectures, and seminar presentations. Development from embryos and development from stem cells are distinct paradigms for understanding and manipulating the emergence of ordered biological complexity from simplicity. This course focuses on the distinguishing features of stem-cell based systems, ranging from the natural physiological stem cells that are responsible for life-long hematopoiesis in vertebrates (hematopoietic stem cells) to the artificial stem cells, ES and iPS cells, that have now been created for experimental manipulation. Key questions will be how the stem cells encode multipotency, how they can enter long-term self-renewal by separating themselves from the developmental clock that controls development of the rest of the organism, and how the self-renewal programs of different stem cell types can be dismantled again to allow differentiation. Does "stem-ness" have common elements in different systems? The course will also cover the lineage relationships among diverse differentiated cell types emerging from common stem cells, the role of cytokines and cytokine receptors in shaping differentiation output, apoptosis and lineage-specific proliferation, and how differentiation works at the level of gene regulation and regulatory networks. Given in alternate years; offered 2024-25.

Reading and discussions of behavioral and electrophysiological studies of the systems for the processing of sensory information in the brain. Given in alternate years; offered 2024-25.

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.

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.

A general survey of the structure and function of the cerebral cortex. Topics include cortical anatomy, functional localization, and newer computational approaches to understanding cortical processing operations. Motor cortex, sensory cortex (visual, auditory, and somatosensory cortex), association cortex, and limbic cortex. Emphasis is on using animal models to understand human cortical function and includes correlations between animal studies and human neuropsychological and functional imaging literature. Given in alternate years; offered 2024-25.

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.

This course will cover 4-5 major discoveries in modern molecular biology, with the goal of analyzing the methods, scientific concepts and logic, research strategies, and scientists that underlie these advances. Students will learn to critique papers in a wide range of fields, including molecular biology, developmental biology, genetics, and neuroscience. As an opportunity to hone their communication and teaching skills, students will develop and implement a hands-on demonstration of a molecular biology concept to local elementary students in the PUSD school system.

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.

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.

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.