In recent years, the field of population biology, encompassing both ecology and evolution and its intersections, has increasingly recognized disease as a centrally important phenomenon. For example, disease may influence the population dynamics of host organisms and the structure of natural communities, and may be an important agent of natural selection and thus evolution. So, there is a growing body of both theoretical and empirical scientific literature on host-parasite population interactions. These studies investigate a wide spectrum of disease problems; for example, the role of host genetic resistance in the spread of an epidemic, the coevolution of parasite and host, or the effect of host density on disease transmission. The organisms studied in this body of work range across the biological spectrum, including microscopic disease agents, and hosts such as wild herbaceous plants, crops, forestry trees, wild animals, insect crop pests, domestic cows, humans - to name just a few. Human disease deserves a special mention. Growing out of this general recognition of the key role of disease in natural populations and the application of evolutionary principles to it, there has been in the past 10 years or so a vigorous effort to apply Darwinian thinking to human disease. For example, is there as adaptationist explanation for fever, and if so should this influence our attitudes toward its treatment? This new field is called Darwinian medicine.

This is your capstone course in Biology, and you bring to it all of your learning and skills from previous courses and experiences. Now you have this opportunity to function at the very top of your scientific ability, applying your knowledge and reasoning to the understanding and communication of ideas and results of research. I expect the very highest quality of effort and outcome from each of you in this capstone experience. Here are the goals:

1. Immersion in the primary scientific literature:

• become comfortable finding, reading, and evaluating original research papers published in the peer-reviewed journals.
• make connections between separate papers that address different aspects of a shared problem
• find new questions to ask, informed by the research you have read about

2. Public speaking in a scientific setting:

• gain experience explaining complex scientific ideas and research to a peer audience.

• develop ability to lead discussion about scientific work
• develop critical listening skills
• gain experience with creating a technology-based presentation

3. Scientific writing

• be able to write a clear, concise abstract or overview of a large body of research.
• be able to write a thorough, well reasoned critique of a scientific paper, drawing on other related papers.

Each class meeting will consist of about three presentations by students, followed by discussion in which the entire class participates, but that is led by a student facilitator. My role is mostly as advisor to you as you develop your presentations, organizer of the schedule, and evaluator of your work. Each person will make two presentations, write one overview and one critique based on the papers s/he presents, act as facilitator twice, and participate in the peer audience for all other presentations.

I will assign a letter grade to each item. Peer evaluations will be factored into the grades for presentations. The quality of effort, preparation, and delivery of papers will constitute the major basis for your grade. For example, reasonable, above average efforts will lead to B grades. Outstanding presentations will lead to A grades. The final grade will be determined by weighting these grades approximately by the percentages given below:

First draft overview/abstract ( approx. 2-3 pp.) 5%

Final draft overview/abstract 5%

Presentation 20%

Written paper critique (approx. 4-5 pp.) 20%

Presentation 30%

Participation 20%

includes facilitating twice, peer audience otherwise

(requires reading and thinking about 1-3 papers per week,

unless you are presenting),

attendance at two Biology Department Seminars.

1. Both presentations should be done with PowerPoint (see Media Center for help).

2. You have about 20 minutes for the presentation, followed by 15 minutes of discussion with the class (35 - 40 minutes total).

3. For everything you say, have a slide that accompanies it. The slide may be text or graphics or photos.

4. Use illustrations as much as possible.

5. Make the presentation very very very organized -- make sure it has a clear flow, make use of summary slides, slides that introduce new sections, etc.

6. Do not try to present everything in the paper equally. Instead, you will probably need to concentrate on some main parts of it - you only have 20 minutes!

7. Start by explaining to the audience why the work you are talking about is important, where it fits into the bigger scientific picture in its field, and also by describing the organisms that were studied (pictures are very useful here).

8. Suggest some interesting questions and further directions to go with this type of work.

9. See attached "Basic anatomy of a scientific paper."

You are the discussion leader for this paper. You should be ready with a list of thoughtful, penetrating questions about the ideas in the paper. Be ready with the first question, and with other questions to ask or points to make when the discussion falters. Be ready to ask a follow-up question of either another audience member or the presenter. All of this means you must be almost as familiar with the paper as the presenter. I will be keeping track of both the quality and quantity of the questions you ask, the comments that you make, and how well you lead the discussion.

