The Great Ideas of Biology
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.
The Biomechanics of Organismal Design
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.
Information Flow in Biology
The storage, readout, and modification of information is core to biological systems. The properties of an organism are primarily encoded in its genome, and how this information (genotype) maps to the morphology, physiology and development of an organism (phenotype) is a major problem of modern biology with practical consequences for personalized medicine and biotechnology as well as conceptual consequences for understanding all of biology from development to evolution. Other core principles of biology will be presented in the context of understanding information flow. May be taken pass/fail if taken in a first-year student's first year. Limited enrollment.
The Great Ideas of Biology: Exploration through Experimentation
Introduction to concepts and laboratory methods in biology. Molecular biology techniques and advanced microscopy will be combined to explore the great ideas of biology: the cell, the gene, evolution by natural selection, and life as chemistry. This course is intended for nonbiology majors. May be taken pass/fail if taken in a first-year student's first year. Limited enrollment.
Current Research in Biology
Intended for students considering the biology option; open to first-year students. Current research in biology will be discussed, on the basis of reading assigned in advance of the discussions, with members of the divisional faculty. Graded pass/fail.
Foundational Principles of Molecular Biology
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.
Introductory Biology Laboratory
An introduction to molecular, cellular, and biochemical techniques that are commonly used in studies of biological systems at the molecular level.
Undergraduate Research with Presentation
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.
Scientific Communication for Biological Scientists and Engineers
This course offers instruction and practice in writing and speaking relevant to professional biological scientists and engineers working in research, teaching, and/or medical careers. Students will write a paper for a scientific or engineering journal, either based on their previous research or written as a review paper of current work in their field. A Caltech faculty member, a postdoctoral scholar, or a technical staff member serves as a technical mentor for each student, to provide feedback on the content and style of the paper. Oral presentations will be based on selected scientific topics, with feedback from instructors and peers. Fulfills the Institute scientific writing requirement.
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.
Order of Magnitude Biology
In this course, students will develop skills in the art of educated guesswork and apply them to the biological sciences. Building from a few key numbers in biology, students will "size up" biological systems by making inferences and generating hypotheses about phenomena such as the rates and energy budgets of key biological processes. The course will cover the breadth of biological scales: molecular, cellular, organismal, communal, and planetary. Undergraduate and graduate students of all levels are welcome. Not offered 2022-23.
Brains, Minds, and Society
Introduction to the computations made by the brain during economic and social decision making and their neural substrates. Part a: Reinforcement learning. Unconscious and conscious processing. Emotion. Behavioral economics. Goal-directed and habit learning. Facial processing in social neuroscience. Part b: History and mechanisms of reinforcement. Associative learning. Mentalizing and strategic thinking. Neural basis of prosociality. Exploration-exploitation tradeoff. Functions of basal ganglia.
Introduction to Data Analysis in the Biological Sciences
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, basic image processing, and resampling-based statistical inference. Students analyze real data in class and in homework.
Statistical Inference in the Biological Sciences
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. Not offered 2022-23.
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; not offered 2022-23.
Have you ever wondered how a penguin swims or why a maple seed spins to the ground? How a flea can jump as high as a kangaroo? If spider silk is really stronger than steel? This class will offer answers to these and other questions related to the physical 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 relate to molecular, cell, and tissue mechanics. The class is explicitly comparative in nature and will not cover medically-related biomechanics. Topics include the physical properties of biological materials, viscoelasticity, muscle mechanics, biological pumps, and animal locomotion. Not offered 2022-23.
Social Media for Scientists
An introduction to the use of social media for scientific communication. Social media platforms are discussed in the context of their use to professionally engage scientific communities and general audiences. Topics will include ethics, privacy, reputation management, ownership and the law, and will focus on the use and impact of social media for personal and professional career development. Lectures will include presentations by invited experts in various specialties, a number of whom will have worldwide recognition. Not offered 2022-23.
Introduction to Biochemistry
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.
Biochemistry of Gene Expression
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 2022-23.
Viruses and Applications to Biological Systems
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; not offered 2022-23.
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; not offered 2022-23.
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.
Morphogenesis of Developmental Systems
Lectures on and discussion of how cells, tissues, and organs take shape: the influence of force on cell shape change; cell migration including chemotaxis and collective cell movement; adhesion/deadhesion during migration; the relationship between cell migration and metastasis; and a review/overview of general signaling principles and embryonic development of invertebrate and vertebrate animals. Students will choose term project involving writing a grant proposal or quantitative analysis of available datasets relating to lecture topics. Given in alternate years; offered 2022-23.
Lecture and discussion course covering basic principles of genetics. Not open to first-year undergraduate students.
