Ben Stephenson

I’m a molecular biologist who finds naturally evolved solutions to difficult problems and puts them to work. My work spans fundamental biology and applied R&D, from studying early animal evolution to developing new technologies for defense, public health, and other government applications.

Some of the work I enjoy most happens outside the lab: finding funding opportunities, building relationships with government customers, and learning what they actually need, then partnering with scientists and engineers to turn those needs into practical solutions.

I’m now looking for roles at the intersection of science, innovation, and commercialization, helping promising technologies move from the lab to the people who need them.

Below you’ll find my research, along with a few of the hobbies that keep me busy in my spare time.

Each location on the map below is a section of the site showcasing one of my interests. Click one to explore it, or scroll to move through the map.Each location on the map below is a section of the site showcasing one of my interests. Tap one to explore it (swipe sideways to see them all), or scroll to move through the map.

Research

From uncovering the molecular mechanisms of early animal evolution to finding and exploiting naturally evolved solutions to difficult problems.

I’m drawn to problems at the intersection of biology and engineering, especially those where an unusual biological system can inspire a practical solution.

My path there began in graduate school with a much more fundamental question: how did early-branching animals such as jellyfish, sea anemones, and corals build their bodies, and what can that tell us about the evolution of more complex groups?

Studying these animals introduced me to highly specialized biological systems unlike anything found in traditional model organisms, from the stinging cells of jellyfish and sea anemones to the underwater adhesives of comb jellies.

After graduate school, I joined Applied Research Associates, where my work shifted toward applied research and solving practical problems, including developing technologies to protect people from airborne pathogens during the pandemic. More recently, those two threads have come together. I now engineer naturally evolved biological systems and explore how their unusual capabilities can be adapted to solve problems in medicine, biotechnology, and defense.

The constant has been curiosity and a belief that some of the most elegant solutions to difficult problems can already be found in biology.

The sections below tell that story in more detail, from my graduate research on early animal evolution, through pandemic preparedness, to my current work engineering naturally evolved biological systems.

  1. Graduate research

    How an anemone lays out its body

    Whitney Laboratory for Marine Bioscience, University of Florida

    Sea anemones and jellyfish branched off early in animal evolution, which makes them a window into how body plans first came together. Working with Mark Martindale, I studied the functional genetics of Hox genes in Nematostella vectensis. We showed that Hox genes and Wnt signaling are already patterning the anemone’s primary body axis before gastrulation begins.

    Read the paper in Nature Communications (2018)

  2. Staff Scientist, my first role at ARA

    A reusable N95 respirator

    Applied Research Associates, Panama City

    I was hired at Applied Research Associates to help build a respirator that didn’t exist yet: a hybrid of an elastomeric respirator and an N95 that could be cleaned and used again. It was designed to survive a hospital washer-disinfector and an autoclave. The work produced a U.S. patent and a sister company, ElastoMaskPro, to manufacture it.

    Our BARDA contract was cancelled before we could seek FDA authorization, so the fully reprocessable medical version never reached hospitals. We did bring a version without reprocessing claims to market to help with the N95 shortage during the pandemic.

    U.S. Patent 10,835,704: Reusable respiratory protection device ElastoMaskPro

  3. During the pandemic

    Measuring protection when it mattered

    Face shields and masks at close range

    In an OSHA-funded project, we used breathing headforms, instrumented mannequin heads that simulate human breathing, to measure how much protection face shields and face masks provide against close-contact droplet transmission of SARS-CoV-2.

    Preprint on medRxiv (2021)

    N95s under extended use and reuse

    With UCSF, we looked at how often N95s failed fit testing after extended use and reuse in an emergency department, then tested those same respirators for SARS-CoV-2 contamination using RT-qPCR.

    Fit failure study on PubMed (2020) Contamination study on PubMed (2025)

  4. Now

    Internal research at ARA

    A few projects I’m developing through internal R&D. I’ll add more detail as results come in.

    Stinging cells as protein factories

    Cnidocytes, the stinging cells of jellyfish and anemones, fire their contents in one of the fastest events in biology. I’m testing whether that mechanism can be used to manufacture and purify protein therapeutics, so the sting itself does the purifying.

    Colloblast glue

    Comb jellies catch prey with colloblasts, cells that release an adhesive that works in seawater. I’ve been collecting Mnemiopsis leidyi in St. Andrews Bay and working to identify the proteins behind the glue.

    ProIRIS biosensor

    A biosensor built on bacteriophage biology: a prophage-based infectious reporter system. Details to come.

