Discussion section assignments

Biology 354

Prof. Toby Bradshaw

http://courses.washington.edu/biol354

 

 

Week 1.  The goals of this week’s discussion section are to:

 

  • meet your TA and classmates;
  • identify a research topic that a group of you will work on for the remainder of the quarter; and,
  • get some tips on how to find and read scientific papers.

 

Below are three observations, for which evolutionary (and perhaps competing non-evolutionary) hypotheses could be developed and tested experimentally.  Discuss them among yourselves.  What is interesting about each observation?  What sorts of hypotheses and experiments can you imagine?

 

  1. Ashkenazi Jews have the highest average IQ test scores of any ethnic group.  Though they represent only 3% of all Americans, Ashkenazi Jews have won 27% of the Nobel Prizes awarded to U.S. scientists.  More than half of world chess champions are Ashkenazi Jews.

 

  1. Two species of monkeyflower, Mimulus lewisii and M. cardinalis, have strikingly different floral morphology, have different pollinators, and essentially never hybridize in nature where their ranges overlap.  Yet fertile F1 hybrids are easy to produce by hand-pollination, and the F2 hybrids (derived from self-pollinating the F1) segregate for all the traits that distinguish the two species.  In the F2 generation grown in the greenhouse there is a slight excess of cardinalis alleles (freq ~ 0.55 instead of the expected 0.50).  If F2 plants are self-pollinated for another 5 generations in the greenhouse, the proportion of cardinalis alleles increases to ~0.75.

 

  1. Invasive species are a leading cause of biodiversity loss.  The freshwater crustacean Daphnia lumholtzi appears to have been introduced into the southern U.S. from a source population in tropical Africa.  The first U.S. record of D. lumholtzi is from a Texas reservoir in 1990-91.  Since then, D. lumholtzi has spread steadily northward in the U.S., reaching the Great Lakes by the late 1990s.

 

Each person should produce a ranked list [1-3 (1=favorite; 3=least favorite)] of the preceding research project topics and turn the list in to the TA.  Your rankings will used to assign each of you to a group that will work on one of these projects for the rest of the quarter.

 

 

Week 2.  The goals of this week’s discussion section are to:

 

  • show your TA copies of the three scientific papers you found and read that provide background for your research topic;
  • discuss these papers with your group members;
  • work with your TA to indentify a paper for which you will write a review; and,
  • get some tips on how to write a review of a scientific paper.

 

A hard copy of this review is to be turned in to your TA at the beginning of the Week 3 discussion section.  A hard copy of the paper you are reviewing should be attached to your review. 

 

Reviews of scientific papers are meant to provide the reader (especially readers who may not be experts in the field) with:

 

  • a clear explanation of the hypothesis being tested, and the alternative (or null) hypothesis;
  • additional background and perspective;
  • a concise overview of the important findings;
  • a critique of any flaws in the experimental design or analysis;
  • an idea of what further questions have been raised by the new findings; and,
  • suggestions for future experiments or observations that might address these questions.

 

Your review should contain all of these elements.

 

To give you a feel for the kind of review we expect, we have made two pdf files available for downloading.  Both of these papers come from the journal Science, the weekly publication from the American Association for the Advancement of Science (AAAS, founded by Thomas Edison).  Science and Nature are the two most widely read (some would say most prestigious) scientific journals that cover the whole range of scientific disciplines, so their papers must be of general interest to all scientists.  Even in these “general interest” journals, the scientific papers can be difficult for scientists in other disciplines to understand, because of the specialized languages of physics, chemistry, biology, etc.  So, many of the most important papers are accompanied by reviews (Science calls them “Perspectives” and Nature calls them “News and Views”) written to appeal to the broadest possible scientific audience.  The Gingerich et al. paper describes the discovery of a fossil that provides insights into the phylogenetic relationship between modern whales and other modern mammals.  The Rose “Perspectives” is a review of the Gingerich et al. paper.  Use these papers to help you understand how your own review (which will resemble the Rose paper in style) should be written.  By reading these papers you will also find out some fascinating details about the evolution of some of Earth’s most charismatic megafauna!  Your textbook (Ch 14) has an excellent section on the controversy surrounding the evolutionary origin of whales, which you will find helpful.

 

A second pair of papers, from Nature, is also available.  Garant et al. is the original paper, and Coltman is the News & Views paper.

