Know Before You Go – Metagenomics Edition

Today (yes, October 12th!) at 4 PM, Dr. Heidi Andersen from Cincinnati Children’s Hospital Medical Center will be presenting her bioinformatics research. Computational genomics is a rapidly advancing field that uses and develops software to detect patterns in biomolecules like DNA, RNA, and proteins. Our guts host many different bacterial species, and Dr. Andersen pieces together their DNA sequences to determine which are present. She is especially interested in tracking the microbes that are multi-drug resistant (those that survive many of the antibiotics we throw at them) across pediatric patients in the hospital. 

A quick brush up on some computational biology vocab before the presentation never hurts:

Metagenomics – the study of the many genomes present in a given environmental sample

Microbiome – the community of microbes in a given environment

Shotgun sequencing – a method of determining the order of nucleotides (A, C, T, G) in a given DNA sequence by breaking it into short fragments, sequencing these, then piecing them back together computationally

Contiguous sequence (“Contig”) – After sequencing the separate DNA fragments in shotgun sequencing, we need to assemble them back together for a longer, more complete sequence (a contig)

16S rRNA gene (“16S”) – a ribosomal RNA gene that is used to identify bacteria and archaea at the genus level

Extra credit – Understanding PCA
If you want to know all the gory details of Principal Component Analysis, a method you will see often in computational biology, check out this post here


The Very Hungry Hornworms

This week, intro bio lab students geared up for their Manduca sexta dissection. These tobacco hornworms had grown significantly since students placed them in their plastic “bachelor pad” cages last week. While all hornworms at least doubled in size, the largest of the group were almost 100 times their weight from last week. Thank goodness that’s pretty impossible for humans to do or Kenyon would need to invest in a better health plan now that Marco’s Pizza accepts K-Cards.

Hornworm fact #1: Time to expand your insult dictionary – the genus Manduca literally means glutton. Try that one at Thanksgiving.

Hornworm fact #2: After a good chomp on a tobacco leaf, Manduca have “toxic halitosis” aka poisonous bad breath from the nicotine which deters spiders from eating them.

Hornworm fact #3: Adult Manduca hawkmoths can eavesdrop on the sonar clicks of bats and drop out of the air to avoid being bat food.

If you know the story of The Very Hungry Caterpillar by Eric Carle, the life of a Manduca is quite similar. Rather than eating sausages and ice cream turning into a beautiful butterfly, though, Manduca hornworms eat the leaves of tobacco, tomatoes and other members of the nightshade family (Solanaceae), then metamorphose into a hawkmoth that can hover like a hummingbird. Reared in the lab, however, the Manduca is a beloved model organism with ease of care, rapid growth rate, and accessible anatomy.

This year, the bio lab sections are testing the effect of diet nutrition on overall growth of the organism. Some Manduca will have less nutrition per bite in their food for 48 hours, perhaps affecting how much they eat, absorb nutrients, or grow in a 48 hour period. After this diet change, students hit the microscopes to investigate.

Whether they named their Manduca after their TA (shoutout to Jeremy Moore ’19), took beautiful anatomical pictures under the microscope (see above), or made a video in their hornworm’s honor like Patrick Olmstead ’21 (below), students found a way to connect with their lab-reared pe(s)ts.

Intro biology lab students share snapshots from their independent research projects

As the culmination of the year-long introductory biology lab course, all students undertake a large independent research project to apply the skills they’ve learned through a wide array of lab exercises, and begin to specialize in their own interests within the broad field of biology. Whereas in the past students worked with their laboratory section instructors on their projects, this year, the course allowed students to select faculty mentors outside of their lab section so they could receive more specialized help in their particular field of interest.

“We aren’t all Renaissance people,” said Dr. Jennifer McMahon, lead instructor and director of introductory labs. In past years, faculty had a difficult time assisting students on projects that fell outside their areas of expertise, so allowing students to pick their own mentors alleviates some of the pressure on the faculty, and lets students find subjects they are truly passionate about. Additionally, the close partnership between students and faculty mentors who share their interests can turn short, 6 week projects into multi-year research endeavors.

