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INSTRUCTOR:       Pascal Gagneux Ph.D. (Professor, Departments of Pathology and Anthropology)



The course will explore the major epidemiological transitions from ape-like ancestors to foraging tribes, farmers and pastoralists, to the global metropolitan primate we now are. We will focus on how diseases have shaped humans and how humans have shaped disease over time.


FORMAT:            1 hour 20 minute  Lectures


READING:           Review article or book chapter.

                             PDF of each reading are posted on the course webpage and will be sent to each student via e-mail in advance of each class

                             Each student is expected to submit a question about the reading by 7am the day of the class.

DAY:                    Tuesday and Thursday

TIME:                  2:00 to 3:20 PM

LOCATION:        Solis 104

EXAMS:              A) Midterm, multiple choice, 1 hour on February 9.

                            B) Final: two hours, multiple choice & simple sentence replies to questions, March 23.


GRADES:           Grades will be based on student participation throughout, reading questions submitted, and Midterm and Final exam        


HONESTY:         This course does not tolerate academic dishonesty and follows UCSD policy on this matter. For more information       

                            see below.


January 5

Lecture 1:          What is disease and how sick are we?

                          Causes of sickness and mortality, unrealized potential, under and over-nourished, stunted, polluted, poisoned, mentally        

                          traumatized, culturally deprived etc. Obesity from status symbol to disease                             

                          Disease now: heart disease, cancer, respiratory disease (COPD), diabetes type 2, influenza/pneumonia, Alzheimers, traffic    

                          accidents, renal failure, septicemia, gun violence

                           READING:      no reading for first lecture.   


January 7

Lecture 2:           From the inside or from the outside (Virchow vs Pasteur/Koch)

                          Theories on the origin of maladies. The germ theory vs Virchow’s inner balance/ cell driven disease. Humors, Qi, Bingdu, Krimi

                           and Miasmas…….Malaria, Plague and leprosy.

                           READING:          Evolutionary Medicine, 2016, Stearns and Medzhitov. Chapter 1: Evolutionary Thinking

January 12       

Lecture 3:           Immunity and immune system & the cost of an effective defense

                   Evolved defenses of longer-lived, multicellular hosts. Life-saving reactions and life threatening over-reactions. Harnessing

                           immunity for prevention and cure.

                           READING:           Evolutionary Medicine, 2016, Stearns and Medzhitov. Chapter 2, part 1 p 28 to p57: What is a patient?

January 14         

Lecture 4:           Host-pathogen co-evolution

                   Arms races and truces between hosts and their pathogens and parasites. Foes become symbionts and symbionts can become


                           READING:         Evolutionary Medicine, 2016, Stearns and Medzhitov. Chapter 2, part 2 p 58 to p857: What is a patient?


January 19         (Hu)Man-made diseases & iatrogenic disease

Lecture 5            Ways of life and cultural practices can create disease. Humans can culturally define/invent diseases. Pellagra, HCV along Nile,

                           Puerperal fever, Toxic shock syndrome, Medication over- and misuse, drug abuse DES (diethylstilbestrol) daughters.

                           READING:           Evolutionary Medicine, 2016, Stearns and Medzhitov. Chapter 3: What is a disease?

January 21         

Lecture 6:           Eco-Health/ Emerging diseases

                   Human encroachment on and disruption of wild ecosystems generates novel diseases. The latest epidemiological Transition?

                           READING:           Evolutionary Medicine, 2016, Stearns and Medzhitov. Chapter 5: Defenses  

                                                       Evolutionary Medicine, 2016, Stearns and Medzhitov. Chapter 5: Pathogen Evolution

January 26        

Lecture 7:           The emperor of all maladies (Cancer)

                   If you have more than one cell, you might get cancer. Cancer perfectly combines nature and nurture.

                           READING:           The Puzzling Origins of AIDS. 2004. James J. Moore Sci. American


January 28        

Lecture 8:          Uniquely human diseases

                   Humans seem to be susceptible to a number of diseases not or only rarely seen in any other primates. The role of evolutionary


                           READING:           Evolutionary Medicine, 2016, Stearns and Medzhitov. Chapter 6: Cancer                   

February 2         Reconstructing past disease, Major epidemiological transitions

Lecture 9:           Paleopathology: how much can we find out about diseases in the distant past?                         