The Biology and Treatment of Cancer
The first part of the course will concern the basic biology of cancer, covering oncogenes, tumor suppressors, tumor cell biology, metastasis, tumor angiogenesis, and other topics. The second part will concern newer information on cancer genetics and other topics, taught from the primary research literature. The last part of the course will concern treatments, including chemotherapy, anti-angiogenic therapy, and immunotherapy. Textbook: The Biology of Cancer, 2nd edition, by Robert Weinberg. Given in alternate years; not offered 2022-23.
The Psychology of Learning and Motivation
This course will serve as an introduction to basic concepts, findings, and theory from the field of behavioral psychology, covering areas such as principles of classical conditioning, blocking and conditioned inhibition, models of classical conditioning, instrumental conditioning, reinforcement schedules, punishment and avoidance learning. The course will track the development of ideas from the beginnings of behavioral psychology in the early 20th century to contemporary learning theory. Not offered 2022-23.
Tissue and Organ Physiology
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.
Tissue and Organ Physiology
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.
Challenges and Opportunities in Quantitative Ecology
Ecosystems are defined by dynamical interactions between groups of organisms, the communities they constitute, and the physical and chemical conditions and processes occurring in the environment. These dynamics are complex and multiscale across both length and time. This course will explore quantitative approaches that observe, measure, model, and monitor ecosystems and the services that they provide society-and the emerging opportunities that could employ these approaches to improve and strengthen global sustainability when it comes to our own ecology. This course will feature lectures each week from different members of the Caltech faculty working on ecological problems from different angles in order to illustrate how fresh insights can emerge by drawing on diverse ways-of-knowing. Given in alternate years; not offered 2022-23.
Introduction to Neuroscience
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.
Neural Circuits and Physiology of Homeostatic Regulation
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 2022-23.
Principles of Neuroscience
This course aims to distill the fundamental tenets of brain science, unlike the voluminous textbook with a similar title. What are the essential facts and ways of understanding in this discipline? How does neuroscience connect to other parts of life science, physics, and mathematics? Lectures and guided reading will touch on a broad range of phenomena from evolution, development, biophysics, computation, behavior, and psychology. Students will benefit from prior exposure to at least some of these domains. Given in alternate years; not offered 2022-23.
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 2022-23.
Comparative Nervous Systems
An introduction to the comparative study of the gross and microscopic structure of nervous systems. Emphasis on the vertebrate nervous system; also, the highly developed central nervous systems found in arthropods and cephalopods. Variation in nervous system structure with function and with behavioral and ecological specializations and the evolution of the vertebrate brain. Letter grades only. Given in alternate years; not offered 2022-23.
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 2022-23.
Molecular Basis of Animal Evolution
We share the planet with well over 1.5 million other animal species. This course covers how the staggering diversity of the animal kingdom came about through underlying molecular evolutionary phenomena, including gene and protein sequence evolution, gene family and genome evolution, the evolution of developmental processes, neural circuit evolution and behavior, and molecular mechanisms that physiologically adapt animals to their environment. Molecular processes involved in speciation will be explained, together with an analysis of constraints and catalysts on the production of selectable variation that have shaped the evolution of animal life. Participants will undertake a laboratory project on evolutionary genomics, involving fieldwork, genome sequencing and comparative genome analysis. The course focuses on the >99.9% of animals that lack backbones.
Physical Biology of the Cell
Physical models applied to the analysis of biological structures ranging from individual proteins and DNA to entire cells. 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.
Cellular and Systems Neuroscience Laboratory
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 Biological Basis of Neural Disorders
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; not offered 2022-23.
Tools of Neurobiology
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.
Microbial Metabolic Diversity
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 2022-23.
Biochemistry and Biophysics of Macromolecules and Molecular Assemblies
Detailed analysis of the structures of the four classes of biological molecules and the forces that shape them. Introduction to molecular biological and visualization techniques. Not offered 2022-23.
Basic principles of modern biophysical and structural methods used to interrogate macromolecules from the atomic to cellular levels, including light and electron microscopy, X-ray crystallography, NMR spectroscopy, single molecule techniques, circular dichroism, surface plasmon resonance, mass spectrometry, and molecular dynamics and systems biological simulations. Not offered 2022-23.
Advanced Topics in Biochemistry and Molecular Biophysics
Discussion of research fields in biochemistry and molecular biophysics at Caltech. Development of skills in literature analysis and information synthesis.
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 2022-23.
Principles of Modern Microscopy
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 2022-23.
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 2022-23.
Plant and Soil Science
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.
Design Principles of Gene Regulatory Networks
This course is focused on the genomic regulatory networks that direct developmental processes. We will discuss concepts that have contributed to our current understanding of gene regulatory networks and their importance in understanding the development and evolution of the animal body plan. Topics will include the developmental control of gene expression, transcriptional control systems, and experimental as well as computational approaches to network analysis. Examples that will be discussed include circuits and networks that operate in mammalian, sea urchin, and Drosophila systems. Given in alternate years; not offered 2022-23.
