BIOL 199 Topics: Introduction to Biological Thinking

The Animal Genetic Toolkit
The overall goal for this course is for you to gain an understanding of how scientists ask questions and test hypothesis through both acute observation and experimentation. In particular, our lens will be how genetic changes in developmental processes have shaped the course of animal evolution (e.g., how can a change in a regulatory gene cause a change in the body plan?). Through the lens of “evo-devo” we will evaluate scientific data from a variety of fields (paleontology, genetics, cell biology, developmental biology and evolution to name a few) to gain an appreciation for how genes and the process of development has shaped the body plans that represent the diversity of animals on the planet. Throughout the course we will also discuss scientific responsibility and the role science plays in our society.

Animal Embryology
Most animals develop from a single fertilized egg cell. That single cell divides mitotically to produce cells that have identical DNA. Yet these daughter cells differentiate and organize themselves into regular, precise and elegant body patterns with as many as 200 different cell types. How do these cells become different from each other if they have the same DNA, and how do they generate such highly organized and specific tissues and organs? And how do we investigate the workings of such a complicated system? This course introduces the questions that developmental biologists ask by focusing on how frog embryos develop into tadpoles. In addition, the course will help students learn to read scientific literature, perform experiments and gather data, write analytically and critically about science, and understand ethical issues of doing and reporting research.

Animals in Extreme Environments
One of the major forces driving evolutionary change is the interaction between individuals and their biophysical environment. Physiological adaptations to environmental challenges (temperature, water, light, salinity, pressure, nutrients, and toxins) shape range limits and organismal responses to variability and change. We will examine the physiological processes associated with hot deserts, arctic climates, freshwater and saline systems, deep sea environments, and integrated responses to environmental stress. We will also examine the human response to physiological stress (temperature, altitude, and exercise). Although we will focus on systems with extremes, an important theme of this course is that evolutionary processes shape physiological adaptations across all variable environments. Laboratory investigations will examine physiological processes in animals, with an emphasis on invertebrate model systems.

Astrobiology
Astrobiology is the study of life in the universe. In this class, we will explore the origins of life on Earth and then look at how the scientific method has been used to generate hypotheses regarding the existence of life elsewhere in the universe. Microbial life forms on Earth (e.g., bacteria, archaea) persist at environmental extremes and therefore serve as model organisms for the study of astrobiology. In lecture and lab, experiments to test these hypotheses, whether performed on Earth, on other planets using remote sensing, or through space exploration (e.g., missions to Mars) will be reviewed. Astrobiology is an interdisciplinary science. A course theme will be how perspectives and methodology from different scientific disciplines integrate in pursuit of an answer to the fundamental question, “Are we alone in the universe?” 2009 was the International Year of Astronomy, commemorating Galileo’s first exploration of the universe with a telescope 400 years ago. This course is a timely opportunity for students to expand their interests, while at the same time building a solid foundation in biological thinking.

The Balance of Life: Evolution and Extinction
The goal of this course is to provide you with an understanding of evolution and how it shapes our lives and our planet. It covers a broad range of topics including: what is evolution, the importance of evolutionary biology, its history, origin of life, extinction and fossils, human evolution, religion and evolution, and conservation biology.

Being Human
The human body is an amazing machine – full of cells, organs, and organ systems working constantly to maintain homeostatic harmony. We will use the scientific method to understand how doctors and scientists made ground breaking discoveries about the structure and function of our body systems. We will discuss and explore how our body systems are impacted by our environment, diet, genetics, and disease. We will consider how humans, as individuals and in populations, have an impact on our ecosystems. We will employ some interactive lab activities to put our own body systems and hypotheses to the test, case studies where we will analyze data and discuss bioethics, and current events where we will consider how we are still learning about human biology every day.

Big Data in Biology
The world today is overflowing with data, and in biology as elsewhere, developing meaningful ways of assessing, analyzing, and interpreting data is one of the big questions of the 21st century. In this course, we will explore how big data has helped to answer key biological questions about the evolution of living organisms. In lab, we will develop skills in conducting biological research with bioinformatic tools.

Biodiversity and Conservation Biology (Cross-Listed as ENVR 199)
Is the current six mass global extinction event a natural phenomenon or human induced? Biodiversity is the diversity of genes, species and ecosystems, and conserving these resources is a growing challenge with a myriad of threats ranging from increasing demands for natural resources to climate change. This course will explore the importance of biodiversity, how biodiversity of studied, and the ecological and evolutionary foundations of the science of conservation biology. We will study biodiversity and conservation in a local and global context, and consider the role of science in decision making.

