Bio 182 Second Meeting

I want to look at three sorts of information access, using Annie (books in our library), Google Scholar (much more than pages on the Web) and Science and Nature(online journals). Each has its place in the spectrum of work you'll be doing, each has peculiarities and conventions, and each has lessons to teach.

And I want to get you started with keeping track of what you find as you do various sorts of searches.

Part 1 of Assignment Two:

So you need to know how to make a hyperlink on that index.html page. Nothing to it. Open FrontPage, use the 'Open' command (File menu) to retrieve your index.html page. Below the material you wrote for this week's assignment, type My logfile. Highlight that text. Click on the GLOBE icon in the menubar. Type log.html to identify what the hyperlink will point to. Save the index.html page (use SAVE AS... to make SURE it's saving it as index.html unless you, like, totally trust Bill Gates...).

Now tell FrontPage that you want to make a NEW page. Put the date on the page. SAVE AS log.html and go to your index.html page in a browser. Click on the "My logfile" link and you should see the page with the date on it. If not, hunt me down and we'll straighten out the problem.

This log.html page is where I want you to keep track of what you do as you search --it's your working space, a place to cache URLs and comments and so on --sort of an electronic lab notebook.


Part 2 of Assignment Two: Try searches on and around your topic in (1) Annie, (2) Google Scholar, and (3) Science and Nature. Write a narrative of your search process and findings in your log.html file. Be sure to report what terms you tried. Always DATE your log entries.

Here's your task: You have some basic terminology in your assigned topic, but (with a few exceptions) you don't know much about the subject. You need to explore to develop a vocabulary about your topic --to figure out what terms you can use to discover more. Each topic demands its own strategy, and you may need to go back and forth between the several starting places.

Every search tells you something. Sometimes the message isn't what you expected --a result of ZERO might be saying that your query was improperly formulated ...or there might be nothing about the subject-as-queried.

So that's what you need to do for this week's assignment, essentially a matter of starting to develop terminology on and around your topic. The question is where to begin? ...and each topic presents a distinctive challenge:

Each of these 'types' (and there may be others too) probably needs a different strategy, and perhaps calls for a different starting place. Here's an example, one I'll be exploring myself over the next two months:
H5N1 declared itself to be a big problem just about a year ago. Over the first six months of 2004, many millions of domestic fowl died or were slaughtered all over East Asia, and more than 30 people died ...not many in the context of the tsunami deaths, but the outbreak was recognized as a crisis by scientists and governments alike.

This has the potential to be or become the great crisis of your lives, on a truly global scale. So we need to figure out how to monitor what's happening as it unfolds into the indefinite future.

The danger is that H5N1 will achieve person-to-person transmission (it's now animal-to-person) and break out as a global pandemic, one with a notably high death rate. The clearest precedent is the 1918 Influenza Epidemic, which killed somewhere between 20 and 50 million people

n.b.: a google search for '1918 influenza total' pointed me to The Threat of Pandemic Influenza: Are We Ready? Workshop Summary (2004) from the National Academies Press
So I'll try to develop examples that explore H5N1... I've been gathering a log file for H5N1 for almost a year

Annie

In cases where you have a pretty clear term, like 'apoptosis', it's often sensible to start with a keyword search in Annie, just because she's friendly and probably will lead you to a starting place for your odyssey. If you get zero, try a more general term.

An Annie search for keyword apoptosis gets 15 hits (though many of them are not about the specific case of plants and apoptosis).

The great POWER of Annie is that many of the books' records include (and search) the Table of Contents, so you can find out important things about what's in books. A couple of years ago this wasn't an option.

But what if an Annie search gets you ZERO hits? The tactic then is to search for something more general. Thus, if I search Annie for H5N1, I get nothing. But I then ask: H5N1 is a kind of what? ...flu [28 hits] ... influenza [55 hits] ...and amongst these I certainly find a number that would be useful to explore further, for background if for nothing else. So I MARKed and EXPORTED a bunch of those, and emailed them to myself. [We might ask WHY I got nothing for such an allegedly important subject?]

Try an Annie keyword search for "embryonic stem cell": 5 hits, useful for background, but not addressing the current scientific issues that will engage most of you in Dr. Wielgus' group.

For one more example, if an Annie search for 'farmed salmon' gets nothing, you might try the more general 'salmon', or back up the more general 'aquaculture'. The same strategy will work for most of you: if a narrow search gets you nothing, make a more general search. The objective here is to find where there may be books that might be useful and go and take a look at them and the surrounding shelves. Secondarily, this exercise will lead you to more words that may be useful as you develop more sophisticated searches and greater knowledge of your topic.

Google Scholar (scholar.google.com)

Every year the Web gets to be more important as a source, but if you rely on search engines you will have to work your way through a lot of questionable stuff to find reliable information. It's astonishing how much you can find that's helpful, especially for the early stages in figuring out the vocabulary of a topic, though generally you won't find primary research articles via Web searches --that's what the specialized databases are for.

Google is not the only one of its kind, but it's pretty good. And Google Scholar is even better --though neither perfect nor comprehensive. I can assume that everybody knows the basic moves of Google, and the basic caveats, but Google Scholar is a different beast, a forerunner of an emerging next generation of Web search tools --one that attempts to limit to a subset of the exhuberant anarchy of the Web. Google Scholar deals in academic literature, searching the sites of a broad stable of publishers. It is not complete or even-handed (it is a Beta, "under development"), but it does work pretty well, and can be used in conjunction with other tools.

