Gaurav Vaidya

Topic pages and biodiversity informatics

PLoS Computational Biology has embarked on a fascinating experiment in scientific publication to Wikipedia: Topic pages. That's a peer-reviewed article published in PLoS Computational Biology designed to be directly incorporated into Wikipedia. Unlike a conventional research paper, a topic paper is designed to comprehensively cover one specific topic. The first ever topic paper was about Circular permutation in proteins, a Wikipedia article which was significantly improved by the changes.

In one elegant step, this ties together Wikipedia and scientific credit: once your topic paper is published, you get the credit due to you, while Wikipedia is greatly improved by your contribution. It also ties together Wikipedia and journal publishing: one of the big problems in taxonomic informatics is tracking the bleeding edge as new species are discovered and named. By writing the articles in a wiki before submitting it for publication, the process of going from scientific paper to Wikipedia article can be simplified and sped up. Finally, by framing the goal of the paper as a "topic paper" rather than as a research question, the content is already in an encyclopedic tone and subject incompatible with a typical, hypothesis-based research paper.

Will we perhaps someday see taxonomic topic pages in which the cutting edge hypotheses about a clade's phylogenetic tree are presented, ready for inclusion into an encyclopedia? Or perhaps taxonomic review topic papers, with the most comprehensive knowledge assembled about a species or clade, summarized by experts, ready to be incorporated into the most widely used encyclopedia on the internet? I do hope so. Daniel Mietchen, the Wikimedian in Residence on Open Science, is already interested in taxonomic treatments, and I can't wait to see what he -- and the PLoS and OKFN teams -- come up with next.

Blogging elsewhere, because I can

While I have been letting this blog fall asleep in the run-up to the ever-so-busy final weeks of school, I have been busily blogging, writing and scheming elsewhere! Here are some updates:

October 11

Co-wrote What’s new, October edition on the Map of Life blog.

November 18

Kicked off a WikiMedia Commons project for the Biodiversity Heritage Library. So far, we've tagged 16 files from BHL, fixing their copyright status and linking back to the BHL website in the process. Jean-Frédéric created this gorgeous template to use as a source template on BHL images. The plan (my plan) is to keep tagging images into the New Year, and see where we are after that.

November 29

Kicked off a project with Robert Guralnick and Andrea Thomer, working closely with the CU Museum of Natural History and with help from the NSIDC (don't you love big-team projects?), to digitize the field notebooks of Junius Henderson, the CU Museum's first curator. We were all surprised at how amazing WikiSource is for managing transcriptions and displaying the results.

December 5

Co-wrote Field Note Challenge Part 2: Veni, Vidi, Wiki on the So You Think You Can Digitize blog.

December 6

Excited by all the taxonomically interesting information already in WikiSource, I created a portal to try to coordinate efforts to annotate, organize and connect these resources with counterparts on WikiSpecies, Wikipedia and (especially) the WikiMedia Commons.

Fun times! I brazenly anticipate even. more. fun as I get a week to push ahead on the Map of Life after Tuesday, followed by a week of fun with sister and cousins in East Brunswick, NJ, followed by another week to code, ruminate and discuss, followed by another two weeks (back in Boulder, now) to work on things before the next semester smashed into my life like a grammarian smashing into someone misusing a simile.

The #SciFund Challenge

I just discovered the #SciFund challenge, a Kickstarter-like project to raise money for scientific projects by promising deliverables created as part of the project. I think it's a great way of getting non-scientists involved in science, to say nothing of getting funded and of creating a concrete science-to-public deliverable system. So: excited!

Here's some of the projects I took a fancy to. Unfortunately for me, as a grad student lacking money, RocketHub (the hosting website) has no mechanism for "subscribing" to a project without paying that I can find. So this might be the only way for me to keep an eye on them (and maybe make a contribution with my next paycheck).

• Collecting ants living nears homes and schools, which sounds like an awesome way to get kids involved in science.
• Genetic surveys of Costa Rican birds and bats, the American pika, and the social tuco-tuco. Because Ctenomys is to love me.
• Hiring local field assistants for elephant research in Sri Lanka, building closer links between researchers and the human residents of the landscapes they study.
• Using Ancient Rome-era DNA to determine the geographical origins of immigrants to the Empire.
• An infrastructure project to deliver vaccines to remote areas by matching up travelers in rural Tanzania with vaccines which need to be delivered to particular villages. That's a really smart idea!
• Do camera traps affect the behavior of their study animals?
• Why do some spinner dolphins have "reversed" fins, which is a fascinating study, mixing up biophysics and evolution/selection pressure research in sexy, sexy ways.
• Tracking dolphin populations through photoidentification, whose project description reminds me that labradors can track killer whales. Which is an awesome thing to be reminded of.
• Parasitic trematodes which change the behavior of the Californian killifish so they get eaten by birds (where the trematode can finish its life cycle).
• Evolution between sunflowers and bees in agricultural fields.
• Explosive duck penis erections, which really needs no elaboration.

The most fascinating part of this enterprise for me is the connection between the science projects and the contributors: the deliverables. Rewards for donating ranged from credit (on websites or in publications), to a copy of the research results, to exclusive access to project blog and Twitter feeds (which make no sense to me: wouldn't you want those feeds to be as public as possible, to encourage more people to join in and contribute?). More interesting deliverables were also on offer, from elephant dung paper and calendars with photos of the research subject, to photos taken during the study, clay sculptures of dolphin fins, lyrics to a Tanzanian children's song, and comics personally drawn for you by Zach Weinersmith of Saturday Morning Breakfast Cereal fame. Allegedly, a comic of "Carl Sagan riding a unicorn" is not out of the question.

One thing I did find odd was the lack of links in the project descriptions. Only a few projects linked to websites, blogs, Facebook pages or Twitter feeds (one project going so far as making the Twitter and blog feeds "contributor only"), although just about all of them had really excellent websites hidden away in the "About Me" section. I love Twitter for letting me follow a project without getting too involved, so more Twitter feeds would have been great to see.

Thinking in the longer term, I wonder how well this would work without the #SciFund banner, though. Unlike music or movie crowdfunding, where artists can put up samples beforehand, it might be harder to prove your scientific worth to a broader audience. For instance, how would I differentiate between a serious project to study bee evolution and some nutjob trying to prove that evolution didn't happen? I could look at the project description, sure, but it's not hard to reference many scientific studies to give yourself an air of authenticity. Perhaps the #SciFund banner will eventually be replaced with institutional banners: if the research is being carried out by the Smithsonian, the University of Colorado or is partially sponsored by National Geographic, you can be pretty sure it's been vetted.