Preparing for Eukaryotic Microbiology Class

For the second year in a row, my advanced microbiology course, Eukaryotic Microbiology, is up and running. Technically this is the 11th iteration of the course, but the second year I'm going to try and blog about the course concomitantly. So the website is went live to students today and has a bunch of business related things about the course and a the first few weeks of modules available.

Before we met, in just under two weeks, there is an online quiz and a number of introductory papers for the course as a primer for the students. The papers are:

• The eukaryotic tree of life from a global phylogenomic perspective. Burki F. Cold Spring Harb Perspect Biol. 2014 May 1;6(5):a016147
• The origin and early evolution of eukaryotes in the light of phylogenomics.  Koonin EV. Genome Biol. 2010;11(5):209.
• The hybrid nature of the Eukaryota and a consilient view of life on Earth. McInerney JO, O'Connell MJ, Pisani D. Nat Rev Microbiol. 2014 Jun;12(6):449-55.
• An archaeal origin of eukaryotes supports only two primary domains of life. Williams TA, Foster PG, Cox CJ, Embley TM. Nature. 2013 Dec 12;504(7479):231-6.
• The common ancestor of archaea and eukarya was not an archaeon. Forterre P. Archaea. 2013;2013:372396. doi: 10.1155/2013/372396.
• A new view of the tree of life. Hug LA., Baker BJ., et al. Nature Microbiology. 2016 Apr 11; 1(article number 16408)
• Predation and eukaryote cell origins: a coevolutionary perspective. Cavalier-Smith T. Int J Biochem Cell Biol. 2009 Feb;41(2):307-22.

Figure 1 from the Hug paper

I ask the students to read the Burki paper first, which is a great overview of the current eukaryotic tree and how it was established. The Koonin and McInerney next, followed by the Williams and Forterre papers. There's a fair bit of overlap among the Koonin, McInerney, and Williams papers that I suggest they skim through. Once those are done, I ask that they read through the Hug paper, which is the only primary research paper of the list. Finally,  the Cavalier-Smith paper on what is a eukaryotic cell in some detail.

I particularly like the two papers by Williams and Forterre as they basically argue different things. This allows me to introduce ambiguity into the course from the beginning, which I think is important. One of my goals is to teach students to think critically about the science they read. This is quite difficult as I think the students have been taught that if it's written in a textbook or scientific paper, it must be correct. Here, I am giving the students two papers, written the same year, that argue two different points of view. Logically they cannot both be correct. It will be interesting to see if this helps students get over the hurdle of being able to question authority or not.