Lessons learned: a retrospective on a newly developed course

This fall, I developed and taught a course called Introduction to Mammalian Microbiomes for the University of Oregon Clark Honors College.  The course objectives were to:

  1. introduce students to basic concepts, laboratory techniques, historical background, terminology, and technology related to microbial ecology in or on mammals,
  2. familiarize students with online resources, including sequence repositories, scientific databases, and analysis tools,
  3. discuss how host-associated microbiomes are shaped by the anatomy and lifestyle of the host, and how the microbiome can reflect onto the health and performance of the host, and
  4. review current literature on host-associated microbial ecology.
As always, include plenty of humor.

Keeping it fresh

While I’ve taught similar material at Montana State University, and have plenty of teaching experience from my graduate teaching assistant days at the University of Vermont, I’ve learned that each student population is different, with a unique core knowledge base and interests.  Thus, I developed this course from scratch, and constantly revised it during the semester to adjust to the pace and learning style of my students.  A draft syllabus, as well as an example of a student’s final project, can be found on my GitHub.

To improve engagement, I tried to make the course (which did not have a lab section) more interactive. I offered a tour of the molecular biology lab I work in, I brought agar plates to class so students could try culturing their own microbiota, and I dressed up like a dead cat.

These students were not science majors, and had had very little science since high school. Even if they had been science majors, I wanted to give a broader look at the field of science than just giving an overview of current knowledge.  At the end of some lectures, I facilitated class discussions on various topics in science: the role of scientists in communicating science and whether we should report only or have an obligation to convince the public; elitism, recognition, and credit for intellectual property in a highly-collaborative working environment; the transfer of maternal microbiota and health status to offspring and how we approach prenatal care and parental leave; air quality (and air microbiota), residential zoning in urban areas, and income inequality; should we eat dirt?, etc.  The students enthusiastically participated in class discussions, and — to my surprise — requested more (see below).

Phone a friend

I wanted to highlight current research in host-associated microbiomes, and hosted three mini-lectures from guest researchers; Deepika Sundarraman, a graduate students in UO physics, Dr. Candace Williams, a postdoctoral researcher who Skyped in from Vienna, and Dr. Edward Pajarillo, a postdoctoral researcher who Skyped in from Florida.

Feedback

I really enjoyed teaching this group of students, and I got regular feedback from them about how the course was going and what was working.  More formally, I volunteered the class to participate in a pilot evaluation for my midterm and end of term review, which asked more probing questions of students than typical teaching evaluations.  For the midterm, only 4 of 15 students responded, but for the final, 13 of 15 responded and I have decided to share those (anonymous) course evaluations for IMM2018: 

Students wanted more in-class discussions, and more group-based work, which was surprising to me as science students tend to prefer fewer of these, or at least the option to opt out. I am already considering additional topics for discussion next year. While there was an option on the final to submit a group project, no one chose to pursue that.  Similarly, students were able to work collaboratively on journal article summaries to improve their comprehension, provided each student submitted a unique response.  Perhaps this option simply needs to be reiterated.

What surprised me most about the evaluations was that several students replied that (the second half of) the course was not challenging enough.  The course content was entirely new to them, and while the assignments drew on skills from their core competency as humanities students (reading and writing), they were required to distill large amounts of scientific information and be able to explain it back to me.  It’s a challenge to serve the learning speed and style of all students in a class, and I try to manage this by varying the format of assignments, as well as to teach skills in the first part of the class which can be refined with successive assignments. 

An example of this was the final project, for which the students needed to create a public outreach presentation in the format of their choice (essay, poster, pamphlet, presentation), which covered a particular topic or discussion point on host-associated microbial communities. Students were able to draw from scientific article summaries they had previously written, or even material from their exams (take-home essays), provided it was more developed and presented in a new and creative way. This flexibility allowed students to choose topics that they were passionate about, and to focus on the message rather the format. I felt this would help them find their voice, and judging by the final projects I received, it was effective.

That being said, if humanities students thought the material too easy, I take credit for communicating it well. I’m pleased with how the course turned out, as well as with the feedback I received from students.  I’ve already begun implementing upgrades to my curricula, and have proposed this course again to the Honors College. Pending approval, I’ll be back at it next year!

