Defeating Bedlam: science on one's computer

[Guest guest]

Defeating Bedlam

Olivia Judson

http://judson.blogs.nytimes.com/2008/12/16/defeating-bedlam/

This week, I want to look at one of the unglamorous, but essential,

parts of science: the problem of how to organize the information you

have so that you know what you've got. For, like everything else in the

digital age, the process of collecting and managing scientific

information has been evolving. Fast.

Here's what I used to do, way back, oh, seven years ago when I was

writing a book about the sex lives of animals. When I wanted to do

research on a topic, I would go to the university library --- how

quaint! --- and photocopy the scientific papers I wanted to read. Papers

such as " Homosexual rape and sexual selection in Acanthocephalan worms "

from the journal Science. Or " Deformed sperm are probably not adaptive "

from Animal Behaviour. If I was looking for something more obscure ---

say, " A review of tool use in insects " from Florida Entomologist --- I

sometimes had to go to a specialist library, like the one in London's

Natural History Museum.

Having collected the papers, I would take them back to my office, type

the bibliographic details (authors, title, year published and so on)

into my computer and put the photocopies into folders with other papers

on the same general topic. In the case of the Acanthocephalan worms, it

was a folder labeled " sabotage " ; for the deformed sperm, it was " other

sperm. " When the time came to write up my discoveries and thoughts on

the subject of sperm evolution, or how males sabotage their rivals, I

went to the relevant folder, read the papers, made notes on them and

started writing.

As a system, it was a little clumsy --- photocopying was a bore, and if

I wanted to spend a couple of months writing somewhere other than my

office, I had to take boxes of papers with me --- but it worked. I knew

what I had and where it was.

Then the scientific journals went digital. And my system collapsed.

On the good side, instead of hauling dusty volumes off shelves and

standing over the photocopier, I sit comfortably in my office,

downloading papers from journal Web sites.

On the bad side, this has produced informational bedlam.

The journal articles arrive with file names like 456330a.pdf or

sd-article121.pdf. Keeping track of what these are, what I have, where

I've put them, which other papers are related to them --- hopeless.

Attempting to replicate my old way of doing things, but on my computer

--- so, electronic versions of papers in electronic folders --- didn't

work, I think because I couldn't see what the papers actually were.

And so, absurdly, it became easier to re-research a subject each time I

wanted to think about it, and to download the papers again. My hard

drive has filled up with duplicates; my office, with stalagmites of

paper. And it isn't just that I have the organizational skills of a

mosquito. Many of my colleagues have found the same thing. (Yes, we talk

about it. Oh, they are lofty, the conversations in university common

rooms.) In short, access to information is easier and faster than ever

before (for a caveat, see the notes, below

<http://judson.blogs.nytimes.com/2008/12/16/defeating-bedlam/#1>, but

there's been no obvious way to manage it once you've got it.

Several pieces of software are now being developed to address this

problem. I want to look at two of them here. The first is called Zotero;

the second, Papers. Both are in version 1 and are still a bit buggy; but

each has the potential, I think, to become a valuable tool for research.

Zotero <http://www.zotero.org/> aims to let you build a library of

useful books and articles that you encounter while surfing online. It's

an extension of the Web browser Firefox, and as you'd expect, it's free

to download and easy to install.

Once you've installed it, each time you visit a Web page that contains

items --- books, newspaper articles, soundtracks, films, etc. --- with

bibliographic information, it extracts that information and allows you

to save it to your Zotero library if you want to.

So, suppose you're interested in books about the psychology of war, and

you go to Amazon and type " On Killing " into the search box. A list of

books appears; Zotero collects the information for all of them and

allows you to select the ones you want to keep. These are then put into

your Zotero library. Once they're there, you can make notes on them, put

them into folders with other items that are related, and so on. If you

ask it to, Zotero will see if it can find a given book in a local

lending library. And, supposedly, you can also pull bibliographic

information from Zotero into documents you're writing, but I haven't

tried that part yet.

It's a powerful piece of software with a lot of capabilities, though not

all of them work as well as they could. For instance, it's hit-or-miss

with newspaper articles --- sometimes it recognizes them, sometimes it

doesn't --- and it can't interpret information from, alas, my local

lending library. It does, however, allow you to screen grab, so you can

still collect such information if you want it. The screen grab also

allows you to add interesting Web pages to your Zotero library. (This is

different from storing the link to a Web site. The screen grab gives you

the page as it was when you looked at it; clicking a link gives you a

site as it is today.)

