A course offered at the University of Maine, Fall 2022 (Course Number: BIO 597-0004)
Instructor: Andy Rominger
Guest instructors: Renata Diaz, Isaac Overcast
- Understanding how and why mathematical and computational models/theories are developed in ecology and evolution
- Understanding the historical and social context of prevalent models/theories in ecology and evolution
- Understanding how to gain insight from real world data with models/theories
This will be a “flipped” course: lectures will be pre-recorded and students are responsible for watching lectures before class meetings. The specific lectures to watch before which class meetings will be clearly communicated in the course schedule included in the syllabus. In class time will be spent on discussion and hands-on coding and analysis. The average weekly amount of time expected of students in this course is 3 hours. Because of the “extra” pre-recorded lectures, the scheduled Friday meeting time is entirely optional and used as office hours.
We will create a learning environment that is safe, welcoming, and supportive of individual needs. This conduct is in part mandated by UMaine policy. Beyond mandates we seek to embrace this ethic as an imperative to make science more just and inclusive. We commit ourselves to not discriminating against our fellow learners based on any aspect of their identity and to celebrate differences as having individual value and collective energy for creativity and good. At the same time, we commit to acknowledging that power imbalances and differences in privilege are attached to diversity by our society and by individuals. We will seek to counter power imbalances and privilege by actively listening to one another’s experiences when they are shared and meeting needs that arise from those experiences. All learners bear responsibility to uphold this conduct, but as the instructor, Andy is ultimately responsible for fostering the learning environment through modeling this code of conduct and maintaining adherence to it. Formal UMaine policies can be found here. Formal Student Accessibility Services accommodation requests (see UMaine policies link) are welcome, as are informal accommodation requests. Please note that as a professor Andy is a mandatory reporter under Title IX.
The University of Maine recognizes that it is located on Marsh Island in the homeland of the Penobscot Nation, where issues of water and territorial rights, and encroachment upon sacred sites, are ongoing. Penobscot homeland is connected to the other Wabanaki Tribal Nations — the Passamaquoddy, Maliseet, and Micmac — through kinship, alliances and diplomacy. The university also recognizes that the Penobscot Nation and the other Wabanaki Tribal Nations are distinct, sovereign, legal and political entities with their own powers of self-governance and self-determination.
In this course we will engage with the social context of ecological and evolutionary theory, including colonialism and scientific racism. The University of Maine, to backup its acknowledgement of occupation of stolen land, has entered into a Memorandum of Understanding with the Penobscot Nation. This MoU will hopefully soon include stipulations about the ethical management of Indigenous data modeled after efforts by Maine-eDNA.
The EcoEvoMatics Lab at the University of Maine is committed to the development of new modes of collaboration, engagement, and partnership with Indigenous peoples for the care and stewardship of past and future heritage collections.Assignment | Percent of grade | |
---|---|---|
Watching lectures and submitting questions/discussion ideas prior to class meetings | 20% | |
Class attendence and participation (multiple modes of participation welcome, please talk with Andy if concerned) | 20% | |
Group project with component parts: | 60% | |
Create groups | (10%) | |
Project github repo created | (10%) | |
Project proposal | (10%) | |
Project write-up | (15%) | |
Project presentation | (15%) |
Lists of thoughts and questions arising from each video should be submitted as "issues" in the github repo containing that video (don't worry, we'll get there together!). Groups for the “group” projects are encouraged, but a group can be a single individual if that person so wishes. Group assignments will be submitted by pushing them to github (again, we’ll get there together!).
