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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 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.

Biochemistry in the Real World (Chemistry 112, counts as Biology 199)
The genomics revolution of the last 10 years has given birth to the “proteome,” emphasizing the central role that proteins play in virtually all life and death processes. Using a semester long research project, this course will explore central features of what proteins look like and how they perform their varied functions in a variety of biological and chemical processes. Discussion will include aspects of cell differentiation, cell death and disease states such as cancer, Alzheimer’s, and AIDS.

Biodiversity and Conservation Biology
Conserving the earth’s biodiversity is a challenge that grows more difficult every year. Human population growth, increased demands for natural resources, and climate change all increase the pressures on many of the earth’s most valued species and ecosystems. This course will explore the ecological and evolutionary foundations of the science of conservation biology. Students will learn to identify a variety of local plant and animal species. We will also study the phylogeny of life, and how specific organisms fit into that phylogeny. 

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.

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.

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
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.

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.