A minor quibble: if you use a small laptop, as I do, you may find the

Zotero window occupies too much of the screen. But I shall certainly

keep using it, though not, perhaps as its conceivers intended. For me,

it'll be a scrapbook of interesting stuff --- books to buy later, press

releases on subjects I think I might write about one day, magazine

pieces about cities I'm thinking of visiting.

For the bulk of my researches, however, I shall use Papers

<http://mekentosj.com/papers/>. This software has been designed for the

Macintosh by two avid fans who call themselves Mekentosj; it only works

on the Macintosh platform. It's not free, but it is quite cheap (20

pounds sterling; 40 U.S. dollars) and, for me, it's been worth the

money. For it solves the problem I started out describing --- how to

keep on top of scientific articles. How to know which ones you have,

where they are, and what else you've got on the same subject.

The makers describe it as iTunes for .pdf files, and that's broadly

right. (For anyone who's never encountered these things, a .pdf file is

a type of document file that any computer can open using a free

downloadable piece of software. This is the form electronic journal

articles come in, and it means they look just as they would have done if

you were reading the journal the old fashioned way. iTunes is a piece of

music management software.) The idea is that, when you download an

article, it goes into your Papers library. The bibliographic information

immediately appears; so does, if you're lucky, the " metadata " --- like

the abstract and the list of subjects that the authors thought their

article touches on. (I say " if you're lucky " because this doesn't always

happen automatically.) The document itself gets neatly filed in a folder

on your hard drive, and renamed by authors and year. Gone are the days

of 456330a.pdf and sd-article121.pdf. Hallelujah.

And that's just the beginning. Not only can you read the papers,

annotate them, find them and create folders of papers on related

subjects, you can also use the software to search the big scientific

databases like PubMed and the Web of Science. (Such databases are where

you go to find out what's already been published on the subject you're

interested in; it's where most scientists find out about the papers they

want to collect.) It doesn't (yet) replace bibliographic software such

as Endnote; but it can be used with it quite neatly.

Papers does have some teething problems. As I said, it's still buggy, so

not everything functions as it should. Moreover, the way it works is not

always intuitive, and there's no formal " help. " Instead, if you have a

question, you have to wade through user forums to try to see if anyone

else has had the same question before --- and, more to the point,

whether anyone has answered it. But after a couple of days of

experimenting, I got it doing exactly what I need.

Organizing materials is always idiosyncratic. I have one friend who

organizes the novels he owns by the year in which the books were

published; another goes by the color of the spine. (The first accused

the second of having the soul of an interior decorator.) But the

important thing is not how you do it, but whether it works --- whether

you can find what you're looking for. These bits of software open up

possibilities; for some people they will be useful, for others they

won't. Some will use both, others neither. For me, well, a few days

after discovering Papers, I put 20 sacks of real paper into the

recycling bin. At last, I'm back to knowing what I have and where it is.

Bedlam has been defeated.

**********

/NOTES:/

/One caveat. I say " access to information is easier and faster than ever

before. " With respect to scientific information, this is true for people

within universities, but not for those without them. One of the

consequences of the scientific journals going digital is that it has

become harder for members of the public to get access to original

scientific information. It used to be the case, for example, that anyone

could get permission to spend a day at the library at Imperial College;

once there, they could read any of the journals on the library shelves.

Now, subscriptions to the paper editions of many journals have been

stopped --- the journals are no longer physically there --- and only

members of the university are allowed access to the online versions.

Some journals give free access, at least to back-issues; but many do

not. Then, if you are not a member of a university and you want to read

some articles, they may cost you as much as $30 each. I think this is a

pity. Perhaps not many people want to read original scientific research;

but somehow, it seems against the spirit of the enterprise./

/In case anyone's interested, here are the full details for the articles

I refer to. For the worms, see Abele, L. G. and Gilchrist, S. 1977.

" Homosexual rape and sexual selection in Acanthocephalan worms. " Science

197: 81-83. For deformed sperm, see Harcourt, A. H. 1989. " Deformed

sperm are probably not adaptive. " Animal Behaviour 37: 863-865. For

insects and tools, see Pierce, J. D. J. 1986. " A review of tool use in

insects. " Florida Entomologist 69: 95-104./

/Many thanks to Austin Burt, Gideon Lichfield and Simpson for

insights,

..

/