COVID-19: Essential Information

David Allen

Assistant Professor in Biology

 
 work802-443-5218
 Mondays 3-4:30pm and Wednesdays 9-10:30am by zoom
 McCardell Bicen Hall 372

Research interests

Forest ecology

I am interested in successional dynamics in oak-hickory forests. Many such forests in eastern North America are under rapid successional change as the oak canopy is replaced by individuals of more mesophytic species. There are multiple hypotheses for the driver of this change: fire suppression, decreasing severity and prevalence of drought, or changes to herbivore communities. Most of this work takes place in a 23-ha forest dynamics plot in Pinckney, MI. This plot is part of the Smithsonian Institution’s ForestGEO global network of forest research plots. As such data from this plot are part of large collaborative studies on other aspects of forest ecology. 

Ecology of tick-borne diseases

I am also interested in the abiotic and biotic drivers of tick-borne disease prevalence. For this project I largely focus on Borrelia burgdorferi, the Lyme disease agent, in Ixodes scapularis, the blacklegged tick. I take a joint empirical-theoretical approach for this project. I am developing a model which predicts enzootic persistence of a tick-borne disease in a given abiotic and biotic context. Then I will parameterize the model with field-collected and literature values. If the model is successfully validated, it will be interrogated to better understand the drivers of disease persistence.This ongoing work takes place in Addison County, Vermont.

For more information on these projects, see my website.

 

Courses

Course List: 

Courses offered in the past four years.
indicates offered in the current term
indicates offered in the upcoming term[s]

BIOL 0140 - Ecology and Evolution      

Ecology and Evolution
In this introduction to ecology and evolutionary biology we will cover the topics of interspecific interactions (competition, predation, mutualism), demography and life-history patterns, succession and disturbance in natural communities, species diversity, stability and complexity, causes of evolutionary change, speciation, phylogenetic reconstruction, and population genetics. The laboratory component will examine lecture topics in detail (such as measuring the evolutionary response of bacteria, adaptations of stream invertebrates to life in moving water, invasive species and their patterns of spread). We will emphasize experimental design, data collection in the field and in the laboratory, data analysis, and writing skills. This course is not open to seniors and second semester juniors in the Fall. 3 hrs. lect./disc./3 hrs. lab DED SCI

Fall 2016, Fall 2018, Fall 2019, Spring 2021

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BIOL 0211 - Biostatistics      

Experimental Design and Statistical Analysis
Experimental design is one of the most important parts of doing science, but it is difficult to do well. How do you randomize mice? How many replicate petri plates should be inoculated? If I am measuring temperature in a forest, where do I put the thermometer? In this course students will design experiments across the sub-areas of biology. We will run student designed experiments, and then learn ways to analyze the data, and communicate the results. Students planning to do independent research are encouraged to take this course. (BIOL 0140 or BIOL 0145). DED

Fall 2018, Fall 2020

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BIOL 0323 - Plant Community Ecology      

Plant Community Ecology
This course will explore the structure and dynamics of plant communities, with a particular emphasis on temperate forest communities. We will investigate patterns in community diversity and structure, explore how plant populations and plant communities respond to environmental disturbances, and investigate the effects of anthropogenic influences (climate change, introduced species, habitat conversion) on plant communities. Labs will emphasize fieldwork at local research sites, and will provide exposure to techniques of experimental design in plant ecology and basic approaches to describing plant community structure and dynamics. (BIOL 0140) 3 hrs. lect./3 hrs. lab. SCI

Spring 2017, Spring 2019, Spring 2020, Spring 2021

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BIOL 0490 - Seminar in Plant Ecology      

Seminar in Plant Ecology
Global climate change has led to a huge effort to collect data on the state of the planet, including measurements of temperature, atmospheric and oceanographic conditions, and species distributions and phenologies. Ecologists have never had access to such quantities of data, and thus need new methods for their description and analysis. In this course we will explore how to use statistical models to make sense of these data: how to develop, choose, and fit the best model for a particular data set. The course will be project-based, culminate in an independent project, and use the statistical software, R. (BIOL 0140 and one statistics course required, no R experience required.) 3 hr. sem./3 hr. lab DED SCI

Winter 2019, Spring 2020

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BIOL 0500 - Independent Study      

Independent Study
In this course students complete individual projects involving laboratory and/or field research or extensive library study on a topic chosen by the student and a faculty advisor. Prior to registering for BIOL 0500, a student must have discussed and agreed upon a project topic with a member of the Biology Department faculty. Additional requirements include attendance at all Biology Department seminars and participation in any scheduled meetings with disciplinary sub-groups and lab groups. This course is not open to seniors; seniors should enroll in BIOL 0700, Senior Independent Study. (BIOL 0211. Approval required) 3 hrs. disc.

Fall 2016, Winter 2017, Spring 2017, Fall 2017, Winter 2018, Spring 2018, Fall 2018, Winter 2019, Spring 2019, Fall 2019, Winter 2020, Spring 2020, Fall 2020, Winter 2021, Spring 2021

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BIOL 0700 - Senior Independent Study      

Senior Independent Study
In this course students complete individual projects involving laboratory and/or field research or extensive library study on a topic chosen by the student and a faculty advisor. Prior to registering for BIOL 0700, a student must have discussed and agreed upon a project topic with a member of the Biology Department faculty. Additional requirements include attendance at all Biology Department seminars and participation in any scheduled meetings with disciplinary sub-groups and lab groups. (BIOL 0211. Approval required; open only to seniors) 3 hrs. disc.

