This weeks PhDetails #83 is with Jimmy Bernot who studies at George Washington University in the USA. Jimmy did his undergraduate degree in Biology at the University of Connecticut, where he worked with Dr. Janine Caira on the taxonomy and systematics of tapeworms of sharks and stayed, completing a masters in the same group. He is now doing his PhD with Keith Crandall at George Washington University on taxonomy, phylogenetics, and genomics of copepods and other crustaceans. You can find Jimmy on twitter @JP_Bernot or at his website HERE
Well let’s start off talking about completely unscientific stuff: What is your favourite band/musical artist pre 1980?
I go through phases in the music I listen to. I’m sort of finishing a disco phase and I’m not sure where I will go next… But if I had to choose a single pre 1980s artist I would pick Fleetwood Mac. I can listen to them anytime.
Favourite band/musical artist post 1980?
The Black Keys.
The Lord of the Rings trilogy.
Do you listen to podcasts? What are some of your favourites?
Yes, some of my favourites are Wait Wait Don’t Tell Me (I listen to this every weekend on NPR One), Radio Lab, Short Wave, Mobituaries, and More Perfect.
Where do you study and who is your supervisor?
I’m doing my PhD at George Washington University with Keith Crandall.
What year of your PhD are you in?
I’m a fifth year PhD student.
Who’s giving you the money – and for how long?
My Phd has been funded off of a number of different grants. I’ve also TA’ed biology courses.
Do you have any publications?
Yes I have 7 publications between my masters and PhD work so far:
Boxshall, G. A., Bernot, J. P., Barton, D. P., Diggles, B. K., Yong, R. Q.-Y., Atkinson-Coyle, T., Hutson, K. S. (in press). Parasitic copepods of the family Lernanthropidae Kabata, 1979 (Copepoda: Siphonostomatoida) recorded from Australian fishes, with descriptions of seven new species. Zootaxa.
Bernot, J.P. and Caira, J. N. (2019). Site specificity and attachment mode of Symcallio and Calliobothrium species (Cestoda: “Tetraphyllidea”) in smoothhound sharks of the genus Mustelus (Carcharhiniformes: Triakidae). PeerJ 7:e7264 http://doi.org/10.7717/peerj.7264
Bernot, J.P. and Boxshall, G. A. (2019). Two new species of parasitic copepods from the genera Nothobomolochus and Unicolax (Cyclopoida: Bomolochidae) from Australian waters. PeerJ 7:e6858 http://doi.org/10.7717/peerj.6858
Hughes, L.C., Somoza, G.M., Nguyen, B.M., Bernot, J.P., González-Castro, M., Díaz de Astarloa, J.M., and Ortí, G. (2017). Transcriptomic differentiation underlying marine-to-freshwater transitions in the South American silversides Odontesthes argentinensis and O. bonariensis (Atheriniformes). Ecology and Evolution. http://dx.doi.org/10.1002/ece3.3133
Bernot, J.P. and Boxshall, G.A. (2017). A new species of Pseudopandarus Kirtisinghe, 1950 (Copepoda: Siphonostomatoida: Pandaridae) from sharks of the genus Squalus L. in New Caledonian waters. Systematic parasitology, 94, 275–291. 10.1007/s11230-016-9692-2
Bernot, J.P., Caira, J.N. and Pickering, M. (2016). Diversity, phylogenetic relationships, and host associations of Calliobothrium and Symcallio (Cestoda: “Tetraphyllidea”) parasitizing triakid sharks. Invertebrate Systematics, 30: 616–634. 10.1071/IS15040
Bernot, J.P., Caira, J.N. and Pickering, M. (2015). The dismantling of Calliobothrium (Cestoda: Tetraphyllidea) with erection of Symcallio n. gen. and description of two new species. The Journal of Parasitology, 101: 167–181. 10.1645/14-571.1
Did you do a masters – where was it and was it about?
Yes I did a masters at the University of Connecticut where I studied taxonomy and systematics of tapeworms from Smoothhound sharks. I am so glad that I decided to do a masters! At the time, I received conflicting advice with some people saying a masters is great, and others telling me it is not so useful if you plan on doing a PhD anyway (I was anticipating doing my PhD eventually). In the end, I decided to do a masters and I could not be happier with that decision.
