Character coding has been called the bete noire of phylogenetic analysis. As you may have seen from class, the definition of "character" is squishy and varies between authors. Although there isn't agreement on exactly what a character is, it is possible to predict how certain character definitions and coding strategies affect phylogenetic analysis.
This activity focuses on character coding, specifically about how different coding strategies can affect analysis. In this exercise we will try to look at different coding strategies by considering the simple shapes below.

(1) What is a character, and what qualities do characters have?
(2) Given the 'morphology' depicted above, what features vary?
(3) Given the variation you identified, come up with as many character codings as you can; i.e., different ways that this variation can be coded into characters.
(4) For each of the coding strategies you come up with in question 3, identify its assumptions, limitations, and strengths.
(5) Identify your preferred coding strategy and defend your choice.

Students asked to define what a character is and to discuss what they 'require', and then to come up with an exhaustive list of coding strategies for the sample morphology. They are then asked to list assumptions/limitations of each strategy.

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This video segment adapted from NASA describes the basic characteristics of our star, the Sun.

To prepare for this exercise students read about the processes that operate at plate boundaries and how they are related to the distinct patterns of seismicity, volcanism, surface elevations (e.g., ridges versus trenches), and seafloor ages characteristic of different boundary types. During the week the assignment is available online, students have access to:
(1) an index map that locates three boundaries they are to study; and
(2) four maps from Sawyer's Discovering Plate Boundaries website that provide the data mentioned above.Â

Student tasks are to:Â
(1) document patterns in each type of data along the three targeted boundaries; andÂ
(2) use these observations in conjunction with their understandings of the processes that operate along different types of boundaries to decide whether each of the targeted sites is most likely to be a divergent, convergent, or shear boundary.Â

This activity gives students practice in map reading, interpreting the likely tectonic setting of a boundary by pulling together constraints from several types of data, and collaborating with their classmates in an online environment. The activity also provides a foundation for understanding a wide range of phenomena that are discussed later in the semester in the context of plate tectonic processes.
Modifications on this activity from the community

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Show LessContributed by Tom Hickson
I also use a version of Dale Sawyer's Discovering Plate Boundaries exercise in an online course. I used the basic idea of this activity and moved in onto Canvas, our LMS. Here is my adaptation of the activity, with maps and examples, illustrating how I have implemented it:

Description of the assignment: Student handout, ONLINE_ Characterizing Plate Boundaries (adapted).pdf (Acrobat (PDF) 166kB Feb19 21)
Answer sheet for students to record observations and interpretations: Target Boundaries: Student answer sheet (Acrobat (PDF) 1MB Feb19 21)
World map with Target Boundaries (Acrobat (PDF) 483kB Feb19 21)

Maps of the "target boundaries" -- my selected areas of focus for the exercise:

Example map, Boundary 3

Provenance: Thomas A. Hickson, University of St. Thomas
Reuse: This item is offered under a Creative Commons Attribution-NonCommercial-ShareAlike license http://creativecommons.org/licenses/by-nc-sa/3.0/ You may reuse this item for non-commercial purposes as long as you provide attribution and offer any derivative works under a similar license.












Example map, Boundary 2

Provenance: Thomas A. Hickson, University of St. Thomas
Reuse: This item is offered under a Creative Commons Attribution-NonCommercial-ShareAlike license http://creativecommons.org/licenses/by-nc-sa/3.0/ You may reuse this item for non-commercial purposes as long as you provide attribution and offer any derivative works under a similar license.












Map example, boundary 1

Provenance: Thomas A. Hickson, University of St. Thomas
Reuse: This item is offered under a Creative Commons Attribution-NonCommercial-ShareAlike license http://creativecommons.org/licenses/by-nc-sa/3.0/ You may reuse this item for non-commercial purposes as long as you provide attribution and offer any derivative works under a similar license.

