Your grade will be determined as described below. In general, you will not be directly tested on the lecture material except as it applies to the papers, or is reflected in the homework. You are encouraged to write the Honor Pledge on your assignments. I encourage you to work together to prepare your presentations and to discuss the papers and homework, but you are expected to prepare your own homework and you are responsible for your own answers.

Papers The goal is to learn how to extract from a paper:
- what claims are being made
- how the results were obtained (i.e. which experiments were done)
- why the experiments were done the way they were
- whether the data justify the conclusions and what caveats remain
- why these experiments were done at all; and why we should care

On the date that a paper is to be discussed, come to class familiar with the paper, and with a copy of the paper in hand. You will be graded on your familiarity with the papers, as judged by your presentations, by your contributions to the overall discussion, and by quizzes. Your familiarity with the papers will be judged by your participation in the discussion, including presentation of material (30% of your grade) and by quizzes (40%; see below). The first part of class meetings on Tuesdays (starting April 7) will be devoted to paper presentations.

I may call on your opinion of some point, ask you to explain a section, or ask you to present a defined section of the paper (usually one figure, or a part of a figure) in front of the class. Each participation grade will appear on Blackboard as "Partic. n," where n is a number between 1 and 9 that indicates the weight of the grade. "Grades" will be -, = or +. In case of presentations, your presentation will be graded based on the clarity with which you cover the following four things:

Everyone is subject to being called on at any time. The selection of students for questions and presentation will be essentially random, and I actually use a random number generator to select names. However, I will try to make sure that everyone has had an opportunity to prove themselves, and I may call on students in order to refocus their attention on the paper. You can decline to present, but it will affect your grade. I will post a simple "grade" for each contribution on Blackboard within a day (the "grade" will consist of a number indicating the degree of your participate (how much you did) and a letter, either M (for -), E (for =) or P (for +), indicating how well you did. I'm not going to spit hairs, just note your participate, so please expect to get Es. In the case of a M (and sometimes in the case of a P) I may send an explanation by email after class, especially if I feel that you would benefit from an explanation. You should also feel free to ask for an explanation.

This year I have abandoned a set of rules used in past years because they grew to be overly complex and do not work well for a larger class. You may volunteer to present. Any contributions to the discussion that aids everyone's understanding of the paper will help your grade. Good questions are especially encouraged. I will never grade anyone down for asking honest questions about the paper.

A quiz may be given on a paper on presentation day. In some cases, there may be a brief quiz before our discussion of the paper. In other cases, the discussion may be replaced by a full one-hour quiz, or the quiz will come at the end. Some quizzes will count more than others. This weighting will be reflected in the total number of points in the quiz.

Homework will be assigned at least one week (two class meetings) before the due date. Homework is due at the beginning of class. In many cases, homework questions will direct your reading to essential points of the paper. However, not all papers will have homework, and not all homework will be specifically related to a paper. There will be less than 8 homework assignments. However, the number of points that are actually graded will vary between assignments. Whether or not I accept late homework, and how much it is discounted, will vary depending on many factors, including whether the homework was discussed in class before the late homework was turned in, and why it was not turned in on time. In order to accomodate the inevitable problems that come up, the lowest homework grade will be dropped before averaging. This will have to be done on a case-by-case basis because different homework assignments will count for different amounts. Not all homework will be graded. Only homework that is graded and returned within one week of the due date will be counted.

Each of you will be assigned a gene. I will send you the accession number for the yeast version of the gene, and you will be required to answer questions about that gene and its homologs in other species on subsequent homework assignments.

At the end of the year, the overall scores for homework and quizzes will be normalized before summing. Presentation grades of +, = and - will be converted to letter grades based on the idea that the default grade in a graduate course is 3.5 (at the boundary of A and B). I generally give roughly equal numbers of A's and B's and only a few C's. But I do have a sense of what it takes to get an A that is independent of your performance relative to the rest of the class, so there is no quota. It's possible for eveyone to get an A.

Being there! Evaluation during class when papers are presented will count for 70% of your grade. You should be sure to attend class. If you must be absent from a class at which a paper is presented you should let me know (by email or telephone, in advance if possible) and explain your absence. In the case of conflicts that you know about in advance, try to let me know as soon as you know that you will be missing the class. Unanticipated absences will be dealt with on a case-by-case basis; but explain your absence as soon as you can. The exact time of your email or voicemail message will be noted.