“The recruitment component of this new approach is very important,” notes department chair, Dr. Drew Kerkhoff. “We want to help students identify potential faculty mentors as early as possible. Hopefully, the changes will break down the barrier for students who otherwise might hesitate to approach one of their professors about research opportunities. It also helps faculty identify talented young students who share their research interests.”

Student research proposals must be approved by both their lab instructor and their faculty member. At the end of the semester, after designing and conducting their research, the students write scientific papers on their project and present their work to their lab mates and instructors, joining a long line of young researchers stretching back 25 years. You can even read papers from past years via Digital Kenyon. And each year, the latest papers are added to the collection, giving students their first taste of scientific publication.

Check out a sample of our students’ diverse and exciting projects!

Congratulations to the 2017 Honors Students!!

On Monday, May 8th, Honors students in Biology, Molecular Biology, and Neuroscience successfully defended their honors theses, bringing to a triumphant close what was, for many of them, years of work.


The 2017 Honors Students in Biology, Molecular Biology, and Neuroscience. Back row, L-R: Kenny Viel, Jiayu Chen, Lauren Michael, Adam Berndt; Front row, L-R: Taylor Jamil, Sarah Mohr, Sarah Naguib

The students had presented their research to peers, faculty, parents, and friends last week, but on Monday, they hosted their outside examiners, established academic researchers in their field who had generously agreed to read and critique their theses, and to come to campus for the day. Researchers came from the University of Dayton, University of Cincinnati, and the Ohio State University, among others.

Each student gave a short presentation to their examiner, then the two of them sat down for an hour to discuss their thesis in detail, as well as the broader area of science to which their work contributes. The examiners asked questions and probed for the limits of the student’s knowledge, but they also shared stories and provided valuable points of reference. The research mentors and other departmental faculty attended the exams, but the conversation is purely between the student and their examiner. One of the students captured the spirit of the event, calling it “intense, but really fun!”

Once the exams were complete, the students, examiners, mentors, and other faculty and staff gathered at Weaver Cottage to celebrate the students’ achievements and to enjoy a wonderful, relaxing lunch.


2017 Honors Students with their mentors. Back row, L-R: Kenny Viel, Jiayu Chen, Prof. Siobhan Fennessy (Biology, mentor to L. Michael), Lauren Michael, Prof. Andrew Engell (Neuroscience, mentor to S. Mohr), Adam Berndt, Prof. Joan Slonczewski (Biology, mentor to A. Berndt); Front row, L-R: Prof. Chris Gillen (Biology/Molecular Biology, mentor to K. Viel, J. Chen, and T. Jamil), Taylor Jamil, Sarah Mohr, Sarah Naguib, Prof. Hewlet McFarland (Neuroscience, mentor to Sarah Naguib).

Science in Writing: Animal Physiology


In Kenyon biology, students learn not only how to perform scientific inquiry but how to communicate their science clearly and effectively. Dr. Christopher Gillen has a passion for understanding how animals work, and his research specializes in salt and water balance physiology, most recently examining salt absorption and secretion in the Aedes aegypti mosquito. His course Biology 243: Animal Physiology is one of the most popular in the department, and students compare complex physiological processes across different organisms under Dr. Gillen’s enthusiastic instruction. In addition to his passion for understanding how animals work, Dr. Gillen is passionate about making scientific research understandable and enaging for all audiences and he is the faculty director of the Kenyon Institute in Biomedical and Scientific Writing. This semester, he launched Kenyon’s first science writing seminar course with Professor Sergei Lobanov-Rostovsky of the English department, where students read and discuss a wide variety of literature with a scientific focus, write voraciously on their own scientific fascinations, and experiment with the many techniques and nuances of the science writing genre.

Dr. Gillen stresses the importance of communicating science in all of his classes, particularly how to write about science for a variety of audiences:

“Pitching complicated research to a general audience is hard. Students must understand the science deeply and frame it with compelling writing and storytelling. And the skills they learn writing for a general audience transform them into better scientific writers.”