Teaching Tips
Adaptations that allow this activity to be successful in an online environment
Sawyer's Discovering Plate Boundaries is a jigsaw exercise in which students collaboratively develop an empirical classification of plate boundaries by first studying an individual data set (e.g., seismicity) and then working as part of a multidisciplinary team to develop a composite classification for the boundaries of a single plate using several types of data. In order for the classification to be truly empirical, students are not introduced to the "traditional" classification of plate boundaries till the end of the exercise.Â

In adapting this assignment to the online environment I have:

(1) asked students to prepare by becoming familiar with the standard classification of plate boundaries and the processes that operate at them;Â
(2) limited their work to three targeted boundaries of different types; andÂ
(3) provided guidance about which features to look for in the each data set. I have found that these modifications help online students, who often work alone "on their own schedules", to avoid getting "lost" and frustrated with the assignment and to compensate for the lack of collaborative input they would receive in a classroom setting.

Elements of this activity that are most effective
The success of this exercise is really seems to depend on how well a student follows the directions. If a student learns about the geologic differences among plate boundaries, makes careful observations, and thoughtfully compares his or her observations to the expected patterns he or she typically does quite well based on answers to the follow-up questions. If, on the other hand, a student simply looks up the types of the targeted boundaries on a map and then attempts to "back out" the observations that he or she thinks should fit, the result is often inconsistency and a poor score on the questions. (I can often tell which approach a student is taking based on the queries they post to the discussion board, but rarely seem to be able to get those who are trying to work backwards through the assignment to change direction.)
Recommendations for other faculty adapting this activity to their own course:
To date my experience developing an engaging online exercise to help students learn the principles of plate tectonics has only been partly successful. I think that having such an exercise is critical, however, because this topic provides the framework for so much of what we learn in the geosciences. Based on my efforts to adapt elements of Discovering Plate Boundaries to an online environment I would offer three recommendations.

(1) Provide examples. Confronted with an unfamiliar map students are sometimes confused when asked to decide if seafloor age, for example, is uniform or variable along the length of a boundary. Showing them what you mean using snapshots from a map can often clear questions like this up quickly. Similarly, for written work a single example that gives them a clear sense of "what you're looking for" and can often head off a lot of questions.
(2) Choose the boundaries you ask students to study carefully. The scarcity of documented volcanism along a mid-ocean ridge or the burial of seafloor age belts by sediment along a trench can result in student observations that are correct, but problematic for correctly assessing the nature of a boundary.
(3) Stay on top of student questions and comments, and be prepared to make well-publicized "mid-course corrections" if something you thought was clear turns out to be misunderstood. These minor corrections happen naturally in face-to-face classes but can require real diligence to catch and correct in the online environment.

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This is the second in a series of modules which detail the research of Charles Darwin and evolutionary theory. This module continues with a discussion of the processes that led to Darwin's formulation of the theory of natural selection.

This module introduces Darwin's Galapagos travels and an introduction to the theory of evolution as a force for biological change and diversification. This is the first in a series of modules which detail the research of Charles Darwin and evolutionary theory.

In this activity, students chart temperature changes over time in Antarctica's paleoclimate history by reading rock cores. Students use their data to create an interactive display illustrating how Antarctica's climate timeline can be interpreted from ANDRILL rock cores.

In this video segment adapted from NOVA, scientists are on the hunt for tornadoes. Using Doppler radar, they gather data in the hopes of solving the mystery of how tornadoes form.

The purpose of this assignment is for students to synthesize field observations, petrography, and whole-rock chemical analyses in order to investigate chemical differentiation processes in a basaltic magma chamber. The students first complete a petrography lab on both hand samples and thin sections that represent a complete stratigraphic section through sill at Fort Lee, NJ. I then provide them with major- and trace-element data and a table of distribution coefficients for common phases that would be crystallizing from basaltic magma. I then ask them to discuss the chemical differentiation of the sill by writing up a 1-2 page interpretative summary based on their petrographic observations and the chemical data.

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This STELLA modeling and writing assignment helps students confront and replace common misconceptions about chemical equilibrium.

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This STELLA modeling and writing assignment helps students confront and replace common misconceptions about chemical equilibrium.

