II. General Information
A. List of Assignments
C. Summaries (sample summary here)
D. Final papers
E. Lab and Lab Reports
V. Schedule of Events
VI. Schedule of Lab Exercises
I. RATIONALE FOR COURSE
Most courses present a panoramic view of the world. From this vantage point, one can see at once all the major oceans and how they are connected and can proceed to subdivide the land masses into progressively smaller parcels for future study. The alternative is to jump into the nearest creek, noting the cold of the melted snow, and wade down to where the creek joins the more rapid flow of a nearby stream. And from there follow the stream to the river and the river down to the ocean. By learning all there is about the creek, you also end up discovering the world, but by this route, connections are made grounded on concrete instances rather than abstractions.
This course focuses on particular problems faced by four bacteria:
Bacillus subtilis: How to time genetic events in precisely the way required to form a spore
Myxococcus xanthus: How to communicate from cell to cell to coordinate communal spore formation
Caulobacter crescentus: How to tie morphological change to particular stages of a complex cell cycle
Anabaena: How to use positional and internal cues to create a pattern of differentiated cells
In addressing these problems, we confront the issues all organisms face in controlling gene expression in time and space. In bacteria we see instances far simpler than any in the animal world of how cells decide how to divide amongst themselves the functions required for a multicellular organism to survive. The simplicity of bacterial differentiation and the powerful genetic tools available permit a deep understanding of the underlying processes that is difficult to obtain in higher organisms.
Much of the course centers around communication, not only communication amongst bacterial cells but also communication amongst humans. We spend a great deal of time learning how to read the currency of science -- the research article. From this process, one comes to realize why scientists are generally irritated by text books, exasperated by what is left unstated behind those pretty three color diagrams. We also spend a lot of time giving written and oral presentations. These are learned skills, probably none more valuable that one can take away from a college education.
II. GENERAL INFORMATION
Elhai (I am not a doctor)
Office - S-202 tel: 8412 fax: 1234
Required text: Science Library
Bacterial Development (1984) Martin Dworkin [on reserve]
Analytical Genetics (1995) Griffiths et al
III.A. List of Assignments
Questionnaire: Please return the attached questionnaire before the end of the week.
Exams: None. No final exam either.
Presentations: Two, each based on one or more papers from the primary literature.
Summaries: One per week (but see Quizzes and Lab reports below) of articles from the primary literature (to be provided). The summary will be due the class period after the paper is discussed unless otherwise noted.
Quizzes Some summaries will be replaced by unannounced quizzes. Quizzes, when given, will always take place on the day of a presentation of a paper. See details below.
Final paper: Does not need to be much bigger than a summary (see details below). The paper is due Monday, Apr 28.
Lab reports: Six (see Lab Schedule), some of which will count as summaries. The last will describe your efforts over several weeks to expand the worlds knowledge concerning bacterial development.
Each participant will give TWO CLASS PRESENTATIONS, each focusing on one or perhaps two research papers from the primary literature (i.e., not review articles!). The presentations will be based on a paper I provide, but suggestions are welcome!
The presentation should make clear to the intended audience:
1. The question the paper addresses, including the larger context. It will probably be necessary to explain pertinent bits of the life history of the organism under consideration and to review previous experimental results that set the stage for the work being presented.
2. The methods used to approach the question experimentally. If a technique is used that is unfamiliar to the audience, then the principle behind that technique should be explained.
3. The experimental results. The experimental basis for any result presented must be made clear. It is not necessary (and generally not desirable) to present all the results within a paper.
4. The implications of the results. To what degree do the results answer the question? What are the limitations on the conclusions that can be drawn? What loose ends remain?
At least one week prior to the presentation, the presenter should meet with me and discuss a STRATEGY OF PRESENTATION. The presenter should bring to this meeting a complete and detailed outline of the proposed presentation (about one line per paragraph-equivalent). The outline should make reference to what visual aids you plan to use and when you plan to use them. Bring withyou either the visual aids themselves or a sketch of approximately what you want.
What is a summary?
A summary should communicate the nature and significance of the problem addressed by the paper, the strategy employed to address the problem, the tools used in the study, the primary results, and important implications. If this sounds faintly reminiscent of what I just said about a presentation, then consider that good communication is good communication.
The summary should be written for an audience of people much like yourself, avoiding jargon and defining any terms you wouldn't expect your colleagues to be familiar with. It should end up about 1½ pages, double spaced, but the optimal length really depends upon the complexity of the paper. A sample is included at the end of this document.
