Biology (Bi) Courses (2019-20)
Bi 1. Principles of Biology-The great theories of biology and their influence in the modern world. 9 units (4-0-5): third term. There are three overarching theories in biology: the theory of the cell, the theory of the gene, and the theory of evolution. Each of them has had major impacts on our lives-for example the concept of the gene has led to treatments for inherited diseases, personalized and genomic medicine, forensic DNA testing, and modern agriculture. Each theory will be discussed from its 19th century origin to its standing in the 21st century, and the scientific understanding and societal impact of each will be sampled. The course will also ask if there is yet a theory of the brain, and if not, how one might be framed. The course is designed to teach what technically adept members of society should know about biology. Instructors: Meyerowitz, Zinn.
Bi 1 x. The Great Ideas of Biology: Exploration through Experimentation. 9 units (0-6-3): third term. Introduction to concepts and laboratory methods in biology. Molecular biology techniques and advanced microscopy will be combined to explore the great ideas of biology. This course is intended for nonbiology majors and will satisfy the freshman biology course requirement. Limited enrollment. Instructor: Bois.
Bi 2. Current Research in Biology. 3 units (1-0-2): first term. Intended for students considering the biology option; open to freshmen. 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. Instructor: Elowitz.
Bi 8. Introduction to Molecular Biology: Regulation of Gene Expression. 9 units (3-0-6): second term. This course and its sequel, Bi 9, cover biology at the molecular and cellular levels. Bi 8 emphasizes genomic structure and mechanisms involved in the organization and regulated 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. Instructors: Guttman, Hong.
Bi 9. Cell Biology. 9 units (3-0-6): third term. 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. Instructors: Chan, Prober.
Bi 10. Introductory Biology Laboratory. 6 units (1-3-2): third term. An introduction to molecular, cellular, and biochemical techniques that are commonly used in studies of biological systems at the molecular level. Instructor: Staff.
Bi 21. Undergraduate Research with Presentation. Minimum 12 units per term (0-11-1): first, second, third terms. 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. Instructor: Staff.
Bi 22. Undergraduate Research. Units to be arranged: first, second, third terms. Special problems involving laboratory research in biology; to be arranged with instructors before registration. Graded pass/fail. Instructor: Staff.
Bi 23. Biology Tutorials. 3 or 6 units: second term. 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. Instructor: Huang.
Bi/BE 24. Scientific Communication for Biological Scientists and Engineers. 6 units (3-0-3): first, third terms. 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. Instructor: MacLean.
Bi 90 abc. Undergraduate Thesis. 12 or more units per term: first, second, third terms. 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. Instructor: Bjorkman.
BE/Bi 101. Order of Magnitude Biology. 6 units (3-0-3): third term. 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 2019-20. Instructors: Bois, Phillips.
CNS/Psy/Bi 102 ab. Brains, Minds, and Society. 9 units (3-0-6): second, third terms. 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. Instructors: O'Doherty/Adolphs, Camerer.
BE/Bi 103 a. Introduction to Data Analysis in the Biological Sciences. 9 units (1-3-5): first term. 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. Instructor: Bois.
BE/Bi 103 b. Statistical Inference in the Biological Sciences. 9 units (1-3-5): second term. 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. Instructor: Bois.
Bi/Ge/ESE 105. Evolution. 12 units (3-4-5): second term. 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 2019-20. Instructors: Phillips, Orphan.
BE/Bi 106. Comparative Biomechanics. 9 units (3-0-6): second term. 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 2019-20. Instructor: Dickinson.
Bi/Ch 110. Introduction to Biochemistry. 12 units (4-0-8): first term. Lectures and recitation introducing the molecular basis of life processes, with emphasis on the structure and function of proteins. Topics will include the derivation of protein structure from the information inherent in a genome, biological catalysis, and the intermediary metabolism that provides energy to an organism. Instructor: Clemons.
Bi/Ch 111. Biochemistry of Gene Expression. 12 units (4-0-8): second term. 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 protein synthesis. Instructors: Campbell, Parker.
