HONR 278K: Evolution, Health, and Medicine

TIME: MW 3-4:15 HJP 1216

Charles F. Delwiche, Professor Dept. of Cell Biology and Molecular Genetics

Humans are living organisms, and as such our health is a biological phenomenon, structured by and subject to the constraints imposed by evolution. This is not just an abstract concept; an understanding of evolution can be used to help predict events that can mean life or death to millions of people every year. Despite this, many people are unaware that evolution plays a role in medicine. We will spend the semester exploring ways in which evolutionary phenomena influence health and medicine. Among the specific phenomena we will discuss will be: the emergence of multiple-drug resistant bacteria (“superbugs”); how natural selection governs the progression of cancer; diseases such as bubonic plague, AIDS, and influenza that have moved from animals to humans; human genetic variation and how it influences our health; and how our health is influenced by the bacteria that live in and on our bodies (the “human microbiome”).

We will use Carl Zimmer’s The Tangled Bank (2nd ed.) as our common reference for evolutionary biology, but more of the readings for the semester will come from news articles, magazines, and the scientific literature. One of our objectives for the semester will be for you to build comfort with reading articles from the scientific literature. We will also read a novel, George R. Stewart’s Earth Abides, which was first published in 1949, and remains a fascinating meditation on the interactions between humans and the natural world.

The course will be primarily discussion-based, with students working in teams to present readings, moderate discussions, and maintain a blog during the semester. Students will peer- review their colleagues work, and will give an oral presentation summarizing their semester blog.

The course will include one or two optional Weekend field trips, to the Smithsonian Institution National Museum of Natural History and/or to the National Museum of Health and Medicine. HONR278K: Evolution, Health, and Medicine

SYLLABUS INFORMATION

Instructor Dr. Charles Delwiche Professor, Department of Cell Biology and Molecular Genetics Office Hours: MW 2-2:50 (or by appointment) email: [email protected] -- this is the best way to contact me Telephone: 301-405-8286 (emergencies only) Gwen Warman @ 5-6991 can also make appointments for me. Office: 2108 BRB (please, during office hours only)

Required Books Zimmer, Carl. 2014. The Tangled Bank: An Introduction to Evolution, 2nd Edition. Roberts & Company, Greenwood Village, Colorado. ISBN-13: 978-1936221448

Stewart, George R. 2006 Earth Abides. Del Rey; Reprint Edition. ISBN-13: 978- 0345487131

Canvas Many course administrative matters will be handled through the Canvas online system (Elms), and it will typically have the most up to date information. All students are expected to make use of this material, and to log onto Canvas regularly. We will make extensive use of the Canvas Wiki tool. Access Canvas at: http://elms.umd.edu

Questions For most classes students are required to submit a one-sentence question on the reading, due at midnight the night before class. Late submissions will not be accepted. Questions will be graded 0-5 points. Five-point questions are those that are especially insightful and run to the heart of key topics in the reading. If two or more students submit the same question (with “sameness” to be determined by the instructor), no points will be given; those students will be assigned to work together to come up with a single, new question that is more imaginative; the grade will then be based on that new question.

Discussions Each student will participate in six group presentations, acting twice as group leader, and four times as an assistant (twice as discussion leader, and twice as foil). Each discussion topic will have background reading, and the entire class is expected to have read these prior to coming to class. The members of each group should work together (in person or via email) to prepare for the topic assigned. 10 points of the each participant’s grade will be a shared grade based on the overall performance, while the remaining points will be assigned based on that individual’s performance in class. Term project Through the course of the semester each student will maintain a blog. Early in the semester each student will pick a specific research topic to focus on in their blog, and to connect to the course subject matter each week. This subject must be consistent with the course theme, and consequently must have both evolutionary and biomedical significance. Five times during the semester the blog will be submitted for grading and peer review. At the end of the semester, taken together, the blog should provide an overview of the topic, information on the evolutionary processes involved, a discussion of history and medical importance of the subject, and figures and literature cited as appropriate. Students will present their projects during the last week(s) of the semester.

