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Pre-SoTL Assignments

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Assignment #1 - Biology Scholars Introduction

 I am an Associate Professor with a primary appointment in the Lyman Briggs College (LBC) at Michigan State University (MSU), a residential college for students majoring in the Natural Sciences.  In Briggs, we focus on undergraduate education, and there is a strong interest in SoTL here and on the MSU campus in general.  As needs arise, I teach both semesters of the Lyman Briggs year-long Introductory Biology sequence, which consists of an Introductory Organismal Biology course and an Introductory Cell and Molecular Biology course.I also teach a graduate level course on Molecular Evolution, emphasizing molecular phylogenetics, every other fall.

Most of the LBC students major in Biology, primarily Physiology and Human Biology.On the first day of freshman year, a large number of our students want to be doctors.By graduation time, many of our students still want to be doctors and go on to successful careers in medicine, dentistry and veterinary medicine.However, many of our students change paths as they move through their college years, and pursue other careers, including scientific research, science policy, environmental law, and business, to name a few.In any case, we have very good and highly motivated students in our college, and it is fun to teach here. 

I have a joint appointment (25%) in the MSU Dept. of Entomology, where I conduct research mainly on the evolutionary relationships of flies in the tephritid genus, Rhagoletis, which are of interest to evolutionary biologists as a model system for studying the processes of speciation and to Michigan’s fruit growers as economically important orchard pests.  Our current focus is microsatellite characterization of variation in cherry fruit fly (Rhagoletis cingulata) populations.

My primary goal in participating in the Biology Scholars Program is to figure out a way to design my courses, in advance, with data collection in mind that will tell me something tangible about the effectiveness of my teaching.I look forward to becoming affiliated with a group of faculty from across the country who can help me move my own efforts in both teaching and SoTL to the next level.

I very much enjoy reading for pleasure.  My most recent books were "Ender's Game", which my wife and I both read along with our 14-year-old son, and Carl Hiaason's "Nature Girl", pure junk that I read as a follow-up to Bryson's, "A Short History of Nearly Everything".  

Outside of work, I, too, enjoy being outdoors, especially working in our yard and garden, having a beer with friends, and hosting the circus of friends our kids bring to our house (my other son is 17) for video and computer gaming.

I am looking forward to meeting and working with everyone.


Assignment #2 - Biology Scholars Reading List Assignment

I have one research problem that I am working on, and one that I would like to work on, in the area of Teaching and Learning.The one that I am working on asks whether or not we can use phylogenetic trees in our Introductory Biology courses to increase student understanding of organismal diversity and evolutionary relationships.Our rationale is that phylogenies serve as representational tools that can help students make connections across taxonomic boundaries.This is the problem that I will most likely address during my virtual residency, primarily because my colleague and I have already done some preliminary work and we have some preliminary data.My second problem, however, may end up being of more interest to a broader community, and might be more fun (it will certainly be more work!)We do a lot of group work in our laboratory classrooms, with student “researchers” working in teams of 3-4 students. What is the optimum team size for these experiences, with respect to student learning and understanding?How can we ensure individual accountability?I think that these are very rich research questions that would be very interesting to pursue.      

One of the main themes from the readings that resonates with my “problems” is that of being learning centered.While we want to increase student learning and understanding, I don’t feel that our research at present is truly learning centered.I mean this in the sense that the data that we have collected doesn’t directly measure student learning and understanding of specific learning goals and objectives.I think we need to give more thought to the nature of the data that we collect.Of the 12 properties of SoTL in microbiology education proposed by Benson, I would say that #8 is particularly relevant.Our research is “Problem Centric”, even though we could do a better job defining the problem(s) in such a way that the data collected will help to address the problem(s) directly.      

With respect to reading the set of papers that we were assigned, I came away a bit surprised by the lack of depth in the research database in the field (of SoTL) and also by the lack of identifiable “big questions”.We need data and we need seminal studies.For example, one major question in microbiology that was addressed relatively recently was the relationship of the three domains.Which was closer to Eucarya, Archaea or Eubacteria?A lot of research went into answering this big question.The 1996 PNAS paper by Balduf et al., “The root of the universal tree and the origin of eukaryotes based on elongation factor phylogeny”, has been cited 144 times.What are the equivalent big questions in SoTL?What is it that we really don’t know?How do the experiments on Teaching and Learning that we conduct in our classes illustrate broader principles?      

What I would like to develop in the next 12 months as a result of my Scholars experience is an experiment that I can run in fall 2008 and/or spring 2009 to test the effectiveness of “tree-thinking” in our Introductory Organismal Biology course.Conversely, it would be fun to come up with an experimental design that would allow us to test the effects of group size on learning and individual accountability in cooperative groups in the Introductory Biology teaching laboratory.I anticipate using the Scholars Experience (and the other Scholars) to sort out which of these two projects is the more promising to pursue, both in the short term and the long term.I see myself presenting the results of one of these experiments at ASMCUE in 2009, but to do so I need a good, solid, experimental plan.I guess that’s where I’d like to begin.      

Assignment #3 - Biology Scholars Annotated Bibliography Assignment

This was a great exercise.  It really forced me to review the literature and find articles that focus directly on my project.

The question I am researching for the BSP is whether or not using a phylogenetic framework, in particular having students work with and learn how to build and interpret phylogenetic trees, leads to increased student learning and understanding of organismal biodiversity and evolution. I am studying the students in an Introductory Organismal Biology course who are studying organismal diversity not by "marching through the phyla", but by examining organisms in a comparative, inquiry-based framework that incorporates what we call, "tree-thinking".  Tree-thinking involves phylogenetic analysis and employs phylogenetic trees as representational tools to understand evolutionary concepts and relationships.

