Class Description

Molecular approaches are advancing at an ever increasing rate. Recent news story like the human genome project and hap-map and the sequencing of the entire genome of the 1918 flu virus are only the tip of the iceberg. Even more exciting is the increasing integration of such new molecular genome-enabled methods with traditional ideas population genetics and evolution (see a nice video from Science Magazine). This integration has some challenges, but also holds great promise for medicine, conservation and our understanding of ecosystems. This class aims to present molecular approaches from different disciplines (genomics, microbiology, ecology, population genetics) and encourage students to think about potential applications of these approaches in their own field of study.

Specifically, the class has three major aims:

  1. To provide students with a broad overview of current molecular methods
  2. To foster interdisciplinary interaction among students
  3. To prepare students for their own molecular research

The course should be particularly beneficial for students using or planning to use molecular methods in their dissertation research. It will also be important, however, for those who wish to enhance their familiarity with molecular methods. Many of the methods covered in this class are rapidly assuming importance in many fields of pure and applied biology not previously associated with these technologies; consequently, gaining familiarity with these methods will increasingly constitute a valuable part of a general scientific education.

Lectures will begin at a very basic level, but will rapidly move ahead to advanced concepts. Every week, scientific papers from the primary literature will be assigned as readings, and discussed in class. Review papers or book chapters will be provided as (required) background reading.

Recommended preparation

There are no specific prerequisites for this class. It will be assumed that students have had general undergraduate training in chemistry and biology including basic genetics. Some prior exposure to the basics of molecular biology would also be helpful. To give you an idea of what prior knowledge I expect, have a look at the lectures in the first two weeks of my FISH 340 class.

Due to the wide range in previous experience within the class, it is very important that you ask me immediately if something is not clear, preferably still in class but also individually by appointment. I would be more than happy to have a few catch-up tutorials with you (preferably as a group) if you need it, but I won't be chasing after you. It is also important that you help each other in and out of class. Remember that teaching is the best way of learning.

Textbook

There is no specific required textbook. Weekly background readings are provided from a variety of sources to complement the lecture material. Each week an article from the primary literature will be assigned for in class discussion. In addition, we will put the following books on reserve:

1. Avise J.C. (2004) Molecular Markers, Natural History and Evolution. Chapman & Hall, New York. Fish-Ocean Class Reserves -- QH438.4.B55 A95 2004. As per the first week of quarter, this book is still in transit, but the previous edition (1994) is available.
2. Hillis D.M., Moritz C., Mable B.K. (1996) Molecular Systematics. Sinauer Associates, Sunderland, Massachusetts. Fish-Ocean Class Reserves -- QH83 .M665 1996
3. Graur D., Li W.-H. (2000) Fundamentals of Molecular Evolution. Sinauer Associates, Sunderland, Massachusetts. Odegaard Stacks QH325 .L65 2000

Exams

The final exam will be a take-home exam that will be distributed on Wed March 8, and is due on Mon March 13. This exam will be on all lectures as well as assigned reading and the topics of student interest covered in class. I will provide example questions in the lectures, and work though them.

Class Assignments and Grading

The major assignment for the course is a research proposal written in the format of a grant proposal, due at the end of the quarter. To ensure that students are "on track" developing their proposals, and to give them feedback on proposal development, a preliminary outline of the research proposal is also required, and due around mid-quarter. There will also be readings designed to reinforce subjects covered in lectures. One take-home exam will be given.

 

Policy on Late Work

All assignments are due at the beginning of the class period on the due date. No credit will be given for papers received after this time. As it is impossible for me to fairly assess special circumstances, I cannot accept a late submission of proposal outline, review or research proposal.

Policy on Cheating

You may want to check out the University Policies on Cheating and Plagiarism. Both are serious offenses, and may have severe consequences ranging from unreported grades to dismissal. In your own interest, don't do it! If there are any uncertainties about group work or appropriate referencing, ask me first. This concern particularly sections 'lifted over' from original PI's proposals or from web pages.