                           READING:   The Changing Disease Scape in the Third Epidemiological Transition. 2010. Kristin Harper and George

                                                       Armelagos  Int. J. Environ. Res. Public Health      


February 4          

Lecture 10:        The three smokes

                   How exposure to environmental, indoor and tobacco smoke kills   


February 9         MIDTERM (one hour on CANVAS)

                   READING: Evolutionary Medicine, 2016, Stearns and Medzhitov. Chapter 8: Mismatch


February 11

Lecture 11:        Disease as a weapon, unintentional and intentional

                          Humans have inadvertently and intentionally used disease as a powerful weapon.

                           READING:           History of biological warfare and bioterrorism. 2014. Barras and  Greub, Clinical Microbiology and Infection


February 16

Lecture 12:        Diseases of other primates & Domesticated disease? Endogenous retroviruses,           

                   transposons etc.

                          What diseases do our closer and more distant evolutionary relatives suffer from?

                           READING:           Primates and the Ecology of Their Infectious Diseases: How will Anthropogenic Change Affect Host-Parasite                                                              Interactions? 2005. Chapman et al. Evolutionary Anthropology.

February 18

Lecture 13:         Reproductive disease

                           Evolution acts mostly on differential reproduction. What are reproductive diseases?

                           READING:           Evolutionary Medicine, 2016, Stearns and Medzhitov. Chapter 7: Reproductive Disease


February 23

Lecture 14:        Cultural attitudes to disease

                          Attempts to make sense of disease. From blaming the victim to patient-interest groups. How culture, technology and commerce

                           can become a viruses’ best friends.

                           READING:           The Anthropology of Infectious Disease. 1990. Inhorn and Brown. Ann. Rev. Anthropol.


February 25

Lecture 15:        Affluenza and SESitis?

                          Do modern humans suffer from microbe deficit disorder. How socio-economic status (SES), affluence or poverty can make you


                           READING:           Sick of Poverty/ 2005 Robert Sapolski. Scientific American.


March 2

Lecture 16:        The mind/brain, our most fail-prone organ?

                          No other organ has such a high failure rate as the human brain. How costly is our most unusual organ?

                          READING:           Evolutionary Medicine, 2016, Stearns and Medzhitov. Chapter 9, Mental disorders


March 4

Lecture 17:        Violence as an infectious disease.

                          Diseased behavior? Can societies have diseases? Epidemics of suicide?

                          READING:           The Transmission of Gun and Other Weapon-Involved Violence Within Social

                                                        Networks, 2016 Tracy et al. Epidemiologic Reviews


March 9

Lecture 18:        Diet and Disease

                          How we humans are eating ourselves sick

                          READING:          Sonnenburg, E.D., Sonnenburg, J.L. The ancestral and industrialized gut microbiota and implications for          

                                                       human health. Nat Rev Microbiol 17, 383–390 (2019).   


March 11

Lecture 19:         Healthy living?

                           Preventive medicine, not as sexy as genetic engineering, but much cheaper!

                           READING:       Will Genomics Widen or Help Heal the Schism Between Medicine and Public Health?

                                                   Khoury, M.J.  et al. Am J Prev Med 2007;33(4)                           

March 16

Lecture 20:         Recap

                           Are we "Homo pathogenic et therapeuticus? Creating our own diseases and cures?

                           READING:       Corbett, S., Courtiol, A., Lummaa, V. et al. The transition to modernity and chronic disease: mismatch and natural

                                                   selection. Nat Rev Genet 19, 419–430 (2018).




March 23              Final exam

                 in person 3-5:59 pm




Statement on Academic Integrity:

“Academic Integrity is expected of everyone at UC San Diego. This means that you must be honest, fair, responsible, respectful, and trustworthy in all of your actions. Lying, cheating or any other forms of dishonesty will not be tolerated because they undermine learning and the University’s ability to certify students’ knowledge and abilities. Thus, any attempt to get, or help another get, a grade by cheating, lying or dishonesty will be reported to the Academic Integrity Office and will result sanctions. Sanctions can include an F in this class and suspension or dismissal from the University. So, think carefully before you act. Before you act ask yourself the following questions: a) is my action honest, fair, respectful, responsible & trustworthy and, b) is my action authorized by the instructor? If you are unsure, don’t ask a friend—ask your instructor, instructional assistant, or the Academic Integrity Office. You can learn more about academic integrity at” (Source: Tricia Bertram Gallant, Ph.D., UCSD Academic Integrity Office, 2017)