I learned a lot in my masters which made the transition to life as a PhD student much easier. For instance, I learned how to budget my time between my own course work, the classes I was TAing, and the research I was doing in the lab. I learned how to see a project through from beginning to end, including writing a couple of manuscripts and tying multiple manuscripts together into a masters thesis. A thesis-based masters can be very similar to a shorter PhD, which is great training to have for a dissertation. During my masters, I also started to figure out what I wanted to focus on in my PhD and to begin planning my dissertation research, which helped me hit the ground running once I started.
Do you do fieldwork? What is the best fieldwork you have ever done and what made it great?
Yes, I’ve done field work in Chile, the UK, Australia, up-state New York at the SUNY Oneonta biological field station, and in Panama.
My most successful field work was in Australia, at a University of Queensland field station on North Stradbroke Island. The premise of this project was just fantastic! Tom Cribb and Scott Cutmore from the University of Queensland assembled an international team of parasite taxonomists to survey all major parasite groups from fish in Moreton Bay, Australia in a 2 week survey. So we had this large, international team, fantastic facilities at the field station, and the Cribb lab was amazingly well organized to collect, identify, and process the fish we collected. In the end, we were able to collect over 1,000 fish, about 200 different species, and we identified hundreds of parasites, including nearly 100 new species!
We basically dissected each fish in an assembly line, with each scientist examining the organs in which the parasites they study reside (e.g., blood was drawn to look for blood parasites, intestines went to the tapeworm and digenean scientists, stomachs went the nematode scientists, gills went to the copepod and monogenean scientists, etc.). That way, we got the most possible information from every fish examined. I worked with Geoff Boxshall on the parasitic copepods so we looked at all the fish heads (most parasitic copepods live on the gills or in the mouth area, or on this skin). We found 130 species of parasitic copepods including 30 new species during this 2-week collecting trip alone!
How many PhDs did you apply for – what were you looking for?
I had 3 PhD programs in mind when I applied. I did this selection based on what I wanted to study (parasitic copepod taxonomy, systematics, and phylogenetics), and which PI’s that would fit well with. There aren’t many people studying copepods so I was limited in that regard, but I searched for PI’s that worked on similar evolutionary questions in other invertebrate systems. I reached out to those professors and let them know what I hoped to focus on for my PhD. If they were receptive to the idea, I applied to that program.
What is the most bodged piece of equipment you have had to use during field/labwork – did it work?
I can’t take credit for this piece of equipment, but it is a great story. I was on a small fishing boat doing field work in Chile to collect shark tapeworms when the fuel pump stopped working, leaving us stranded in the water during a bit of a storm. The Chilean boat driver, who we subsequently nicknamed “MacGyver” (side note: it was hilarious trying to explain “MacGyver” to him in Spanish), used his pocket knife to cut a sliver from one of the wooden ores, cut a fingertip off his heavy rubber work gloves, then placed the wooden sliver inside the rubber finger and used that combination to plug an opening in the fuel pump. He did it all in about 5 minutes, and it worked like a charm to restart the fuel pump and get us back to dock safely. Never underestimate the ingenuity of people that know their craft (especially fishermen)!
What one piece of advice would you give to a masters student applying to PhDs now?
Spend time looking for a PI and finding a lab that works for you. Any work you put in at this stage (Googling PI’s, reading their papers, writing them emails, contacting their graduate students to ask about life in the lab) will pay dividends in the long run.
How often do you meet with your supervisor?
About once a month.
What supervisor traits are important to you?
Open and honest communication, investment in their student’s goals, particularly when those goals may differ from their own.
What do you think are the worst supervisor traits?
Lack of empathy and lack of time for their students.
In one sentence what is your PhD about?
Taxonomy and phylogenetics of parasitic copepods.
What has been your academic highlight of the last year?
Publishing the last chapter of my masters thesis http://doi.org/10.7717/peerj.7264. It is probably the piece of work I am most proud of up until now. It took a few years of work in the lab, and the manuscript was >80% done when I started my PhD, but then it was hard to finish with all the other things going on in my personal and professional life, so it hovered at 80-90% finished for years. But I kept working with my masters advisor and we both stayed focused on polishing and improving it amid all the other things in our lives and we finally ended up with a much-improved finished product that we were both very proud of!
Have you had an academic low-point of the last year – if so what happened?