 

Your review should be no more than three pages long (including any illustrations, figures, tables, and references), double spaced,  with 12pt font and 1 inch margins, neatly printed single-sided on white paper.  Reviews will be graded on originality of thought, thoroughness in dissecting the paper under review, and clarity of expression.  Your TA will return your graded review to you, and you will have the opportunity to revise your review if you wish.

 

Your written review is to be an individual effort.  Please read and understand the UW policy on plagiarism.

 

Week 3.  This week you will formulate evolutionary hypotheses to explain the observation you are studying.  Alternative hypotheses (which may or may not be evolutionary) should also be developed.  Begin to think about, and discuss among yourselves and with your TA, what sorts of experiments might be designed, or observations made, to distinguish between alternative hypotheses.  Your TA will approve a hypothesis and an alternative for which you will develop experimental tests by next week.

 

 

Week 4.  Bring your individually-written experimental design (max 3 pages double-spaced, including any figures or tables) to the discussion section.  Typical elements of an experimental design include:

 

Hypothesis(es) and alternative(s)

Description of experimental treatment(s) or observation condition(s)

Description of and rationale for control(s)

Sample size(s)

Data to be collected (what type, how much, methods for collection)

Method(s) of data analysis

Expected outcomes under each hypothesis

 

Within each group, you will discuss the pros and cons of each person’s experimental design, and arrive at a consensus design that satisfies the whole group.  You will bring two copies of a written consensus experimental design (same format as above) to next week’s discussion section.

 

 

Week 5.  Each group will read the experimental design of another group, and discuss strengths and weaknesses of the design.  A critique consisting of a bullet list of strengths and weaknesses will be written and explained by the critics to the group that developed the experimental design.  Each group will consider the criticisms received when preparing to present its finalized experimental design to the whole discussion section in Week 6.  Each group will schedule a meeting with the instructor and TA, to take place before the Week 6 discussion section, to review and approve the experimental design.

 

 

Week 6.  Turn in a hard copy of the final experimental design to your TA.  Presentations of your experimental design should be brief – no more than 12 minutes, to leave time for questions and comments from your classmates.  The presentation should have clear and meaningful visuals (PowerPoint or overheads) providing:

 

A statement of the observation that initiated your project

An evolutionary hypothesis and one (or more) alternative hypotheses to explain the observation

An experimental test that distinguishes between the competing hypotheses

The rationale for the chosen experimental design, including controls

The type of data to be collected (what is measured, how it is measured, sample sizes)

The method(s) of analysis to be used

The expected outcome if your primary hypothesis is true

Limitations and caveats on your experimental design

 

 

Weeks 7-8.  Download your data.  Meet with your group to discuss and analyze the data you have been given.  Ask advice from your group and your TA on what sorts of statistical analyses are appropriate, and what inferences can be drawn from the results of those analyses.  Consider how you will intepret your results in light of your hypotheses.

 

 

Week 9.  Bring hard copies of the figures and tables for your individual papers to review with your group mates and your TA.

 

 

Week 10.  Work with your TA to put the final touches on your paper.  FINAL PAPERS MUST BE TURNED IN BY FRIDAY 10 MARCH BEFORE 5PM.  There will be boxes in the Plant Lab (L-14 on the campus map) labeled with your TA’s name.  Put your paper in the appropriate box.

 

Your final paper must be an individual effort.  Please read and understand the UW policy on plagiarism.  Your paper should be no more than 5 pages long (including figures, tables, and literature cited), single-spaced with 12pt font and 1” margins.  The general format of your paper should follow the style of a regular paper in the journal Evolution http://lsvl.la.asu.edu/evolution/instruct.html.  If you have never read a paper in Evolution, look through some recent issues of the journal to become familiar with the style.  Papers will be graded on the appropriateness of the hypotheses, the quality of the experimental design, the thoroughness and rigor of the data analysis, the thoughtfulness of the discussion, and clarity of expression.  Your paper should contain the following elements:

 

An informative title

An abstract summarizing the hypotheses, experiment(s), results, and discussion

An introduction giving some background and perspective on the project

Materials and methods (experimental design, methods of data collection and analysis)

Results (often summarized in tables, graphs)

Discussion (how your results fit into the “big picture”, what can and cannot be inferred from your data, alternative interpretations that could also explain your results, specific suggestions for future directions this work might take)

Acknowledgments

Literature cited