In Animal Physiology, students were asked to complete a News and Views assignment where they write two essays on the same scientific research article: one essay that makes an argument about the research to an audience of scientists and another essay that explains the research to a broader audience of non-scientists. Here is one such article for a general audience, written by junior neuroscience major John Wilhelm:

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Perspectives in Research: Rachel Schafer joins researchers at the 2017 Society of Toxicology National Conference

Note from Sarah: This is a guest post written by Rachel Schafer ’18. Schafer’s work in the Powell lab focuses on the effects of environmental toxins on the thyroid pathway in African clawed frog development.


Me and Dr. Wade Powell in front of my poster.

This spring break, I was fortunate enough to attend the 2017 Society of Toxicology National Conference in Baltimore, Maryland.  I went with my professor, Dr. Wade Powell, to present a poster on the interaction of an environmental toxin, TCDD, and the thyroid hormone pathway in Xenopus laevis metamorphic development.  Our findings demonstrated a discrepancy between gene expression in our X. laevis cell line and in the exposed tadpoles.  I was also privileged enough to win the Pfizer SOT Undergraduate Travel Award, which generously funded my costs at the conference. Continue reading

Mishaps in the Lab: Biology faculty tell tales of experimental failure

Perhaps the most exciting aspect of experimental biology is its unpredictability. No matter how meticulously you design your procedure, check and quadruple-check every measurement and work with the utmost professionalism, things still manage to go awry. 

This time of year, Higley Hall bustles with exciting research: 50 different independent projects by introductory lab students in Biology 110, lab research on everything from plant and animal physiology to gene manipulation, the ongoing work of faculty and their student research groups, and seniors working tirelessly to finish their honors theses.

Today and every day, Higley Headlines and the biology faculty celebrate the wacky world of experimental biology and remind everyone that failure, no matter how embarrassing and frustrating, is a critical, not to mention hilarious part of the scientific process. It may not have been amusing when it ruined your entire data set and set back your research by six months, but as you’ll see, everything is funny in retrospect.

Poor Timing

“I once thought I’d be a good lab citizen and adjust the lab clock for Daylight Savings Time. I hadn’t realized it was held up with only a thumbtack! When I replaced it on the wall, it came crashing down – right onto the safety shower lever below and causing a flood of water from the shower above. I’m glad that the safety shower was in good working order, but I didn’t really need to be drenched just for adjusting the clock! I’ll never hang anything over the safety shower lever again (especially with thumbtacks).”

Dr. Sarah Petersen, Ashby Denoon Assistant Professor of Neuroscience

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Nat Carruthers ’10 Returns to Fischman to Fix ‘A Fetch of Fittings’


Nat Carruthers ’10 contemplates his work on ‘A Fetch of Fittings’ in Fischman Wing.

When Nat Carruthers was preparing to graduate from Kenyon in 2010, he knew he wanted to leave some lasting impact on his environment: “I wanted to leave an imprint on Kenyon as much as Kenyon was going to leave an imprint on me. I mean, I was going to think about Kenyon all the time, but would Kenyon ever think about me?”

He designed his legacy as his final project in a studio art class, where he was asked to create a piece that incorporated one hundred handmade objects. His one hundred (estimated) beautiful dragonflies are now suspended from the ceiling of Fischman wing in Higley Hall. Biology students and faculty alike marvel at ‘A Fetch of Fittings’ as they pass underneath on their way to lab or travel the second floor hall between Higley and Tomsich. The work’s enticing ‘fidget-quality,’ as Nat pointed out, inevitably led to the sculpture becoming tangled, so this year biology department chair Drew Kerkhoff invited Nat back to campus to refit his fittings.

Nat was thrilled to have a Kenyon homecoming: “I think there are probably fewer schools you can come back to where you can hug faculty and chat with professors and go have a drink with someone you haven’t seen, you know, do that kind of stuff and feel that they still really care about you. Kenyon is special in that way.”