Yes, within a 40 day period this year I had the following things happen (mixed personal and professional):
- I broke up with my boyfriend of the past 3 years and had to move out of the place we shared
- I lost a chapter of my dissertation (about 3 full months' worth of work and some invaluable and irreplaceable specimens) when I discovered there was a transcriptional error in a protocol I was given
- a tree branch fell on my car and broke my windshield
- my bike (my primary means of transportation to, from and around campus) was stolen
- I wasn’t paid for a teaching position for 2 months
-And my PI asked me to graduate a semester sooner.
So yeah… that was a rough period and I was definitely feeling low and questioning my future and was filled with more doubt than I have ever been before. But I reached out to family and friends and mentors for support and got one particularly inspiring pep-talk from a mentor, which really helped me put things in perspective and forge ahead. I got through it, and if anyone else is struggling with something and reading this I believe you can get through it too! It gets better! Also, if you are having a hard time and want someone to talk to, the Samaritan Line is available 24/7 at (877) 870-4673 (or 116 123).
Which academic idol/scientist have you met?
Geoff Boxshall is basically the world expert on copepod taxonomy and diversity, and I’ve been lucky enough to meet him a number of times and even spend two three-month stints working with him at the London Natural History Museum. The first time I met him, I was too much of a noob to even know how big of a deal it was that I got to sit down one-on-one to ask him questions about copepods. He is genuinely one of the nicest, friendliest people I’ve ever met, and it has been an absolute pleasure to work with him and learn from him. I really hope I get to continue that for many years to come.
Which academic idol/scientist would you most like to meet?
I’d really like to meet Jens Høeg – he is the expert on barnacles. If you search for a paper on barnacles, its more than likely that he or one of his students is one of the authors. I’ve heard he is a super nice guy with diverse interests in music and art in addition to all his scientific work. I met one of his graduate students and if they were any indication, Jens must be a really cool dude.
Who has been your academic role model/inspiration and why?
My undergraduate and masters adviser Dr. Janine Caira. I’m pretty sure she would be embarrassed to read this but it is true! She embodies what professors aspire to be: an expert scientist, researcher, teacher, communicator, and mentor. Her students that have gone on to academic positions talk about trying to live up to her example. She never does anything halfway, everything she does is done to the highest standard. She is extremely dedicated to her students and places the interest and goals of her students above her own, even when they may conflict.
Do you have a favourite paper?
That is a tough one! I have a favorite academic book: Boxshall and Halsey (2004) An Introduction to Copepod Diversity. It is basically the bible of copepod taxonomy. It details every family of copepods (there are about 200) and all of the genera within each family, including keys to each genus. It is the piece of academic literature that I reference the most frequently. It has certainly made copepods, which are a diverse and at times challenging group to work with, MUCH more approachable.
What has been your favourite conference so far – why?
The International Workshop on Cestode Systematics in Lawrence Kansas in 2011. I was at a bit of a crossroads trying to decide if I should go to med school or grad school at that time. This was the second conference I presented at, and I had such a good time with friends and colleagues at that meeting (and drinking beers in hotel rooms and bars late into the night, I’m looking at you The Bourgeois Pig) that it made me realize how much I loved the parasitology research community. I decided that I wanted to be able to study parasite diversity more broadly, and not be limited to just to a few parasites and diseases of humans, and that I wanted to keep working with these people and others like them.
What hours do you typically work?
It varies a lot but I often default to a late schedule, working from 11am or noon to 8PM or later.
How do you avoid procrastinating?
“200 crappy words per day.” I read an interview with a prolific author (I forget who now) and he was asked how he managed to write so many books each year throughout his career. He replied that he told himself he has to write 200 crappy words each day. This was an attainable enough goal that is was easy to complete each day, yet once started he often wrote much more than that.
I find that getting started on challenging tasks is usually the hardest part, so when I find myself procrastinating on them, I break them down into much smaller tasks – something so easy it is hard not to attain it. Then once I’m started it’s easier to continue. Sometimes I only complete the minimum goal I set, other times I look up and a few hours have gone by and I’ve made great progress.
What motivates you in your day to day PhD life?