Reviews of peer’s blogs Each student will review two blogs prepared by other students on each submission. They may comment on the blog as appropriate (the original author will, of course see comments posted to the blog). The student can also submit a brief review to the instructor. The blog will be graded on the basis of: 1) relevance to the course subject matter, 2) originality and creativity of thought, 3) quality of reasoning, logic, and use of evidence-based argumentation, and 4) presentation, including language and grammar, formatting, use of graphics, etc.

Grading Presentations 100 points (20 for Leader, 15 for assistants) Participation 25 points (awarded one per class session) Questions 100 points (5 points per question) Blog entries 100 points (20 points per 5 submissions) Reviews 50 points (5 pts each, 2 per submission) Final presentation 25 points Final Exam 100 points

Total: 400 points

Participation points and questions are considered minor graded exercises and cannot be made up. All other exercises are considered major graded exercises. When practical, emergency absences will be accommodated by rescheduling the (entire) presentation. If this is not practical, then the missed exercise will be made up by oral exam or written assignment (at the same level of difficulty). The blog and reviews are not in-class exercises, cannot be excused, and late assignments will not be accepted.

Grading will use the letter grade +/- system, and will be based on rank in the course. Rank is determined by the average percentage of points earned. To earn a given grade, students must demonstrate an understanding of the course subject matter in keeping with the Undergraduate Catalog: A -- denotes excellent mastery of the subject and outstanding scholarship; B -- ; C -- denotes acceptable mastery of the subject. D -- denotes borderline understanding of the subject. It denotes marginal performance, and it does not represent satisfactory progress toward a degree; F -- denotes failure to understand the subject and unsatisfactory performance. The grade of A+ will be given to exceptional students, A- to students at the lower end of the "A" range, B+ to students at the upper end of the "B" range, etc. Students with the same point average will always receive the same grade, and those with a higher point average will always receive the same or higher grade.

Participation: This is a discussion-focused class. Attendance is technically not mandatory, but students should be aware that it is strongly correlated with grades. Students are expected to attend class, participate in class discussions, and behave in a professional manner. All assignments are required, and must be completed at the scheduled time. Students who anticipate schedule conflicts, including religious observances and athletic events, must identify themselves and the date of the anticipated conflict within the first two weeks of the semester. Students requesting accommodation for disability are expected to identify themselves and provide appropriate documentation within the first two weeks of the semester, and at least one week prior to each exercise for which accommodation will be requested.

Electronics: Cell phones and other gadgetry should be silent and unobtrusive at all times. Initially we will determine whether electronics of any kind are allowed in class each day by the toss of a coin; after an initial trial period we may choose to adopt one or the other approach permanently. Under any circumstances, a ringing cell phone must be turned over to the lecturer for the remainder of the class. Advance permission is required to record lectures. The lecturer may ask any student to leave at any time.

Academic Integrity Any lapses of academic integrity will be handled through the Honor Council, which has requested that the following information be provided:

The University of Maryland, College Park has a nationally recognized Code of Academic Integrity, administered by the Student Honor Council. This Code sets standards for academic integrity at Maryland for all undergraduate and graduate students. As a student you are responsible for upholding these standards for this course. It is very important for you to be aware of the consequences of cheating, fabrication, facilitation, and plagiarism. For more information on the Code of Academic Integrity or the Student Honor Council, please visit http://www.shc.umd.edu.

To further exhibit your commitment to academic integrity, remember to sign the Honor Pledge on all examinations and assignments: "I pledge on my honor that I have not given or received any unauthorized assistance on this examination (assignment)."

CourseEvalUM The provost has asked that the following be included in the syllabus:

Your participation in the evaluation of courses through CourseEvalUM is a responsibility you hold as a student member of our academic community. Your feedback is confidential and important to the improvement of teaching and learning at the University as well as to the tenure and promotion process. CourseEvalUM will be open for you to complete your evaluations for fall semester courses during the last two weeks of classes. Please go directly to the website (www.courseevalum.umd.edu) to complete your evaluations. By completing all of your evaluations each semester, you will have the privilege of accessing online, at Testudo, the evaluation reports for the thousands of courses for which 70% or more students submitted their evaluations.

Reading List See “Pages” online.

Schedule See Online.Supplementary Information: Topic Ideas for Projects These are some ideas for potentially interesting topics. There are many other possibilities. Bear in mind that some of these will be much more difficult than others.