This time around, Nat is able to operate the lift on his own!

Returning to Higley Hall brought back strong memories of Nat’s time at Kenyon, where he was on a pre-medical school track for most of his career in the biology department. Though his greatest fascinations were on the cellular level, Nat was curious about all the aspects of biology he studied, from animal physiology and genetics to wetland ecology. He also recalled throwing all his papers and binders off the third floor of the chemistry building following his final exam as a senior and watching all the papers rain down. “But we cleaned it all up afterwards.”

As a student, Nat spent many hours studying in the lounge chairs on the second floor of Fischman and Higley. He was drawn to the large windows and the bright open space filtering natural light like he was used to in his hometown of Boulder, Colorado. Designers, Nat said, are always “tortured by their environment,” and he designed Fetch of Fittings to fit this space in the true spirit of the biological mantra ‘form fits function.’

“I had thought it would look cool here because of light and the amount of students who pass by here- I always thought it would be cool to have something take up that space.” The curve of the dragonflies spiraling up to the ceiling on their invisible fishing wires draws the eye upward, and the overall shape of the piece is reminiscent of the spiral of a DNA double helix, mirroring the classic ball and stick DNA models that rest on the shelf in the corner of the wing.

The idea came to Nat as a slow buildup from his final studio art project, where students were instructed to create a sculpture that incorporated 100 identical handmade items. While most students designed pieces to sit on the ground or on top of a table, Nat, who has always been fascinated by flight, wanted something that could hang and move in the air and something that also reflected his love of biology. He chose dragonflies as his 100 items, fascinated by the elegant mechanics of their flight and their history as an evolutionarily ancient animal: “they symbolize that elegance, simplicity, and yet how complex they are as little creatures.”

The process of making ‘Fetch of Fittings’ was an experiment in patience, perseverance, and trial after trial. Nat worked closely with now-retired professor of  art Barry Gunderson, who advised him on optimizing and simplifying his design. At first, Nat was adamant about making his metal dragonflies intricate with as much biological accuracy as possible, but after trials and errors in reproducing the iron insects which turned out “really quite bad,” Nat learned that simplicity was key to a good design. “On the same sense as it’s handmade, it also has to be mass-produced,” a mentality he now applies when tackling projects with his design firm: “it’s about finding that place that has as little design as possible but also communicates the effect fully.” Nat finally settled on a simple design of a silver bolt with nuts as clamps for the wire mesh wings.

Once complete, Nat sold his sculpture to the biology department to hang in Fischman Hall, exactly as he’d designed it. He spent an entire day during his senior week before graduation on a lift with a maintenance worker who helped him operate the machinery while he fitted his design to the ceiling of Fischman. Once complete, all that was left was to classify his creation. Nat chose ‘Fetch of Fittings’ as a comment on both the concept and the materials of the work. A ‘fetch’ is the term for a group of dragonflies, and ‘fittings’ calls attention to the materials that produce them and the mechanics of the sculpture itself.

“I hope the source of delight is when you see them from a distance, you think wow those are really cool, and then as you come closer you see how they slowly move and you want to reach out and touch them, and I wanted that ‘fidget quality,’ that fiddle-with desire. For me, and I think my love of design comes from the fact that I like art that you want to touch, that really grabs your attention and draws you to delighting in the details, the simplicity of it.”


Nat adds one last fitting to his fetch.

Nat had the opportunity to fiddle with his creation once again on Wednesday and Thursday. He crafted extra dragonflies for the occasion, some he had left over from the original creation as a senior and some he made in his hotel room at Kenyon the night before his repair work began. He added two as I watched to fill empty spaces, but decided to leave the design mostly unchanged, instead distributing the extra fittings among faculty and passing students.

“Whenever you make anything, there’s a little bit of obsession, you know everything about it: always tweak, always perfect. I had dreams and aspirations of filling the whole space, just having hundreds of them raining down, but once again there’s this sort of constant reigning myself back.”