My motivation varies a lot from day to day, but I definitely enjoy a sense of accomplishment, so I try to use that as a motivator. I make lots of lists and use Google calendar to set tasks and (attempt) to keep myself on track with my plans. I also use little rewards, like working hard up until 2PM then allowing myself to take a midday gym break, or working really hard on a Friday evening because I know I’m going to feel accomplished and enjoy a day off on Saturday if I finish one more thing. That latter one in particular works really well for me – I usually find Friday evening to be my most productive time. For example, I am finishing these interview questions, which have been on my to-do list for weeks, right now at 9PM on Friday haha!
What do you do when you’re not working – how do you balance it with your PhD?
I try to maintain a social life, and slow down in the evenings or weekends to read, sit in a park, play an instrument, watch TV, or play some video games. I also love playing volleyball and racquetball. I really enjoy going out with my friends to a gay bar or club to have a good time, dance, and just be my wacky self: social butterfly, gay, nerd, and all! I think “work hard play hard” is a great motto.
If a genie could grant you one wish to help with your PhD what would you wish for?
To finish one of my projects that I’ve been working on for about 3 years but it just keeps expanding and getting larger and more complicated with every analysis and I DON’T KNOW IF IT WILL EVER BE DONE!
Jimmy: Here are some drawings I made of a few new species of copepods I am describing
What would be your dream job?
I just want to be able to learn about how copepods work and teach people about invertebrate diversity – so a professor or museum curator.
Where do you see yourself in 5 years?
Hopefully I just finished up postdoc-ing and have an academic job!
One word to sum up your future in academia:
What do you want to achieve outside of academia in the coming year?
I want to improve my ability to be present and not let my thoughts run away with me.
What essential tool hardware/software could you not do your PhD without?
A microscope and my laptop.
Where is somewhere you would like to work in the future?
I really want to go to Japan and do some field work there. There is a history of quality work on parasitic copepods of Japanese fish and inverts, and I would love to go to some of the same field sites to collect and sequence many of these copepods for the first time.
Do you have a favourite organism?
I suppose copepods are my favorite organisms, but I love invertebrates in general. They are the crazy, wacky, unsung, not to mention largest, portion of animal diversity! I think the spectacular forms invertebrates have taken and the strategies they have evolved to make their unique ways of life are so fascinating. I mean, just try imagining what life is like for a ctenophore, starfish, or tapeworm! It is almost unfathomable, but I find the exercise of trying to understand how they perceive and interact with the world to be endlessly interesting.
Are there any social interactions/meetings which have enhanced your PhD experience?
Absolutely! Conferences in general are a scientific and also social event. I try to chat with different people at the coffee breaks and attend all of the conference dinners, grad student socials, etc. -- that is where there is the most time to network and build relationships. I also try to go to all the seminars I can, whether they are my department or not, or my university or a neighbouring institution. There are often informal meet ups before or after seminars, and I have gotten so much out of the interactions and conversations that take place there. People might not remember you after a couple of meetings over the course of a few years, but most people will after seeing you half a dozen times.
More graduate student meets up and events with optional faculty participation. I think informal graduate student seminars are great, and so are things like grad student pub crawls. Anything that helps build a student cohort and bridge relationships between students and faculty is really helpful in a department.
What major question in your subject area is yet to be addressed – why is it important and why isn’t anyone addressing it?
How are the major groups of copepods related to each other? The application of molecular sequence data is only in its infancy in copepod systematics and phylogenetics. The deeper level relationships in copepods (e.g., between families of copepods) is still largely unknown. Especially among parasitic copepods that have lost many of the appendages and structures typically used for classification, we know very little about how they are related to other copepods. Although evolutionary biology has made great strides, especially in the last 20 years, there are still many unresolved parts of the arthropod tree of life, and the larger invertebrate tree of life. These are really interesting areas to explore as a researcher, and with the advent of all sorts of new imaging and sequencing technologies, it is such an exciting time to be a scientist!
One general piece of advice to graduate students (or anyone!):
Don’t forget to look back and appreciate how far you’ve come! It is easy to get caught up in the moment and in the pressure to do more, know more, learn more. Try to regularly take time to reflect on what you have learned and what you’ve accomplished. When you feel like you still have so far to go, try asking yourself, “If I told myself 1/3/6/12 months ago that this is where I’d be now, how would I feel?” I find that when I am feeling inadequate, if I take time to go through this mental exercise, I find that I am nearly always pleased with my progress. It is easy to lose sight of our progress when we don’t take time to reflect on it.