BIOL 101
General Biology
Module 1
Elaine Reynolds (Biology), Jeff Pfaffmann (Computer Science)
This module uses an agent-based model of cell division in culture, so that students will run virtual experiments altering nutritional conditions or the number of cells originally plated in culture. They can then compare their lab experiments with the model predictions. In addition, they will alter the program to change the culture conditions of the model or the features that are responsible for contact inhibition to see how these changes affect the cell growth curve. This module has two main objectives: first to show student how computational models can be used as a tool in discovery, and second to give students familiarity with some basic features of model programming.
Module 2
Robert Kurt (Biology), Mary Armstrong (Women’s and Gender Studies)
A major goal of this interdisciplinary module is to make students in this first year biology course more aware of gender issues in science. There are three discussions spread throughout the semester. The first is a conversation on Gender, Science and Objectivity. For this discussion students read two articles. The first article is “Gender and Science” by Evelyn Fox-Keller, and the second article is “Gendered Experiences in the Science Classroom” by Molly Dingle. The second discussion is focused on Gender and Culture. For this discussion students read “The Egg and the Sperm” by Emily Martin, and the chapter on Biology from “Has Feminism Changed Science?” by Londa Schiebinger. The final discussion is focused on intersex, and for this discussion students read “Should There be Two Sexes” by Anne Fausto-Sterling. As a result of this interdisciplinary module students should come away from the course with a greater appreciation and understanding of gender issues in science, as well as the values of diverse viewpoints in science.
BIOL 102
General Biology
Module 1
Anna Edlund (Biology) and Jim Toia (Art)
This module focused on scientific illustration and visual skills. The Guild for Natural Science Illustrators website opens by asking us to: “Imagine a description of a yellow butterfly in words only! What shade of yellow? What is the wing shape? What does the color pattern look like?” Illustrators mix scientifically-informed observations, technical and aesthetic skills to accurately portray a subject. Lafayette’s Biology students currently lack training in observational, technical and aesthetic skills. Currently, an art student, while drawing a natural history specimen, is likely to observe it more closely than a science student ever will. Similarly, a Design student will explicitly discuss the elements of effective visuals, while a science student may never do so. With this infusion, we aim to redress this, and to make Biology students aware that sketching and laying out illustrations can transform raw observations into explanations and evidence. It can help scientists (or anyone, actually) to observe, abstract, recognise pattern and find meaning (Root-Bernstein, 1989). This infusion includes a hands-on drawing exercise in the laboratory with dissected or sectioned specimens, short readings (such as the Scudder, S.H. “Look at your fish” essay on Louis Agassiz’s observational science (1874)), a short lecture on the history of scientific illustration and its tools, and an exercise on visualization of quantitative data and relationship, for example Bioinformatics graphics.
Module 2
Eric Ho (Biology), Nancy Waters (Biology), John Drummond (Biology)
For this infusion we created a new molecular phylogeny module. The goal of this module is for students to understand evolutionary relationships between species based on a phylogenetic tree, which is constructed by computational methods. The module consists of a lecture followed by a computer lab exercise. In the lecture, we discuss the theory of speciation with the emphasis on quantifying differences between species, and the procedure to construct phylogenetic trees from biological sequences such as DNA and protein sequences. In the lab, each student is required to build a phylogenetic tree of a randomly assigned gene using the computational molecular evolution tool MEGA6. Through this new module, students learn how to use the computational method to study a biological problem (phylogeny in this case), and to treat computational work as an experiment in which the results must have proper controls and they must be validated in the same way as bench experiments.
BIOL 110
Edible Ethics
Module 1
Megan Rothenberger (Biology), Ben Cohen (Engineering Studies)
This module begins with an introductory lecture by Prof. Cohen on the Green Revolution and the history of agricultural technology. As a homework assignment, students are asked to explore the popular literature (i.e., Grist, NY Times, Orion, etc.) to identify 5 differing perspectives on the topic of genetically modified (GM) foods. On the class website, they write short “blurbs” describing each of these perspectives/arguments for or against GM crops. We spend time in class listing and discussing these different stakeholders and arguments as a way to appreciate the complexity of these ethical issues. Later in the semester (and with a more sophisticated understanding of the issue of agricultural technology, GM crops, and sustainable agriculture), students engage in a role-playing debate in which they act as United Nations delegates who have come together to discuss and debate a variety of issues surrounding world hunger, including the capacity of agriculture to meet current and future needs, food aid, and biotechnology (e.g., should genetically modified (GM) maize be included in food aid shipments to developing nations?).
