Land acknowledgement
McMaster University (and this class) is on the traditional
territories of the Mississauga and Haudenosaunee nations, and within the
lands protected by the “Dish with One Spoon” wampum agreement.
(Why? See “Beyond
Territorial Acknowledgements”
Course goals
Primary: To learn about the ecology and evolution of
infectious diseases and parasites in general, both (1) the E&E
of infectious diseases (how E&E principles apply to
pathogens) and (2) the effect of pathogens on the E&E of their host
organisms and communities.
Secondary: to practice a variety of skills including
critical and creative thinking; critical reading of papers from the
primary and secondary literature; scientific writing and review; web and
literature searches for scientific information.
Check out Perry Jr. (1997).
Expectations
- attend and participate in class (on time); do the reading; ask
questions (including submitting your discussion questions online and
participating in class and online discussions); think critically and
creatively. Please let me know if you can’t participate in class
discussion (shyness, internet/remote-participation issues,
etc.).
- know basic ecological and evolutionary principles (from BIO 1M03,
2C03, 2F03, 3FF3) but more importantly to ask questions, in or
out of class, when you don’t understand something. There is no
such thing as a stupid question. If you don’t know something you’re
probably not the only one in class.
- behave responsibly in online and in-person settings
- do your own work, don’t plagiarize, reference sources appropriately,
credit group work appropriately: see honesty.html.
- Appropriate use of generative AI (see citation
guide)
Readings and discussion
In addition to the textbook, we will read papers from the primary and
secondary literature and discuss them in class every Friday (starting
September 12). I hope to do reading-based interactions on Perusall,
still working out the details.
Recordings and notes
- I will post lecture notes beforehand; recordings will be available
by request. Don’t expect them to be comprehensive.
- There will be some ‘spoiler’ blocks in notes.
- If you prefer notes in another format, ask.
Writing
Writing is hard. The only way to get better is to practice.
- We will give you lots of feedback. Grading will be based primarily
on evidence of appropriate effort, critical thinking, and creativity
(and improvement).
- The Writing
Centre offers appointments to help you with your writing
- Here are some of my style
preferences
Referencing
- Primary literature (usually journal articles) is best
- Wikipedia is a great start and generally reliable. You should often
dig down into the references
- Google Scholar is great (use the
author: tag if you’re
looking for something in particular)
- follow references backward and forward
- Other web resources are OK, reputable sources (CDC, WHO, …)
preferred
Citations
- Cite anything you use
- Never cite anything you haven’t read (OK to cite
“Jones 1910, referenced by Smith (1999)”)
- Use whatever complete citation format you like (I like
author-date)
- Articles: include authors, year, source (journal title),
volume/issue/page numbers, DOI if possible. URL alone is
insufficient.
- For web resources include author/title/date, access date, URL.
Reputable resources preferred (Wikipedia, CDC, WHO, …)
- I strongly recommend that you use a bibliographic database system.
Zotero is my favourite.
Reading papers
- Reading research papers (primary literature) is hard but
important
- Carey, Steiner, and Petri Jr (2020);
Some
advice from a guy I know
- Focus first on introduction, figures, conclusions; try to get the
big picture
- Try to understand the overarching logic. What are the questions?
What are the primary data? (How) do the data and the arguments in the
paper go together to answer the questions?
- “What if they did X?” “Why didn’t they do Y?” are secondary to
engaging with the details of the paper
- Try not to get bogged down in details, unless you have time and
energy.
- Math and statistics
- don’t panic
- connect verbal descriptions → model equations and model results
(figures or equations) → verbal conclusions
- e.g. \(dS/dt = b -\beta S I - \mu
S\)
- Don’t be afraid to ask questions
Topics
- Way too much interesting stuff:
- how does the ecology (“distribution and abundance”) of parasites/ID
work? Classic ID epidemiology, population dynamics. Variation in space
and time.
- how do parasites/ID evolve? Phylogenetics, population genetics;
phenotypes, genotypes
- how do parasites/ID affect the ecology of their hosts? Biocontrol,
conservation biology, apparent competition, trophic cascades
- how do parasites/ID affect the evolution of their hosts?
Coevolution
- The important questions:
- How do we know? Population genetics, phylogenetics,
historical records, surveys, experiments, statistics, mathematical
models, meta-analysis …
- So what? Why are we bothering with the details of a
certain fact or definition?