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


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).

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.’