Reading William Gunn’s recent blog posting, Could this be the Science Social Networking killer app? got me thinking more about the many online scientific reference list repositories like Connotea, CiteULike and 2Collab, and why they are failing to catch on. William is suggesting a Pandora-like system of expert reviewers tagging papers to set up a recommendation system. I’m not sure this would be really helpful–what you get from a scientific paper is very different from what you get from listening to a song, and their interconnectedness works in very different ways. And it brings to mind the failings of organizing your references by tags.

If you’ve ever dealt with any of these social bookmarking sites, you know how incredibly tedious they are to use. Even for journals like CSH Protocols, where we have buttons on every article to add it directly to these sites, you still end up jumping through hoops, filling out forms, writing summaries, adding tags. You’re on the spot at that moment to come up with a list of tags that will remind you about the content of that paper. As your worldview changes over time, and with it your research priorities, you’re probably going to want to revisit many papers and add additional tags. Even with all this time-consuming work, you still may not have added an appropriate tag to let you find what you want to find at a given moment. Did you add a tag for every method used in the paper? Every conclusion, every subject referenced? That band on the gel in figure 3 that you’re ignoring today might be very important to you tomorrow. How are you going to tag the paper in case you need to find it again?

It’s more work than it’s worth, particularly given the ability to do full-text searches on your collection of articles through programs like Papers (out for the iPhone this week, by the way). Why tag every single aspect of a paper when you can just do a quick search? Even Google Scholar and PubMed strike me as much easier tools to use for these purposes than social bookmarking sites. It’s why Apple, Microsoft and Google have spent so much time and money on desktop search applications over the last few years. Investing efforts in organizational schemes is pointless when you can call up the file you need via a quick search. Sure, with Papers or the search engines, you lose the social aspects of things, the use of the network as a discovery tool. Then again, your hard work adding tags isn’t helping you discover new papers, it’s helping other people. You have to hope that others are tagging papers as relentlessly as you and that they’re tagging the aspects of papers that fit your interests.

The tedium of tagging versus the relative ease of searching brought to mind this recent article from John Gruber on the Daring Fireball site, Untitled Document Syndrome. Gruber talks about friction, the number of tedious steps involved in so many programs:

“There’s the stuff you want to do, and there’s the stuff you have to do before you can do what you want to do. People have a natural tendency to skip the have to do stuff to get right to the want to do stuff if they can get away with it. Friction is resistance.”

His example is writing a Word document. How often do you find yourself starting a new document, and writing for a long while without actually saving it? Saving changes to an already saved document is trivial, a keystroke away, but a new document means you have to go through that dialogue box, figure out where you’re saving it, come up with a title, etc.

“The obvious problem with Untitled Document Syndrome is in the rare cases where you lose data because you never saved it. The non-obvious problem is that the mental friction posed by the Save dialog often keeps you from ever even creating or saving small items of data in the first place.”

Gruber talks about the different approach taken by programs like Apple’s iLife suite, where you just dump in music, video or photos, and you don’t have to worry about naming them, or deciding where to store them. The program does it for you. It’s no surprise then, that programs like Papers or Yojimbo, which are based on the same iLife-style interface, are so much easier to use for organizing your scientific research list. Given the time demands faced by scientists, it’s no wonder I’ve heard rave after rave about Papers, but never really receive much more than a shrug when discussing online reference sites with folks at the bench.

One other caveat–if you are going to invest your time in tagging, be sure to regularly extract your account’s information and back it up. Sites may disappear at the drop of a hat. Some of the science paper bookmarking sites are clearly unaware of the Napster and Grokster court decisions and their willingness to become redistributors of copyrighted material places them only a lawsuit away from the abyss. And even with those backups, uploading them to the next site is never as clean as you’d like it to be. Be prepared to repeat a lot of your efforts.