Encyclopedia of Life Blog

UPDATE! (July 31, 2008): The code sprint will now take place September 8-11, 2008

The Encyclopedia of Life has been keenly interested in content management systems and social networking phenomena, especially relating to how well these might be of benefit to practicing taxonomists who are under pressure to get online. So, we have been getting serious about Drupal and want to make a stab at hosting sites called “LifeDesks” that as a start will focus on particular groups of organisms and will be similar to Scratchpads, a most amazing collection of Drupal-based sites hosted at the Natural History Museum in London, England. LifeDesks would sit just to the side of EOL, but will have the advantage of providing some extra, distinct visibility for participants while still feeling part of the EOL dream. A bit of work needs to be done on Drupal to make this work and we’re interested in sharing developments with the wider Drupal community.

So, although it’s short notice, we’re going to host a Drupal code sprint August 11-14 in Chicago, Illinois to kick-off our relationship with Drupal. Please visit http://sprint.eol.org to see what we have in store and please also spread the word to any Drupal developers you know.

This June the BioSynC had some very exciting visitors! On the 4th, we were honored to give a tour to Dr. Ashok Khosla, the former director of the United Nations Environmental Program. On the 12th staff from the offices of Illinois Senator Dick Durbin and Congresswoman Melissa Bean came by for a tour.

Outside of the Field Museum, Rick attended the Consortium for the Barcode of Life meeting in San Diego the week of June 23rd, specifically to go to a session on data visualization, presenting BioSynC’s efforts to develop interactive tools with Adobe.

Mark and Darolyn left the Evolution meeting (previous post) in Minneapolis on the 23rd to travel to Keelung, Taiwan for an organism-focused synthesis meeting on Decapods (shrimps, crabs, crayfish and lobsters) from the  25th to the 29th. This meeting was an exceptional example of the power of organism-focused meetings to bring together key scientists focused on a megadiverse group to develop great taxonomic, phylogenetic, and conservation resources for the broader community on a scale not previously seen. Hosted by Professor Tin Yam Chan, the meeting developed ties between the US decapod crustacean biologists working on the Decapod Tree of Life project with their counterparts in Australasia. These groups have exceptionally complementary talents and resources, and combining their efforts proved very productive. It could be said that they made a quick and effective leap forward in the fundamental understanding of decapod diversity. The meeting involved around 24 specialists and six students from 9 countries, with the goal of among other things, creating the first comprehensive species list for decapod crustaceans, no small feat given that there are over 15,000 known species. Darolyn will be posting in greater detail about how the meeting went really soon.

Staff Update

Here is a group photo of our staff and summer interns (we always look this good), unfortunately all the postdocs were out that day, from left to right: Alta Buden, Kate Harney, Nick Lilly, Krista Larson, Audrey Aronowsky, Darolyn Striley, Mark Westneat, and Rick Ree

On June 9th our new summer interns started! Three of them are from the BitMap program, which means they are trained in bioinformatics, (Krista Larson, Scott Bradley and Pratima Maiti) and two others hail from the University of Chicago (Kate Harney) and Princeton (Nicholas Lilly).

Here is a little bit about each of them and some photos (that may or may not be photoshoped) we took with the Olmec head at the Field Museum:

Krista Larson

Krista is a graduate student in computer science with interests in biology and bioinformatics.  Her work history is diverse, starting with working in the pharmaceutical industry, moving on to IT consulting, and then as IT support for an investment consulting firm until she finally realized what she wanted to do when she grew up.  Currently she is working with Rick Ree on an application for grafting and editing phylogenetic trees.  Always up for a new challenge, she also recently worked as a ‘crystal expert’ doing chandelier restoration at a hotel in downtown Chicago.

Scott Bradley

Scott has a degree in Electrical Engineering from Purdue University and is completing a Master’s in Computer Science at DePaul University where he has focused his course work in artificial intelligence and software development for the sciences. Scott has been doing systems and software design and development for over 14 years across many fields, including telecommunications, manufacturing, architecture, and web application development. His most recent work has been on projects for Siemens Corporate Research, and AT&T. Scott’s broad academic background also includes a degree in theology. His research has included theological inquiry into the nature of human creativity, and his current interests include search and discovery and the general application of programming and artificial intelligence to creative and scientific pursuits. He was once called “some sort of academic hippy” in a job interview, and well, he didn’t get that job anyway, but that might be why we like him.

Our other BitMap intern Pratima Maiti will be posted soon.

Nick Lilly

Last year Nick graduated from Princeton University where he majored Ecology & Evolutionary Biology and minored in Creative Writing and Environmental Studies. For his thesis, he wrote a novel centered around green sea turtle conservation and based on his own field research at the green turtle nesting beaches of Tortuguero, Costa Rica.  In the future, he hopes to publish his book and to continue to combine his interests in biology and creative writing. Nick is currently working on research for a virtual coral reef project. He is also going help us out this summer by getting together information to contribute to EoL turtle pages as well as helping to translate science speak on some of the EOL fish pages. He spends much of his free time both in and out of the BioSynC either eating or preparing baked goods (as do many of us here). Among the many places on Earth he enjoys, he feels particularly attached to the tent he slept in while studying in Kenya, to Rome, to Fassi souks and medersas, to Costa Rican sea turtle nesting beaches and cloud forests, to the Field Museum and Brookfield Zoo, and to his home in the Midwestern United States.