Introduction to Computational Biology and Bioinformatics
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.
Vision: From Computational Theory to Neuronal Mechanisms
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; not offered 2022-23.
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.
Human Genetics and Genomics
Introduction to the genetics of humans. Subjects covered include human genome structure, genetic diseases and predispositions, the human genome project, forensic use of human genetic markers, human variability, and human evolution. Given in alternate years; not offered 2022-23.
The Cell Cycle and Genomic Stability
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; not offered 2022-23.
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.
Introduction to Systems Biology
The course will explore what it means to analyze biology from a systems-level point of view. Given what biological systems must do and the constraints they face, what general properties must biological systems have? Students will explore design principles in biology, including plasticity, exploratory behavior, weak-linkage, constrains that deconstrain, robustness, optimality, and evolvability. The class will read the equivalent of 2-3 scientific papers every week. The format will be a seminar with active discussion from all students. Students from multiple backgrounds are welcome: non-biology or biology students interested in learning systems-level questions in biology. Limited enrollment. Not offered 2022-23.
Mathematics in Biology
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.
Mentoring and Outreach
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.
Introduction to Programming for the Biological Sciences Bootcamp
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.
Deep Learning for Biological Data
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.
Stem Cells and Hematopoiesis
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.
Behavior of Mammals
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; not offered 2022-23.
Central Mechanisms in Perception
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 2022-23.
Genetic Dissection of Neural Circuit Function
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 Structure of the Cytosol
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".
Methods in Modern Microscopy
Discussion and laboratory-based course covering the practical use of the confocal microscope, with special attention to the dynamic analysis of living cells and embryos. Course topics include: basic optics, microscope design, Kohler illumination, confocal microscopy, light sheet microscopy, spectral unmixing and fluorescence correlation spectroscopy, three-dimensional reconstruction of fixed cells and tissues. Students will construct a light sheet microscope based on the openSPIM design, and perform time-lapse confocal analysis of living cells and embryos. Enrollment is limited. Given in alternate years; not offered 2022-23.
Optogenetic and CLARITY Methods in Experimental Neuroscience
The class covers the theoretical and practical aspects of using (1) optogenetic sensors and actuators to visualize and modulate the activity of neuronal ensembles; and (2) CLARITY approaches for anatomical mapping and phenotyping using tissue-hydrogel hybrids. The class offers weekly hands-on LAB exposure for opsin viral production and delivery to neurons, recording of light-modulated activity, and tissue clearing, imaging, and 3D reconstruction of fluorescent samples. Lecture topics include: opsin design (including natural and artificial sources), delivery (genetic targeting, viral transduction), light activation requirements (power requirements, wavelength, fiberoptics), compatible readout modalities (electrophysiology, imaging); design and use of methods for tissue clearing (tissue stabilization by polymers/hydrogels and selective extractions, such as of lipids for increased tissue transparency and macromolecule access). Class will discuss applications of these methods to neuronal circuits (case studies based on recent literature). Given in alternate years; offered 2022-23.
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.
Molecular Geobiology Seminar
Critical reviews and discussion of classic papers and current research in microbiology and geomicrobiology. As the topics will vary from year to year, it may be taken multiple times. Not offered 2022-23.
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 2022-23.
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.
Topics in Molecular and Cellular Biology
Lectures and literature-based discussions covering research methods, scientific concepts and logic, research strategies and general principles of modern biology. Students will learn to critique papers in a wide range of fields, including molecular biology, developmental biology, genetics and neuroscience. Graded pass/fail.
Topics in Systems Biology
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.
Topics in Systems Neuroscience
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.
Topics in Developmental, Stem Cell and Evolutionary Biology
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.
Current Research in Cellular and Molecular Biology
Presentations and discussion of research at Caltech in biology and chemistry. Discussions of responsible conduct of research are included.
Responsible Conduct of Research
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.
Advanced Topics in Biochemistry
Hours and units to be arranged. Content will vary from year to year; topics are chosen according to the interests of students and staff. Not offered 2022-23.
Topics in Emotion and Social Cognition
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.
This special topics course will examine the neural mechanisms of reward, decision making, and reward-based learning. The course covers the anatomy and physiology of reward and action systems. Special emphasis will be placed on the representation of reward expectation; the interplay between reward, motivation, and attention; and the selection of actions. Links between concepts in economics and the neural mechanisms of decision making will be explored. Data from animal and human studies collected using behavioral, neurophysiological, and functional magnetic resonance techniques will be reviewed. Given in alternate years; not offered 2022-23.
Biological Research: Fellowship Application and Science Communication
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.
Special Topics in Biology
Students may register with permission of the responsible faculty member.
Special Topics in Computation and Neural Systems
Students may register with permission of the responsible faculty member.
Students may register for research units after consultation with their adviser.