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Assignments for Fall 2013

BISC 830:  Community Ecology and Macroecology                       Cypress Park         

Nick's Collection on Communication

Reading Papers

A major component of this course will be reading and discussing the primary literature.  Although you are already reading a lot, it's likely that you aren't doing it as effectively as you could.  Critical evaluation of the literature means paying attention to particular things as you read.  Quite alot has been written about this.  We recommend the following resources:
From John Little and Roy Parker, U. Arizona:  How to Read a Scientific Paper
From Purdue, a Quick Tutorial on Reading Science Papers

Summaries of readings, in the style of The Economist 

In graduate school and beyond, you will have to communicate with other scientists (by writing papers, presenting at meetings, and so on) as well as with non-scientists (your family, natural history groups, and so on).  Nick and Elizabeth believe we all have a duty to communicate science to the broader community.   Our aim for these weekly summaries is threefold:  to ensure you've read the papers, to get you writing regularly so writing itself becomes a habit rather than a scary and time-consuming ordeal, and to give you practice in how to communicate complex scientific concepts to non-scientists (which is truly the best way to demonstrate you understand the scientific concepts).

Each week we will read 3 papers, one classic and 2 contemporary, chosen by classmates (this may change depending on enrollment).  For one of the contemporary papers, we ask you to write a short summary of the main points and why they are interesting, using the summaries of exciting findings published in The Economist as a guide.  Summaries should be 500 words, emailed to the instructor who taught the topic the papers are about before class (this may not be the person teaching that week!), and in word (not pdf) format to facilitate instructors making comments in the document. Note that whenever you email something to an instructor, your name should be part of the document name.

Here are two good examples of the sort of summary we are looking for from the Economist, and the scientific paper they are based on:
Sexual Selection in Birds, Economist
Original paper in PNAS

Plant Communication via Mycelial networks, Economist
Original Paper in Ecology Letters

For our first class meeting, please read one of these two pairs of papers so we can discuss how this sort of writing is done.  

Note the structure of these summaries;  they start with a paragraph introducing the general topic, then there are several paragraphs about a new paper, including what was studied, how, what the major findings are, and (importantly!) ending with a statement about why it is interesting.  Jargon is avoided, sentences are short and to the point, and being stylistically clever is encouraged.  

Here's a great piece by Tim Radford, former science editor of The Guardian:  A manifesto for the simple scribe

If you are leading a discussion in any given week, you don't have to turn in a summary.  

Leading a discussion

Each week we will discuss 3 papers, one classic and 2 that are contemporary.  Discussions of papers will begin with a brief discussion of the classics by the class, followed by a student-moderator lead discussion of a companion paper published in the last 5 years.  We prefer that these papers be data papers rather than reviews.

In the first class, you will sign up to present on one or more of the topics.  Although your companion paper must be on that general topic (ie, competition, predation, diversity estimation) it doesn't have to match the classic directly.  Your paper must be circulated to the class (the course e-mail list will work) by the Tuesday before our Friday class, along with 3-5 questions to stimulate discussion of the paper.  

When you are moderator, we expect a brief overview of the context of the paper (why it is interesting), hypotheses being tested or presented, and main findings--this should take no more than 5 minutes and preferably less (we've all read the papers!).  Your overview is not a presentation or a lecture (no powerpoints!).  Then, proceed to your list of insightful and stimulating discussion questions;  these should be open-ended, to stimulate discussion, and may include things like whether the methods adequately address the hypotheses, what caveats the authors should have considered, and whether the results or interpretations are supported by the data.  Total discussion time for each paper will be 30 minutes.  That actually isn't very long, so moderators need to put some effort into thinking about what the major concepts of the papers are and what the class should talk about.  We encourage moderators to use the classic paper and lecture material as a jumping-off point.

More tips on effective leading of discussions can be found here:
From T. W. Sherry of Tulane, Leading a Discussion of a Scientific Journal Article
P. Suber of Earlham College has some ideas of how to Plan your Discussion
From a Physics Teacher Training Program at Illinois State, How NOT to Lead a Discussion

The Review Paper

The final assignment in the course will be to write a review (or opinion) paper in the style of Trends in Ecology and Evolution.  From their website:

TREE Reviews are concise reviews of recent research in rapidly progressing or emerging areas.  They should briefly set the background and then concentrate on setting recent findings in context.  They should provide a balanced view of developments, even in fields that are controversial, and authors must never concentrate unduly on their own research.  

TREE Opinions should present a personal viewpoint on a research-related topic, rather than a balanced review of the topic.  The aim should be to stimulate debate or new research, cover controversial topics, or provide a new framework for, or interpretation of, an old problem or current issue, or speculate on the implications of some recent research.

Our audience ranges from student to professor and so articles must be accessible to a wide readership.  Please avoid jargon, but do not oversimplify:  be accurate and precise throughout.  

You should choose some area of community ecology that is of interest to you, and that ideally has some connections to your research.  Topic areas must be OK'd by your instructors during our class-wide discussion of the reviews on October 11.  Your review should be approximately 3000-3500 words (10 double-spaced pages). The review can be emailed to your instructors on November 29 by noon.  We will then do a round of peer review, and you will have a chance to revise your papers, but the final, no-excuses deadline to turn in your revision is 5 PM on December 13.

Information on format and content of TREE papers on their website.

Peer Review

In addition to encouraging you to critique each other's work informally during the term, we will ask you to perform formal peer review of  TREE papers written by two of your classmates.  Crtical assessment is an essential part of science, and learning how to provide useful feedback is definitely worthwhile.  Ideally, you want to provide specific but tactful feedback on the strengths and weaknesses of any work that you review, and this feedback should go beyond editorial comments to the larger issues of the work.

Your reviews should be short (1-2 pages), and should follow the following fairly typical format:  a summary paragraph (3-5 sentences) where you describe the main points of the paper;  a paragraph where you note more specifically major concerns with the paper, including, where relevant, suggestions for improvement;  and finally a list of concerns (by page and line number is helpful), often divided into major concerns and minor concerns.  

You should email your anonymous reviews to the Associate Editor (Elizabeth or Nick--whoever sent you the paper) by 5 PM December 5.  The AE will then make a decision (minor revision, major revision, etc) and return the paper and reviews to the author.  We'll also blind copy you on that correspondence so you can see our decision and the other peer review of the manuscript, as feedback for how you did.

Here are some resources about peer review.
An article from Bioscience, directed more at research papers and pre-submission review, but a great starting point.
The Ten Simple Rules collection;  there's lots of good stuff in here, but if you go through the list you'll see advice on reviewing.
And a long but useful guide on peer review from the British Ecological Society

Course Evaluation Breakdown:

TREE paper:  35%
Your review of two TREE papers written by classmates:  10%
Weekly write-ups, 5% each, * 6 = 30%
Discussion:  15% as moderator, 10% as participant