Encyclopedia of Life Blog

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?

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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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