Informational Interview by Ally Weir, ASPB Conviron Scholar 2018
Dr. Joshua Der is an assistant professor at California State University Fullerton. He is also the curator of the MacFadden Herbarium at CSUF, as well as a research associate at the Rancho Santa Ana Botanic Garden. AT CSUF he studies the evolution of plant biodiversity and adaptation in natural systems such as ferns, parasitic plants, and California native plants. His research includes the topics of conservation, genomics and other bioinformatics, population genetics, and molecular evolution. We spoke about his career path, research interests, and life as a professor. Below is a portion of our discussion.
• How did you become interested in plant research? Have you always been interested in plants?
I went to college wanting to go into environmental ecology or environmental science, and I didn’t get excited about the classes available in that major, so I decided to switch to biology. My freshman year I had to take a botany class, and I just got so amped with plant diversity, and the evolution of lifecycles. My professor was super enthusiastic. He was a person who would climb to the tops of the tallest redwood trees to measure them and to document the canopy biodiversity. It all just got me so excited about plants, so I took as many plant related classes as I could and ended up becoming a botany major. I went to graduate school to get my master’s and studied parasitic plants. That was my first lab experience and opened up perspective on other plant research areas that I didn’t have exposure to as an undergraduate.
• When did you start researching ferns?
I first learned about them as an undergraduate. I liked the ferns that were under the understory of the redwoods, but there weren’t that many of them, maybe, 10-15 species? And I knew them all! But in my master’s program, I took a took tropical plant systematics course in Costa Rica and one of the teachers was a fern specialist, so walking around in the jungle of Costa Rica learning about all these different species of ferns made me more excited about fern diversity and fern biology. When I was thinking about a PhD project I had initially wanted to explore ecological speciation related to pollination of flowering plants, but I never really found a system where I felt like I could make a significant contribution. I picked up a side project on the bracken fern that I ended up following through to publication. After having invested so much time on this project I ended up expanding that work to encompass genomics. That is how I really got involved in the fern community, and I’ve stuck with this community for a long time.
• Is this how you got into the field of computational biology?
Yes, my dissertation had several genomic aspects to my work, that led me into the world of genomics. At the time, my work was at the cutting edge of fern genomics. I am largely self-taught. I had received a small grant to sequence the chloroplast genome and transcriptome of my fern to study RNA editing in chloroplast genome. We were using some of earliest next generation sequencing technology, and I had to learn computer programming all on my own in order to manage all of those data.
• What was it like to be working with such new technology?
I had a committee member who had done bioinformatics in yeast, so they were able to help me a little bit, but all of the tools for processing so much data didn’t exist back then. It was a lot of sloppy code and trying to invent my own bioinformatic methods by patching together pieces of software, writing my own scripts trying to change data formats…yeah, it was pretty piecemeal.
• It seems that with the direction the field is going in, researchers need to know how to code and manipulate data, do you have any suggestions to biologist who wants to get more into bioinformatics?
Yeah, most projects involving molecular sequences are going to have high throughput data, and in order to handle all those data, you need to have strong computational skills. Part of that is going to be learning how to use the command line, so that you can access computers that are able to process larger datasets. There are a number of tutorials for how to learn the command line. I have started to get involved with Data and Software Carpentries. They offer weekend workshops that get scientists up and running with computational skills, and they have some modules that involve genomic data. These workshops are put on at conferences, or universities where there is a group that wants to learn these skills. There are two parts to this organization, one focuses on data carpentry which teaches skills related to handling large amounts of data, and the other focuses on software carpentry which teaches the coding skills. I think both programming and data management skills are applicable to biologists.
• Have you always wanted to work in academia?
I didn’t realize that I wanted to work in academia until I got into graduate school and worked as a TA, where I had more of a chance to get a feel for what working in a classroom was like, and also have firsthand experience in research. I went into graduate school thinking I would get my masters and then go into botany, and work a field job, or work for the forest service. As an undergrad, I didn’t have a lab-mentored research experience, so I didn’t really know what it meant to be a professor until I went to grad school and had a closer look.
• How do you balance work and outside life?
In the past few years I have been reading fiction to give myself a mental break. Getting out and spending time on the weekends with my family helps a lot. My whole family is happiest when we are outside, so in our spare time we go hiking, kayaking, camping, you name it. My wife is also a biologist, and she specializes in bees, but she is also a really great botanist as well. We are always looking at insects and plants, my kids are pretty good naturalists now. My wife has a longer commute, so I tend to pick the kids up after school. When I’m at home I spend the early evening with my family. If I have more work to do that I didn’t get done during the day sometimes I’ll get back to work late in the evening when the kids go to bed. When at school, I try to block off times for different activities; I have blocks for teaching prep, writing, and time when I am working with students. A lot of times I end up having to just put out the most urgent fires though.
• In your opinion, what is one of the most important characteristics of a researcher?
Well, I think curiosity, and wanting to understand how things work is a key trait in a researcher. Being organized, dedicated, and committed are also important characteristics, but you have to be curious, and want to know how the world works in order to stay with science, and to have that creativity to sort of think outside the box, to design an experiment and to solve those problems.