Woodworking

A scientist pretending to be a craftsman, faking it till I make it.

It started with an empty shed.

When I bought my house in 2021, I walked into the empty shed out back and realized I finally had room for something I’d wanted to do for years: learn to make fine furniture. Five years and a ton of expensive mistakes later, I’ve started making what I consider fine furniture, mostly with hand tools. Here’s a little about that journey.

Learning the basics

My first pieces came out of The Weekend Woodworker course, working mostly in pine and plywood to learn basic cutting, joinery, and finishing techniques. I highly recommend this course for anyone just starting out. It gets you in the shop, building quality furniture from scratch on day one.

Coffee tableA framed top with a stained plywood panel, set on a painted base.
Spaghetti benchA complex-looking piece that was surprisingly easy to build. It’s affectionately known as the spaghetti bench because it’s built up in layers.
Paper trayAn oak desk tray with a monogrammed centerpiece and a purpleheart stripe.

Moving to hardwoods

Once the basics felt solid, I moved on to hardwoods, figured grain, veneer, and the details that separate fine furniture from an ordinary build.

Keepsake boxes: simple but elegant

Mitered boxes with continuous grain wrapping around the corners, reinforced with contrasting splines and fitted with inset box hinges. The lids pair walnut with figured maple and padauk with soft maple. Small projects like these taught me a lot, because once you can build a truly square box, you can build just about anything.

Walnut bookcase

The case and adjustable shelves are American walnut, the back panels are figured European walnut, and the drawer front is walnut burl framed in white oak, with an ebony bead lining the top and bottom of the case. At least, that’s how it looks. This build was my experiment with veneer: the casework is actually eucalyptus, and all of that beautiful walnut is a thin layer on top. I learned that veneer has an important place in fine furniture, but you really shouldn’t build a whole project out of it!

Wall cabinet No. 1, after Mike Pekovich

Built from Mike Pekovich’s wall cabinet design in The How and Why of Woodworking. An oak case with exposed joinery on the sides and a pair of burl drawer fronts with brass knobs.

Hiking

One multiday hiking trip a year brings me closer to nature and reminds me just how good we have it with modern conveniences.

Once a year, a group of friends and I pack up for a multiday hike.

Recent trips have taken us through Yellowstone and the Grand Tetons, up Mount Mitchell, and along stretches of the Appalachian Trail.

Code & Create

Questions from the lab turn into code projects in my free time.

I’ve always dabbled in code, writing simple Python scripts to handle mundane tasks, but in 2021 I started learning in earnest. I began with Harvard’s CS50x and CS50P courses, then leaned heavily into bioinformatics, working through Bioinformatics Algorithms: An Active Learning Approach by Phillip Compeau and Pavel Pevzner. My coding projects are sporadic, but I’ll add them here as I build them.

Codon optimizer for Nematostella

A Python tool that rewrites a gene’s coding sequence to match the codon preferences of the starlet sea anemone, so a protein designed elsewhere has a better chance of expressing well in the animal. It reads compressed FASTA files with Biopython, builds a codon usage table from the anemone’s genes, and began as coursework for CS50’s Introduction to Programming with Python.

Protein:

The sample is the start of green fluorescent protein, which comes from a jellyfish. Cnidarians get everywhere.

Code challenge · Bioinformatics Algorithms, Chapter 1

Finding where replication begins

This project is my solution to the final code challenge in Chapter 1 of Bioinformatics Algorithms: find where replication begins in a bacterial genome. Bacteria copy their circular chromosome starting from a single spot, the origin of replication, or oriC. My Python code finds oriC in the Salmonella enterica genome, along with the DnaA boxes inside it: the short sequences where the protein that kicks off replication binds.

The first clue is GC skew. Cytosine mutates to thymine more often on one side of the origin than the other, so the balance of G to C flips right around oriC. Walking the genome and adding one for every G and subtracting one for every C, that running total bottoms out near the origin.

GC skew across the genome

Running total of G minus C, from the start of the genome to the end

The skew narrows the search to about a thousand bases. My code then slides a 500-base window across that stretch, finds the most frequent 9-letter words in each window (allowing one mismatch and counting both DNA strands), and keeps the window whose frequent words match the DnaA box consensus, TTATCCACA. Inside that window it reports every 9-mer within one mismatch of the consensus on either strand.

Proposed origin in

Positions , with the four DnaA boxes my code found

    Running the same code on E. coli finds an origin with the same four DnaA boxes, a good sign that the method works beyond the genome I built it on.

    See my Chapter 1 solutions on GitHub