Encyclopedia of Life Blog

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.

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).

From June 20-24th BioSynC staff members Mark Westneat, Audrey Aronowsky, Darolyn Striley and myself hosted a booth at the 2008 Evolution meeting. The meeting attracts leading phylogeneticists, systematists, and evolutionary biologists from around the world making it an ideal conference to recruit scientists to EOL and also to solicit interest in synthesis meetings. It was held in Minneapolis at the University of Minnesota and had an attendence of about a thousand people. Our booth got lots of attention (we were only ones with candy :)) and we met several people who are going to propose synthesis meetings. Our booth was across from the NEScent booth and we had alot of fun getting to know our fellow synthesis meeting organizers, who, for the record are still leaps ahead of us in terms of booth set-up.

Mark gave a 15 minute talk to a full audience titled: “Phylogenetic visualization tools and phyloinformatics in the Encyclopedia of Life”. In the presentation, Mark used his own fish research ( a phylogenetic dataset) which incorporates systematics, developmental genomics, and biogeography to demonstrate the many kinds of data that EOL will be able to handle and also how the research communities that focus on each of these kids of data could work together using EOL. Here are some pictures of us and the booth in action:

March came in like a fifteeen degree Lion of Tsavo here at the Field Museum, Mark Westneat wasn’t affected because he was at the Assembling the Tree of Life Annual PI Meeting (AToL) from March 7-9 which happened to be in warm New Orleans, Louisiana. Besides carousing in the music-filled New Orleans air, Mark and Paddy gave presentations to the meeting on the EoL and BioSynC accompanied by much (two hours!) of productive discussion. Mark returned to Chicago to find that construction of the new Synthesis Center had been completed and on March 12 the staff moved in to their comfortable, well-lit, energy efficient new offices. Have I mentioned that we are now the greenest part of the Field Museum? Almost everything in the new space is recycled or energy efficient, down to our potato-starch eating utensils.

The new Synthesis Center has quickly become a place where people from all over the museum feel comfortable stopping by to say hello and talk about science. Audrey has found that if she leaves baked goods out on the counter, which she often does, they will be gone by the end of the day and our lounge is almost always filled during lunch time. We finished construction in time to debut it at Museum Members night (March 27-28th) which had a record high attendance of 10,687 guests in two nights. We had mild but constant traffic and screened the EOL demo video in our large conference room on a loop the entire time. We also encouraged people to explore the web site live on our new computer consoles in the lounge.

Moving on to April, from the 18th to the 20th, we hosted our first in-center Synthesis Meeting:

“MegaTree: Mega-Phylogeny Assembly by Literature-Mining and Grafting”

This method-focused meeting, led by Rick Ree (featured in the second picture) was designed to refine approaches for assembling large phylogenies (evolutionary trees) and to train students in their use. The goal was to assemble a “knowledge-based” phylogeny for vascular plants that synthesizes the information from various sources using a method that allows grafting of information from different sources while simultaneously keeping track of the origin of the information. Basically this crew has found a way to take the large number of smaller evolutionary trees that have been created for plants by different people using different computer programs and graft them all together so that they still make sense. This way they can begin to piece together an extremely detailed and large evolutionary tree (a megatree!) for plants.

Here is the crew all together:

That’s Darolyn peeking out behind them.

Here they are in action:

(This meeting was not, as I had originally hoped, about a group of electric cars that through transformer-like powers could form a tree that would use solar power to charge their batteries, thus battling evil by eliminating parking lots and oil-dependence. sigh, you can’t have it all.)

Now that the EoL is up and running, the “Biodiversity of the Week” blog post will feature creatures that actually have species pages! As you may or may not know, many (most) of the EoL species pages are incomplete and the majority are just stub pages, meaning they pretty much only have a name at the top. But, as time goes on, more and more will be fleshed out and this genre of blog post will hopefully highlight that process as it happens. These entries are meant to show stellar species pages and to give an appreciation for the real meat of the EOL: the organisms it has been created to preserve. The hope is that by giving everyone a weekly dose of species fun-facts, people will be encouraged to not only spread the word about the organisms they learn about, but also continue to learn about them on their own. On that note, get ready to be amazed by the supreme:

Click HERE to actually go the page. (there are some great videos there of chicks hatching and feeding)

This bird of prey is spectacular for many many reasons. For starters, it’s a looker, enough said. These beauties are about the size of a crow and can live up to 15 years in the wild. They also mate for life. Second of all, they are THE FASTEST ANIMALS ON EARTH!! Here is a video of a speed enamored scientist/pilot doing crazy aerial experiments to measure a peregrine’s speed. He finally clocks one at 242 mph!

At that speed all peregrines have to do to kill their prey (usually other birds) is stick out a clenched foot as they zoom by. Their abilities also mean that their bodies have evolved some incredible features that allow them to both go that fast and to withstand the gravity and other forces that would wreak havoc on the bodies of most creatures (think about your ears popping during airplane landings, but A LOT more intense.) Here is a video of a peregrine divebombing a flock of starlings:

The final amazing thing about them is actually two-fold. The first part is their conservation story, which is featured in the introduction on the EOL species page. But briefly, in North America in the 1950’s they were nearly extinct, largely because of a common pesticide called DDT which thinned the shells of their (and other birds of prey’s) eggs causing them to break prematurely. This was a little known fact until the publication of the book Silent Spring, by biologist Rachel Carson in 1962, which was widely read and highlighted the plight of the peregrine as evidence for the effects of pesticides on the environment (a previously unstudied topic). Not only did the book create a public outcry which resulted in the ban of DDT in 1972, but it is also credited with starting the environmental movement in the U.S. So the successful comeback of the peregrine is even more heartwarming for its connection to the movement to save the environment in general.

