Your grade will be determined as described below. Over half of your grade will be based on the six papers. Lecture material will apply to the papers, and will be reflected in the homework, quizzes, and a final exam. 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 to take the quizzes on your own.

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 (or on some reliable electronic device with a sufficient charge). You will be graded on your familiarity with the papers. This familiarity will be assessed by your presentations, by your contributions to the overall discussion, and by quizzes. The first part of class meetings on Tuesdays (starting the second week) will be devoted to paper presentations.

    Discussion and presentations (about 200 pts. 40%)

    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 a short section, such as the abstract or conclusions, one figure, or a part of a figure) in front of the class. The points assigned to each participation grade will vary between 5 and 25. The expected grade is 80% (e.g. 4 out of 5) and I will not explain giving that grade. Any grade other than 80% will be for a reason.
    In case of presentations, your presentation will be graded based on the clarity with which you present the section. In the case of the abstract, introduction or discussion, you will be evaluated on your ability to convey the relevant ideas. In the case of a figure, you will be evaluated based on your presentation of four things:

  • 1) the overall point of the figure or section
  • 2) the techniques used
  • 3) the results
  • 4) the interpretation
  • Everyone is subject to being called on at any time. The selection of students for questions and presentation will be essentially random, and I 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 multiple times in one session in order to refocus their attention on the paper. You can decline to respond or present, but it will affect your grade (you will receive 0, but out of a smaller total). Again, I'm not going to spit hairs, just note your participation, so please expect to get 80%, which is the grade I give as default. In the case of grades that are significantly different from 80% 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.

    Any contributions to the discussion that aids everyone's understanding of the paper will help your grade. Good questions are especially encouraged. I will not assign low grades for asking honest questions about the paper.

    Quizzes in class (about 100 pts. 20%)

    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. The total number of in-class quiz points is not set. That way, you won't know whether or not I will be giving a quiz. However, the total number of points assigned to quizzes and presentations and discussions together will be 300.

    Homework and online quizzes (100 pts. 20%)

    Written homework will be assigned at least three days (50 hours) before the due date. Usually, this means it will be distributed on Thursday (or online, before Thursday) and due on Tuesday. Homework due on Tuesday will be assigned no later than Friday night. Homework is due at the beginning of class. I want hard copy. In many cases, homework/quiz 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 (or online quizzes), perhaps as few as four or five. The number of points that are actually graded will vary between assignments, and there is no guarantee as to how many points will be assigned in total. 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. Missed or late assignments will be dealt with on a case-by-case basis because different homework assignments will count for different amounts.

    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.

    Final Exam (100 pts. 20%)

    The final exam will be comprehensive, covering key points from the lectures and essential points from the papers.

    Being there! (Priceless)

    Evaluation during class when papers are presented will count for 60% 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 will be noted.

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