Bi 114. Immunology. 9 units (3-0-6): second term. 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. Instructors: Bjorkman, Yui.
Bi/BE/BMB 115. Viruses and Applications to Biological Systems. 9 units (3-2-4): third term. 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 2019-20. Instructors: Bjorkman, Gradinaru, Van Valen, Bjorkman.
Bi 116. Microbial Genetics. 9 units (3-0-6): second term. 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 2019-20. Instructors: Mazmanian, Newman.
Bi 117. Developmental Biology. 9 units (3-0-6): second term. 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. Instructor: Bronner.
Bi 118. Morphogenesis of Developmental Systems. 9 units (3-0-6): second term. 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; not offered 2019-20. Instructor: Stathopoulos.
Bi 122. Genetics. 9 units (3-0-6): first term. Lecture and discussion course covering basic principles of genetics. Not open to freshmen. Instructors: Hay, Sternberg, Staff.
Bi/BE 129. The Biology and Treatment of Cancer. 9 units (3-0-6): second term. 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 2019-20. Instructors: Zinn, Campbell.
CNS/Psy/Bi 131. The Psychology of Learning and Motivation. 9 units (3-0-6): second term. 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 2019-20. Instructor: O'Doherty.
Bi 145 a. Tissue and Organ Physiology. 9 units (3-0-6): first term. 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. Instructor: Tydell.
Bi 145 b. Tissue and Organ Physiology. 9 units (3-0-6): second term. Building on the foundations of Bi 145a, Bi 145b 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. Instructor: Tydell.
Bi/CNS/NB/Psy 150. Introduction to Neuroscience. 10 units (4-0-6): third term. 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. Instructors: Adolphs, Lester.
Bi/CNS/NB 152. Neural Circuits and Physiology of Appetite and Body Homeostasis. 6 units (2-0-4): third term. An advanced course of lectures, readings, and student presentations focusing on neural basis of appetites such as hunger and thirst. This course will cover the mechanisms that control appetites both at peripheral and central level. These include genetics, neural manipulation, and viral tracing tools with particular emphasis on the logic of how the body and the brain cooperate to maintain homeostasis. Given in alternate years; not offered 2019-20. Instructor: Oka.
Bi/CNS/NB 154. Principles of Neuroscience. 9 units (3-0-6): first term. 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 2019-20. Instructor: Meister.
Bi/NB/BE 155. Neuropharmacology. 6 units (3-0-3): second term. 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. Psychiatric diseases: Nosology and drugs. The course is taught at the research level. Given in alternate years; not offered 2019-20. Instructor: Lester.
Bi/CNS/NB 157. Comparative Nervous Systems. 9 units (2-3-4): third term. 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 2019-20. Instructor: Allman.
Bi/CNS 158. Vertebrate Evolution. 9 units (3-0-6): third term. 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 2019-20. Instructor: Allman.
Bi 160. Molecular Basis of Animal Evolution. 9 units (3-3-3): third term. 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. Instructor: Parker.
Pl/CNS/NB/Bi 161. Consciousness. 9 units (3-0-6): third term. 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 Bi/CNS 150) is strongly recommended and students with such background will be preferentially considered. Limited to 20. Instructors: Eberhardt, Adolphs.
Bi/CNS/NB 162. Cellular and Systems Neuroscience Laboratory. 12 units (2-4-6): second term. 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. Instructor: Bremner.
NB/Bi/CNS 163. The Biological Basis of Neural Disorders. 6 units (3-0-3): second term. 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 2019-20. Instructors: Lester, Lois.
Bi/CNS/NB 164. Tools of Neurobiology. 9 units (3-0-6): first term. 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. Instructor: Meister.
Bi 165. Microbiology Research: Practice and Proposal. 6 units (2-3-1): first term. The course will serve to introduce graduate students to 1) the process of writing fellowships to train students in preparing effective funding applications; 2) ongoing research projects on campus involving the isolation, culture, and characterization of microbes and microbial communities as well as projects in other fields; and 3) presentation of research and asking questions in research presentations. The first half of the class will involve training in grant writing by drafting an NSF-GRFP proposal. The second half of the class will involve giving chalk talk research presentations. Students can apply from all departments; priority will be given to those in microbiology. Enrollment is limited to instructor approval. Instructor: Hoy.
