Encyclopedia of Life Blog

The Encyclopedia of Life is gearing up to join the National Geographic Society (NGS) and the National Park Service in support of the Indiana Dunes BioBlitz <!–[if !supportAnnotations]–>, May 15-16, 2009.  During this 24-hour event teams of scientists, students, volunteers and community members will observe, identify and record as many plant and animal species as possible at the Indiana Dunes National Lakeshore.

EOL is also partnering with NGS to pilot Fieldscope, their online mapping program. High school students will input their findings from the BioBlitz into Fieldscope and eventually this information will be served on EOL.  Students will also be using EOL as reference resource prior to going to the field and will be using information from EOL in the field to help them identify plant species in the park.  After the BioBlitz students will continue to upload their findings to EOL.

The Encyclopedia of Life staff will be in the field as well as in the Scientist Tent at West Beach at the Indiana Dunes National Lakeshore. We will be collecting data and helping participants upload their images and contribute their information to EOL through tagging images and leaving comments about their species observations. Last but not least we will be reporting live from the BioBlitz. So, stay tuned for blog posts, images and videos from the event!

EOL hosted a synthesis meeting on the peracarid crustaceans April 3-6, 2009.  The meeting took place on beautiful Catalina Island, CA at the USC Wrigley Marine Science Institute.  The meeting was organized by Gary Poore, Regina Wetzer, and Dean Pentcheff and co-sponsored by the EOL Biodiversity Synthesis Group and the Species Pages Group. Peracarids are a large and diverse group of crustaceans that range from marine to freshwater and terrestrial habitats. They include the major sub-groups Amphipoda, Isopoda, Mysidacea and other, less well-known groups.

The 16 participants came from the Argentina, Australia, Canada, Italy, Norway, Poland, and the U.S.  Specialist foci ranged from molecular systematics to alpha taxonomy to host-parasite symbioses. Taxonomic specialists covered all orders within the Peracarida.

Audrey Aronowsky (Synthesis) and David Shorthouse (Informatics) introduced the community to EOL, BHL, and EOL informatics and discussed the role that EOL can play throughout the ontogeny of a taxonomic project.  The peracarid research community is already involved with a number of EOL data partners including WoRMS and uBio and will use these established channels as pipelines for EOL content.  The workshop resulted in participants agreeing to use these channels to share and contribute databases on every order of Peracarida.  Co-organizer Dean Pentcheff will coordinate the community’s efforts to integrate and collate their diverse digital and non-digital resources for web dissemination. Dean will also coordinate the integration of several excellent literature databases and catalogs to which the community contributes.  The community’s discussion and progress will be centralized on the new peracarida.org website. They are excited to leverage EOL’s wide array of data partnerships and ability to aggregate content from these partners to have a centralized location for data on peracarids.  The meeting stimulated the group to begin preparing an NSF AToL proposal with EOL as a primary avenue for research dissemination.

A group of seven researchers, including two students, from three countries (Bulgaria, Germany, and the USA) working on millipedes (Diplopoda) met at the Zoologische Staatssammlung in Munich, Germany from March 21–25 to discuss ways to update the classification and species catalogue of the megadiverse arthropod taxon Diplopoda. This meeting was organized by Dr. Petra Sierwald from the Field Museum of Natural History and sponsored by the Biodiversity Synthesis Center and the Species Pages Group of the EOL.

Group photo (from left to right): Peter Decker, Pavel Stoev, Michael Brewer, Jörg Spelda, Petra Sierwald, Jason Bond, Roland, Melzer, Hans Reip, Torsten Dikow. (photo taken by Rüdiger Bieler)

There are about 13,000 species of millipedes known to science today and many more species are certainly still undetected. General information on millipedes can be found at myriapoda.org.

Harpaphe haydeniana (image by W. Leonard) + Chicobolus spinigerus (image by R. Shelly)

The main aim of the meeting was to merge three comprehensive databases of taxonomic names and literature developed by three researchers to provide a consensus classification down to the species level. This updated classification will serve the Diplopoda research community as well as be displayed on the Encyclopedia of Life millipede pages in the future. The Diplopoda classification was updated using the powerful classification editing tool in LifeDesk on a big screen and the millipede LifeDesk will be used in the future by the community to exchange information on this interesting group of arthropods.

