Molecular Biology (BIO304) Spring 2010
Lecture MWF at 12:30 (Chambers 2146 )
Dr. A. Malcolm Campbell - Dana 221: phone x2692 email: macampbell@davidson.edu
Office Hours Mon. 2:00-3:30 and Wed. 10:30-12:30
Three Free Texts required for this course:
1) Online! by Harnack and Kleppinger
2) Life 8th Edition by Purves et al. (you can borrow a copy)
3) This web site and its online readings
Grades:
|
Components |
Percentage Final Grade |
| 2 exams during the semester and 1 during finals |
60% |
| Your Favorite Protein web page |
10% |
| Your Favorite Orthologs web page |
10% |
| Jmol tutorial web page |
10% |
| 1 literature review paper on web | 10% |
| Extra Credit for Summary Selected Talks |
+2 pts/+1 for good Question |
Notes:
1) Class participation can change your grade by one increment
(up/down +/-).
2) Any assignment turned in late will be docked one letter grade for every day it is late,beginning the day it was due.
Attendance policy: I will take attendance every day to facilitate a more objective means for assigning the class participation grade. In order to receive a passing grade in this course, you cannot miss more than 5 classes without a legitimate reason. You may not miss any labs without a legitimate reason. Legitimate means medical, legal circumstances, or college sponsored events; it does not mean lots of tests that day, spring frolics, etc.
Grading Scale:
| B+ = 91 - 89 | C+ = 82 - 80 | D+ = 73 - 71 | ||
| A = 100 - 95 | B = 88 - 86 | C = 79 - 77 | D = 70 - 68 | F = < 67 |
| A- = 94 - 92 | B- = 85 - 83; | C- = 76 - 74 |
I am very excited about this semester's molecular biology course. I have been working on this course for several years I think it is a good one. The best aspect of this course is the use of virtual reprints. Virtual reprints are research publications reproduced on the web. For the first three weeks of the course, we will use the introductory biology textbook to revisit some materials to make sure everyone is on the same page and we all know how to use some basic tools of molecular biology. Then we will have a test on this material. After this section, we will turn our attention to the virtual reprints. I have selected some papers on related topics to be covered as "chapters". For each chapter, there is some introductory material that you should read first. The papers have a strong bias towards cell biology using genomic organisms. I have outlined an ambitious agenda for us; there is a lot to learn and we don't want to miss out on any of it. However, if we find that this is unrealistic, we will adapt (or die?). We will try to read all the papers as outlined, but we might abbreviate some sections if necessary.
This has to be one of the cheapest courses you will every take. If you bought the intro text by Purves and Online! for your introductory biology courses, then you don't have to buy any more books. If you don't have copies of these, borrow them from someone. Online! is a great book that will teach you a lot about the WWW, how to investigate the quality of a web site, how to contact the person who set up a web site of interest, and how to properly cite internet resources using CBE (Council of Biology Editors) style. You must use CBE style for all your citations and the name, year format for in-text refrences (Campbell, 2005). The contents of Online! will not be tested directly, but you will have to use this information for your web assignments and proper citation style will be a part of your grade. Life will be used extensively during the first three weeks, and then occasionally after that. You must use a copy of Biology eighth edition to match the page assignemts.
You have 3 exams total (see some old exams) during the semester (see the schedule).You will have multiple days to complete the final exam. All exams are take home, closed book, answers are to be typed, and are due at the next class meeting. Exams are not to be turned in late unless you have made prior arrangements with me. Acceptable reasons for delay include: death in the family, personal illness requiring doctor's care, etc. Unacceptable reasons include: intramurals, Patterson Court functions, other tests or exams, etc. The exams will be distributed at the end of classes. The final exam is also a take home test and will be identical in format to the second test.
I want each of you to create a web homepage (see some examples of WWW homepages from previous years) and learn how to work with HTML. You may use Dreamweaver. Biology lab computers (Macs and PCs) have both Netscape and Dreamweaver so you can use them if you do not have access to a computer. ITS computer labs also have Dreamweaver. Your homepage will be graded on its clarity of information and it must meet certain minimal standards. Each of you will be given a folder on the biology web server which will be password protected. You can load any course-related files in this space either through the campus network or an FTP program (e.g. Fetch or CyberDuck on a Mac and CuteFTPon PCs). You have 4 assignments that require you to make web pages. The third assignment is a challenging one where you will have to learn a little bit of computer programming (benefit of no lab! :-).
The forth web assignment is to post your review of a paper (see some examples of old review papers) you will write will be a critique/review of primary literature (you will choose from a short list of options that I provide). Your review of this paper will be presented on your web page. You will need to explain briefly and evaluate the data presented in the paper and then explain what direction you would follow for future research (see review paper requirements). The proposed future research should be accompanied by some specific experiments you would perform to answer the question(s) you are posing
The format of the class will require each of you to read that day's assignment BEFORE you come to class. Each class will begin with a period where you can ask specific questions related to the previous day's material or specific areas you do not understand from the current day's assignment. We will try to stick to the syllabus schedule because there is so much to learn and so little time. Therefore, if we do not cover a topic in class, but it is covered in your reading assignment, you are responsible for it. We will discuss some topics as a group, I will call on you randomly to answer a question or lead a discussion, and I will present some information in the traditional lecture format. If I call on you to answer a question, it is OK to say, "I got this part, but this other section lost me." It is not OK to say, "I didn't read it." I understand that occasionally you might fall behind a day or two but do not make this a practice since class participation is also graded. After the first three weeks, I will call on you to explain parts of the virtual reprints and this format will be used almost exclusively.
My Objectives (in no particular order):
Finally, I do not know everything. If you think I have said something that is incorrect, please point this out. When you ask me a question that I cannot answer, I will research it and get back to you. If you have tried to understand the material but just can't get it, then come talk to me either during my office hours or make an appointment. I am happy to work with you as much as is necessary.
"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."
All of your tests are closed book, closed notes, take home exams. You do not have a time limit for these tests other than the days allotted, and you can take them any place you want. This form of testing is only possible because of the honor code. If you violate my trust in you or the honor code, we will have to take the tests during the 50 minutes of class. You are required to not cheat on these tests, and to report to me or the Dean of Students any violations you observe or hear about second hand. This means that even your lab partners or best friends must be reported if you know they are cheating. The entire system will break down when individuals make exceptions to the rule in order to spare their friends.
It is considered an honor code violation if someone takes credit for work he or she does not deserve. The content of web assignments are also covered by the Honor Code. Each person must write his or her own web pages. The content is what I will be evaluating, not the layout. Therefore, you may work collaboratively to create the layout for your web pages. For example, it is fine to ask someone for help in creating relative links, inserting chime files, how to use a particular public web site for sequence analysis, etc. However, it is unacceptable for you to "borrow" text from another student or any document, or electronic source unless you explicitly cite the reference. You can consult the Biology Department's plagiarism web page for help in this area.
Accommodations for Students With Disabilities
Full accommodations are the legal right of students with all kinds of disabilities, whether learning disabilities or physical disabilities. I am happy to provide these accommodations. If you are a student with a learning disability documented by Davidson College who might need accommodations, please identify yourself to me within the first week or two of class, so that I can learn from you as early as possible how to best work with your learning style. Students with other disabilities are also encouraged to self-identify if there is any way in which I can make accommodations that will enhance your learning experience. All such discussions will be fully confidential unless you otherwise stipulate.
Week begining: