Syllabus

OVERVIEW: We are entering a very exciting period when the study of infectious disease and the study of evolution are intersecting like never before. Evolutionary insight is yielding important advances in understanding the nature of disease, and evolutionary approaches are becoming widely used not just for tracking the origins and spread of humanity’s current batch of plagues, but also for controlling them. At the same time, pathogens are yielding key insights into the nature of the evolutionary processes that shape all of life on Earth. The goal of this course is to use evolution to understand infectious disease and to use infectious disease to understand evolution. We will cover a diverse range of topics related to these themes, including fundamental evolutionary theory, the diversity of infectious disease agents, vertebrate immunology, molecular phylogenetics and epidemiology, evolution of virulence, Darwinian medicine, pathogen evolutionary genomics, impacts of pathogens on human genetics, antimicrobial drug resistance, and the control of disease using evolutionary knowledge. We will also focus on some important pathogens, such as HIV and influenza, as case studies.

LECTURES: Tuesdays and Thursdays, 3:30-4:45 ILC 137

INSTRUCTOR:
Dr. Michael Worobey
Dept. of Ecology and Evolutionary Biology
Biosciences West, Room 324
Phone: 626-3456
worobey@email.arizona.edu
Office hours: Tuesdays, 8:00 - 10:00 a.m.

TA:

USEFUL (BUT NOT REQUIRED) TEXTS:

No available textbook adequately covers the scope of the course. The instructor will provide handouts, PDFs, and web-links, but the following books will also be useful:

Frank, Steven A. (2002) Immunology and Evolution of Infectious Disease. Princeton University Press. (This book is available as a freely downloadable PDF from http://stevefrank.org/antiVar/antiVar.html)

Stearns Stephen C., ed (1999) Evolution in Health and Disease. Oxford University Press.

Page, R.D.M. and Holmes, E.C. (1998) Molecular Evolution: A Phylogenetic Approach. Blackwell Science.

Nesse, R.M. and Williams, G.C. (1996) Why We Get Sick: The New Science of Darwinian Medicine. Vintage Books.

Ewald, P.W. (1994) Evolution of Infectious Disease. Oxford University Press.

Janeway, C.A. et al. (2005) Immunobiology, 6th edition. Garland Science Publishing.

ACADEMIC AND GRADING POLICIES:

A 100-90%
B 89-80%
C 79-70%
D 69-60%
E <60%

The revised grading scheme is as follows: The higher of your two midterm scores will count for 25% of your overall grade. The lower one will be downweighted to 10%. The term paper will be worth 25%.

If you do NOT want to downweight one of your midterm scores, you can opt for the alternative scheme where both midterms are worth 25% and the term paper is worth 10%. You need to email me on or before Monday Dec. 5 to request this option, though (no need to do this again if you've already done so).

Undergraduate students will be required to choose a single, original research article from a peer-reviewed journal (not a “review” article, and not a “news” article) on a topic that interests them, then write a 1000 word paper that communicates (1) what question was addressed by the study and what methods were used, (2) what conclusions were reached, (3) whether there were any identifiable problems with the study, and (4) how the study contributed to the understanding of the evolution of infectious disease.

Graduate students, in addition to taking the midterms and final exam, will have to write a 3000 word term paper and give a ten-minute presentation on the same topic to the rest of the class. Topics will be chosen with the help of the instructor during the first three weeks of class. The goal will be to choose any subject relevant to the evolution of infectious disease, learn about it by reviewing the scientific literature, then communicate the “state-of-the-art” on that topic in both a written paper and live presentation.

SUGGESTED TOPICS AND SCHEDULE (check the Schedule page for the most up to date information):

T Aug. 22 -- Hand out syllabus, introductions
R Aug. 24 -- Course Overview

T Aug. 29 -- A brief introduction to evolutionary thinking
T Aug. 31 -- The central role of parasites in evolution

T Sep. 5 -- Diversity of infectious disease agents (I)
R Sep. 7 -- Diversity of infectious disease agents (II)

T Sep. 12 -- Immunology and disease: how vertebrate immunity works
R Sep. 14 -- Immunology and disease: how vertebrate immunity works

T Sep. 19 -- Immunology and disease: how vertebrate immunity works
R Sep. 21 -- EXAM

T Sep. 26 -- Exam Discussion
R Sep. 28 -- Antigenic variation in parasites

T Oct. 3 -- Guest lecture: Dr. Nancy Moran on Symbiotic bacteria in animals
R Oct. 5 -- Guest lecture: Dr. Howard Ochman: Genomics of pathogens

T Oct. 10 -- Trees and disease: phylogenetics and molecular epidemiology
R Oct. 12 -- Trees and disease: phylogenetics and molecular epidemiology

T Oct. 17 -- Trees and disease (cont.) : phylogenetics and molecular epidemiology
R Oct. 19 -- Evolution of virulence

T Oct. 24 -- Darwinian medicine
R Oct. 26 -- EXAM

T Oct. 31 -- Exam review, Impact of infectious disease on human evolution
R Nov. 2 -- Darwinian Medicine

T Nov. 7 -- Evolution of antimicrobial drug resistance
R Nov. 9 -- Evolutionary approach to vaccines

T Nov. 14 -- Case study: influenza virus
R Nov. 16 -- Case study: HIV

T Nov. 21 -- Graduate student presentations I
R Nov. 23 -- NO CLASS (THANKSGIVING BREAK)

T Nov. 28 -- Graduate student presentations II
R Nov. 30 -- IN CLASS FINAL EXAM

T Dec. 5 -- Last class: review of course, the future of infectious disease