LifeDesk classification editor dragging a species from an alternative classification (right) to the master classification (left) (example from Leptogastrinae LifeDesk).

The millipede community has been very active already in databasing information and making it available online, e.g., the extensive millipede literature database with more than 13,000 titles. Quite a few of these publications have been digitized by the Biodiversity Heritage Library to this day (see list at EOL Diplopoda page), but many more will become available soon as the meeting participants submitted a list of the 30 most important works on millipedes to be digitized by the BHL. Another initiative started years ago is the Global Myriapd Information System that provides the current Diplopoda classification to the Catalogue of Life from where the EOL imports it. As this meeting focused on enhancing the current classification changes to the EOL species catalogue will certainly appear in the near future.

Overall, this meeting was a successful synthesis meeting focusing on a megadiverse arthropod taxon.

The BioSynC’s latest initiative in digital learning, a virtual coral reef, is live online! The reef learning environment, called WhyReef, just launched in Whyville.net.  You can access the reef directly (after an intro screen) at reef.whyville.net . Its free to join or you can sign in as a guest.

WhyReef’s goals are to teach about the diversity of life on reefs, the interconnectedness of species, collaborative counting of reef species, and how to mobilize to “fix” the reef if/when something goes wrong. We will report back in a few weeks on progress and lessons learned.

We set a pretty insane timeline for ourselves and had only 90 days from grant to launch! Our team included staff at BioSynC (Beth Sanzenbacher, Mark Westneat, and Audrey Aronowsky), Field Museum (Johanna Thompson, Elizabeth Babcock, and Krystal Villanosa) and Numedeon, the parent company of Whyville (including Jen Sun, Jim Bower, Mark Dinan, CJ Circo, and Alfred Lo). It has been an exhausting stretch, but Beth, Jo, and Mark D have been amazing!

The virtual reef project is funded by MacFound DML and is our first major foray into virtual worlds and education. We have collaborated on some smaller scale, pilot projects with Global Kids; including the fantastic “I Dig Tanzania!” pilot in Teen Second Life.

We are excited to announce that we’re now indexing videos as well as images from Flickr.  Videos uploaded to the EOL group in Flickr and tagged with a species name will now be featured in EOL species pages.  Visit the Honeybee (Apis mellifera) page to see some recent video additions by Arthur Chapman and Valter Jacinto . Since the group began less than 6 months ago contributors have submitted over 13,000 photos and now over 200 videos which are shown in EOL species pages. Follow the instructions on our group homepage and learn how to submit and tag your photos and videos. We encourage everyone to check out the EOL Flickr group and start submitting photos and videos today!

Charles Darwin was born on this day in 1809! Hooray for the great man who took the first steps that brought us here! As Theodosius Dobzhansky so nicely put it: “nothing in biology makes sense except in the light of evolution.” So, thanks Darwin, thanks for evolution.

We hope we are making Darwin proud by continuing to observe and learn from the natural world around us and push scientific thinking to new horizons.

To help celebrate this glorious day check to see what events are being hosted in your city, or host one yourself!

After a few weeks of preparation, we are now ready to release the code that runs the www.eol.org website into the open source community.  The code is written in Ruby on Rails and is released under the MIT License.  There are many moving parts to the system, including code needed for data indexing, harvesting, names finding algorithms, data model creation, as well as all the code used to generate the actual web pages.   This release includes all of the Ruby code used to generate the webpages for the www.eol.org website, including the full data model and includes all the code to set up your own miniature version of eol.org running on your Mac (or PC…).  All that is missing is all of the wonderful data, but the code comes with enough sample data, called “fixtures”, to get you going!  Some other parts of the system written in PHP (such as indexing and names finding algorithms) will be released separately.

To get started, check out the project homepages on Google Code or GitHub.

At the Biodiversity Synthesis Center, one of our core interests is phylogeny, especially how to incorporate it into the EOL.  This post is about phylogenetic synthesis, and highlights in particular a new BioSynC tool in development called Phylografter.  But first some background.