ESE/Bi 166. Microbial Physiology. 9 units (3-1-5): first term. 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. Instructor: Leadbetter.
ESE/Bi 168. Microbial Metabolic Diversity. 9 units (3-0-6): second term. 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; not offered 2019-20. Instructor: Newman.
BMB/Bi/Ch 170. Biochemistry and Biophysics of Macromolecules and Molecular Assemblies. 9 units (3-0-6): first term. 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 in 2019-20.
BMB/Bi/Ch 173. Biophysical/Structural Methods. 9 units (3-0-6): second term. 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. Instructors: Clemons, Jensen, and other guest lectures.
BMB/Bi/Ch 174. Advanced Topics in Biochemistry and Biophysics. 6 units (3-0-3): first term. Discussion of research fields in biochemistry and molecular biophysics at Caltech. Instructors: Clemons, Hoelz, Shan and various guest lecturers.
CNS/Bi/Psy/NB 176. Cognition. 9 units (4-0-5): third term. 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; Not offered 2019-20. Instructor: Shimojo.
Bi/BE 177. Principles of Modern Microscopy. 9 units (3-0-6): second term. 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; not offered 2019-20. Instructor: Collazo.
Ge/ESE/Bi 178. Microbial Ecology. 9 units (3-2-4): third term. 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. Offered in alternate years; not offered 2019-20. Instructor: Orphan.
Bi/BE 182. Animal Development and Genomic Regulatory Network Design. 9 units (3-0-6): second term. This course is focused on the genomic control circuitry of the encoded programs that direct developmental processes. The initial module of the course is devoted to general principles of development, with emphasis on transcriptional regulatory control and general properties of gene regulatory networks (GRNs). The second module provides mechanistic analyses of spatial control functions in multiple embryonic systems, and the third treats the explanatory and predictive power of the GRNs that control body plan development in mammalian, sea urchin, and Drosophila systems. Grades or pass/fail. Given in alternate years; offered 2019-20. Instructors: Stathopoulos, Peter.
Bi/BE/CS 183. Introduction to Computational Biology and Bioinformatics. 9 units (3-0-6): second term. 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. Instructors: Pachter, Thomson.
Bi/CNS/NB 184. The Primate Visual System. 9 units (3-1-5): third term. This class focuses on the primate visual system, investigating it from an experimental, psychophysical, and computational perspective. The course will focus on two essential problems: 3-D vision and object recognition. We will examine how a visual stimulus is represented starting in the retina, and ending in the frontal lobe, with a special emphasis placed on mechanisms for high-level vision in the parietal and temporal lobes. An important aspect of the course is the lab component in which students design and analyze their own fMRI experiment. Given in alternate years; not offered 2019-20. Instructor: Tsao.
Bi/CNS/NB 185. Large Scale Brain Networks. 6 units (2-0-4): third term. This class will focus on understanding what is known about the large-scale organization of the brain, focusing on the mammalian brain. What large scale brain networks exist and what are their principles of function? How is information flexibly routed from one area to another? What is the function of thalamocortical loops? We will examine large scale networks revealed by anatomical tracing, functional connectivity studies, and mRNA expression analyses, and explore the brain circuits mediating complex behaviors such as attention, memory, sleep, multisensory integration, decision making, and object vision. While each of these topics could cover an entire course in itself, our focus will be on understanding the master plan-how the components of each of these systems are put together and function as a whole. A key question we will delve into, from both a biological and a theoretical perspective, is: how is information flexibly routed from one brain area to another? We will discuss the communication through coherence hypothesis, small world networks, and sparse coding. Given in alternate years, not offered 2019-20. Instructor: Tsao.
CNS/Bi/EE/CS/NB 186. Vision: From Computational Theory to Neuronal Mechanisms. 12 units (4-4-4): second term. 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 2019-20. Instructors: Meister, Perona, Shimojo, Tsao.
