Student Profile: Jonathan Karnes

How would you describe your area of study to your grandmother?

I’m studying a recycling program that occurs within cells called autophagy.  Breaking this word down into its Greek roots, it means “self eating.” During autophagy, the cell breaks down parts of itself into raw materials which it can use for energy or to build new proteins. This process allows cells to survive stress, such as a lack of food, for short periods of time. Autophagy can be used by cancer cells to help survive treatment with chemotherapies and it may allow brain cells to survive for longer periods of time, thus preventing neurodegenerative diseases such as Parkinson’s disease. Our laboratory is studying autophagy to better understand how it is regulated and how we might influence it in the context of cancer or neurodegenerative diseases. My particular area of autophagy study is to look at a gene whose function is currently unknown but which we believe regulates autophagy.

What is your primary motivation for persevering through graduate school?

Finishing. Probably a typical third year graduate student response. Secondary motivations could be listed as contributing to the body of scientific knowledge, satisfaction from what I’m learning, and looking forward to interactions with colleagues.

What do you want to do with your degree?

I have not entirely made up my mind, but I’m currently considering pursuing a full-time research career, teaching, or going into the field of molecular diagnostics to help diagnose diseases in a clinical setting.

Did you take time off before starting your Ph.D. degree or come directly from an undergraduate or master's degree program?

Yes, I worked for five years after finishing my undergraduate degree before continuing with graduate school.  I worked for almost two years in the Human Leukocyte Antigen laboratory at Michigan Community Blood Centers doing DNA sequencing to match bone marrow donors to patients at Helen DeVos Children’s Hospital. Following this, I worked for just over three years in the Molecular Diagnostics lab at Spectrum Health testing patient samples for diseases that could be diagnosed through analysis of DNA or RNA.

How has your previous coursework contributed to your breadth of knowledge?

I studied biochemistry as an undergraduate. Though biochemistry and molecular biology sound like similar subjects and the same research problems are often studied in both, the respective disciplines really approach problems from different angles. My background in biochemistry often helps me in thinking about what may be happening at a chemical level within the cell even as I’m approaching the problem from a top-down molecular and cellular biology level.

Do you think there is any value in social networking with other graduate students in non-related fields?

Networking with graduate students in non-related fields is of great value for a couple of reasons. First, it is great practice in communicating one’s research with others who may not be familiar with the highly specific language used in one’s field.  It is also a great way to get the perspective of how another person might approach your own research problems from their field’s point of view, often leading to new experimental ideas or solutions. 

How do you think earning an advanced degree will change your role in society?

In my particular case, I’m very interested in being involved in discussing and forming public policy as it relates to science at some point in my career. I think an advanced degree is a necessary part of achieving this goal as the knowledge and skills developed while pursuing the degree are needed in order to be a helpful contributor to policy debates. 

Did your past experiences in life or education help prepare you for graduate school or did you have to develop different strategies to succeed?

Many of my undergraduate experiences and career experiences were useful in developing as a graduate student, particularly study skills and interpersonal interaction skills. In many ways, however, graduate school is very different from either of these previous experiences and I have had to develop strategies to overcome many problems unique to the graduate student experience. A few examples would be dealing with direct and sometime harsh criticism without taking personal offence, critically evaluating other people’s research, quickly formulating new thoughts into concise wording, and, perhaps most importantly, independently investigating and organizing new subjects.

What is your favorite stress-reduction technique?

Playing and performing music.

What accomplishment (academic or other) are you most proud of?

I tend not to rank my accomplishments as I often have varied reasons for being proud of accomplishing things and comparing any two of them to one another is difficult. I will list some accomplishments that I am proud of, in no particular order: being a National Merit Scholar, winning my college orchestra’s concerto competition as an undergrad, passing my comprehensive examinations in graduate school, and getting married and having a family.

Are you involved in other community activities and if so, how have they shaped your graduate experience?

I am a semi-professional musician in the Grand Rapids area. Playing music is a great way for me to reflect and maintain perspective on what is important in life. Though practicing and performing occasionally puts time stress on my life as a graduate student, overall it gives me more energy for pursuing science by providing an opportunity to exercise a different portion of my brain.

Has your perception of this Ph.D. program changed since you began the program?

Not really, most of it has met my expectations of what it would be. This is partially due to the amount of research I did into the program before applying and partially due to the well written description of the program in the Graduate School Catalog.

If you were asked to put something in a time capsule for each year you have been in the program and this capsule would not be opened for 25 years, what would you contribute?

Year 1:  Grant proposal written for the first module of the program.
Year 2:  Comprehensive exam write-up and commentary received back.
Year 3:  Picture of lab bench.

If you hadn’t been admitted to graduate school, what do you think you would be doing right now?

Still working at Spectrum Health or in law school.

Is there anything else you would like us to know about your doctoral education experience?

It is simultaneously one of the hardest and also most rewarding things I will attempt career-wise in my life.

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