Kate Harney

Kate is entering her fourth year at the University of Chicago majoring in the biological sciences and mathematics. She spent the past semester studying tropical ecology in Ecuador where she spent a month in the rainforest and also traveled to the mountains, coast, and Galapagos Islands. At the UofC Kate is a member of the women’s ice hockey team, something one would not suspect from her calm demeanor.  At BioSynC she is working on background research for a virtual coral reef project and learning Drupal with Alta in order to help redesign our website.

We also have one of our new post-docs starting this month:

Jim Parham

Jim, our second Postdoctoral Research Associate, is a broadly trained herpetologist (although clearly he is into turtles). He is arriving in Chicago from California, where he recently completed a postdoc in molecular systematics at the Joint Genome Institute following his PhD work in paleontology at U.C. Berkeley. Before that he studied geology at the University of Rhode Island. He is primarily interested in how human activities impact our ability to reconstruct natural patterns of reptile diversity (through extinction), distribution (through extirpation and exotic introduction), and phylogenetic relationships (through genetic pollution). He also studies the evolution of major turtle lineages by integrating paleontology with molecular systematics.

I joined the Encyclopedia of Life a few weeks ago as the Director of the Species Pages Group. I’’m based at the Smithsonian Institution, along with the EOL secretariat, but will be working regularly with the other four components of EOL: the Informatics group at Woods Hole, BioSynC at the Field Museum in Chicago, Education and Outreach at Harvard University, and the Biodiversity Heritage Library at many institutions.

That said, as the Director of the Species Pages Group, my primary companions will be the global scientific community. Our goal of 1.8 million species pages in ten years can only be met with intense, coordinated effort. We need to prioritize sharing of digital information already in databases, and target key areas where little information exists online. We need to enrich species pages with knowledge from specialists such as ecologists and physiologists, with observations from museum collections and citizen scientists, and with excellent images and video.

My group works with prospective data partners and will administer a new EOL Fellows program. We’ll be building a curatorial network that will help authenticate contributions from the general public.

How did I get here? My doctoral work in biology at University of Michigan was on the social behavior and communication of crows (Corvus brachyrhynchos) and I’’ve studied the evolution of magpies (Pica) using DNA sequence and behavior. For the past ten years I’’ve worked on a variety of informatics projects. With the Animal Diversity Web I led the development of species pages by college students, negotiated licensing, and developed software for children observing diversity in their schoolyards. At the Human Computer Interaction Lab at University of Maryland we explored ways to visualize biological trees and food webs. More recently, at both University of Maryland at College Park and at Baltimore County, I’’ve worked on semantic web and social technology for scientists (particularly moth and butterfly experts) and for citizens (ecoblogging). In my spare time, I’m a Flickr fan and a geocacher.

Discerning readers will note a trend. – I resist narrow research bins and just want to find the best ways to build and share knowledge about biological diversity. That’’s my passion, and that’’s why I’’m now with the Encyclopedia of Life.

As I work on the human connections that will build the content of the Encyclopedia of Life I welcome your ideas. You can leave them as comments here, or send me a message via the Contact Us form.

Many thanks to all of you who have already volunteered to help curate pages, and who are busy collecting information to contribute to species pages once our tools are ready. How many people do you think will ultimately be involved in the effort?

Torsten Dikow, net in hand.

This past weekend (July 27-28) BioSynC post-doc Torsten Dikow, expert on robberflies, was invited to participate in the 2008 Middlefork Savanna Bioblitz. On Saturday, he ventured into Middlefork Savanna, one of the “most important sites for biodiversity in northeastern Illinois” according to Chicago Wilderness, to look for specimens of robber flies. Here is the one he found (it was very windy, not stellar for fly catching).

Bioblitzes are an brilliant way to simultaneously raise public awareness about local biodiversity and to collect scientific data: Torsten will now identify that fly and ad it to his research data. In addition the park preserve now has a better idea of what species live there, and thus how to better look out for them. This bioblitz featured over 100 scientists and many more civilians combing the preserve for 24 hours to attempt to identify as many species as possible. They discovered at least 1054 species and more are still being counted by participating scientists and taxonomists. Check out their blog to see how the event progressed.

Bioblitzes are usually centered around a “Tally Tent” where people bring photographs and specimens for documentation, and where the public can watch scientists at work. These events have exciting implications for the EOL; we hope that in the future the EOL can both serve as a resource for people identifying species in them as well as act as a host for the detailed regional data that they produce. Here is the flickr link to the best photos that they took like the one below of a shy and elusive eastern milk snake (Lampropeltis triangulum triangulaum).