Module 2
Megan Rothenberger (Biology), Tara Gilligan (Women’s and Gender Studies)
To prepare for the first part of this module, students are asked to read excerpts from The Sexual Politics of Meat by Carol J. Adams and to generate 3 good questions for discussion based on the reading. The first session is a joint discussion of the readings with Gender & Environmentalism students. Students in both courses are divided into 3 mixed groups (i.e., containing approximately even numbers of students from the 2 courses). Each group meets during the lunch hour in Gilbert’s Café to discuss specific questions constructed by the students (questions drawn randomly from a hat). For the second session, a panel of guest speakers, including Lynn Prior of PA’s Buy Fresh Buy Local and other local farmers and food businesses, talk about their experiences, approach, and mission in sustainable agriculture and food. Students in both this course and Gender & Environmentalism attend.
BIOL 224
Plant Form, Function and Adaptation
Module 1
Megan Rothenberger and Mike Butler (Biology), Dave Sunderlin (Geology and Environmental Geosciences)
This module begins with a lecture by Prof. Sunderlin on the fields of paleobotany and paleoecology (e.g., questions asked, research methods, etc.) and the origin, diversification, and structure of the earliest plants. Next, we introduce the students to the specific ANCIENT plant and animal interaction on which we will be focusing: the coevolution of grasslands and grazing ungulates. Each of us paint a part of this Miocene picture for the students. Prof. Sunderlin discusses the paleoecology of a Miocene grassland. Prof. Rothenberger discuss the diversification of the graminoids (i.e., true grasses, sedges and rushes) during the Miocene, and the structure and function (anti-herbivory?) of phytoliths. Prof. Butler discusses the diet and digestive anatomy and physiology of grazing ungulates. The students get an opportunity after this introduction to read and discuss some of the literature on these topics and to eat some grass to experience phytoliths for themselves! During the second practicum session, Prof. Sunderlin discusses plant-insect interactions in the fossil record and shares fossils with students to demonstrate ways in which paleobotanists can learn about these plant-herbivore relationships of the geological past.
Module 2
Megan Rothenberger (Biology), Bill Bissell (Anthropology and Sociology)
This module begins with an introductory lecture by Prof. Bissell on the field of cultural anthropology and ethnobotany (e.g., foundations, themes, questions asked, research methods, etc.). Students do some cooperative brainstorming to consider the following questions: 1) What different uses are there for plants and plant products?, 2) People attribute special properties to material substances, including plants. What are some different ways in which humans classify and value plants?, 3) How and why might this change across different cultures?, and 4)What information about a culture could an anthropologist or ethnobotanist gain from learning about the plants found in that culture? Students complete an assignment in which they select a plant product (e.g., food, herb, medicine, drug) and trace it back to its source. They write a paper that includes both biological information (scientific name, classification, distribution, life cycle) and cultural information (story of origin – description of first uses, history of cultivation, cultural/social significance and how changed over time) about the plant. The second part of the module focuses on bioprospecting – the logistical, methodological, and ethical aspects (e.g., issues of compensation and intellectual property rights for plant derived drugs) of ethnobotanical field work. For this part of the module, students read articles and watch a film that demonstrate bioprospecting in practice.
BIOL 225
Microbiology
Module 1
Laurie Caslake (Biology), Andrea Smith (Anthropology & Sociology)
This module is intended to explore social justice – the fair distribution of resources – in the American health care system. In 1999, Congress commissioned a report on the health care quality and experiences of racial and ethnic minorities in the US, resulting in the Institute of Medicine’s report, Unequal Treatment: Confronting Racial and Ethnic Disparities in Health Care (IOM, 2003). Focusing on the Tuskegee syphilis experiments, the goal for this module is for students to understand the “experiment”, the historical context, and be able to identify at least two other disparities in our current health care system based on race and ethnicity.
BIOL 251
Human Physiology
Module 1
Mike Butler (Biology), Justin Hines (Chemistry)
In preparation for this laboratory exercise, students read Misaka 2013 (Molecular mechanisms of the action of miraculin, a taste-modifying protein, Seminars in Cell & Developmental Biology 24:222-225), a short review on how scientists think miraculin works. Miraculin is a protein that comes from a fruit that is commonly known as the miracle fruit. This protein seems to bind to the sweet taste receptor on the tongue that is affected by pH; specifically, when an individual eats a sour food, the sweet taste receptor undergoes a change in shape, creating the impression of sweetness. In other words, individuals can eat miracle fruit, and then for up to an hour later, acidic foods such as lemons or pickles can taste sweet. Upon arriving in class, students answer one or two group-based questions to solidify their understanding of the material and expose any weaknesses in their understanding. They then eat a series of naturally acidic and naturally sweet foods and subjectively assess the sweetness and acidity of those foods, and then generate predictions regarding how those foods will taste after eating miracle fruit. Then, they eat some miracle fruit and eat the same foods again and rate their sweetness and acidity. After this, Prof. Hines and Prof. Butler lead a discussion analyzing the figures from Misaka 2013. Students learn about topics such as protonation, shape change in proteins, and the function of receptors. They also apply these lessons to understanding the concepts within Misaka 2013 more clearly, and then use this understanding in a discussion regarding their opinions on the value of exploring the use of miraculin as an artificial sweetener.