1918 flu epidemic Alcohol tolerance & flush response Andean and Himalayan adaptation to high elevation BRCA1 Bubonic plague Changes in HIV through course of infection Clostridium difficile Cold adaptation in Inuit (Eskimo) populations Cold adaptation in Jul’hoansi and Australian aboriginals Cystic fibrosis – genetic basis for disease Cystic fibrosis – evolution of the pathogen during the course of disease Dengue fever E. coli O157 H7 Ebola Epigenetics and parental care Familial, sporadic, and acquired prion diseases G6PD Deficiency Gonorrhea Influenza Hansen’s disease Hanta virus Hemochromatosis Homosexuality Lactose tolerance Malaria – antibiotic resistance Malaria – human adaptations Mitochondrial ND3 and ATP6 and the arctic Neanderthal cold adaptation Obesity & gut flora Origin of HIV p53 and skin cancer Plasmodium falciparum SARS Sickle cell disease (see also malaria, above) Skin color Smallpox and Cowpox Tuberculosis West Nile Virus Spring 2015 Reading Assignments (From ELMS WIKI)

January 26

Supplementary reading

About the MMR Vaccine Lancet fraud mentioned in class on 1/26: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3136032/ More about measles: http://www.cdc.gov/measles Ebola: http://www.cdc.gov/vhf/ebola/ Influenza: http://www.cdc.gov/flu/

January 28

1. Streicker, D.G. 2013. From persistence to cross-species emergence of a viral zoonosis. Science 342: 1185-1186. DOI:10.1126Science.1247566. http://www.sciencemag.org/content/342/6163/1185.full.pdf? sid=bffae677-a8e9-4ba4-b063-c5b8271b2533

The Tangled Bank, 2nd Edition (2015 Notes)

2/2/15

Chapter 1: Introduction to Evolution

Chapter 2: A Brief History

2/4/15

Chapter 3: What the Rocks Say

Chapter 4: The Tree of Life

2/9/15

Chapter 5: Evolution's Raw Materials

Chapter 6: The Ways of Change

2/11/15

Chapter 7: Molecular Evolution

2/16/15

Chapter 8: Adaptation

Chapter 9: Sex and Family

2/18/15

Morbidity and Mortality 1. Armstrong, G.L., Conn, L.A., and Pinner, R.W. 1999. Trends in infectious disease mortality in the United States during the 20th Century. JAMA 281:61- 66. doi:10.1001/jama.281.1.61 http://jama.jamanetwork.com/article.aspx?articleid=768249 2. http://www.washingtonpost.com/opinions/why-science-is-so-hard-to-believe/2015/02/12/2ff8f064-b0a0- 11e4-886b-c22184f27c35_story.html?hpid=z6 Supplementary

Why today is the best time to live in human history: http://www.pri.org/stories/2015-02-16/why-today-best- time-live-human-history

2/23/15 Chapter 10: Darwin's First Question

Chapter 11 Macroevolution

2/25/15

Chapter 12: Intimate Partnerships

3/2/15

Chapter 13: Minds and Microbes

Supplemental:

Since we have been talking about the separation between what we perceive and what our senses are actually registering, we can engage this: http://www.washingtonpost.com/blogs/wonkblog/wp/2015/02/27/12-fascinating-optical-illusions- show-how-color-can-trick-the-eye/?hpid=z1 3/4/15

Chapter 14: A New Kind of Ape

3/9/15

Chapter 15: Evolutionary Medicine

3/11/15

Discussion

1. Carrol S.P. et al., 2014. Applying evolutionary biology to address global challenges. Science 346: http://www.sciencemag.org/content/346/6207/1245993.full 2. Please review readings from 2/18/15 as well. Supplementary

Palumbi, S.R. 2001 Humans as the World's Greatest Evolutionary Force. Science 293:1786- 1790. DOI:10.1126/science.293.5536.1786 http://www.sciencemag.org/content/293/5536/1786.full? sid=19bd60bf-bb61-4fef-b4d5-7a4841c4ee7c

