Biology

Provides a complement to the BCMB core curriculum. Student reads research papers relating to a core lecture topic. Discussions are led by a student while a faculty member from Biochemistry or MMI act as facilitator. Helps students to develop skills in reading the primary literature and provides an introduction to the experimental paradigms underlying the concepts presented in the core course.

This course reinforces the topics covered in AS.020.151. Students participate in a semester-long project, identifying bacteria from Homewood campus soils using molecular biology techniques. Other laboratory exercises cover aspects of evolution, genomics and biochemistry. Students who have credit for AP Biology but take General Biology Lab I will lose four credits of AP Biology credit. This course is offered in fall terms only.

Prerequisite(s): Students must have completed Lab Safety training prior to registering for this class. To access the tutorial, login to myLearning and enter Laboratory Safety Introductory Course in the Search Box to access the proper course. Click here to access the Laboratory Safety Introductory Course;AS.020.151 can be taken prior to or at the same time as AS.020.153.

Distribution Area: Natural Sciences

AS Foundational Abilities: Science and Data (FA2)

The demand for computational genomics and biology in industry, academia, and government is rapidly growing. Genomic data have the potential to reveal causes of disease, novel drug targets, and relationships among genes and pathways in our cells. However, identifying meaningful patterns from high-dimensional genomic data has required development of new computational tools. This course gives a broad introduction to statistics, machine learning, and computational tools for modern computational genomics real-world problems. Assignments include project sets including programming, and a project component. Genomic applications will include single-cell RNA-sequencing, genome-wide association studies, epigenetics, spatial transcriptomics, heritability and genetic risk prediction, long-read RNA-sequencing, and ethics in genetics.

Prerequisite(s): EN.580.475

Distribution Area: Engineering

AS Foundational Abilities: Science and Data (FA2)

Focuses on reproductive physiology and biochemical and molecular regulation of the female and male reproductive tracts. Topics include the hypothalamus and pituitary, peptide and steroid hormone action, epididymis and male accessory sex organs, female reproductive tract, menstrual cycle, ovulation and gamete transport, fertilization and fertility enhancement, sexually transmitted diseases, and male and female contraceptive methods. Introductory lectures on each topic followed by research-oriented lectures and readings from current literature.

Distribution Area: Natural Sciences

AS Foundational Abilities: Science and Data (FA2), Projects and Methods (FA6)

This course introduces students to widely used biophysical techniques, combining theoretical foundations with practical applications. Students will gain familiarity with key experimental methods in biophysics and develop skills to critically read and interpret primary scientific literature. The course format includes lectures, analysis of scientific articles, and group discussions.

Prerequisite(s): AS.250.315 OR AS.020.305

Distribution Area: Natural Sciences

AS Foundational Abilities: Writing and Communication (FA1), Science and Data (FA2)

Writing Intensive

Introduces the computational hardware and programming model upon which analysis tools and languages are based. Introduces and uses three main languages (Python, Perl, SQL) and their underlying rationale to develop computer science concepts such as data structures, algorithms, computational complexity, regular expressions, and knowledge representation. Draws examples and exercises from high-throughput sequence analysis, proteomics and modeling of biological systems. Reinforces key concepts through lectures with live computer demonstrations, weekly readings, and programming exercises. Has students working with a High Performance Compute Cluster and the Amazon cloud.

Principles and methods for the design and optimization of new biological systems, from a molecular perspective. Topics include: introduction to genetic parts and modern methods for their assembly; synthesis and incorporation of nucleic acids at the level of nucleotides, genes, and genomes; design of genetic programs; library generation and screening; directed evolution and its application to create new proteins and metabolic pathways; computational design of protein and RNA?using physical and bioinformatic approaches; non-canonical amino acids and genetic code expansion. This course will also feature critical evaluation of the primary literature in this fast-paced field, and practical experience with relevant software and computational tools.