In this exercise students utilize data from geochemistry databases to analyze inputs and outputs associated with arc volcanism.

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This tombstone weathering lab is designed to provide students with tangible understanding of chemical weathering and weathering rates. To prepare for this lab, students will have learned in previous labs to identify common minerals and rocks and will have attended lectures about the process of chemical weathering. During the first part of the lab we travel to the city cemetery to collect data on the age and extent of chemical weathering of tombstones that are made of limestone and igneous rocks. After collecting data for ~1 hour, we return to the computer lab where students use Microsoft Excel to analyze and interpret their data. Their task is to calculate a chemical weathering rate for limestone for our region and compare that rate to those from other regions. This activity gives students experience in the process of scientific inquiry: data collection, data analysis and data interpretation. Students develop Microsoft Excel skills: writing formulas, producing charts, understanding trendlines and R2 values.

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In this video produced for Teachers' Domain, learn about MIT professor Cathy Drennan's research into microorganisms that remove carbon dioxide, a greenhouse gas, from the atmosphere.

From the scientific viewpoint, this evaluation will help the students see a process instead of just a data collection event, and they will get to practice estimating amounts. They will also need to determine the products of any reactions performed during the experiment. From the standpoint of sustainability, this evaluation is intended to help the student recognize the environmental "cost" of an experiment-in consumables used and in waste products generated.

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As a segment in PBS's Coping with Climate Change series, Hari Sreenivasan reports on the actions the city of Chicago is taking to mitigate climate change in an urban landscape.

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Click to watch Alain Plattner discuss his activity or watch the full webinar.We use MATLAB functions available from https://github.com/NSGeophysics/Seism-O to simulate the superimposition of different seismic waves recorded in a simple near-surface geophysics setting. The choice of the geophone layout influences how easy it is to discern the different wave types, which is crucial for the success of a near-surface seismics survey. Students learn which parameters they should try to estimate before the survey, why these parameters are crucial, and how they influence the setup of the survey.

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Students research various options for new appliances and make purchasing decisions based not merely on purchase price, but also on energy efficiency, which has implications for the planet AND for longer-term personal finances. Students calculate the "payback period" for the more energy efficient appliance and calculate long-term savings.

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In an upper-level seminar course, students bear significant responsibility for their learning. This activity provides the framework to help them identify the exact topics that they will discuss throughout a course in Environmental Analysis. The students are given constraints so that they don't either wander completely aimlessly through the environmental literature or pick only papers on their favorite topic. They are instead asked to dip into the literature to find papers that deal with analysis of pollutants in air, water, and solid matrices, and to have at least one that is relevant to climate change.

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The 'A Civil Action' 1-D Contaminant Transport Game is an EXCEL spreadsheet that enables students to compute concentrations of TCE traveling in the groundwater flow system toward well H that emanate from the W.R. Grace site. The idea of the game is to draw students into learning some of the fundamental concepts about (1) how contaminants move in the subsurface and (2) how models can be used to test hypotheses. These concepts are taught within the context of the famous 'A Civil Action' trial described in the book by Jonathan Harr (1996) and the movie starring John Travolta (1998).

The spreadsheet computes values of hydraulic head, advective flow velocities and traveltimes, contaminant velocities, and contaminant concentrations at 20 locations along the flowpath from W.R. Grace to the Aberjona River. Breakthrough curves showing changes in concentration versus distance and changes in concentration versus time pop-up automatically (see below). The spreadsheet also creates graphs of advective and contaminant velocities versus distance.

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Students were provided with drawings of snowflakes and were asked to construct a cladogram of the snowflakes. The drawings were provided by the students themselves during a quiz a few weeks earlier. (The quiz was 1: write your name, 2: draw a snowflake). There were 17 students and therefore 17 snowflakes. Students are asked to construct a character table and determine various character states. Then students construct a second table showing each snowflake and its state for each of the characters. Finally, students are asked to use this to construct a cladogram, as best they can, from their character matrix. Students note homologies and count the steps in their cladograms.

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