The modern concept of phylogeny (genealogical history tracing the common ancestry of species) was one of Darwin’s most significant contributions to science.  In On the Origin of Species, he described how species have proliferated using wonderful botanical imagery:

“As buds give rise by growth to fresh buds, and these, if vigorous, branch out and overtop on all sides many a feebler branch, so by generation I believe it has been with the great Tree of Life, which fills with its dead and broken branches the crust of the earth, and covers the surface with its ever branching and beautiful ramifications.”[1]

Since then, great strides have been made in reconstructing the Tree of Life, using DNA sequences, morphological traits, and other evidence observed in both living and fossilized organisms.  But these strides have necessarily been piecemeal. Individual studies in the primary literature are inherently limited in scope to resolving local “ramifications”: the branch holding the lemurs, for example, or the deepest splits near the root.   This is because for any given problem, representative organisms and data must be sampled very judiciously.  As a result, even with continuing advances in data acquisition, analytical methods, and computational power, our understanding of the whole Tree depends fundamentally on focused, hierarchically nested research efforts.  I think it is even safe to say that it will never be practical or worthwhile to try and estimate the phylogeny of all known species in a single analysis, from scratch.

At the same time, mounting interest in phylogeny as a means of understanding broad-scale patterns in biodiversity has heightened the need to synthesize primary research — to effectively link together published results, forming ever more inclusive phylogenetic “megatrees.”  Synthetic phylogenies of this sort can be powerful tools for testing hypotheses about the tempo and mode of evolution.  So, how does one go about doing this — “grafting” together published  trees into a greater whole, while keeping track of the sources of the parts?

Read the rest of this entry »

I typed furiously to capture the chatter of the teachers who were viewing EOL at a professional development workshop for kindergarten to high school teachers at Martha’s Vineyard Regional High School in Oaks Bluff, MA.  Watching and listening to teachers as they learned about the features of EOL was a great experience. Not only did the participants think that EOL was a “neat” resource, but they had many questions and suggestions about how to make EOL more user friendly for educators and students.  A few highlights…Teachers are eager to use the tagging tools to organize lists of local biodiversity by having students create tags with categories such as location, habitat or traits. They envision having students create accounts on EOL and creating “mini EOL’s” or lists of species that they want to study for different purposes. Tagging on EOL species pages is a new feature and it would be interesting to test it out by having an entire class tag to create a species list for their own study. The teachers provided helpful comments on features such as search tools and a suggestion to create an explanation of taxonomic classification on the EOL website, along with relevant educational resources.

I felt very lucky to have the opportunity to observe teachers as they experienced the Encyclopedia of Life and viewed the website through an educational lense.  This experience makes me wonder what other users might think of the EOL website, especially the new features.  Your comments are welcome here. Thanks!

Click below for an introductory lesson on the Encyclopedia of Life created by high school biology teacher Elliott Bennett, who facilitated the professional development workshop on EOL.

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Hi Folks,

As some of you may or may not have noticed, without any fanfare, we released a substantial update to the Encyclopedia of Life website on January 5, 2009.  We are calling it version 2, and in fact, if you look at the footer of the www.eol.org pages, you will now see our internal version number right there (today at 2.0.11).

So what’s new, you ask?  Well, a whole bunch actually:

1. You can now tag images and then search for species associated with those images (e.g. “blue”, “marine”).  You can tag any image you want and once several people tag an image in the same way, it is promoted to a “public” tag viewable by all.
2. You can comment on species, images or blocks of text.  Content providers will then be able to see your comments to help improve their material.
3. You can add your own images to the EOL Flickr Group that, when tagged correctly, will automatically appear in EOL species pages.
4. We now distinguish between “trusted” and “unknown” content with clear messages and colors and will soon invite curators to help indicate the trust level of content.
5. And of course, many new species pages and more content, adding to the overall richness of the experience.

For a more complete listing of what’s been added, along with some screen-shots, head on over to the “What’s New?” page.  We’ve already begun working on the next set of features to add, with some great additions like public APIs high on the list.  The real fun will begin once the APIs are released and we begin seeing mashups between EOL and other projects - we can’t wait.

Thanks and enjoy,

Peter