CNS/Bi/Ph/CS/NB 187. Neural Computation. 9 units (3-0-6): first term. Programming will be required. This course investigates computation by neurons. Of primary concern are models of neural computation and their neurological substrate, as well as the physics of collective computation. Thus, neurobiology is used as a motivating factor to introduce the relevant algorithms. Topics include rate-code neural networks, their differential equations, and equivalent circuits; stochastic models and their energy functions; associative memory; supervised and unsupervised learning; development; spike-based computing; single-cell computation; error and noise tolerance. Not offered 2019-20. Instructor: Perona.
Bi 188. Human Genetics and Genomics. 6 units (2-0-4): third term. 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; offered 2019-20. Instructor: Wold.
Bi 189. The Cell Cycle. 6 units (2-0-4): third term. The course covers the mechanisms by which eukaryotic cells control their duplication. Emphasis will be placed on the biochemical processes that ensure that cells undergo the key events of the cell cycle in a properly regulated manner. Instructor: Dunphy.
Bi 190. Systems Genetics. 6 units (2-0-4): first term. 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 2019-20. Instructor: Sternberg.
BE/CS/CNS/Bi 191 ab. Biomolecular Computation. 9 units (3-0-6) second term, (2-4-3) third term: . 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. Not offered 2019-20. Instructor: Winfree.
Bi 192. Introduction to Systems Biology. 6 units (2-0-4): first term. 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. Instructor: Goentoro.
Bi/CNS/NB 195. Mathematics in Biology. 9 units (3-0-6): first term. 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. Instructor: Meister.
BE/Bi/NB 203. Introduction to Programming for the Biological Sciences Bootcamp. 6 units: summer term. 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. Instructor: Bois.
Bi 206. Biochemical and Genetic Methods in Biological Research. 6 units (2-0-4): third term. This course will comprise discussions of selected methods in molecular biology and related fields. Given in alternate years; offered 2019-20. Instructor: Varshavsky.
Bi 214. Stem Cells and Hematopoiesis. 9 units (3-0-6): third term. 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. Instructor: Rothenberg.
Bi/CNS/NB 216. Behavior of Mammals. 6 units (2-0-4): first term. 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 2019-20. Instructor: Allman.
Bi/CNS/NB 217. Central Mechanisms in Perception. 6 units (2-0-4): first term. Reading and discussions of behavioral and electrophysiological studies of the systems for the processing of sensory information in the brain. Given in alternate years; not offered 2019-20. Instructor: Allman.
Bi/CNS/NB 220. Genetic Dissection of Neural Circuit Function. 6 units (2-0-4): second term. 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. Not offered 2019-20. Instructor: Anderson.
Bi/BE 222. The Structure of the Cytosol. 6 units (2-0-4): third term. 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." Instructor: Kennedy.
Bi/BE 227. Methods in Modern Microscopy. 12 units (2-6-4): second term. 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 will begin with basic optics, microscope design, Koehler illumination, and the principles of confocal microscopy as well as other techniques for optical sectioning such as light sheet fluorescence microscopy (also called single plane illumination microscopy, SPIM). During the class students will construct a light sheet microscope based on the openSPIM design. Alongside the building of a light sheet microscope, the course will consist of semi-independent modules organized around different imaging challenges using confocal microscopes. Early modules will include a lab using lenses to build a cloaking device. Most of the early modules will focus on three-dimensional reconstruction of fixed cells and tissues. Later modules will include time-lapse confocal analysis of living cells and embryos. Students will also utilize the microscopes in the Beckman Institute Biological Imaging Facility to learn more advanced techniques such as spectral unmixing and fluorescence correlation spectroscopy. Enrollment is limited. Given in alternate years; offered 2019-20. Instructor: Collazo.
Bi/CNS/BE/NB 230. Optogenetic and CLARITY Methods in Experimental Neuroscience. 9 units (3-2-4): third term. 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 2020-21. Instructor: Gradinaru.