Discusses molecular, biochemical, cellular and immunological methodology and approaches for the mechanistic understanding, treatment and prevention of human diseases, and for understanding disease susceptibility. The focus will be on the application of biological methods and approaches to such critical issues as infectious disease, cancer, neurodegenerative disease, COPD, environmental toxicant effects on early development, and reproductive anomalies and their treatment.

Provides an opportunity for students to, in consultation with a faculty mentor from the Dept of Biochem and Molecular Bio, Environmental Health or Molecular Microbiology and Immunology, prepare a critical, scholarly paper on an agreed upon subject area.

Provides a broad understanding of the different levels of public health prevention: primary, secondary, and tertiary and discusses the impact of each level on prevention in population health. Emphasizes the role of epidemiology in prevention and control; compares and contrasts the descriptive epidemiology, natural history, and pathologic and biologic characteristics as well as factors related to their etiology. Presents the impacts of recent advances in human genomics/genetics, immunology and metabolism on prevention strategies for chronic and acute disease. Introduces basic principles, theories, and methods in the field of prevention science. Identifies public health interventions that operate at multiple ecological levels, including the community, family, and individual. Introduces the role of resilience. Discusses case studies related to the prevention of different physical, mental, behavioral and infectious disease health problems.

Emphasizes the need to establish the credibility of the evidence, based on the rigor of the methods used in generating it (e.g., type of studies, rules of causality, the nature of errors) before employing evidence to advance knowledge, practice, or policy. Discusses the bases for debate about recommendations for particular interventions that impact a population’s health, how to weigh their benefits and harms, the ethics of scientific conduct, and effective communication in building evidence. Uses illustrative case examples, such as breast and prostate cancer screening, vaccines for measles and cervical cancer, nutritional sodium reductions, and the opioid epidemic.

Focuses on the basics of cellular and molecular biology, genetics, and infectious agents. Explains concepts that link basic biology to disease and population health. Illustrates application of biologic and genetic principles to population health using case studies.

This First-Year Seminar is designed to introduce students to the fundamental physical and chemical origins of color and how we perceive them - from the vivid palette provided by the natural world to the brightly colored clothing we wear. Beginning with the basic principles of light and color, we will embark on an interdisciplinary investigation of color, including, but not limited to: color chemistry; color in biology; the physiology of the eye; how color affects human psychology; the history of color and light; and the use of color in art. Discover the physical and chemical explanations behind several noteworthy phenomena such as sunsets, color-blindness, rainbows, fireworks, chameleons and the Aurora Borealis.

This First-Year Seminar will explore the neuroscience of choice. In addition to exploring the neurobiology of choice, we will dabble with philosophical ideas of free will and determinism. We will also touch on questions related to culpability. For example, are people who break the law but suffer from brain damage responsible for their actions? Sound interesting? Well, why stop there? Let’s sit back, eat some popcorn and take a look at how popular culture depicts the neuroscience of choice in the movies. Yes, with your help, we can do it all – but will you choose to???

Most people think the strongest kind of evidence in a criminal case is a confident eyewitness. Most students think re-reading textbook materials or class notes is the best way to prepare for an exam. And all too many people think that measles vaccines cause autism. All three of these ideas are wrong. In this First-Year Seminar, we will explore what modern psychology has uncovered about how our intuitions concerning human nature deceive us, and lead to incorrect ideas such as the ones just mentioned. We will discuss a wide variety of topics including “the attention economy,” groupthink, and subliminal perception.

We often think of bacteria in the context of dangerous or annoying infections. However, bacteria themselves can be infected by even smaller and more abundant entities: viruses called bacteriophages. This First-Year Seminar will combine readings and discussion of the fundamental biology of phages and their role in controlling populations of bacteria, with lab work to discover new phages from the Johns Hopkins campus. Phages identified in this class will be added to the Science Education Alliance’s archive which is comprised of phages from over 100 academic institutions worldwide and is a resource for phage biologists and physicians directly involved in developing phages as a treatment for disease.