Thus, if I do a search for "embryonic stem cell" diabetes I get nearly 1000 hits (without the quotes to force the phrase, it's nearly 5000...). These may be a very good start. Look at what we get, by looking in some detail at the first record in the set: a 1998 article in Science, with a LINK to its full text... and another link to 579 citers of the article. We do have to ask: where is the diabetes connection? Anothher article: Insulin Production by Human Embryonic Stem Cells Suheir Assady et al. Diabetes 50:1691-1697, 2001 seems like another good place to begin.

Another example: alcoholism ethnicity gives a good start, though with fewer citations of the articles.

Obviously there's a lot more to it than just plugging in a phrase, but clever browsing and trying various combinations of likely terminology can produce very useful things. I'll be happy to consult on a 1:1 basis if you're having problems with your topic.

Science and Nature

The third place your assignment is sending you is to two of the essential NEWS conduits of the sciences, read (or at least monitored and skimmed) by many of the world's scientists on a weekly basis. IMPORTANT events and discoveries show up in these magazines, which also publish PRIMARY articles that the editors select as particularly significant. It's a VERY big deal to have an article accepted by either of these --which have 90+% rejection rates. They also function as bellwethers --the first news of discoveries and events of interest to people across the disciplines of the sciences. Watson and Crick "Molecular structure of Nucleic Acids" Nature April 2, 1953 is arguably one of the most important scientific 'events' of the last 51 years, and it first appeared as a Letter in Nature.

Here's an example of a News story in the very latest Nature: Red meat is strongly linked to cancer: Diet experts urge move to poultry, fish and beans after results of long-term study (Helen Pearson, Nature 11 January 2005])

...and here's one that looks to me like it's ABSOLUTELY in the court of William Young's topic: Human immunodeficiency virus: Nuclear RNA export unwound BRYAN R. CULLEN Nature 433, 26 - 27 (06 January 2005)

...and in the just-posted Nature, I found this: Infectious disease: Vietnam's war on flu Nature 433, 102 - 104 (13 January 2005)

Having suffered heavily from avian influenza in 2004, Vietnam might now be brewing the next human flu pandemic. Yet, as Peter Aldhous discovers, local researchers don't have the resources to investigate the risk properly.
The ways in which HIV can subvert cellular processes for its own ends seem boundless. The latest discovery — a cellular enzyme that helps to export HIV RNA from the nucleus — reveals a possible drug target.

Science is an essential source, accessible to you in two places: October 1995-present at www.sciencemag.org, and 1880(!!)-1997 via www.jstor.org. Both allow keyword searching of full text of articles, and of course one can search by author too.

I happen to know that Ian Wilmut is one of the Big Names in cloning (Dolly the Sheep, and all that). If I do a search in the online current Science for 'wilmut' as author I get five hits, one of which is Human Factor IX Transgenic Sheep Produced by Transfer of Nuclei from Transfected Fetal Fibroblasts (Angelika E. Schnieke et al. Science Volume 278, Number 5346, Issue of 19 Dec 1997, pp. 2130-2133. --Ian Wilmut is one of the authors)
What have we here? It's a 1997 article, very widely cited by subsequent writers. The sidebar gives us a lot of options... and at the bottom is a list of citers. There's also a link to Science's Subject Collection on Genetics, and the smart money tries the "search for similar articles" feature.

Science is interesting with the non-scientific term 'pharming', yielding 180 hits in full text (mostly in the News domain) --but it turns out that Science stems the search words --so my search for 'pharming' turns into a search for 'pharm-' and therefore gets 'pharmaceutical' and 'pharmacy' and so on... but a search in quotes ("pharming") gets the 7 Science articles that contain the word. Interestingly, it turns out that there's a Dutch biotech company with the name Pharming.

The Science site includes 1996-2005 issues of the magazine. In addition, we have access to Science from 1880 to 1998 via JSTOR.

Just for fun, I tried a search for "human cloning" in the General Science collection of JSTOR (which includes other titles in addition to Science). One of the 10 items I found was How Close Are We to Implementing Gene Targeting in Animals Other Than the Mouse? (a Commentary by Mario R. Capecchi, in Proceedings of the National Academy of Sciences of the United States of America [PNAS], Vol. 97, No. 3. (Feb. 1, 2000), pp. 956-957). A subsequent search for "gene targeting" got 200+ hits, and the "highest scoring" of these projected me right into the middle of the topic...

Nature is the British-based 'twin' of Science, accessible on campus via www.nature.com/nature/, with an archive 1997-2003.
A search for "endocrine disrupting chemicals" got 7 hits... and gave me a good start in my quest to learn more in this area. One of the hits was Frogs put in the gender blender by America's favourite herbicide (REX DALTON, Nature 416, 665 - 666 [18 April 2002])

On the Nature Advanced Search page I noticed a button for CrossRef Search, so I tried a search for 'genetic alcoholism', which found a LOT of material. One link led to an article in The Pharmacogenomics Journal (2003) with a link to a pdf. Its bibliography looks like a really good springboard into that literature.

Please observe that I've captured links to a number of articles, a procedure that's possible with some sources (like JSTOR, Science, Nature) but isn't with others. Where possible, adding links into your log files is a very good idea, but it's also wise to collect the detailed bibliographic data as well --since you'll need that if you're including a source in a bibliography.

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A new idea for combating pathogens points to an article in the current issue of Journal of Theoretical Biology: Virus evolution within patients increases pathogenicity Yoh Iwasaa, Franziska Michor, and Martin A. Nowak