You should also come prepared with thoughtful, penetrating questions about the ideas in each paper. Thus you must read the papers carefully before class. I will keep track of both the quality and quantity of the questions that you ask and comments that you make.

You will also act as peer evaluator for one of the presentations each week.

1. You will pick a subtopic within the topic of the seminar, for which you have found and chosen a review article (see list at the end for possible ideas). Pick this paper after looking at many others, so that you are sure to choose one that interests you the most. While the focus of the seminar is on the primary literature, you will start off with a review article as the centerpiece of your first presentation. This will teach you how to look at and evaluate an overall body of work. For a review article the author reads all of the relevant recent literature on a topic and then writes an article that gives an overview of the topic at that point in time. An important reason for doing this is to illustrate areas where future work needs to be done.

2. After you have read the article, pick 5 other papers from its bibliography and read those also.

3. One week before you present:

• give me one copy of the review article, and give me a good first draft of an overview/abstract of your talk (probably about 2-3 pages, typed double spaced). I will comment and return to you in about two days. Make sure you correctly cite the other 5 papers and the review paper (see the method for citing used on the list below).
• put one copy of the review paper on reserve at the library.
• For every day you are late your presentation grade will be reduced by one half letter.

4. In your presentation, your job is to teach the class about this subtopic, using the review article as your guide, and bringing in mention of the work in the other 5 articles to emphasize some of the points.

5. On the day of your presentation, hand in the final draft of your abstract.

1. Pick three papers from the primary literature. To find papers that interest you, that you understand very well, and that you think can be presented well in the time allotted, you should plan to spend 5-10 hours in the library finding and reading papers. It is VERY likely that you will want to send away for some papers through interlibrary loan, or you may want to visit a different library (the Biology Library at Princeton University, for example). So you must PLAN AHEAD!!! Give inter-library loan about a week to get a paper for you (sometimes as long as two weeks).

2. Give me copies of these papers AT LEAST two weeks before you are scheduled to present. Within about two days I will look at them and help you choose which one to present and critique. I will keep the copy of the one you will present.

3. One week before you present:

• Hand in a written critique (only the final draft for this one) of the paper. This will be about 4-5 pages,

consisting of an abstract of the paper ( your own version, not the paper's own abstract), and valid criticism of a) the science of the paper - the reasoning, the methods, the conclusions, the interpretation, etc. (no paper is perfect - there is always some criticism to make); and b) the fine details of the paper -- spelling or math errors, wrong figure captions, unclear tables, etc. (this part is less important than the first part). For the first part of the critique you should draw on at least three other papers that address similar questions or use a similar methodology, but that have a different perspective or reach different conclusions. In addition to giving you more experience with scientific writing , the purpose of this assignment is to prompt you to read a paper more carefully and critically than you ever have before, and to ensure that you have understood the paper thoroughly before you start to prepare your presentation. You will truly develop the skill of reading scientific papers.

• Put one copy of the paper on reserve.
• For every day you are late, your presentation grade will be reduced by one half letter.

4. In this presentation you will talk about the paper as if you had done the study (but not in first person voice). You will present an introduction, the methods, the results, and the interpretation and conclusions, following the guidelines listed above.

Scientific topics are presented in a very large number of sources. For this seminar, with the exception of the first review article, you will be reading only peer-reviewed research papers from scientific journals. These papers present original research done by scientists, and then reviewed by other scientists and a board of editors of the journal before it is accepted for publication. These journals may also publish research reviews, book reviews, commentary, etc. You will only read the research papers (except for the first review article).

If you have a question about the appropriateness of a journal or paper, then ask me early.

1. Browse the journals - look in recent copies in the reading room, or look through the bound volumes. The December issue of each year will have an index.

2. Check out the bibliographies of papers to see titles of other related papers.

3. Check out the bibliographies of review papers for titles of research papers.

4. Search for papers using a computerized database, including Cambridge Scientific Abstracts, BIOSIS, AGRICOLA, WILNOW. Ask the reference librarians to help you.