Biology of Mammals
The purpose of this course is to introduce students to the process by which scientists develop and address biological questions and we will accomplish this goal by exploring different aspects of mammalian biology through integration of concepts and information, observational and experimental research, and interpretation and communication of research findings. Mammals are some of the most familiar organisms to us, yet they are a remarkably diverse group in terms of anatomy, physiology, behavior, and ecology. Study of such an interesting and varied group requires consideration and exploration of many facets of science and we will integrate information and approaches from multiple areas within and outside of biology throughout the course. We will start by considering the evolution and diversity of mammals and we will develop research questions and projects to explore mammalian behavior, population dynamics, and population genetics. We will also spend time considering extinction and conservation of mammals, ways wild mammals interact with and impact humans, and ethical considerations when performing research involving mammalian species.

Biology to Save the World
How can an understanding of biology help us solve the problems of the world? In this course, we will explore how biologists develop solutions to environmental and health-related issues, from curing diseases to using synthetic biology. Synthetic biologists manipulate DNA to build an organism that helps us answer biological questions. In lab, we will engage in synthetic biology by harnessing the power of molecular engineering to deepen our understanding of biological systems and begin to address real-world problems. We will also grapple with the ethical dimensions of groundbreaking advances, from the creation of novel life forms to the future of human genetic engineering.

Coastal Marine Ecology (Cross-Listed as ENVR 199)
The ocean covers more than 70 percent of our planet?s surface and contains 97 percent of the Earth's water. Coastal ecosystems provide a number of valuable ecosystem services on which humans depend for food, recreation, transportation and economic activities and yet, our use of these resources is increasingly threatening these fragile habitats. In this class we will examine the interactions between organisms and their environment exploring the physiological and behavioral adaptations that allow species to persist in this unique ecosystem and consider the new challenges that climate change will bring. Students will gain experience asking and answering questions through observation and experimentation in both the lab and on field trips to the coast. Students will learn how to interpret and communicate data to a variety of audiences. As a service learning class we will have the opportunity to work with regional conservation agencies as well as fifth graders at a local elementary school. This course is cross-listed as ENVR199. This course fulfills the life science requirement for the Environmental Studies major or minor.

Genes, Neurons, and Behavior
This course examines the genes and neurons responsible for generating human behaviors like our biological clocks, learning, memory, and sexual attraction. We will look at what is learned from experiments and from animal models to learn where these behaviors come from within us.

The Genetics of Being Human
Human heredity is a topic of considerable interest and relevance in today’s world.  Advances in our understanding of genes and how that information relates to inheritance of specific traits gives us insights into our own lives and how science and society interact.  We will work with these important issues and to help each of you to develop critical thinking skills that will lead to informed decision-making regarding issues that continually affect our society. Some of the material that will be covered in this course will include (but is not limited to): information on stem cells, chromosomal inheritance of disease, genetic basis of inherited diseases, reproductive technologies, biological gender determination, genetic testing, biotechnology for forensics, genetic testing and finding cures for genetic disorders, human evolution, genetics of the immune system and population genetics.

A Gut Feeling
The human body is an amazing machine – one that works tirelessly and requires an abundance of fuel in order to stay operational. We will spend the semester learning to think and ask questions like scientists, and will use our digestive tract as a lens to explore our body’s capabilities. We will investigate how our bodies meet the challenges of acquiring, utilizing, and storing fuel, as well as what happens to the byproducts and wastes from these processes. We will discuss how features of the human body have evolved over time, and will consider and make predictions about the changes that are ongoing. We will employ the scientific method to conduct interactive lab activities to put our own body systems to the test, will develop and test some of our own hypotheses, will analyze data and discuss bioethics in case studies, and will tie in current events to keep things in perspective.

Infectious Diseases
Microorganisms have influenced society and history in significant ways. The realization that bacteria, viruses, protists, and fungi are the causative factor behind many of the most menacing diseases moved humanity to a new era of understanding its relationship to the world around it. The sciences of microbiology and infectious disease studies has matured since these early discoveries, with genetics, molecular biology, and biochemistry providing a mechanistic grasp on the dynamics of infection. These areas have, in turn, augmented humanity’s ability to prevent the transmission or the persistence of these germ-derived diseases. In this class we will inspect diseases caused by bacteria and viruses under a mechanistic eye, using scientific methodology and literature to better understand how infections arise, are transmitted, progress, and lead to illness. Discussions will also address the role society has played in the emergence of many “new” diseases. Labs are designed to dissect disease transmission, evolution of antibiotic resistance in bacteria, and the importance of structure to a bacterial toxin’s function, among other topics.