Introduction to Mammalian Microbiomes

Since the end of September, I’ve been teaching a course for the UO Clark Honors College; Introduction to Mammalian Microbiomes.   And in a novel challenge for me – I’m teaching the idea of complex, dynamic microbial ecosystems and their interaction with animal hosts … to non-majors.  My undergraduate students almost entirely hail from the humanities and liberal arts, and I couldn’t be more pleased. So far, it’s been a wonderful opportunity for me to pilot a newly developed course, improve my teaching skills, and flex my creativity, both in how I explain concepts and how I design course objectives.

I enthusiastically support efforts towards science communication, especially in making science more accessible to a wider audience.  My students likely won’t be scientific researchers themselves, but some will be reporting on science publications, or considering funding bills, and all of them are exposed to information about human-associated microbial communities from a variety of sources. To navigate the complicated and occasionally conflicting deluge of information online about the human microbiome, my students will need to build skills in scientific article reading comprehension, critical thinking, and discussion.  To that end, many of my assignments are designed to engage students in these skills.

I feel that it’s important to teach not only what we know about the microbial community living in the mouth or the skin, but to teach the technologies that provide that knowledge, and how that technology has informed our working theories and understanding of microbiology over centuries.  Importantly, I hope to teach them that science, and health sciences, are not static fields, we are learning new things every day.  I don’t just teach about what science has done right, but I try to put our accomplishments in the context of the number of years and personnel to achieve publications, or the counter-theories that were posited and disproved along the way.

And most of, I want the course to be engaging, interesting, and thought provoking.  I encouraged class discussions and student questions as they puzzle through complex theories, and I’ve included a few surprise additions to the syllabus along the way.  Yesterday, University of Oregon physics Ph.D. student Deepika Sundarraman taught us about her research in Dr. Parthasarathy’s lab on using light sheet fluorescence microscopy to visualize bacterial communities in the digestive tract of larval zebra fish! Stay tuned for more fun in #IntroMammalianMicrobiomes!

 

2017 Year in Review

The end of 2017 marks the second year of my website, as well as another year of life-changing events, and reflecting on the past year’s milestones help put all those long hours into perspective.  I reviewed my year last year, and found it particularly helpful in focusing my goals for the year ahead.

Looking Back

In the first half of 2017, I was working as a post-doctoral researcher in the Menalled lab at Montana State University, researching the interaction of climate change, farm management (cropping) system, and disease on soil bacteria in wheat fields, as well as the legacy effects on subsequent crops.  I am still working to analyze, interpret, and publish those results, and hope to submit several manuscripts from that project in early 2018.  In June, I began a position as a research assistant professor in the Biology and the Built Environment Center at the University of Oregon.

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This involved another large move, not only from Montana to Oregon, which has led to some awesome new adventures, but also from agriculture and animal science to indoor microbiomes and building science.   So far, it has been a wonderful learning experience for incorporating research techniques and perspectives from other fields into my work.

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2017 has been another extremely productive year for me.  I presented some work at two conferences, the Congress on Gastrointestinal Function and the Ecological Society of America meeting (additional ESA posts here and here).  While at ESA, I was able to attend the 500 Women Scientists luncheon to discuss inequality in academia as well as recommendations we could make to improve ESA and other conferences ,such as offering affordable on-site child care, and action items we could take ourselves, such as attending training workshops to combat implicit bias or making sure job searches recruit a diverse candidate pool.

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500 Women Scientist group at ESA 2017

This year, I added four new research publications and one review publication to my C.V., and received word that a massive collaborative study that I contributed to was accepted for publication- more on that once it’s available.  In April, I hosted a day of workshops on soil microbes for the Expanding Your Horizons for Girls program at MSU, and I gave a seminar at UO on host-associated microbiomes while dressed up as a dissected cat on Halloween.  In November, I participated in a Design Champs webinar; a pilot series from BioBE which provides informational discussions to small groups of building designers on aspects of how architecture and biology interact.

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I published 34 posts in 2017, including this one, which is significantly fewer than the 45 I published in 2016.  However, I have doubled my visitor traffic and views over last year’s totals: over 2,000 visitors with over 3,200 page views in 2017! My highest-traffic day was April 27th, 2017.  While I am most popular in the United States, I have had visitors from 92 countries this year!