Baquero, F. and J. Blazquez. 1997. Evolution of antibiotic resistance. Trends in Ecology and Evolution 12:482-487.

Burdon, J.J. and P.H. Thrall. 1999. Spatial and temporal patterns in coevolving plant and pathogen associations. The American Naturalist 153 (supplement): S15-S33.

Caldararo, N. 1996. The HIV/AIDS epidemic: Its evolutionary implications for human ecology with special reference to the immune system. Science of the Total Environment 191(3):245-269.

Ebert, D. and W.D. Hamilton. 1996. Sex against virulence: the coevolution of parasitic diseases. Trends in Ecology and Evolution 11:79-81.

Grenfell, B. and J. Harwood. 1997. (Meta)population dynamics of infectious diseases. Trends in Ecology and Evolution 12:395-399.

Hamilton, W.D., R. Axelrod, and R. Tanese. 1990. Sexual reproduction as an adaptation to resist parasites (a review). Proceedings of the National Academy of Sciences 87(9):3566-3573.

Harvell, C.D. 1990. The ecology and evolution of inducible defenses.

Quarterly Review of Biology 65(3):323-340.

Hudson, P. and J. Greenman. 1998. Competition mediated by parasites: biological and theoretical progress. Trends in Ecology and Evolution 13:387-390.

Jarosz, A.M. and A.L. Davelos. 1995. Effects of disease in wild plant populations and the evolution of pathogen aggressiveness. New Phytologist 129(3):371-387.

Johal, G.S., J. Gray, D. Gruis., and S.P. Briggs. 1995. Convergent insights into mechanisms determining disease and resistance response in plant - fungal interactions. Canadian Journal of Botany 73 (Supplement 1):S468-S474.

Leitmeyer, K and R. Rico-Hesse. 1997. Viral evolution and epidemiology.

Current Opinion in Infectious Diseases 10(5):367-371.

Martin, F.N. and J.E. Loper. 1999. Soilborne plant diseases caused by Pythium spp.: ecology, epidemiology, and prospects for biological control. Critical Reviews in Plant Sciences 18(2):111-181.

Michalakis, Y. and M.E. Hochberg. 1994. Parasitic effects on host life-history traits: A review of recent studies. Parasite 1(4):291-294.

Moller, A.P., P. Christie, and E. Lux. 1999. Parasitism, host immune function, and sexual selection. Quarterly Review of Biology 74: 3-20.

Nice, C.S. 1994. The dissemination of human infectious disease by birds. Reviews in Medical Microbiology 5(3):191-198.

Parker, M.A. 1994. Pathogens and sex in plants. Evolutionary Ecology 8(5):560-584.

Penn, D. and W.K. Potts. 1998. Chemical signals and parasite-mediated sexual selection. Trends in Ecology and Evolution 13: 391-396.

Poulin, R. 1996. The evolution of life history strategies in parasitic animals. Advances in Parasitology 37:106-134.

Richardson, L.L. 1998. Coral diseases: what is really known? Trends in Ecology and Evolution 13: 438-443.

Schmid-Hempel, P. and J.C. Koella. 1994. Variability and its implications for host-parasite interactions. Parasitology Today 10(3):98-103.

Sheldon, B.C. and S. Verhulst. 1996. Ecological immunology: costly parasite defences and trade-offs in evolutionary ecology. Trends in Ecology and Evolution 11:317-321.

Sorci, G., A.P. Moller, and T. Boulinier. 1997. Genetics of host-parasite interactions. Trends in Ecology & Evolution 12(5):196-200.

Thornhill, R. and A.P. Moller. 1997. Developmental stability, disease and medicine. Biological Reviews of the Cambridge Philosophical Society 72(4):497-548.

Wennstrom, A. 1999. The effect of systemic rusts and smuts on clonal plants in natural systems. Plant Ecology 141:93-97.

Williams, G.C. and R.M. Nesse. 1991. The dawn of Darwinian medicine.

Quarterly Review of Biology 66(1):1-22.

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