Ge/Bi 244. Paleobiology Seminar. 6 units (3-0-3): third term. Critical reviews and discussion of classic investigations and current research in paleoecology, evolution, and biogeochemistry. Instructor: Kirschvink.
Ge/Bi/ESE 246. Molecular Geobiology Seminar. 6 units (2-0-4): second term. 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. Instructor: Orphan.
CNS/Bi/NB 247. Cerebral Cortex. 6 units (2-0-4): second term. 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. Not offered 2019-20. Instructor: Andersen.
Bi 250 a. Topics in Molecular and Cellular Biology. 9 units (3-0-6): first term. 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. Instructors: Aravin, Voorhees.
Bi 250 b. Topics in Systems Biology. 9 units (3-0-6): third term. 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. Instructors: Elowitz, Bois.
Bi/CNS/NB 250 c. Topics in Systems Neuroscience. 9 units (3-0-6): third term. 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. Instructor: Siapas.
Bi/BMB 251 abc. Current Research in Cellular and Molecular Biology. 1 unit: . Presentations and discussion of research at Caltech in biology and chemistry. Discussions of responsible conduct of research are included. Instructors: Sternberg, Hay.
Bi 252. Responsible Conduct of Research. 4 units (2-0-2): third term. 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. This course is required of all trainees supported on the NIH training grants in cellular and molecular biology and neuroscience, and is recommended for other graduate students in labs in the Division of Biology and Biological Engineering labs. Undergraduate students require advance instructor's permission. Graded pass/fail. Instructors: Meyerowitz, Sternberg, Staff.
Bi 253. Reading, Writing, Reviewing, Experimental Design and Reproducibility. 6 units (2-0-4): second term. This course will consider scholarly communication in molecular and cellular biology, broadly defined. Students will learn about data standards, the minimal information required to describe an experiment and computer code. Discussion will include long term storage of data and informatics workflows. Appropriate citation of other article and resources will be considered. We will discuss evaluation of scientific premise, rigorous experimental design and interpretation, appropriate statistical power, authentication of key biological and chemical resources, data and material sharing, record keeping, and transparency in reporting data and observations. Students will learn to read papers critically and practice reviewing short articles from Micropublication: biology, which are short enough to allow a thorough analysis of methods necessary to ensure reproducibility. Graded Pass/Fail. Instructors: Sternberg, Hay, Meister, Staff.
Ch/Bi 253. Advanced Topics in Biochemistry. 6 units (2-0-4): third term. 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 2019-20.
Psy/Bi/CNS 255. Topics in Emotion and Social Cognition. 9 units (3-0-6): third term. 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. Instructor: Mobbs.
CNS/Bi/NB 256. Decision Making. 6 units (2-0-4): third term. 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. Instructor: Andersen.
Bi/BE/Ch/ChE/Ge 269. Integrative Projects in Microbial Science and Engineering. 6 units (3-0-3): second term. A project-based course designed to train students to integrate biological, chemical, physical and engineering tools into innovative microbiology research. Students and faculty will brainstorm to identify several "grand challenges" in microbiology. Small teams, comprised of students from different graduate programs and disciplinary backgrounds (e.g. a chemical engineer, a computer scientist and a biologist) and a faculty member, will work to compose a project proposal addressing one of the grand challenges, integrating tools and concepts from across disciplines. Student groups will present draft proposals and receive questions and critiques from other members of the class at check-in points during the academic term. While there will not be an experimental laboratory component, project teams may tour facilities or take field trips to help define the aims and approaches of their projects. At the end of the course, teams will deliver written proposals and presentations that will be critiqued by students and faculty. Instructor: CEMI Faculty.
Bi 270 abc. Special Topics in Biology. Units to be arranged each term: first, second, third. Students may register with permission of the responsible faculty member.
CNS/Bi 286 abc. Special Topics in Computation and Neural Systems. Units to be arranged: . First, second, third terms. Students may register with permission of the responsible faculty member.
Bi 299. Graduate Research. Units to be arranged: first, second, third terms. Students may register for research units after consultation with their adviser.