Course description: This seminar will focus on specific human genetic conditions, using a case-study format with primary research papers as our main resource. We will explore 1) the methods by which the associated gene(s) for each condition were identified; 2) the biology at the organism, tissue, cell, and molecular level; and 3) gene therapy and other treatment methods.

Course objectives: This seminar is designed to refine and extend your fluency (both verbal and written) in genetic concepts and techniques. Through the dissection of research papers on many human genetic conditions, you will understand the experimental approaches that are appropriate under different circumstances, and you will learn to think critically about experimental design. You will devise and propose hypothetical experiments to address unanswered questions in human genetics. You will appreciate the peer review process through critiquing the mock grant proposals of other students and having your own proposal critiqued. You will attain a realistic view of the sociology, politics, and serendipity of science.

Prerequisite: Bio201 (Genetics). I expect that you have good background knowledge of basic principles of classical and molecular genetics. It is your responsibility to review appropriate materials as necessary.

Textbooks: Our primary readings will consist of research papers and review papers from the literature, as well as selections on the web.
Required book: Decoding Darkness: the Search for the Genetic Causes of Alzheimer Disease by Tanzi and Parson (Perseus, 2001).
Optional resource textbook: Human Molecular Genetics, 3rd edition by Strachan and Read (Garland Science, 2004). It is feasible for students to share this book or for students to borrow my copy and read it in the Biocenter, Dana 211.
Optional writing resource: A Short Guide to Writing about Biology by J. Pechenik (Addison-Wesley; any recent edition will do).

Email: I will regularly send important announcements via email. You are responsible for any information/assignments/instructions I send by email, so check your messages each day.

Attendance and Participation: Since this seminar meets only once a week, your attendance is essential. An unexcused absence will result in a penalty of one +/- increment on your course grade. A second unexcused absence will result in a failing grade. Your participation grade will be based on the extent to which you ask questions and contribute to discussion.

Grading: Your final grade for the course will be calculated as follows:

Reading assignments: Since we meet only once a week, it's crucial to pace yourself and spread your reading across many days. Papers are available as PDFs in my public folder at Biology\Hales\Bio363Spring2013. Some are also available online. Bring printed copies to class of all papers designated "background" and "main" unless otherwise noted. To avoid printing difficulties, download files to your local computer before sending to the printer. Since some papers have color figures in which the color is essential to the meaning, you should view these on a computer and/or obtain color printouts.
*Three important notes:
1) Background reading and papers designated as "main" papers should be read very carefully before class. As you read, write detailed notes directly on your copies of the papers, particularly to annotate the figures, so that you can quickly recall the meaning. I will provide study questions (hyperlinked in the schedule below) to guide your reading. Come to class prepared to explain to the class anything covered in the reading.
2) If you don't understand something in the reading, be proactive and look up the concept in a textbook and/or online.
3) For papers designated as "supplementary," read the introduction and conclusions carefully, and skim the results section (UNLESS you are a discussion assistant for that week, in which case you should read and understand the data carefully and be ready to help others work through the paper).

Weekly class routine: We will break the class time into three portions each week, with short breaks in between.
First portion: Discuss background information on the condition in question. Start main paper.
Second portion: Dissect main paper, sometimes in smaller groups. Discussion assistants then lead class as we explore the supplementary paper.
Third portion: Student presentation. (Student can alternatively choose to present at the beginning of class).

Laptop computer: If you have a laptop with wireless capability, bring it to class to facilitate in-class searches on questions that come up

Roles of discussion assistants: Twice during the semester, you and a partner will be designated as discussion assistants. Your jobs are to read the supplementary paper carefully ahead of time and then stand up in front of the class to explain the main point of the paper and to lead the class (interactively) through the most important data figure(s).

Decoding Darkness: This book is a personal account of attempts to elucidate the genetic causes of Alzheimers. You are expected to read the whole book by the day when we focus on Alzheimer's disease. Take notes as you read to help you remember the important points. On the schedule below are suggested intermediate deadlines for reading particular chapters.

Formal presentation: You will give one 20 minute formal presentation during the semester on a genetic disorder of your choice; it must be one that we do not otherwise cover. No two students can choose the same topic, so clear your topic with me early to get first dibs on it. Background information on the disease should take up about half of your presentation. Analysis of an original research paper should take up the other half. I must approve your research paper choice and you must have it in hand at least seven days before your presentation. Don't try to explain the entire paper--instead, pick the most crucial two or three figures and explain those in detail. You must prepare a handout with an outline and any important images to distribute to the class. During your preparation, I encourage you to take advantage of the Speaking Center, a campus resource to help you develop a comfortable and effective public speaking style. The grading rubric is as follows: background section, 50 points; explanation of research paper, 50 points; fielding questions from audience, 20 points; handout, 10 points; effectiveness of presentation method (powerpoint, etc.), 10 points; public speaking presence (voice, posture, enunciation),10 points.

Research paper/mock grant proposal: You will write a paper in the style of an NIH grant proposal. You will read original research papers on a human genetic disorder (one that we are not covering in class) and then propose the next research questions to address, explaining the experiments you would perform to answer those questions. Most students choose to expand upon the topic covered in the formal presentation. The mock grant proposal will include the following sections: abstract, specific aims, background and significance, experimental design and methods, conclusion, and references. Refer to Pechenik's A Short Guide to Writing about Biology for basic strategies. Go to this NIH page to download sample grant proposals; note that for you, the three relevant sections are Specific Aims, Background and Significance, and Research Plan. REMIND ME and I will send you a sample grant proposal from a previous year. I want to select one that does not focus on a disorder that any of you have chosen. The mock grant proposal should be at least 2500 words, not including references. For information on proper citation of sources, refer to the Pechenik book and the Davidson Department of Biology statement on plagiarism.
A topic proposal & bibliography is due in Februrary (see schedule below) by email. You must put significant effort into acquiring and reading references before writing the topic proposal. It should be at least 250 words, including a few sentences of background on the disease, a few sentences on recent research, and a few sentences on the types of experiments you will propose. Use proper citation format as described here: Davidson Department of Biology statement on plagiarism. The title of the file you email must begin with your last name.
The actual mock grant proposal is due in April (see schedule below); email the file to me and to your peer reviewers, who are the two people listed after you on the class roster at the top of the schedule below. The title of the file you send must begin with your last name.

Peer critiques: You will receive the grant proposals of two other students by email. For each one, your main tasks are to evaluate the clarity and completeness of the background and significance section, and to assess the plausibility, logic, and value of the proposed experiments. You are to write a 500-700 word critique for EACH of the two proposals that you read. These critiques are due to me as email attachments by the date indicated on the schedule below. Also send your critique to the original author of each paper.

Honor Code: Your signature on every assignment will affirm your respect for and compliance with the Davidson Honor Code. The full Honor Pledge reads as follows: "On my honor I have neither given nor received unauthorized information regarding this work, I have followed and will continue to observe all regulations regarding it, and I am unaware of any violation of the Honor Code by others." Plagiarism is an Honor Code violation and is defined as representing another person's words and ideas as one's own. Paraphrasing (taking another person's sentences and changing a few words here and there) is NOT equivalent to writing something in your own words, and it is considered plagiarism unless proper citation is made. Please see the Davidson Department of Biology statement on plagiarism for comprehensive information.

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