-- Spring Break --

Multiple Drug Resistant Bacteria

3/23/15

1. Levy, Stuart B. 1998. The Challenge of Antibiotic Resistance. Scientific American 278:46-53. doi:10.1038/scientificamerican0398-46. 2. Groopman, J. 2012 Sex and the Superbug New Yorker 88:26- 30. http://search.ebscohost.com/login.aspx?direct=true&db=f5h&AN=82215679&site=ehost-live 2015-03-23 Course Notes

3/25/15

1. Cannon, B. 2014. Resistance Fighters. Nature 509:S6. http://www.nature.com/nature/journal/v509/n7498_supp/pdf/509S6a.pdf 2. Watch the frontline episode on Multiple-Drug Resistant Tuberculosis: http://www.pbs.org/wgbh/pages/frontline/tb-silent-killer/ Supplementary:

And on other multiple-drug resistant bacteria: http://www.pbs.org/wgbh/pages/frontline/hunting-the- nightmare-bacteria/ McDonald's stops using antibiotics in chicken: http://wapo.st/1GkhHkv 2015-03-25 Course Notes

Earth Abides I

3/30/15

Cancer

PBS is running a series called The Emperor of All Maladies. This is based on the book by Siddhartha Mukherjee, which is excellent, so I imagine the TV series will be well worth watching as well.

4/1/15

1. Merlo, L.M.F. et al., 2006. Cancer as an evolutionary and ecological process. Nature Reviews Cancer 6:924-935. doi:10.1038/nrc2013

2. Greaves, M. and Maley, C.C. 2012. Clonal evolution in cancer. Nature 481:306- 313. doi:10.1038/nature10762 http://www.nature.com/nature/journal/v481/n7381/full/nature10762.html

2015-04-01 Course Notes

4/6/15

1. Murchison et al., 2014. Transmissible dog cancer genome reveals the origin and history of an ancient cell lineage. Science 343: 437- 440. DOI: 10.1126/science.1247167 2. Nowell, P.C. 1976. The clonal evolution of tumor cell populations. Science 194:23-28. Supplementary:

Hiding in plain sight - an ancient dog in the modern world. [News piece describing transmissible cancer in dogs (Murchison et al. 2014)]: http://www.sciencemag.org/content/343/6169/376.summary An NPR piece on the same topic (transmissible dog cancer): http://www.npr.org/blogs/health/2014/01/23/265236618/contagious-cancer-in-dogs-leaves- prehistoric-paw-prints 2015-04-06 Course Notes

Zoonotic Diseases

4/8/15

Kilpatrick, A. Marm, and Randolph, Sarah E. 2012 Drivers, dynamics, and control of emerging vector- borne zoonotic diseases . The Lancet 380:1946-55. Faria, Nuno R., et al. 2014. The early spread and epidemic ignition of HIV-I in human populations . Science 346:56-61. See also news & views in same issue: Cohen, Jon. 2014. Early AIDS virus may have ridden Africa's rails . Science 346:21-22. It is probably a good idea to read this piece first, then read the primary article. 2015-04-08 Course Notes

4/13/15

Morse, Stephen S. et al., 2012. Prediction and prevention of the next pandemic zoonosis . The Lancet 380:1956-1965. Taubenberger, Jeffrey K., and Kash, John C. 2010. Influenza virus evolution, host adaptation, and pandemic formation . Cell Host & Microbe 7:440-451. 2015-04-13 Course Notes

Supplementary:

Nice data graphic on vaccination: http://graphics.wsj.com/infectious-diseases-and-vaccines/ Earth Abides II

4/15/15 - Second discussion of Earth Abides

Human Genetic Variation

4/20/15

1. Campbell, M.C., and Tishkoff, S.A. 2010. The Evolution of Human Genetic and Phenotypic Variation in Africa. Current Biology 20:R166- R173. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2945812/ 2. Barbujani, G., and Colonna, V. 2010. Human genetic variation: frequently asked questions. Trends in Genetics 26:285-295. 2015-04-20 Class Notes

Supplementary: A more recent update of the Campbell and Tishkoff article from 4/20/15: http://cshperspectives.cshlp.org/content/6/7/a008524.long

Human dispersal:

http://www.sciencemag.org/content/347/6223/708.full?sid=01bc83cc-59f3-49eb-ad20-96591945d250 Race and ethnic identity:

Skin color: http://www.sciencemag.org/content/346/6212/934.full

Admixture: http://www.nytimes.com/2014/12/25/science/23andme-genetic-ethnicity-study.html?_r=1 http://www.cell.com/ajhg/fulltext/S0002-9297(14)00476-5 4/22/15

1. Leslie, S. et al. 2015. The fine-scale genetic structure of the British population. Nature 519:309- 314. http://www.nature.com/nature/journal/v519/n7543/full/nature14230.html 2. Vernot, B., and Akey, J.M. 2014. Resurrecting surviving neanderthal lineages from modern human genomes. Science 343:1017-1021. doi:10.1126/science.1245938 http://www.sciencemag.org/content/343/6174/1017.full?sid=8f95b8b2- bce0-440a-b1fe-c50e88565925 Supplementary:

Callaway, E. 2014. The Neanderthal in the family. Nature 507:414. http://www.nature.com/news/human- evolution-the-neanderthal-in-the-family-1.14932 Chimerism in humans and its developmental effects on sex:

Ainsworth, C. 2015 Sex redefined. Nature 518:288-291 http://www.nature.com/news/sex-redefined- 1.16943 Evolution and the biology of homosexuality:

http://www.bbc.com/news/magazine-26089486?ocid=global_bbccom_email_18022014_magazine Gay animals: http://www.nytimes.com/2010/04/04/magazine/04animals-t.html?_r=0 Warfare and Cooperation

Bowles, S. 2009. Did warfare among ancestral hunter-gatherers affect the evolution of human social behaviors? Science 324:1293-1298. http://www.sciencemag.org/content/324/5932/1293.full Pennisi, E. On the origin of cooperation. Science 325:1196-1199

http://www.sciencemag.org/content/325/5945/1196.full?sid=6f432e72-caee-4989-8db8-2111180fb62c

Human Microbiome

4/27/15

1. Cho et al., 2012. The human microbiome: at the interface of health and disease. Nature Reviews Genetics 13:260-270. http://www.nature.com/nrg/journal/v13/n4/full/nrg3182.html 2. Turnbaugh, P.J., et al. 2006. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444:1027-1031. doi:10.1038/nature05414 Supplementary, but recommended:

Pennisi, E. 2011. Girth and the gut (bacteria). Science 332:32- 33. http://www.sciencemag.org/content/332/6025/32.full.pdf?sid=e134b71c-e657-4e3b-a160- 13377aaaec85 A nice "News & Views" piece about the article: http://www.nature.com/nature/journal/v444/n7122/full/4441009a.html Composition of gut microflora and obesity: http://www.nature.com/nature/journal/v444/n7122/full/4441022a.html

4/29/15

1. Collins, S.M., Surette, M., and Bercik, P. 2012. The interplay between the intestinal microbiota and the brain. Nature Reviews Microbiology 10:735- 742. http://www.nature.com/nrmicro/journal/v10/n11/pdf/nrmicro2876.pdf 2. Garrett, W.S. 2015. Cancer and the microbiota. Science 348:80- 86. http://www.sciencemag.org/content/348/6230/80.full.pdf?sid=61af1800-3dc4-4b66-96be- 3bd52d139218 Supplementary:

Your microbes follow you from house to house: http://www.sciencemag.org/content/345/6200/1048 The vaginal microbiome during pregnancy and postpartum: http://www.nature.com/srep/2015/150311/srep08988/full/srep08988.html More on cancer and the gut microbiota: http://stm.sciencemag.org/content/7/271/271ps1.full? sid=ce0f8084-283f-42e0-9119-3dec99e56f25 Drugging the gut microbiota: http://www.nature.com/nbt/journal/v33/n3/full/nbt.3161.html Mental health: thinking from the gut: http://www.nature.com/nature/journal/v518/n7540_supp/full/518S13a.html The End Game

5/4/15 - Discussion

Supplementary:

There is an outbreak of bird flu going on right now (April 2015) in Iowa, and millions of chickens are going to have to die: http://www.washingtonpost.com/news/morning-mix/wp/2015/04/21/millions-of-hens-to-be-euthanized-at- iowa-farm-with-bird-flu/ 5/6/15 - Presentations

5/11/15 - Presentations