For Nat, the process of creating a ‘Fetch of Fittings’ was exemplary of how Kenyon shaped him as a student and a thinker, helping him to modify and tweak his goals until he eventually realized his dreams:

“I think why Kenyon is an amazing place is because brilliant ideas can come very quiet, and some of those barely formed thoughts, when they’re given the space to grow, can evolve into something amazing. And that’s where students come in is having the space to allow for that exploration, right? Because the general goal is to create a great education for people, but when you actually give space for ideas as opposed to just teaching there are incredible results, and that something that’s really special about Kenyon.”

As part of his visit to campus, Nat gave a talk to students and faculty on Wednesday entitled “If Art and Science had a Baby” about how his education at Kenyon as a biology major and studio art minor led him to his current career as the head of his own industrial design firm: Dezyn Group, LLC. He spoke enthusiastically about his long journey from avid student of biology at Kenyon to sales and operations manager at Zybek Athletic Products to head salesman for Audi automobile manufacturers to graduate student at the Metro State University of Denver to managing his own industrial design company, and he offered the students valuable tips on ‘designing your life.’

A Kenyon Homecoming (Undergraduate Thoughts on an International Conference)

Note from Drew: This is a guest post from Toby SantaMaria ’17, a senior in the Kenyon Biology Department. In the Kerkhoff Lab, Toby studies forest carbon cycles. She is also is lab social media tsar and an indefatigable lab TA. 

593c5603-5863-47ce-846a-14913ccf166fIn January, I was blessed to be taken to the 2017 biennial International Biogeography Society Conference —which happened to be in my hometown of Tucson, Arizona. I went as a member of Dr.Kerkhoff’s macroecology lab at Kenyon College to co-present a poster with Dr.Kerkhoff. We presented on how Kenyon’s Ecology Lab class used R and some publicly available databases (like GBIF) to teach undergraduates how to make species distribution models. If you don’t know what that is, it’s basically a model that uses climatic and animal occurrence data to tell you where your animal of choice will or will not find favorable habitat based on climate, whether today or at some point in the future. As the course TA, I helped Dr.Kerkhoff teach the classes and stayed after-hours with a lot of the students to help them figure out their models. One of the goals of the poster is to show scientists that undergraduates can do real climate change science, so he felt that it was it was best if I present the poster with him at the conference.

When Dr. Kerkhoff invited me to the conference, it was really funny to me that all these biogeography and macroecology experts, for whatever reason, were going to have this huge conference literally 15 minutes from my home in South Tucson! I was equal parts excited and nervous, but more than anything, I was really hopeful about the meeting: hopeful that I would meet nice new people, hopeful that I would do a good job presenting my piece of the work I did with Dr. Kerkhoff, and mostly just hopeful that it would be a good experience. I’d had moments at Kenyon where I was really unsure of my place in the biological sciences, and I felt like a conference like IBS would be a litmus test for whether I stayed in science or not.

I wasn’t disappointed! At first, I thought the amount of information would be too overwhelming for me—we had long symposia all morning where big names like Sal Keith presented their big research results, and in the afternoons were smaller lectures given by still bigger names in biogeography like Marten Winter and Jacquelyn Gill, or huge posters sessions like the one where we presented. However, at the start of the symposium session on Monday, I noticed that we were asked to live-tweet the conference. So, true to my inner social media queen, I tweeted a LOT under the #ibstucson; which helped keep me pretty focused and practiced my science communication skills. I tried to include the most important points of every talk along with the most important figures, which apparently made my Twitter feed a crowd favorite at IBSTucson (according to Dr.Kerkhoff).

I was also super lucky to make good acquaintance with a lot of big names during the conference. I was fortunate enough to be in a lunchtime discussion and network session with Marten Winter, Dov Sax (the macroecology and conservation bio guy at Brown University – who was also Dr. Kerkhoff’s lab TA when he took his first undergraduate ecology class!), and Fausto Sarmiento (who studies the decolonization of science, University of Georgia). I also just plain hung out with a lot of really cool people. I got to talk about my research in multiple languages, I spoke to a lot of Master’s students on how to find a good graduate school mentor, and I got to share a lot of really happy moments with my lab mates and advisor. Being the real Tucson native amidst my lab mates meant I got to share a lot of what makes me who I am—from the good places to chill out at the student union, to the coziest restaurants on Congress Street, to playing pool and eating cheap pizza at SkyBar after the last poster sessions.