Day | Date | Videos to watch before class | In class activity | Location | Assignments | |
---|---|---|---|---|---|---|
2 | M | 8/29/22 | Getting started | Ferland 236 | ||
3 | W | 8/31/22 | GitHub Orientation | Ferland 236 | List of thoughts and questions | |
4 | F | 9/2/22 | Optional office hour | Murray 303 | ||
5 | M | 9/5/22 | No class - Labor Day | |||
6 | W | 9/7/22 | What is Biodiversity? | What is Biodiversity? | Ferland 236 | List of thoughts and questions |
7 | F | 9/9/22 | Optional office hour | Murray 303 | ||
8 | M | 9/12/22 | Why Theory? | Why Theory? | Ferland 236 | List of thoughts and questions |
9 | W | 9/14/22 | No class | Ferland 236 | ||
10 | F | 9/16/22 | Optional office hour | Murray 303 | ||
11 | M | 9/19/22 | Equilibrium Theory of Island Biogeography | Equilibrium Theory of Island Biogeography | Ferland 236 | List of thoughts and questions |
12 | W | 9/21/22 | Discussing anti-racism in ecology and evolution | Ferland 236 | ||
13 | F | 9/23/22 | Optional office hour | Murray 303 | ||
14 | M | 9/26/22 | The Neutral Theory of Biodiversity | The Neutral Theory of Biodiversity | Ferland 236 | List of thoughts and questions |
15 | W | 9/28/22 | Simple Metrics of Biodiversity | Simulating the Neutral Theory of Biodiversity | Ferland 236 | List of thoughts and questions |
16 | F | 9/30/22 | Optional office hour | Murray 303 | ||
17 | M | 10/3/22 | GitHub and RMarkdown | Github | Ferland 236 | List of thoughts and questions |
18 | W | 10/5/22 | GitHub and RMarkdown | Rmarkdown | Ferland 236 | List of thoughts and questions |
19 | F | 10/7/22 | Optional office hour | Murray 303 | ||
20 | M | 10/10/22 | No class - Indigenous Peoples Day | |||
21 | W | 10/12/22 | Simulating the Neutral Theory of Biodiversity | Simulating the Neutral Theory of Biodiversity | Ferland 236 | List of thoughts and questions |
22 | F | 10/14/22 | Optional office hour | Murray 303 | ||
23 | M | 10/17/22 | Simulating the Neutral Theory of Biodiversity | Ferland 236 | ||
24 | W | 10/19/22 | Working on roleR package installation | Ferland 236 | ||
25 | F | 10/21/22 | Optional office hour | Murray 303 | ||
26 | M | 10/24/22 | Working on roleR package installation | Ferland 236 | ||
27 | W | 10/26/22 | The Lotka-Volterra Model | The Lotka-Volterra Model | Ferland 236 | List of thoughts and questions |
28 | F | 10/28/22 | Optional office hour | Murray 303 | ||
29 | M | 10/31/22 | The Lotka-Volterra Model | The Lotka-Volterra Model part 2 | Ferland 236 | List of thoughts and questions |
30 | W | 11/2/22 | No class | Ferland 236 | ||
31 | F | 11/4/22 | Optional office hour | Murray 303 | ||
32 | M | 11/7/22 | Modern Coexistence Theory | Modern Coexistence Theory | Ferland 236 | List of thoughts and questions |
33 | W | 11/9/22 | Modern Coexistence Theory | Ferland 236 | ||
34 | F | 11/11/22 | No class - Veterans Day | |||
35 | M | 11/14/22 | Model Fitting: Likelihood Methods | Model Fitting: Likelihood Methods | Ferland 236 | List of thoughts and questions |
36 | W | 11/16/22 | No class | Ferland 236 | ||
37 | F | 11/18/22 | Optional office hour | Murray 303 | ||
38 | M | 11/21/22 | Planning the rest of semester and brainstorm final project ideas | Ferland 236 | One sentence project idea | |
39 | W | 11/23/22 | No class - Thanksgiving | |||
40 | F | 11/25/22 | No class - Thanksgiving | |||
41 | M | 11/28/22 | Work on Projects | Ferland 236 | Project proposal | |
42 | W | 11/30/22 | The Importance of Temporal Dynamics | Work on Projects | Ferland 236 | |
43 | F | 12/2/22 | Optional office hour | Murray 303 | ||
44 | M | 12/5/22 | The Full MESS | Work on Projects | Ferland 236 | |
45 | W | 12/7/22 | Work on Projects | Ferland 236 | ||
46 | F | 12/9/22 | Optional office hour | Murray 303 | Project write-up | |
47 | M | 12/12/22 | Final Presentations | Ferland 236 | Project presentation | |
48 | W | 12/14/22 | Final Presentations | Ferland 236 | ||
49 | F | 12/16/22 | Final Presentations | Ferland 236 |