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Map of home countries for 2017 website visitors.

My most popular post is currently “Work-life balance: what do professors do?”, with over 610 views! My least popular is “Presentation on juniper diets and rumen bacteria from JAM 2016 available!” with just 2 views, granted, that one appeals to a much narrower audience.  This year, in addition to updates on publications, projects, and positions, I wrote about writing; including theses and grants. I wrote about getting involved in science, be it through education, participation, or legislation.  I described outreach in academia, and the process of interviewing.  I gave some perspective on the effect of climate change and anthropological influence on agriculture and ecology, as well as on the debate surrounding metrics of success in graduate study.

I also added some “life” to my work-life balance; in November, I married my best friend and “chief contributor“, Lee Warren, in a small, stress-free ceremony with some local friends in Eugene, Oregon!!

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Looking Ahead

I have high hopes for 2018, notably, I’d like to finish more of the projects that have been in development over the last two years during my post-docs.  Nearly all academics carry forward old projects: some need additional time for experimentation or writing, some get shelved temporarily due to funding or time constraints, some datasets get forgotten and gather dust, and some which got cut short because of the need to move to a new job.  This is a particular concern as grant funding and length of job postings become shorter, forcing researchers to cut multi-year projects short or finish them on their own time.  After defending in early 2015, I had two one-year postings and started at UO in June 2017, making this my fourth job in three years.  I’m looking forward to roosting for a bit, not only to clear out unfinished business, but also to settle into my new job at BioBE.  This fall, I have been analyzing data on a weatherization project, writing a handful of grants, and developing pilot projects with collaborators.  I have really enjoyed my first six months at BioBE, and Lee and I have taken a shine to Eugene.  In the next few months, I hope to have more posts about my work there, exciting new developments in BioBE and ESBL, and more insights into the work life of an academic.  Happy New Year!

I’m now writing for the UO BioBE blog

The Biology and the Built Environment center here at the University of Oregon has a blog, and I’ll be writing updates and blog posts for them, as well.  I will be cross-posting my posts, but you should also check them out!

My first week at the University of Oregon

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My new work home.

Last week was my first week as a Research Assistant Professor in the Biology and the Built Environment Center (BioBE) at the University of Oregon, and my first full week in Eugene.  Combined with the Energy Studies in Buildings Laboratory, our collaborative team of architects and biologists researches how to make buildings more efficient, sustainable, pleasant, and healthy.

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Delta Ponds, along my new bike route to work.

My first day started auspiciously as I charted a new bike route to work, about 4.5 mi of which is along a path snaking next to the Willamette River.  It goes through several parks, and by a few small lakes and swamps which are home to dozens of species of birds, mammals, amphibians, and reptiles.  I haven’t seen any river otters yet, but I have been keeping a close eye out.

Arriving on campus, most of my first day, and first week, were spent visiting the various places around campus to get myself established as a new employee- obtaining my ID card and email address, filing out paperwork, attending orientation, and finding all the coffee places within walking distance of the building.  ESBL is renovating and expanding its offices across several large, pluripotent rooms to accommodate a growing research team, so I got a brand new standing desk, chair, shelving, and computers (on order), all to my specifications.  The flexibility of working position, screen size, and screen angle provided by my new station are comfortable and great for productivity, and it’s neat to design the new space into offices, meeting tables, and storage which are based on our personalized usage needs and preferences.  And of course, there is plenty of space for all the mementos and science toys I’ve accumulated.

Most importantly, my first week was spent acclimating to my new department and getting up to speed on the ongoing and planned projects.  BioBE and ESBL have dozens on ongoing or planned projects on the built environment, with a combination of building and biology facets.  Over the course of the summer, I’ll be writing several grants and organizing new projects that explore how building use, occupancy, and human habits affect human health and the indoor microbiome, as well as contributing to the BioBE blog,  providing building microbiome posts to Give Me the Short Version, and getting some older projects out for publication.  On top of that, I’m looking forward to exploring the Pacific coast and the Northwestern landscape, and availing myself of the Willamette Valley wine industry.

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Photo Credit: Alen Mahic