This First-Year Seminar will explore seminal ideas in macroevolutionary theory through both classic and cutting-edge studies. Topics will include the relationship between evolution and development, how fossils shape our understanding of biological systems, and the logical basis of evolutionary inference. Students will also gain an appreciation for the historical development of these ideas and their application in modern science and beyond. This course will explore these topics using foundational texts in biology, such as The Origin of Species and writings by the evolutionary biologist Stephen Jay Gould. It will feature guest lectures from curators from natural history museums across the country as well as offer students their own opportunity to go into the field to collect fossils here in Maryland.

Johns Hopkins University Homewood campus and its surroundings is a wonderful green space in the middle of Baltimore City. This First-Year Seminar will introduce students to both the visible and cryptic organisms living above- and belowground. A combination of observational and sampling techniques will be used to demonstrate how ecologists collect data about plants, insects, and other organisms. In the classroom, these field observations, combined with reading material will be used to discuss global environmental issues including climate change on biodiversity, invasive species, and human impacts on the landscape. By the end of the course students will be able to generate research questions based upon field observations and appreciate the diverse life forms both in Earth and in our backyard. Students should be prepared to spend many hours outside.

This First-Year-Seminar covers concepts of biology taught through the lens of microbes and antibiotic resistance. Using environmental samples, students actively engage in the hunt for novel antimicrobials. Broader concepts include the meaning of disease, how that meaning has changed over time, and the implications of widespread antibiotic resistance for society. This is a research-based project lab course in which students participate as part of an international consortium of undergraduates at other colleges. Students will isolate and characterize antibiotic-producing bacteria from the environment using modern molecular biological techniques. This seminar is open to all students, regardless of major. No prior lab experience necessary.

In the age of Molecular Biology, DNA sequencing allows the identification of genes. Biochemical assays allow the measurement of gene expression. Reverse transcriptase and PCR are used to determine the RNA made by activated genes. These tools allow the study of disease organisms on the molecular level with emphasis on particular genes, known as virulence genes, which enable the disease organisms to attack the human body. This First-Year Seminar will introduce students to the disease tuberculosis, to human innate and adaptive immune systems and to the molecular biology of Mycobacterium tuberculosis, an intracellular pathogen which infects humans and manipulates the human immune response to escape detection and elimination. We will even grow cultures of Mycobacterium smegmatum, M. tb’s harmless relative. In addition, millions worldwide have tuberculosis, and this disease is a case study in the measures that are being used to control the spread of an epidemic disease. Students will learn through by readings from books such as The White Plague by Rene’ and Jean Dubos, The Microbe Hunters by Paul de Kruif, The Aetiology of Tuberculosis by Robert Koch and Fever by John Fuller, videos, class interactions and discussions, and after the introductory portion of the course, by presentations of research papers about M. tuberculosis pathogenesis and treatment. Finally, we will explore recent genomic research that has yielded specific Mtb peptides that give evidence of being the basis of first effective vaccine for tuberculosis.

Animals have evolved a vast array of sensory systems that support a rich repertoire of natural behaviors. Some animals live in dark environments and use tactile, chemical, electrical and auditory sensors that allow them to operate in the absence of light. Other animals rely heavily on vision and take advantage of colors that humans cannot see. In this First-Year Seminar, we will explore extraordinary adaptations of sensory systems in animals that live on land and under water. Our focus will be on sensory systems that guide navigation and foraging behaviors in species as diverse as star-nosed moles, weakly electric fish, honeybees, and echolocating bats. As we delve into understanding the extraordinary sensory systems of selected species, we will also consider how these animals have inspired literary and visual artists. We aim to introduce students to a rich interdisciplinary experience that opens their eyes to new areas of inquiry as they take advantage of local resources, such as the National Aquarium, Baltimore Zoo, Wyman Park, Peabody School of Art, and Baltimore Museum of Art.

