Your paper will count for approximately 40% of your grade. You will seldom take tests after Stanford, but you may frequently need to write. In past years, almost without exception, students have enjoyed writing the paper and learned a great deal in the process, while grumbling a bit initially about the time required. Unlike an exam, a paper should not evoke anxiety, and I have set up a process that should further reduce any concerns you might have.

You have the option of collaborating with another student to write a joint paper.  All other aspects of the assignment are identical except that two of you would share the work.  The resulting paper would be the same length as the others, but should be twice as good.  In the real world, most scientific papers are collaborative efforts.

At the time of the 4^th class, please turn in a brief (1 page maximum) outline or abstract of the paper you would like to write. You can do two of these if you are uncertain about topics. You are not committed to write about what you propose, but of course it would be useful if you did.  The preferred method of submitting your outline/abstract is via email, as an attached word file.  Be sure to give your filename a unique identified: preferred is your last name-a one word clue to your topic-then 121 or 228-then a version identifier: eg: yourname-CF-121-draft2.doc.  Identify your final submission as such: yourname-CF-121-final.  If you use a Mac, be sure to save versions of your files in PC-compatible formats.

By Friday of week 6, please turn in your first draft if you want feedback. The preferred method of submitting your outline/abstract is via email, as an attached Word file. If you use a Mac, please save your file as a PC or RTF file to make it easier for me to open.  I will provide a written critique, and return it on Monday of Week 8. The deadline for the final paper is the first day of finals week (see academic calendar). That date is firm. If you miss or ignore the first deadlines the quality of feedback you get will be compromised. If you miss the last deadline, you automatically adopt NC, so be sure to send whatever you have even if it doesn't meet your standards for perfection.  (NIH and NSF are similarly unforgiving about grant deadlines).  Again, the final draft should be sent via email.

Style of paper.  No strict guidelines are imposed, but the more successful papers are often similar to a Perspective in Science or a News & Views article in Nature.

Topics and scope of paper. Most topics that we have covered or will cover in class are appropriate, but so too are many topics that we will not have time to cover, but which are clearly relevant to the subject. Here are some titles of papers by students in prior years:

Topic 2 focuses on explaining a technique. You would need to convince me that it was worth doing a technique-oriented paper.

Topic 3 could go in several directions. The focus could be molecular, or (better) an attempt to link these molecules to behavior and medicine.

Topic 4 focuses on a particular aspect of a particular molecular entity. This is the most focused topic in the list, and in general a narrow focus yields the strongest papers.

Topic 5 takes a whole secretory response as its subject. This can be of more interest than the narrower topics, but requires considerable skill to carry it off. These are just examples to get you started—I’m confident you will have better ones. Ideally you should have some deep curiosity about the topic you pick.

The length maximum is 1200 words of text, with one or two figures that you draw yourself.  Drawing a figure allows you to summarize the main points of your paper in a visual way or to illustrate structural features that would be difficult to convey with words alone.  Don't forget a figure caption (it counts in the word total so keep it brief but informative).  If you don't usually draw with your computer you might find the drawing features of Power Point an easy way to start.  If you want to draw by hand you will need to know how to scan in your image so as to have a small file size.  Both of these are skills you will be glad to have.

Don't forget to number the pages! Use section headings liberally, and keep paragraphs short. Scientific writing is dense, and needs leavening. Use any standard reference style you like, but it must include full titles to all referenced articles.

You are encouraged to use PubMed and an automatic reference database and bibliography maker such as EndNote. I will offer a brief tutorial on PubMed and EndNote if there is interest. You may begin your literature search with a review article, but you should then go to the original literature. Don't try to be comprehensive with regard to the literature, but instead try to select excellent papers and study them thoroughly. Usually there aren't many of them. You may need to use Science Citation Index during the literature search for your paper.

The Web is a rich source of material, including figures. Avoid "elephant & fleas" approaches. That is, if we agree that you will write about elephants, don't say: "elephant's have fleas", and then write about fleas because you lose your way when researching your original topic. Do not write about a topic that has only a tenuous link to the course topics. Of course, a paper you have done for another course should not be re-worked for this one.  If you don't now sleep with a copy of Strunk & White under your pillow, you should buy one soon (it is always available in paperback) and read it before, during, and after writing your paper. Strunk's original text, without E.B. White's  lovely introduction, is on the web.

You are encouraged to give your drafts to one another and get comments on them before giving them to me. Virtually every scientist seeks opinions from colleagues on drafts of papers. For some reason, most of us have difficulty detecting when our writing is unclear (we know what we mean); so if someone has trouble with what you write—assume the fault lies with you and not them.

Grading. The grade range in the past has been from A+ to B- for students who finish the paper. This narrow range is appropriate for a small, graduate style class.  Anyway, the main reason for writing the paper isn't the grade.

Wikipedia Alternative

     If you prefer, you can do your paper assignment as a Wikipedia entry, assuming you know how, or are willing to learn for this purpose.  To get started, set up an account with Wikipedia, which is free, takes a minute or so but requires you to makeup a username and password.  It is optional, but recommended, that you also list your email address so they can confirm you have an account.

The general requirements in this case do not differ, but there are great advantages.  You can find out what is already known--you don't want to do an entry on something that is extremely well covered--but you might find that what seems to be well-covered is actually not.  This option lets you take advantage of the hypertext functions of the web to expand on terms and link to references.  The directions for doing all of this are part of the Wikipedia project.  But perhaps the greatest advantage is that your entry could be read and be useful to many people.