Module 2
Mike Butler (Biology), Jenn Rossmann (Mechanical Engineering)
Because students sometimes have difficulty understanding some of the complexities regarding generation and maintenance of blood pressure along all points of the circulatory system, Prof. Rossmann helped develop a laboratory exercise to illustrate some of these concepts more clearly. We use water that can be raised and lowered along a vertical axis and a series of tubes of different diameters to model the effects of vasoconstriction, changes in body position, and other factors that affect blood pressure. The work is group based, and involves students using a worksheet to make predictions, collecting data, and revising their understanding of the rules regarding fluid dynamics. After each lesson that uses water, students are challenged to apply this understanding to human circulation by answering questions on their worksheets about blood flow.
Module 3
Mike Butler (Biology), Daniel Stroembom (Mathematical Biology)
The focus of this module is the role of probability and stochasticity in physiological systems. Because of terminology that insinuates a consciousness or intention of molecules (e.g., hemoglobin drops off oxygen when it gets to capillaries), this module was developed to demonstrate that physiological patterns can emerge because of changes to probabilities at the molecular level. To this end, we developed an Excel spreadsheet that allows students to use what they know regarding how oxygen binds to (and dissociates from) hemoglobin in a variety of microenvironments to predict the net change in oxygen-hemoglobin binding. By refreshing this spreadsheet, which has a number of probability-based formulas, students can see that there is no intentional “dropping off” of oxygen anywhere. Rather, because the chemical microenvironments differ between the lungs and the muscles (e.g., pH), the likelihood that oxygen will bind to or dissociate from hemoglobin is different. This difference results in the emergent pattern of a net dissociation of oxygen from hemoglobin in the muscles. Thus, a net drop off of oxygen occurs at a specific site in the body, without hemoglobin’s “knowing” that it was at a particular place where it needed to drop off anything.
BIOL 256
Neurobiology
Module 1
Elaine Reynolds (Biology), Jeff Pfaffmann (Computer Science)
This module uses an agent-based model of decision making during the developmental process where cells decide to become nervous system or skin. This module was used in class as a demonstration of how cellular signaling pathways influence patterning of the nervous system. The main objectives of demonstrating the model was to show student how computational models can be used as a tool in discovery. The model was introduced and then students developed hypotheses that we tested on the model in class. After running the model we discussed the results and the limitations of modeling.
Module 2
Elaine Reynolds (Biology), Jim Toia (Art)
In this module students developed infographics that explained specific ideas about neurotransmitters. The main objective was to introduce a discussion of visual communication as a means of communicating scientific ideas and to give students some practical experience in this technique. Jim Toia spoke in class about visual design after the project was introduced and the class discussed tools to use, parameters that defined the project and then we reviewed the module as a class. Students created infographics about a particular neurotransmitter and then presented their work poster style to their peers in the class. Students rated each others’ work and discussed the positives and challenges of each presentation. Jim Toia also reviewed the work after the presentations and gave feedback for improvement of the module.
Biol 270
Behavioral Ecology
Module 1
Mike Butler (Biology), Lisa Gabel (Neuroscience), Elaine Reynolds (Biology)
This module is focused on the mechanistic underpinnings of behavior. In particular we developed a laboratory section that brings the neuroscience perspective to behavioral ecology by highlighting the important role genetics can have in shaping behaviors. By using Drosophila mutants, we explored how specific genetic lines have predictable differences in behavior, and that these differences manifest in specific environments (e.g., at specific temperatures).
Module 2
Mike Butler (Biology), Jonathan Lafky (Economics)
This module is focused on using economic principles to understand behavioral ecology. For this purpose, Profs Lafky and Butler developed a laboratory module that uses different games (the term that behavioral economists use) to allow students to interact with each other in a diversity of circumstances to compete for resources (i.e., money). These games investigated phenomena such as altruism, trust, and the importance of repeated interactions in shaping how humans interact with each other when there is a monetary benefit. At the conclusion of each game, we discussed how these principles apply to the behavioral ecology of non-human animals, which compete for survival and reproductive success, rather than money.