Fall 2016, Winter 2017, Spring 2017, Fall 2017, Winter 2018, Spring 2018, Fall 2018, Winter 2019, Spring 2019, Fall 2019, Winter 2020, Spring 2020, Fall 2020, Winter 2021, Spring 2021

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BIOL 0701 - Senior Thesis      

Senior Thesis
Seniors majoring in Biology who have completed one or more semesters of BIOL 0500 or BIOL 0700 and who plan to complete a thesis should register for BIOL 0701. In this course students will produce a written thesis, deliver a public presentation of the research on which it is based, and present an oral defense of the thesis before a committee of at least three faculty members. Additional requirements include attendance at all Biology Department seminars and participation in any scheduled meetings with disciplinary sub-groups and lab groups. Open to Biology and joint Biology/Environmental Studies majors. (BIOL 0211 and BIOL 0500 or BIOL 0700 or waiver; instructor approval required for all students) 3 hrs. disc

Fall 2016, Winter 2017, Spring 2017, Fall 2017, Winter 2018, Spring 2018, Fall 2018, Winter 2019, Spring 2019, Fall 2019, Winter 2020, Spring 2020, Fall 2020, Winter 2021, Spring 2021

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BIOL 1230 - DataScience Across Disciplines      

Data Science Across Disciplines
In this course we will gain exposure to the entire data science pipeline—obtaining and cleaning large and messy data sets, exploring these data and creating meaningful visualizations, and communicating insights from the data in a meaningful manner. During morning sessions, students will attend a combined lecture where they will learn the tools and techniques required to explore new and exciting data sets. During afternoon sessions, students will break out into smaller groups to apply these tools to domain-specific research projects in Art History, Biology, Economics, or Japanese and Linguistics.
Students enrolled in Professor Abe’s (Japanese) afternoon section will use the tools of data science to create visualizations of social and emotive meanings that surface through Japanese language/culture materials. Participants will use these visualizations to engage in various theoretical and pedagogical topics pertaining to (educational) linguistics.
Students enrolled in Professor Allen’s (Biology) afternoon section will use the tools of data science to investigate the drivers of tick abundance and tick-borne disease risk. To do this students will draw from a nation-wide ecological database.
Students enrolled in Professor Anderson’s (History of Art and Architecture) afternoon section will use the tools of data science to create interactive visualizations of the Dutch textile trade in the early eighteenth century. These visualizations will enable users to make connections between global trade patterns and representations of textiles in paintings, prints, and drawings.
Students enrolled in Professor Myers’ (Economics) afternoon section will use the tools of data science to create an interactive visualization of the landscape of abortion policy and access in the United States. This visualization will allow users to explore how abortion access varies across the country and how this variation in turn correlated with demographic, health, and economic outcomes.
This course will utilize the R programming language. No prior experience in statistics, data science, programming, art history, biology, economics, or Japanese is necessary. DED SCI WTR

Winter 2021

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ENVS 0700 - Senior Independent Study      

Senior Independent Study
In this course, seniors complete an independent research or creative project on a topic pertinent to the relationship between humans and the environment. During the term prior to enrolling in ENVS 0700, a student must discuss and agree upon a project topic with a faculty advisor who is appointed in or affiliated with the Environmental Studies Program and submit a brief project proposal to the Director of Environmental Studies for Approval. The expectations and any associated final products will be defined in consultation with the faculty advisor. Students may enroll in ENVS 0700 as a one-term independent study OR up to twice as part of a multi-term project, including as a lead-up to ENVS 0701 (ES Senior Thesis) or ENVS 0703 (ES Senior Integrated Thesis). (Senior standing; Approval only)

Fall 2020, Winter 2021

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ENVS 0703 - Senior Integrated Thesis      

Senior Integrated Thesis
This course is the culminating term of a multi-term independent project, resulting in a senior thesis on a topic pertinent to the relationship between humans and the environment and that meaningfully integrates perspectives, methodologies, and/or approaches from multiple academic divisions (e.g., humanities/arts, natural sciences, social sciences). Approval to enroll is contingent on successful completion of at least one term (and up to two) of ENVS 0700 and approval of the Environmental Studies Program. The project, carried out under the co-supervision of two faculty advisors from different academic divisions of whom at least one is appointed in or affiliated with the Environmental Studies Program, will result in a substantial piece of scholarly work that will be presented to other ENVS faculty and students in a public forum and defended before the thesis committee. (Open to Senior ENVS majors) (Approval Only)

Spring 2021

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FYSE 1413 - Lyme Disease      

Lyme Disease
Lyme disease is fascinating from medical, public health, and ecological perspectives. In this seminar we will explore the disease in an interdisciplinary fashion. We will look at the history of—and controversy around—its diagnosis, treatment, and control. Because Lyme has a tick vector and animal reservoirs, we will consider how the local environment affects it. Connections to other zoonotic diseases (SARS, West Nile, EEE) will be made. Readings will come from Bull's Eye: Unraveling the Medical Mystery of Lyme Disease by Eldow, Lyme Disease: The Ecology of a Complex System by Ostfeld, and primary sources. 3 hrs. sem. CW SCI

Fall 2016

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Department of Biology

McCardell Bicentennial Hall
276 Bicentennial Way
Middlebury College
Middlebury, VT 05753