Cells and Molecules
Biology 152

Class time/location: Napier 201, MWF 10:10 - 11:05 am

Instructor: Dr. Bonnie K. Baxter

Office hours:

Mon and Wed 11:15 - 11:55 am
Thurs 10:10 - 10:55 am
(I'm also available on a drop-in basis, or by appointment)

Office: 207 Rosenberg
Phone: 315-781-3598
Email: bkbaxter@hws.edu

Course web site: http://people.hws.edu/bkbaxter/bio152web_fall02

Textbooks (all required, all available in the College Store):

• Biological Science, by Scott Freeman
• A Student Handbook for Writing in Biology, by Karin Knisely
• Bio152 Lab manual, Bonnie K. Baxter, Fall 2002

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I will be making the case to you this semester that the biology of cells and molecules is the essence of all biology. You'll notice as we go through the course this semester that we will make few distinctions between organisms. At the molecular level, a mushroom is much the same as a rhinocerous, a California redwood, an intestinal parasite, or you. It is these fundamental similarities that have allowed molecular biology to advance with jaw-dropping speed over the last 40 years or so. It is these same similarities that have led to advances in biotechnology that have been welcomed with enthusiasm (the use of bacteria to produce human insulin for the treatment of diabetes) or with great trepidation (the insertion of a bacterial gene into crop plants to generate herbicide resistance).

Should you decide to pursue a career in biology, at whatever level, a fundamental understanding of cells and molecules will be essential to your success. Even more important, though, are the decisions you'll need to make in your life that will be impacted by your understanding of molecular biology and biotechnology. For example, what is the embryonic stem cell debate all about, and should it affect how you vote? If you or a loved one is faced with cancer, how should you decide which treatments to pursue? How does cancer treatment work, and what new developments are in the offing? How does HIV cause the devastation that it does? How do anti-HIV drugs work? We'll be discussing each of these topics in Bio152 this semester. In lab, we'll also explore the genetics of fruit flies, the effects of herbicides on plants, and the technology used in DNA fingerprinting. We'll use these topics as a context for learning not only how to understand what is known about molecular biology, but also how to formulate new questions and design original experiments. My hope is that you will leave the course armed with both new knowledge and new skills (see course goals, below).

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Above all else, science is a way of thinking. A well-trained scientist is best characterized not by the accumulation of knowledge of "facts," but rather by an inquisitive, analytical, and critical approach to information. A scientist uses existing knowledge to formulate interesting questions, develop new models and hypotheses, and design rigorous experiments. She or he then carefully analyzes the data from these experiments in regard to the original models and hypotheses, adjusts or discards the models, and begins again.

In order for this process to be useful, however, scientists must not work in isolation. If knowledge is to progress, each new set of data must be presented to the community as a whole for critical analysis and then incorporated into an overall understanding. A working scientist must therefore be not only a careful thinker and experimentalist, but also a voracious reader, a clear and precise writer, and an active member of the scientific community. He or she must be skilled in critical reading and in the synthesis of many disparate pieces of information into a coherent whole.

Obviously, skills like these are not gained in a single semester. You have been learning and refining them throughout your academic career so far, and they will continue to be emphasized as you move on into upper-level courses in your chosen discipline. Your time and efforts in Biology 152 should make a significant contribution. Here are the goals as I see them for Bio 152 students:

1. To gain a solid understanding of existing concepts in cell and molecular biology, including an idea of how these concepts were developed by scientists over time
2. To gain proficiency, confidence, and experience in experimental design, analysis, and written presentation, particularly in relation to the field of cell and molecular biology

The classroom and laboratory components of the course have been designed to work together toward these two goals.

