How to become a protist nerd

Lisa Schneider, MixITiN ESR11, unveils her tools to becoming a protist nerd.

June 2020

When I started my PhD 2 years ago, I was completely new to the world of plankton, protist physiology, photosynthesis and marine ecology. I thought I knew something but that quickly turned out to be wrong. And now 2 years later I am still quite new to that world and am only scratching the surface, but I starting to feel at home in that invisible world of marine protists. 

While the MixITiN workshop that we ESR’s got over the past 2 years were incredibly useful, I also realized I needed to step up my game. So, I devised my own study plan with the goal to become a “data-driven, numerically inclined, protist nerd”. And so far, I am really enjoying my path to get there. I thought other people might be interested in the different resources I used and so I decided to compile a list for this blog. Enjoy 😊

Over the past four years I have become a huge fan of MOOC (massive open-online courses). MOOCs are great! You can watch whenever and wherever you want, you can repeat and rewind as often as you needed and you can even playback at 2x speed (sometimes very useful 😊). In the last year I followed three MOOCs and I can recommend all three of them.

Water quality and the biogeochemical engine. EPFLx – WaterBiogeochemistryX. École polytechnique fédérale de Lausanne. This is a great course. It runs over 13 weeks and covers the major microbial metabolisms, biogeochemical cycling and natural water treatment processes. I especially liked the lectures given by Prof.  Rizlan Bernier-Latmani.

Tropical Coastal Ecosystem. UQx – TROPIC101x. The University of Queensland Australia. This is also a great course. It runs over 9 weeks, is very interactive, well made and entertaining. They start by explain very visually which organisms one can find on a reef, then go more in depth into the different ecosystem processes taking place and conclude with lecture on marine spatial planning. I especially liked the lectures by Sophie Dove and Ove Hoegh-Goldberg.

Khan Academy – biology course. This is the best to refresh high school biology knowledge. Sal Khan is such a great educator, so enthusiastic that even in front of my laptop screen I couldn’t stop myself from becoming incredibly excited about everything I was learning!

I have always been a huge book lover, but it has taken me some time to find scientific (text)books that inspire instead of bore. But I found some of them and really enjoyed reading them.

“A Practical Guide to Ecological Modelling: Using R as a Simulation Platform” written by Karline Soetaert and Peter M. J. Herman. This is such a great book! It made me realize that I am in the right field. I highly recommend it to anyone who wants to work in ecological modelling.

“Marine Carbon Biogeochemistry – A Primer for Earth System Scientists” written by Jack J. Middleburg. Also, one of my favorites. I really like his concise style of writing, the structure of the book and the fact that he mentions ball park number which I had unsuccessfully been trying to find since the beginning of my PhD.

“Marine Plankton – A practical guide to ecology, methodology and taxonomy” edited by Claudia Castellani and Martin Edwards. This is a huge, thick book, but has wonderfully concise summaries of the different functional plankton groups.

“Wonders of a Drifting World” written by Christian Sardet. For a non-microscope person like me, this book and the accompanying website is a gift from heaven!

“Life’s Engines” written by Paul G. Falkowski. Such an interesting, beautifully written and personal book. I really enjoyed reading it. And I also liked his book recommendation at the end. More books to add to my list 😊

“Ecology – The Analysis of Distribution and Abundance” written by Charles J. Krebs. A great, thick book. I especially liked the questions posed at the end of each chapter. They really help recap the chapter and if you read on, the answers are provided somewhere in the following chapters. Note: I am still working on this one!

“Aquatic Photosynthesis” written by Paul G. Falkowski and John A. Raven. I really liked the introduction, but I am still working on this one as well.

“Dynamic Ecology – The art of simulating trophic dynamics” by Kevin J. Flynn. This book give a nice introduction into protist physiology for modelers.

I just enjoy coding (in R) and really like the Rstats community.

“R for data science” written by Hadley Wickham. A MUST for everyone who wants to learn R, work in R or just upgrade their R skills. I cannot stress this enough! It is an incredibly good resource!

“RLadies Twitter account”. I really enjoy following this twitter account (even though I do not have twitter myself). The account has a rotating curator and you learn so much about different applications of R and new developments. Very good work.

Creating good visualization is so important for scientists. In my opinion, good, aesthetically appealing and scientifically sound visualizations are really the heart of the story and they really take some effort to create. But I found some really nice resources that help along the way.

“dataViz” website. A great website to get ideas on which type of graph to use for different types of data. A really good starting point!

“Visual cinnamon” by Nadia Bremer. I really like her visualizations. They are beautiful and inspiring. Eye candy 😊