My research is not concerned so much with students ability to understand phylogenetic trees per se, but more with how the trees can be used as a tool to organize thoughts about groups of organisms.  I also want students to see a phylogeny as a hypothesis, and to use data and observations to discern between two competing hypotheses (phylogenies), which may help move evolutionary biology in my students' minds away from being dogma and towards being experimental science .

I am looking for literature pertaining to how students interpret phylogenetic trees, and how to assess whether or not using phylogenetic trees in our Intro Organismal course has led to increased learning and understanding of organismal relationships.

1. Baum DA, Smith SD, Donovan SSS. 2005. The Tree-Thinking Challenge. Science 310:  979-980. [DOI: 10.1126/science.1117727].
This paper is really the "call to arms" with respect to tree-thinking, referring to the use of phylogenetic trees to study evolution.  These authors point out that phylogenetic analysis, which is used to infer phylogenetic trees to interpret ancestor-descendent relationships, is rarely employed outside the realm of professional evolutionary biologists.  The authors would like to raise the status of tree-thinking as a major theme in our students' evolution training, arguing that phylogenetic trees are the most direct representation of ancestor-descendent relationships, which are the core concept of evolutionary theory.   I have heard anecdotally that many people have used the Tree-Thinking Quizzes that are included in this paper as supplemental material available online.

2. Gregory TR. 2008. Understanding Evolutionary Trees. Evolution Education and Outreach 1:121-137. [DOI 10.1007/s12052-008-0035-x]
This paper provide an extensive introduction to evolutionary trees with guidelines about how to read and interpret them.   The author then examines, with excellent examples, ten common misconceptions about phylogenetic trees that he claims represent "fundamental barriers to understanding how evolution operates". This paper is really nice in that it provides the reader with a reference to the tree-building quiz developed by Eli Meir et al. (contained in EvoBeaker), is well referenced, and has many useful links to online resources for understanding evolution and tree thinking.

3. Brewer S. 1996. A Problem-Solving Approach to the Teaching of Evolution.  Bioscene 22(2): 11-17.
Brewer's work with John Jungck on the computer program Phylogenetic Investigator, available through BioQuest, has inspired some of my own teaching efforts.  The goal of Phylogenetic Investigator was to have students use phylogenies in a problem-posing, problem-solving and peer-evaluation instruction model.  I used Phylogenetic Investigator with a group of Honors students one semester in my Intro Organismal course to study the evolution of HIV.  The Bioscene paper, while not particularly well focussed, has much valuable information on problem-solving as a general educational method with comments to its applicability to the teaching of evolutionary concepts.  Again, it is argued that the historical and comparative approaches, which are important for really understanding the significance of evolutionary theory, are really given short shrift compared to natural selection and the functional perspective.  This paper derives from Brewer's Ph. D. dissertation in Science Education.

Reference #3 was found only by using ERIC.

4. Julius ML, Schoenfuss HL.  2006. Phylogenetic Reconstruction as a Broadly Applicable Teaching Tool in the Biology Classroom: The Value of Data in Estimating Likely Answers. Journal of College Science Teaching 35: 40-45.
This paper describes an exercise that is very similar in spirit to the one that we developed in our course.  Julius and Schoenfuss used a set of vertebrate skulls to have students develop a character matrix for phylogenetic analysis.  Julius and Schoenfuss emphasize scientific literacy, which gets to the heart of the matter with respect to why I wanted to use phylogenies in my class in the first place.  They do a really nice job of bringing in Popper's 1959 book, "The Logic of Scientific Discovery", in which the importance of using data to discern between competing hypotheses is brought out.  This is the key concept I want to teach.  Phylogenies are hypotheses of the evolutionary relationships of groups of organisms, and we have objective criteria (data and methods) that we use to decide which of two competing hypotheses is preferred.  This is the key thing that makes evolutionary biology science.  This paper also includes some assessment of student learning in summary form.  Senior level students who had completed this laboratory performed better on the evolution section of a summative exam (65% vs. 34%), while students in lower level courses who had completed this laboratory were found to perform an average of 11% better in an exam covering systematics and evolution.  Unfortunately none of the actual data were included in the paper.  .

Reference #4 was found only by using ERIC.

5. Singer F, Hagen JB, Sheehy RR. 2001. The comparative method, hypothesis testing & phylogenetic analysis – An Introductory Laboratory. The American Biology Teacher 63: 518 – 523.

The paper by Singer et al. is one of two papers (the other is: Giese AR. 2005. Using inquiry and phylogeny to teach comparative morphology.The American Biology Teacher 67: 412 – 417.) whose methods we merged to create our own laboratory stream.  One goal of this work was to have students learn that phylogenetic trees are graphical representations of hypotheses about evolution.  The authors also point out that practicing phylogenetic analysis provides practice in critical thinking, strengthening students' logical and mathematical abilities, and their problem-posing and problem-solving skills.  Singer et al. provided skeletons of five animals (opossum, dog, cat, rat and rabbit) to their students, who were then asked to generate a character matrix based on observations of these skeletons.  Using this matrix, and other information on the anatomy, physiology, behavior and ecology of these animals, students were asked to propose a hypothesis of evolutionary relationship, using the extinct Megazostrodon as an outgroup (there are 105 possible hypotheses).  Students then tested this "tentative statement" using DNA sequence data to infer a phylogeny of these five animal group, showing the students that hypothesis are tentative statements that are open to testing and revision using additional data or data from a different source.  In our own work, we have used the opossum as outgroup, and then show the students that there are only 15 possible phylogenies.  Our students are given two of these 15 trees, and then asked to develop an explanation of why one is better than the other by mapping individual characters onto their trees and applying the principle of parsimony.