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1. To share with you my delight and amazement at the way that life works at the molecular and cellular level
2. To design course materials that effectively serve the course goals
3. To facilitate your learning as effectively as I know how
4. To design assessments (exams, grading criteria, etc) that are a reasonably accurate measure of your mastery of course content, and to use these materials to provide you with frequent feedback on your progress
5. To be available to you, and to listen to you with respect and attention

Your responsibilities (as I see them):

1. To commit the time and energy necessary to allow you to progress (see hints for success below)
2. To manage your time effectively so that you can complete assignments on time and be prepared for class and for exams
3. To work collaboratively, cooperatively, and respectfully with your fellow students and with me
4. To participate actively in your learning and to let me know promptly when you are confused

I cannot emphasize this last point enough! You must not be shy. I cannot teach effectively without feedback. I need you to tell me when you do not understand something, preferably by asking questions in class where others may benefit. Alternatively, come see me in my office or send me a note by e-mail. You should never feel a question is too trivial to ask. I enjoy these interactions very much, and they can be invaluable to me, to you, and to your fellow students. The more promptly we can discuss a topic after it has come up in class, the more effective and useful the discussion.

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Research has shown that one of the *least* effective ways to further understanding is to sit passively and listen to a lecture, no matter how well-organized and clear the lecture may be. Your own experience may bear this out. If you wanted to learn to make quiche, for example, which do you think would be more effective: watching a beautifully presented program on public television or going into the kitchen and attempting to follow a quiche recipe?

It’s not that you wouldn’t be interested in the TV program, or motivated to learn from it. Rather, it is simply that the more different ways you can engage your brain in processing a concept the more effectively you learn. Doing something is more effective than reading about it, and explaining something is more effective yet.

If you are to gain an understanding of cell and molecular biology, you must actively engage the material. What does this mean?

1. First, read the textbook. But don’t just run your eyes over the page. Make notes to yourself. Underline important areas. Ask yourself to restate the main point of each section. Examine the figures. Work through the equations. Answer the textbook’s study questions.
2. Next, come to class. But don’t just sit there! If you do you are likely to gain little. Take careful notes. Process the information as you go. Does this make sense? Do you understand what the point is? Do you see how this fits with the material in your text and in previous class sessions?
3. Ask questions!! Of me, of each other, of yourself. In class, in the hallway, in my office, over e-mail. Asking questions means that you are attempting to process and make sense of the material, and is therefore enthusiastically welcomed. I will have regular office hours for this purpose, and they are much more interesting when students show up. If these hours are not convenient, feel free to come by, call, or e-mail at another time. If I am not available right then, we can make an appointment.
4. Form or join a study group with 2 or 3 of your fellow students. Meet regularly to discuss the course material and review for exams. You will often find that you can synthesize a much clearer and more complete understanding as a group than as individuals. Also, the practice you get in explaining concepts within your study group will prove invaluable on exams.
5. Manage your time well. Bio 152 is a demanding course. Your other courses this semester are likely to be demanding as well, and you are presumably balancing this course load with other commitments and a personal life. Be aware that it is my expectation that you will spend 1 - 2 hours outside of class on coursework for every hour in class, which means at least 5 - 10 out-of-class hours weekly on Bio 152. If you are spending 10 outside hours every week on Bio 152 and are still struggling to keep up with the course, come and see me so we can problem solve together. I may be able to suggest ways to arrange your study time more efficiently. If you cannot make this kind of time commitment for each of your classes and still meet your other responsibilities, rethink your courseload.

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I will give occasional homework assignments to encourage you to keep up with your reading and preparation for class. Because they are designed to encourage preparation, they will generally include material that we are about to discuss in class, but haven’t covered yet. Each homework assignment is worth points toward your final grade. You should use your textbook and your classmates as resources. It is perfectly acceptable (even encouraged!) for you to work together on these assignments. Each person, however, should construct each answer in his or her own words (see "plagiarism," below).

Periodically, I will also give in-class assignments. These will be completed during class, sometimes with the collaboration of your colleagues. They will be used to facilitate discussion and encourage preparation, and they will not be announced in advance.

Because homework assignments are designed to encourage advance preparations, they will not be accepted late. Also, any in-class assignments that you miss cannot be made up. Inevitable conflicts will arise for many students. To accommodate this, I will drop your lowest homework score and your lowest in-class score before calculating your final grade.

