Week 3

Refining your topic in the light of what you've found and read is a main goal for this next week, since you're heading toward a meeting with your faculty supervisor in the week of March 2-6, for which you need to have

a title for your project and
hard copy of all citations found to that date.

Accordingly, the next few weeks will require a good deal of searching and thinking. Your citations need to be in the appropriate form (the journal format specified for your group), and you need to be reading and annotating as well as finding, and delivering the citations and annotations to your faculty supervisor.

It's important to move beyond the simple searching with which exploration of a topic begins --to find new vocabulary and other ways to narrow your searches, and to gradually elaborate an understanding and develop a focus. Your report to me (assignment #2) should reflect your progress with this elaboration. To accomplish these goals you'll need to use the more specialized databases (PubMed, Cambridge Biological Abstracts, perhaps others as well) and explore some of their advanced searching features.

We'll consider the anatomy of the article to make clear what 'primary' and 'secondary' are and how to tell the difference. And what to do with each, how to mine bibliographies, how to make sense of abstracts, how to manage unfamiliar terminology.

The example of Bollinger et al. Inbreeding avoidance increases dispersal movements of the meadow vole (Ecology vol 74 pp 1153-1156, 1993) summarizes handily.

There's a sense in which the primary literature isn't written to be read: it establishes ownership and priority for ideas and findings, validates its authors' professional identities, serves as a permanent record of scientific progress. It's read by specialists --and by students who are preparing to become specialists. It's customarily written in a pretty rigid style (generally avoiding the first person, often favoring the passive voice, spending little energy on verbal niceties). Few people read primary literature for pleasure.

Secondary literature exists to improve access to the riches of primary literature: to interpret, summarize, adjudicate, review --but primarily for specialist or at least scientific audiences.

Specialized databases are the key to the research and review literatures. We have quite a few to choose amongst, to learn to use, to experiment with, so the first question is how to choose? Most are accessible via links on the Biology Department page.

It seems that it's useful to distinguish between topics that are

ethological (BasicBiosis in FirstSearch, Biological Sciences in Cambridge Scientific Abstracts --but not only those), and
more-or-less
medical (Cambridge Scientific Abstracts, PubMed [MEDLINE], probably others)
PubMed offers a "see related articles" feature that may be very useful once you've found an article that seems right on target. Just what the algorithm is for similarity I'm not sure, but a recent article on finding plagiarism in Science (Jan 23 1998: pg 474) comments favorably:
One of PubMed's most valuable features, designed by the National Center for Biotechnology Information (NCBI), is a push-button function labeled "find related articles." NCBI director David Lipman explains that this "neighboring" function was developed by John Wilbur, an M.D. with a Ph.D. in mathematics. It uses statistical algorithms to identify root words in a selected article and scans the entire Medline database for other records that use the same words and are likely to cover the same topic. After its first pass through the database, it concentrates the search by giving extra weight to root words that appear more than once in the initial batch of candidate records.

Other databases that could be of use to all of the above include NSF grants (and for some NIH grants) and the Conference Papers Index in CSA, and of course UnCover. A link to a list of publishers' search utilities exemplifies the wave of the future.

Review articles present a specific sort of finding problem.

A basic skill to master is using the descriptors, identifiers and other coded fields (when available) to focus searches.

With any of these databases, a basic question is do we have the journal? [answer the question with a Title search in Annie], and often the answer is negative. While in theory it is possible to get almost anything by InterLibrary Loan (usually not possible to get MA and PhD theses), for Bio182 you are supposed to restrict your efforts to what we have at W&L, plus a small number of appropriately-chosen (and negotiated with me and your faculty supervisor) ILL transactions if necessary.

Most of these specialized databases offer abstracts, from which it's possible to learn a lot (and which often are sufficient basis for deciding whether to pursue an article). You should make extensive use of abstracts --e-mail them, save them, print them out, use them to enlarge your understanding of your topic.
You do have to be careful not to claim to have read an article because you've read its abstract, and it's just plain unfair (and intellectually dishonest) to adjust the text of abstracts to construct bibliographic annotations.

Another question for each database: what is its coverage? Thus, BasicBIOSIS is limited to 1994 to 1997, a fact you really need to consider in using it. AGRICOLA goes back to 1970. UnCover starts in the early 1990s, Cambridge Scientific Abstracts goes back to 198?, and so on.

Examples: skunks, ebola, and surrogacy