How we become unique is one of the deepest questions that we can ask. The answers, where they exist, inform how we think about morality, public policy, faith, health care, education, and the law. Although investigating the origins of individuality is not just an endeavor for biologists, many of this topic’s most important aspects involve fundamental questions about the development, genetics, and plasticity of the nervous system. The good news is that recent scientific findings are illuminating this question in ways that are exciting and sometimes counterintuitive. The better news is that it doesn’t just boil down to the same tiresome nature-versus-nurture debate that has been impeding progress and boring people for years. Genes are built to be modified by experience. That experience is not just the obvious stuff, like how your parents raised you, but more complicated and fascinating things like the diseases you’ve had (or those that your mother had while she was carrying you in utero), the foods you’ve eaten, the bacteria that reside in your body, the weather during your early development, and the long reach of culture and technology.So, let’s dig into the science together. Our sources will be not only books and articles but also visits by guest scientists and artists as well as engagement with films and stories that explore human individuality. It can be controversial stuff. Questions about the origins of human individuality challenge our concepts of nation, gender, and race. They are inherently political and incite strong passions. Given this fraught backdrop, we’ll do our best to play it straight and synthesize the current scientific consensus (where it exists), examine the controversies, and point out where the sidewalk of our understanding simply ends.

This First-Year Seminar explores the scientific-technological, philosophical, social, and ethical dimensions of using animals for scientific research from the early nineteenth century to present. Why did scientists use animals and how did they choose “the right animal for the job”? How did philosophers define a “model organism”? What were the political economies formed within research communities sharing research animals? How did financial and material infrastructure take shape for large-scale, long-term maintenance of genetically standardized mice or zebrafish? How did the interpretations of animals reflect the social imaginaries of researchers and our society? And how did animals “speak” back? These are questions we are going to examine through reading scholarly publications, watching documentaries, visiting laboratories, and doing mini research projects together.

"This First-Year Seminar is an introduction to the field of biological anthropology, which is broadly a mixture of social studies and biological studies that focus on human evolution and human biosocial variation. We will explore evolutionary theory and mechanisms of inheritance, the diversity of living primates, the fossil record, human evolution, and modern human biological variation. We will begin the semester by learning the basic principles of evolution and natural selection as proposed by Charles Darwin. We will then move on to consider the primate condition across species and through time. This involves examining the taxonomy of extant monkeys and apes as well as the fossil and archaeological record of our hominin ancestors that begins some 7 million years ago. This will involve excursions to local zoos and museums, as well as visits to labs right here at Hopkins. Following a survey of human biocultural evolution, we will consider how this history has influenced contemporary human biological variation.

This multidisciplinary course explores the origins of life, planet formation, Earth's evolution, extrasolar planets, habitable zones, life in extreme environments, the search for life in the Universe, space missions, and planetary protection. Recommended Course Background: Three upper level (300+) courses in sciences (Biophysics, Biology, Chemistry, Physics, Astronomy, Math, or Computer Science).

Prerequisite(s): Students may not register for this class if they have already received credit for AS.020.334 OR AS.020.616 OR AS.171.333 OR AS.171.699 OR AS 270.335 OR AS.360.671

Distribution Area: Natural Sciences

AS Foundational Abilities: Science and Data (FA2), Ethics and Foundations (FA5)

This multidisciplinary course explores the origins of life, planet formation, Earth's evolution, extrasolar planets, habitable zones, life in extreme environments, the search for life in the Universe, space missions, and planetary protection. Recommended Course Background: Three upper level (300+) courses in sciences (Biophysics, Biology, Chemistry, Physics, Astronomy, Math, or Computer Science).

Prerequisite(s): Students may not register for this class if they have already received credit for AS.020.616 OR AS.020.334 OR AS.171.333 OR AS.171.699 OR AS.270.335 OR AS.360.339.