Module 3
Mike Butler (Biology), Daniel Stroembom (Mathematical Biology)
Behavioral ecologists use a diversity of tools to investigate behavioral patterns; one is to mathematically model populations and examine how varying initial conditions or program rules affect population size. To a) demonstrate the value of modeling tools and b) to reinforce concepts on factors influencing population size, we developed a module for the laboratory section of behavioral ecology. Students used the computer lab and a script to test ideas related to how population size changes as a function of multiple factors. Students performed a series of modifications to the model, evaluated how population size differed, and discussed the reasons for these observations. They also made predictions regarding how population size would change when other factors were modified, allowing them to evaluate their own comprehension of the underlying concepts.
BIOL 314
Anatomy of Vision
Module 1
James Dearworth (Biology), Chris Anderson (Chemical and Biomolecular Engineering)
This module began with a lecture by Professor Dearworth on how an electron microscope works. He described how the technology has advanced over the decades including its greater ease of use. Chemical and Biomolecular Engineering possesses a desktop Phenom Prox SEM (scanning electron microscope) that is this easy-to-use type of instrumentation. A project was described done by Professors Dearworth and Anderson with Science Horizon Students Sze Cheng BIOL ꞌ17, Olivia Erdman BIOL ꞌ17, and Amy Lau BIOL ꞌ18 to image the topology of the posterior side of the iris in the turtle. Results of these images were reported in September 2015 at the 31st International Pupil Colloquium in Oxford, England and were shared with the students. The students then were taken to Acopian Engineering Center 315 where the SEM is housed. There, Amy Lau and Professor Anderson demonstrated how to prepare and image samples using the SEM.
Module 2
James Dearworth (Biology), Joe Sherma (Chemsitry)
This module began with a lecture by Professors Dearworth and Sherma on how high-performance thin-layer chromatography (HPTLC), spectrophotometry, and high-performance liquid chromatography are done. Students were shown developing tanks, plates, and pipettes. A project was then described which was done by Professors Dearworth, Sherma, and Dr. Chejlava working alongside with neuroscience majors Lauren Hartnett ꞌ13 and Melroy D ꞌSousa ꞌ13. Iris tissue was isolated and analyzed by the techniques to detect for vitamin A. Results revealed that vitamin A is present in the iris and thus can support a functional melanopsin in the iris of the turtle. The results found using these techniques, which were presented at the Society for Neuroscience held in Washington DC in fall 2014, were shared with the students.
BIOL 317
Physiology of Extreme Animals
Module 1
Mike Butler (Biology), Dave Sunderlin (Geology and Environmental Geosciences)
Within this module, Profs. Sunderlin and Butler use their respective areas of expertise to explore different physiological mechanisms in prehistoric animals. They primarily focus on dinosaurs, and try to answer two questions: 1) were dinosaurs endothermic?, and 2) how did sauropods maintain blood pressure to the head? Cell- and organismal-level differences in endothermy and ectothermy are described, and then groups discuss whether it was likely dinosaurs generated significant amounts of body heat (i.e., were endothermic). Students are expected to describe the sort of evidence they’d need to draw conclusions, and Profs Sunderlin and Butler describe what sort of evidence exists. When students get stuck, fossil evidence or examples in extant organisms are mentioned. At the end, general opinions among paleontologists are reviewed. For the second component of this module, basic challenges facing a long-necked dinosaur are discussed; that is, any large change in height of the head could result in drastic changes in blood pressure, leading to fainting or to ruptured blood vessels in the brain. Discussions draw on recent literature and evidence from extant animals such as giraffes.
Module 2
Mike Butler (Biology), Steve Nesbit (Mechanical Engineering)
Prior to class, students read about differences at the tissue level between chimpanzee and human muscle tissue. During this process, it will become apparent that chimps are approximately six times stronger than the average human, a significant difference. After thinking about this difference at the physiological level, we discuss possible biomechanical reasons. At this point, we will use equipment to track the biomechanics of human motion, with the students as the subjects. After analyzing captured videos to quantify various metrics of strength and speed, we compare these data to those that are available on chimpanzees, highlighting that small differences in physiology or anatomy between similar species can result in fairly large changes in function.