Invasions in Biology (Cross-Listed as ENVR 199)
Humans act as the greatest vehicle for species to move from one location to another. Why do some organisms that are normally benign suddenly become noxious pests or do direct harm to humans when introduced into a new environment? We will explore how scientists use approaches from diverse biological disciplines (i.e. genetics, ecology, evolutionary biology, physiology) to study invasions in biology both at the ecosystem and the microbiological levels. We will develop research projects to explore the population dynamics, spatial distributions, and molecular mechanisms of invasions, in part based on an overnight field trip. This course provides a timely opportunity for students to examine the origins and consequences of invasions in biology, while gaining first-hand experience with how scientists ask and answer questions through both observation and experimentation.

The Life of Birds
A football-sized Arctic tern migrates tens of thousands of kilometers each year, chasing perpetual summer nearly from pole to pole. Ground-bound cassowaries shift entire plant populations uphill against the pull of gravity. Atop Everest, climbers struggle for the summit while bar-headed geese fly over top. Babbling babies and song sparrow sopranos mirror each other in vocal development and gene activation. Birds are studied in nearly every subfield of biology, but how did these descendants of the dinosaurs come to colonize every continent – and what comes next? In this course we explore the breadth of avian diversity, including their genetics, physiology, behavior, ecology, and evolution, to learn the analytical skills and communication essential for biological study. Trips to nearby habitats and hands-on lab and field techniques will familiarize students with local Virginia birds by sight and sound and contribute to citizen science efforts.

Mesoamerican Ethnobotany
This course is about plants that are important to the people of Mesoamerica, both past and present, as a platform for consideration of: 1) the nature of the scientific process; 2) the myriad connections among scientific disciplines and human culture; 3) sustainability of human life; and 4) basic elements of botanical science.

Microbial Stress
The overall goal for this course is for the student to gain an understanding and appreciation of how scientists ask and answer questions through both observation and experimentation. To this end, the following will be considered: How do scientists choose what to study and select the questions to be answered? How do scientists design good experiments? What tools exist to study the natural world? How is scientific data analyzed, interpreted, and disseminated? What does it mean to be an ethical scientist? Why is this important? The course will address these questions through the prism of the stress biology of microorganisms (microbes), organisms invisible to the naked eye. Microbes are the most numerous, most diverse and most important organisms on earth. In their natural environments, microbes must appropriately respond to numerous adverse conditions in order to grow or, at the least, survive. This course will consider how microbes survive adverse conditions such as thermal stress, radiation, predation, antimicrobial chemicals, and the human immune system. These survival mechanisms are inherently interesting to scientists from a wide range of disciplines and have numerous implications in diverse areas including public health, food production, and evolution.

Molecular Mechanism of Medicine
The primary aim of this course is to introduce you to how scientists think, work, and communicate. We will build these skills by studying the molecular mechanism of certain drugs and the diseases that they treat. We will focus on experimental design in model organisms that can be used for drug development and discuss the uses and ethics of human research. Additionally, we will look at examples of "alternative medicines" that are tested via the scientific method and discuss the ramifications of "alternative therapies" that escape this scrutiny. Finally, you will explore recent research that is leading to the next generation of innovations in medicine.

Neural Communication
As the basis for animal behavior, an understanding of how nerve cells communicate is fundamentally important. How is electrical activity generated in a nerve cell? How is electrical activity converted into chemical information at the nerve specializations known as synapses? How is a synapse built and maintained by guidance cues and neural activity? How is synaptic function altered in development, learning, and drug addiction? Throughout the course, we will appreciate how biologists generate questions and how they answer them. What are the hallmarks of good experiments? Why should scientists have good observational skills? Which tools and approaches assist our ability to answer questions? Once data are collected, how do we make sense of them? We will also discuss scientific responsibility and the role science plays in our society. Integrated laboratory experiments will provide opportunities to learn laboratory skills and gain experience with experimental design, measurement, analysis and communication of results.

Stem Cells and Regeneration
This course introduces the process of biological discovery by studying stem cells which are important in development and in the repair of biological tissues following injury or disease. How are stem cells used to create new tissues? Some animals also have the capacity to regenerate injured body parts; what signaling molecules and cellular processes are needed for regeneration and could these be useful in designing therapeutic approaches? We will examine what is known about stem cells and regeneration and how these discoveries were made and then generate research questions to be addressed using the scientific process. Student-driven research projects will provide opportunities to learn laboratory skills, solve problems, and gain experience with experimental design, measurement, analysis, and the communication of results. This course will also examine ethical questions about stem cell therapies and, in the context of the scientific process, what it means to be an ethical scientist and why this is important.