Distribution Area: Natural Sciences

Introduces students to the major global causes of child mortality and the strategies and interventions to reduce child mortality. Includes specific topics: malaria, HIV, measles, pneumonia, diarrhea, neonatal disorders and nutritional deficiencies. Additional topics may include maternal mortality, eye diseases, demography and anthropometry. Focuses on and emphasizes a theme through the different lectures, with the tension and balance between horizontal approaches to child survival, such as Integrated Management of Childhood Illness (IMCI), and vertical programs such as disease eradication programs. Discusses several papers published as part of the Lancet Child Survival and Lancet Neonatal Survival series, and gain hands-on experience applying different child survival strategies using the Lives Saved Tool (LiST).

Provides an overview of the biologic basis for development and evaluation of new viral, bacteriologic, parasitic, and cancer vaccines. Address the fundamental immunologic concepts of correlates of protective immunity underlying current and new strategies for immunization. Emphasizes the use of new technologies for expression of vaccine antigens, including recombinant DNA techniques and use of novel adjuvants and antigen-carrier systems to enhance the delivery/presentation of specific immunogens to effector sites.

Provides students with an overview of protein bioinformatics including computational and experimental approaches. Introduces amino acid and protein physical properties as well as the alignment and evolution of protein sequences. Presents protein structure and methods of structure determination as well as the use of protein databases and software for visualizing proteins and generating publication quality figures. Discusses methods for secondary and tertiary protein structure prediction including homology modeling. Also covers methods for modeling small/molecule-protein interactions within the context of rational drug discovery and design. Finally, introduces students to experimental and computational aspects of mapping protein interaction networks.

Acquaints students with the central concept of causation across the biomedical and public health disciplines. Discusses how cause and effect relationships govern today's research and evidence-based decision-making based on the social, physical, political, and economic determinants of health. Compares how fields and sub-disciplines in biomedicine and public health approach causation using research case examples that illustrate major morbidity and mortality-related health problems. Examines strategies to mitigate the limitations of causal inference.

What does a rat exploring its environment tell us about memory? How can a mouse help us better understand schizophrenia? This course will focus on procedures that are routinely used to study behavior in animal models of cognition and neuropsychiatric disorders, with a focus on rodent models. Topics will include motor function, emotional and motivational states, cognition, and disorders such as dementia and schizophrenia, among others. Throughout the course, we will read and discuss original research articles to illustrate and compare some of the measures and results from the various procedures. Through this process students learn to assess animal models, to critique results presented in original research articles, and learn about the various techniques used in neuroscience to generate and evaluate various animal models.

Prerequisite(s): AS.200.141 OR AS.080.306 OR instructor permission.

Distribution Area: Social and Behavioral Sciences

AS Foundational Abilities: Science and Data (FA2)

This course is an advanced survey of the scientific study of learning and memory. Different perspectives will be used to review the science of learning and memory including the cellular-molecular basis of synaptic plasticity, the functional circuitry involved in learning and memory and memory systems in the brain. The course is designed to provide a deep understanding of the issues and current debates in learning and memory research and focuses specifically on animal models of memory and memory impairment. This is an interactive lecture course with a strong emphasis on student participation.

Prerequisite(s): AS.200.141 OR AS.080.306 OR (AS.020.312 AND AS.020.306) or instructor permission.

Distribution Area: Natural Sciences

AS Foundational Abilities: Science and Data (FA2)

(Formerly Nervous Systems I) Neuroscience: Cellular and Systems I is a fully integrated, two-semester course that surveys the cellular and molecular biology of neurons as well as the structure and function of the nervous system. Students must register for Neuroscience: Cellular and Systems II offered in the second term. Course open to JHU undergraduates only.

Prerequisite(s): AS.200.141 OR AS.080.105 OR AS.050.105 or instructor permission.