BIOL 338
Biological Pattern Formation
Module 1
Anna Edlund (Biology), Daniel Stroembom (Mathematical Biology)
According to scholars Sarah Otto and Troy Day (2007), a full 60% of American Naturalist articles in 2006 “reported predictions or results obtained using mathematical models,” and if statistical analyses are included, virtually ALL Biology articles are found to hold underlying mathematical models. Yet Biology students remain unaware of this, or only discover it once they begin reading primary literature, often hopping their eyes over any equations they encounter while reading, searching below the symbols and numbers in hopes of finding a figure legend or translation into prose. It is especially fruitful to approach the mysteries of Biological Pattern Formation using models and algorithms. Branching patterns in vasculature are reminiscent of fractals; zebra stripes have periodicity or frequency; spirals in shells or plants expand with predictable character. This infusion includes primary literature readings that illustrate distinct types of models, a hands-on exercise using NetLogo for its programmable modeling environment and participatory simulations, and a journaling assignment on individual response to Quantitative Biology.
Module 2
Anna Edlund (Biology), Jenn Rossmann (Mechanical Engineering)
According to the Biomimicry Institute, one approach to innovation is to look to animals, plants, and microbes as “consummate engineers” that have, through deep time, “already solved many of the problems we are grappling with.” For example, we might find the optimal angle for the man-made fiber wrappings of a fire hose by looking to the natural fibers around such other hydrostatic skeletons as earthworms or penises. We might better design architectural ventilation after studying termite mounds or lungs. We might better predict the behaviors of self-patterning arrays, after studying the equal spacing of spots across an embryonic animal hide. This infusion includes a short lecture on the use of biomimicry for addressing engineering challenges, readings (such as excerpts from Janine Benyus’s book Biomimicry: Innovation Inspired by Nature, 1997), and a problem-based learning exercise focused on biomimicry.
BIOL 341
Environmental Issues in Aquatic Ecosystems
Module 1
Megan Rothenberger (Biology), Kira Lawrence (Geology and Environmental Geosciences)
The first interdisciplinary module is focused on the topics of paleoclimatology and paleooceanography (i.e., using lessons learned from Earth’s climate history to understand the climatological impact of human activity on modern marine biodiversity). The first part of this module is focused on the Paleocene Eocene Thermal Maximum (PETM) as an analog to modern climate change. Students read two introductory readings about the “last great global warming” that occurred ~56 million years ago, and Professor Lawrence gave a guest lecture that covered the causes and consequences – particularly for marine organisms – of the PETM. She also shared with the students a replica ocean sediment core that showed the clay layer of the PETM. Students were then be asked to work in groups to use their new understanding of past warming events to brainstorm about the consequences of current climate change – which is occurring 10 times faster than the PETM – to some of the major marine ecosystems that we discussed earlier in the semester (e.g., estuaries, coral reefs, kelp forests, pelagic areas, rocky intertidal). Students were then introduced to modern methodological approaches for studying the impact of climate change and acidification on marine biodiversity (i.e., modeling vs. experimental approaches). Students discuss the pros and cons of each approach, and, for their assignment, they were asked to construct a research proposal for measuring some change in biodiversity in the marine ecosystem as a result of warming and/or acidification.
Module 2
Megan Rothenberger (Biology), Art Kney and Dave Brandes (Civil & Environmental Engineering)
The second module provides more information on technological solutions to water quality and quantity problems and focuses on green infrastructure and stormwater management. This module began with a field trip to the Sullivan Park constructed wetland where Prof. Brandes talked to the students about the design, maintenance, monitoring, and challenges of the wetland. Routine monitoring of the wetland up until now has identified two potential management problems: 1) the presence of several aggressive invasive plants and 2) seasonal algal blooms. As a result, Biology 341 students are separated into 2 groups. One group is asked to characterize the wetland plant community and document the current mean percentage coverage of invasive species, and the second group is asked to assess the relationship between nutrient concentrations and ratios and the development of algal blooms in the retention pond. Students learn the field sampling techniques required to address these research questions, and they learn to process initial samples and analyze the data in a separate practicum back in the lab. The first visit to the wetland served as introduction to the problem and to the sampling/analytical techniques. Throughout the rest of the semester, students are required to use the sampling and analytical methods they learned to collect data on their own again in October and in November. For their assignment, students are responsible for working with their teammates to write an environmental assessment report detailing key findings and proposing potential management strategies for contending either with invasive species or noxious algae.
BIOL 490
Biology Capstone
Module 1
Laurie Caslake (Biology), Nancy Waters (Biology), Katalin Fabian (Government & Law)
Students read several articles relating to global health equity and disparities. They then apply that knowledge in discussion and debates to articulate the biological, social, and political aspects of health care delivery in two countries beyond the United States.
Module 2
Laurie Caslake (Biology), Nancy Waters (Biology), Jason Alley (ITS Senior Instructional Technologist)
Students read guides on enhancing communication through visual/social media. They then apply that knowledge to how they prepare and present graphs, tables and drawings for a semester-long project culminating in a juried public poster event.