The nicest part of IBS Tucson for me-if I had to pick a singular moment and not just all of it- was the beginning. Dr. Kerkhoff, Cecina Babich Morrow (another lab member), Kiri Staiger (a graduate of the Kerkhoff Lab) and I went downtown to historic Fourth Avenue for a lab reunion dinner. It felt strange at first to be leading my lab mates down from the University to Fourth Avenue. I saw people I had grown up with my whole life casually walking down the same streets as people I’d only known at Kenyon. I had walked down Fourth Avenue maybe a million times—from when I was a toddler being carted around the University of Arizona by my young mom, to when my best friend and I would walk up and down the street just to grab the oatmeal cookies from Epic Café. For me, growing up in South Tucson made the place itself feel like an illusory home. It was a place my great grandfather settled his 16+ member family in 1940, where everyone knew me and I knew everyone because of the vast nature of my family tree, and where I inherited a lot of unmitigated negative feelings from the Tucsonan underbelly that had nothing to do with me but everything to do with who I ended up being. Tucson always felt like a transitory place to me, like a bad incubator from which I was always supposed to burst forth and move past and leave behind. South Tucson was always a place where as a brown girl, everything was to be quiet and soft and unseen lest you distract from the people of real importance.

But those feelings went away when I was at the conference with my lab group and advisor. Being able to sit with people who knew me, the real me in the rainbow hat that people call Toby and not Tayler with thick hair and the inescapable narrative of being a brown girl in South Tucson, was freeing. It freed me from the fear that this “research stuff” that I loved doing at Kenyon was evanescent and impossible to pursue, from the fear that South Tucson was who I would end up being my whole life. And mostly, it freed me from feeling that the only way to be a good scientist in my future was to erase all traces of my past. Eating and celebrating science at IBSTucson with my lab group proved to me that I am the biology that I love, and not just who loves and had loved me. My past in Tucson stopped feeling like an insurmountable wall and I stopped feeling like an impostor. Instead, in that starting moment of IBSTucson were I was sharing fry bread with my lab mates and celebrating science with people from all around the world, I finally felt…well, they say a picture is worth a thousand words.ibs

Celebrating Darwin’s 208th Birthday!


A beautiful birthday cake, courtesy of The 8 Sister’s Bakery

Every few weeks the biology department gathers in Fischman 103 for Biojournal club, an informal gathering of faculty and students. Student leaders mine recent journal publications for exciting research papers, and we carefully select an intriguing study to discuss as a department. We gather at 12 for pizza and beverages to accompany delving into deep scientific literature. At the small discussion tables, students and faculty alike delve into the texts of the papers, deciphering statistics, interpreting graphs, and raising questions about methods and conclusions. Every meeting yields a new discussion with topics ranging from plant physiology in seed dispersal mechanisms to rapid-scale bacterial evolution to editting the human genome.

In joint celebration of Charles Darwin’s 208th birthday and Valentines Day, our paper focused on sexual selection and the sex-driven ornamentation driving speciation of finches. Discussion was lively, and all involved felt the love for evolution, Darwin, and biology. The discussion ended with Dr. Slonczewski showing pictures from her trip to the Natural History Museum in London, England, which is proclaimed as a temple of sorts to Darwin and his revolutionary theories of evolution.

The paper discussion ended early so attendees could sing ‘happy birthday’ to our dear friend, Chucky D, and enjoy his delicious chocolate-vanilla layered birthday cake. We may have temporarily lowered our fitness by consuming all of this sugary cake, but rest assured that the long-term benefits of celebrating Darwin as a department outweighed any costs.