Distribution Area: Natural Sciences

AS Foundational Abilities: Science and Data (FA2), Ethics and Foundations (FA5)

Every day decisions often require us to weigh the costs and benefits of engaging in a particular course of action in order to obtain some expected outcome. Unfortunately, we often lack the information necessary to obtain our desired goal with complete certainty. Economists have long been interested in understanding human decision-making under these circumstances. In parallel, neuroscientists have made great strides at describing the underlying neural basis of simple decision-making. However, despite much progress in both fields, our understanding of how the brain makes decisions is incomplete. In order to strengthen and further research in both fields, the interdisciplinary field of Neuroeconomics arose. This course will survey the field of Neuroeconomics focusing on theoretical concepts developed by economists and the role these theories are playing in guiding current experimental neuroscience.

Prerequisite(s): AS.080.306 OR AS.200.141 OR AS.020.312

Distribution Area: Natural Sciences

AS Foundational Abilities: Science and Data (FA2), Ethics and Foundations (FA5)

Class designed to give students first-hand knowledge of the behavioral procedures and techniques used to study behavior in the field of neuroscience. Students will gain hands-on experience by carrying out some of the behavioral tasks used to assess animals under specific behavioral domains, discuss why certain aspects (i.e. genotype, environment conditions, group size, etc.) are important factors to consider when designing, planning, and carrying out such experiments, and learn the relevance of behavioral research in translational medicine. Note, this course can NOT be substituted for, or take the place of, the Neuroscience Lab core course requirement for the Neuroscience or Behavior Biology majors.

Prerequisite(s): AS.200.141 OR AS.200.250 OR AS.080.301 OR AS.080.306 or permission by instructor.

Distribution Area: Natural Sciences

AS Foundational Abilities: Science and Data (FA2), Projects and Methods (FA6)

This is an advanced course discussing mainstream and frontier topics in the five areas of: 1. Cosmology and galaxy, star, black hole and planet formation. 2. Discussions on the astrophysics of (exo-)planets including atmospheres, non-equilibrium atmospheres and biosignatures. 3.Future missions including the Habitable Worlds Observatory. 4. The hazards of space flight and how to overcome them 5. Significant existential questions for life’s continuance over the vast timeline of the Universe.

Distribution Area: Natural Sciences

AS Foundational Abilities: Science and Data (FA2)

A survey of neuropsychology relating the organization of behavior to the integrative action of the nervous system.

Distribution Area: Natural Sciences, Social and Behavioral Sciences

AS Foundational Abilities: Science and Data (FA2), Ethics and Foundations (FA5)

This course examines how and why animal behaviors are produced across the animal kingdom. Neurobiological, hormonal and developmental mechanisms and adaptive function of behaviors are examined in an evolutionary context. Behaviors include survival, acquiring food, reproduction, communication, parental care, and cooperation. Students will also learn how to develop hypotheses and predictions for scientific questions and interpret graphical results.

Prerequisite(s): AS.200.141 OR Permission of Instructor.

Distribution Area: Natural Sciences, Social and Behavioral Sciences

AS Foundational Abilities: Science and Data (FA2), Ethics and Foundations (FA5)

This class will survey the behavioral and biological science of human memory. Historical perspectives as well as modern controversies will be discussed. Intersections with other fields such as law, education, medicine, and technology will be highlighted. The course will be a mixture of lectures and group discussions.

Distribution Area: Humanities, Social and Behavioral Sciences

AS Foundational Abilities: Science and Data (FA2)

This course examines both the evolution and mechanisms of hormonal effects on behavior across animals, including humans. Topics will include the effects of hormones on sexual differentiation, reproductive behavior, parental behavior, stress and social behavior. Additionally, this course emphasizes developing skills in hypothesis testing and critically assessing the scientific literature. Course Recommendations: Introductory or advanced courses in biology and an introductory course in neuroscience (e.g. Foundations of Brain Behavior and Cognition) are highly recommended for success in this course.

Distribution Area: Natural Sciences, Social and Behavioral Sciences

AS Foundational Abilities: Science and Data (FA2), Ethics and Foundations (FA5)