Attendance:

As outlined below, attendance at exams and at laboratory sessions is absolutely mandatory. Attendance at all class sessions is strongly recommended. The vast majority of people find regular class attendance an essential part of mastering the course material. Further, if an in-class assignment is given on a day when you are not in class, you will receive no points for that assignment. It is my assumption that since you are adults who are paying good money to enroll in this course, you will not miss class unless circumstances absolutely require you to do so. If you do have to miss a class (as opposed to a lab or an exam), you need not explain your absence to me. Simply find another way to get the material that you missed. Your classmates' notes, your textbook, and the class web site are all good resources in this regard. I am happy to answer your questions, but do not expect me to re-teach a missed class.

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Exams:

There will be four midterm exams, each covering 6-8 class sessions, and one cumulative final exam. The exams will cover material presented in lecture and in the reading assignments. Each midterm is scheduled for a regular class session, as outlined in the class schedule. These dates are firm, so mark them in your calendar now (see "missed exams" below). You will be required to complete each exam within the 55-minute class period (or the 3-hour final exam period); extra time will not be given (see "accomodations" below). As each exam approaches, we will discuss in more detail its content and format.

Missed Exams:

Out of fairness to everyone in the class, I insist that everyone take the exams at the time they are offered, not earlier or later. I do not make exceptions to this rule for anything except 1) a college sponsored trip, 2) a serious (and documented) illness, or 3) a family emergency that takes you out of town. I must formally approve any exceptions before the exam occurs. You should contact me by phone or e-mail as soon as you know there is a problem. I do not give makeup exams. I cannot reschedule the final exam for anyone. Plan your end-of-semester travel accordingly.

Accomodations for special exam needs:

Every student is expected to take every exam as scheduled, within the 55-minute time frame allotted (or the 3-hour time frame for the final exam). If you have a learning disability which necessitates extra time on exams or any other accomodations, it is your responsibility to consult the Center for Academic Support Services (CASS). The director is Joyce Dillon (x3351, jdillon@hws.edu). CASS will require documentation of your needs. You can then ask the Center to forward this information to your professors. Without a request (in advance!) from CASS, I cannot make special arrangments for any student. Please note that you need to ask CASS each semester to notify your course professors of your needs. In the interests of confidentiality, they will not forward this information without your request.

If you suspect that you have an undiagnosed learning disability, please go to CASS for a consultation. It makes sense to address this problem as early as possible in your college career, so that you can develop strategies for success.

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Missed Labs:

Per biology department policy, attendance in laboratory is absolutely required. This means that if you miss a lab session, you will fail the course. I do not make exceptions to this rule for anything except 1) a college sponsored trip, 2) a serious (and documented) illness, or 3) a family emergency that takes you out of town. I must formally approve any exceptions before the lab occurs. You should contact me by phone or e-mail as soon as you know there is a problem. (Does this sound familiar?) Make-up labs are generally not possible.

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Your overall grade for the course will be determined from the number of points you earn over the course of the semester. The points will be distributed as follows:

This course is not graded on a curve; your grade will be based solely on the number of points you earn over the course of the semester, according to the scale below. This means that everyone can get an A; you are not in competition with each other for a limited number of high grades. I hope you will therefore work together to help each other by forming study groups. Such collaborative groups can substantially improve your study habits and your grade. Here is the grading scale:

Exception: The drawback to a non-curved grading scale is that there is no allowance for exams that are too difficult for most students. If there is an exam on which the average score is less than 75%, I will adjust the scores upward so that the average is 75%.

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Plagiarism and data fabrication

The world of science, and of academia in general, relies utterly on the honesty of its contributors. When data are presented in a scientific paper, they are taken as fact. When an analysis of a topic is presented and not credited to an external source, it is assumed to be the creative product of the author of the paper. Violation of these norms does irreparable damage and must not be tolerated. It will not be tolerated in this course. If I find that you have fabricated data, plagiarized, or cheated on an exam, I will respond. At minimum, you will fail the relevant assignment or exam. More commonly, you will fail the course. I will also report the occurence to the Deans and to the Colleges' Committee on Standards.

Particularly on first entering college, some students may be confused about what constitutes data fabrication or plagiarism. A former colleague of mine at Lewis & Clark College, Paulette Bierzychudek, has written a useful summary called Honesty in Science, complete with examples relevant to introductory biology. With her permission, I've adapted this summary for this course and included it in your lab manual. Ignorance of what constitutes plagiarism or data fabrication will not constitute a valid excuse.

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