The major part of the summary will discuss the paper presented in class. In addition, you will also connect that paper to one the related paper assigned to you (or found by you). Young Hemingways in the class are free to use any appropriate format to realize these goals, but the rest of us should seriously consider the following:
Paragraph 1: Describe problem addressed by the presented paper and what should lead the authors to address it
Paragraph 2: Describe the experimental strategy employed in the paper
Paragraph 3: Describe one or more important experimental result(s)
Paragraph 4: Describe implications of the result
Paragraph 5: Describe how your own paper overlaps with the presented paper and briefly compare the two
Needless to say, there may be occasions where two paragraphs are necessary for one of the tasks outlined above.
Each paragraph should have a goal. If a phrase does not contribute towards the goal, then it detracts from it and should be deleted. Many people profit from writing an outline before attempting to write deathless prose. The outline need not be formal -- just setting down the substance of each paragraph without needing to worry about the niceties. Doing this after writing a rough draft may also be useful, often makes comically clear how rambling a paragraph really is.
III.D. Final Paper
Maybe I shouldn't call it a final paper. It sounds so... final. This exercise is intended as an opportunity for you to go a little further than you will in the summaries. The topic may be anything of your choosing, even a topic of a previous summary or a topic on which you gave a presentation. In fact, the paper may be not much more than a transcription of your presentation. The only limitations are:
1. The paper must discuss and relate results from at least three research papers (not reviews).
2. The paper must have the same degree of organization as you give summaries. This is an opportunity for you to extend your powers of organization, not an opportunity for you to relax and throw words -- splat -- on the page.
You are encouraged to turn in the paper early. If you do, I will look at it early and return it to you with suggestions but without a grade. You may take those suggestions to heart, if you wish, and turn in a (hopefully) improved version. Any draft turned in April 18 or later will be considered a final draft.
III.E. Lab and Lab Reports
You will be handing in two types of lab reports: brief and full. "Brief" does not mean "unintelligible", and "full" does not mean "encyclopedic". Brief reports will be used for those labs in which you are provided detailed protocols. Full reports will be used for those labs in which you devise much of the protocol. In either case, the audience for which you are writing consists of people like you, before taking this course.
Brief reports: Begin with a reminder of what the goal of the experiment was and what methods were used to achieve that goal. A few sentences should suffice. Then lead the reader through the data you obtained, telling a story, and referring to labeled tables and figures as you go. Don't begin the report with a table of numbers that the reader couldn't possible understand. English first!
Full reports: Divide the report into four sections: Introduction, Materials and Methods, Results, and Discussion.
The Introduction should start with general questions and proceed from them to an exposition of the specific question (not necessarily a hypothesis!) that your experiment addressed. In the cases of Labs 2 and 4, you will need to provide a rationale for the papers on which those Labs are based.
The Materials and Methods section should allow the reader to see the principles behind your experiment and how it might lead to results that bear on the questions they address. On matters of protocol, you may refer freely to any handout provided for this course, but you must detail any modifications or specifics particular to your experiment.
The Results section should be as described for brief reports.
The Discussion should first of all tie the results to the issues raised in the Introduction. Make a cogent argument for your conclusions, appealing to elements of your results. To what degree did the results resolve the issue? What is left unresolved? If you believe your data to be inconclusive, state why and what might have caused the ambiguities. Be sure that any explanations you put forward to explain deviations from expected results can quantitatively account for your actual results!
All assignments will be assigned a numerical grade based on the usual scale of 90-99=A, 80-89=B, etc. The final grade will be calculated based on a weighted average of all assignments. The weights are as follows:
Summaries/Quizzes 88 (11 x 8). The two lowest non-zero grades will be dropped.
Presentations 80 (40 x 2)
Final paper 40
Turning in assignments late makes life difficult for those of us who have to grade the assignment, and, eventually, to those of you who would like to receive the assignment back in a timely fashion. The purpose of late penalties is to discourage antisocial behavior but at the same time to encourage you to turn in something, sometime. To this end, every day late costs, but it is always much better to turn in the late paper than to not do it at all (which would generate a zero). An assignment is deemed late if it is turned in later than 5:00 P.M. on the day due. The maximum grade obtainable by a late paper will be calculated according to the formula:
where d is the number of weekdays late.