Biology 3596a Genomics and Beyond A laboratory Course

Biology 3596a What Wilhelm von Humboldt had to say about university education.

Just as primary instruction makes the teacher possible, so he (she) renders himself (herself) dispensable through schooling at the secondary level. The university teacher is thus no longer a teacher and the student is no longer a pupil. Instead the student conducts research on his (her) own behalf and the professor supervises his (her) research and supports him (her) in it. Because learning at university level places the student in a position to apprehend the unity of scholarly enquiry and thereby lays claim to his (her) creative powers. Der Konigberger und der Litauishe Schulplan

Biology 3596a Where do you fit in this scheme?

Biology 3596a Why this course exists Course information Course philosophy Course sections Mark breakdown Expectations Safety

Why this course exists Preparation for fourth year and graduate studies. This course emphasizes technical accomplishment.

Why technical accomplishment?

Why this course exists This course emphasizes independent learning through reading the primary scientific literature.

Course information Major source of course information is found on the web site or Tony: WSC rm#305 Your TAs

Tony’s office hours Monday 3:30-4:30PM and 6:30-7:00PM Appointments Drop by fine for simple things

Lab Web Site You are expected to read the lab web site, because it contains the expectations and consequences.

Feedback Feel free to give feedback on the organization of the web site or course. I have included movies demonstrating some techniques, I would appreciate your feedback on their usefulness.

Course philosophy The experiments should work and the results should be marked. The experiments should focus on a problem, and not just a technique. The student should do as much of the experiment as possible. The experiments should be modern.

Course philosophy All information should be available on the Web. The course should prepare you for the future as an independent experimental research scientist.

Course Sections Lectures will introduce the content of the labs. Preparation for the final examination.

Lectures The Lectures are in part pre-lab talks. This information will not be tested on at the final exam, but is intended to prepare you for the lab and assignment. The Lectures, through your reading of the assigned material, are a preparation for the final examination. There is no memorization component in this course.

Lectures Lecture powerpoint will be posted on the web site by Friday afternoon. Depending on the day, the lectures will be between 1 and 2 hours long.

Course Sections Introductory lab: a warm up for things to come.

Course Sections Experiment 1: The Honeybee EST project. You will sequence an EST with the aim of analyzing a novel DNA sequence. This is as close as you will get to a real research problem.

Course Sections Experiment 2: Mouse murder mystery You are part of a mouse crime scene investigation unit. The point is not necessarily to solve the mystery, but rather what you can say from the analysis.

Course Sections Experiment 3: Basic cloning To introduce basic methods for the manipulation of DNA

Course Sections Experiment 4: Light regulated genes To investigate light regulated gene expression in plants. RT-PCR analysis

Course Sections Experiment 5: Mutant Characterization and Complementation analysis To characterize novel mutations by complementation analysis. Easiest experiment to do/ hardest to understand.

Mark Breakdown Results 22% Assignments 23% Final examination 35% Lab notebook 13% Lecture preparation 7%

Principles/Guidelines to ensure fair grading for all students

Expectations for Results If the lab works, you are expected to get it to work too. You will be working together in groups; therefore, all members are expected to participate in the experiments, and all members are to work as a team.

Expectations for Lab Notebook The protocols and pre-lab preparations must be in your notebook before coming to the lab. This will be checked by the TA. Data is recorded in your lab book during lab time. Checked by TA. Results will be entered into your notebook. A notebook does not have to be tidy, but needs to be complete for later reference.

Lab Cleanliness The web site lists a set of particular chores. This will be checked by the TAs. Marks will be deducted for a lack of cleanliness.

Safety Labs are dangerous places. Lab coat must be worn at all times. Eye protection must be worn at all times. No Food or Drink in the lab. No dangerous fooling around. Dressed from the neck down, closed shoes. See web site for more on safety.

Waste disposal You will be exposed to hazardous wastes which need to be disposed of properly. Read the page on the Web site. Marks will be deducted for not following the rules.

Absence from the Lab If no medical/compassionate documentation is supplied to the Dean’s office, missing a lab will result in 5 marks lost from your final mark. If you plan to be absent from a lab, for an athletic or cultural event, you must inform me well before the event, and have a note from the coach or organizer of the event.

Late penalty If more than 15 minutes late for the lab, 2 marks will be deducted from your final mark. You are letting down your lab partners by being late.

Lecture Preparation For 7 lectures you are required to answer 3 questions on a scientific article that you have read. To make sure that you read the paper before the lecture. The throw of a dice will determine which question I will mark.

Final Examination You will read an assigned paper. I will not answer questions on the paper. The final exam will be a set of 7-13 questions based on the paper. You will be allowed to bring in any paper you wish with notes, one textbook, and one dictionary to the exam.

Marks and Privacy Marks can no longer be posted on walls or web sites, ed, or given out over the phone. At the last lecture, I will give you an individual summary of your marks to that date.