The second really exciting part of that is that today, peregrines and other falcons are so prevalent that they have found a new niche in cities, commonly nesting on tall buildings and bridges and feeding on pigeons and other delicious city creatures. In New York City in 2005 there were 18 documented pairs of peregrines.

This new proximity to people has created a really interesting phenomena that not many species enjoy, and that is the 24 hour webcams of their nests! Here are links to all the “falconcams” that I could find, but I bet there are more out there: Derby Cathedral (UK), Shenandoah National Park, VA, Richmond, VA, Brisbane, AU, Plymouth, Devon (UK), Rochester, NY, and Harrisburg, PA. Have fun stalking our cute feathered neighbors!

February is coming to a chilly end in the heartland. Besides sitting around in long underwear and rhapsodizing about how warm and lucky all the people going to the upcoming TED conference next week in Monterrey, California (Feb. 28th) are going to be, the BioSynC has been active in several areas. We have been hosting visitors, working on outreach and planning future meetings, here is the latest:

Construction of the center is buzzing along, with lights, ceiling, and doors installed recently, and we are excited to see that the colored accent walls have been painted-heralding the final push to finish by the end of March. Here are some pictures of the unfinished (but getting close) space:

On February 5, we were happy to have a visit from Jamee Field, new member of the Board of Trustees at the Field Museum (and daughter of Marshall Field) in order to see the progress of the new center facilities.

On February 7th Audrey Aronowsky, Rick Ree and Mark Westneat had a conference call with the team at Adobe Systems and got an update on the progress of new phylogenetic tree visualization that they are creating as a portal to the EOL. Visualization tools for evolution and biogeography are a central goal of BioSynC, and we are looking forward to having our collaborative visualization tool demonstrated by Adobe at TED.

On Feb. 8, Mark Westneat presented a seminar to the High School Transformation Project of the Education Department, entitled “Coral Reef Fishes: Biodiversity, Evolution and Bioinformatics”, highlighting potential uses of the Encyclopedia of Life for teachers and students.

On February 11th Audrey Aronowsky attended a meeting at the MacArthur Foundation along with Field Museum’s Elizabeth Babcock (Education) and Steve Strohmeier (Institutional Advancement) to discuss a digital learning initiative that MacArthur is interested in funding that will involve both the Field Museum and the EOL.

BioSynC is participating in and hosting two upcoming synthesis meetings. The first one, “IEDG 2008: Integrating Evolution, Development and Genomics” will take place May 28th-30th at UC Berkeley and will be hosted by Berkeley graduate students led by Jan Vendetti. The second one, “Mega-phylogeny Assembly by Literature-mining and Grafting” will take place April 18th-20th, and will be the first meeting to take place in the completed center. It will be led by Assistant Director Rick Ree and will focus on assembling a phylogeny of North American vascular plants. The main purpose of the meeting will be to train students how to use numerous computer applications to assemble and graft together phylogenetic trees.

Today is the Chinese new year! Despite an intense cold-snap stranding millions, China celebrated The Year of The Rat with traditional fireworks and fanfare. We will celebrate by examining some of the wonders of a very controversial mammal who, according the an ancient Chinese tale, beat all the other animals in a race to be the first in the zodiac, it managed to especially irritate the cat by betraying its trust, accounting for their uneasy relationship to this day. People born in this year are expected to possess qualities associated with rats, including creativity, honesty, generosity, ambition, loyalty, a quick temper and wastefulness.

There are approximately 56 species of rat, the two that we are familiar with, many of us on a daily basis, are: the Norwegian Rat, Rattus norvegicus, found in both the sewers of our cities, and your local pet store, and the black rat, rattus rattus, also found in the sewers but preferring the warmer cities and generally kept out of pet stores.

Assuming everyone already knows a bit about rats, for example the fact that they live 2-3 years, are social, intelligent, and are important prey for many predators, as well as that they play an important role in scientific research, I would like to highlight some of the lesser known things about them. (For a more practical and informative bit of info on rats, check out what rat expert Robert M. Corrigan had to say in response to people’s questions about them in a recent blog session. Part I, Part II, Part III.)

One thing I learned today, is that rats are ticklish, and they laugh when you tickle them, check out this video of an odd scientist tickling a rat.

People have very intense positive and negative relationships with rats. For one, there was the bubonic plague, which was transmitted by them, like the cat incident, many people still have not forgiven the rat for its involvement in the plague. Some people, however are not bothered by rats per se, they even keep them as pets. Some of those people take it to the next level by showing their rats in rat shows, for a “Best in Show”-esque view of what that scene is like check out this 25 minute spot on Fancy Rats in Australia, it’s actually amazing and worth your time.

In India, there is a temple where people worship rats. They feed them and touch them and feel especially blessed if they can eat the food that the rats have touched:

Other human-rat affection can be found in the recent movie “Ratatouille”, which manages to tackle our greatest phobia of rats, by associating them positively with our food. Also, my personal favorite the character Master Splinter from teenage mutant ninja turtles. Here he is “making a funny”.

The Biodiversity Synthesis Center has been very active in the past three months: we have hosted three synthesis meetings, had a booth at the Society for Integrative and Comparative Biology Conference in San Antonio, TX, and begun construction on our new conference center. We have also added two new employees to our team (as mentioned in a previous post) and are interviewing more post-docs.

Synthesis Meetings
Two of our meetings were the product of an exciting collaboration with a team at Adobe Systems in San Fransisco. The first was a small meeting between Adobe staff and BioSynC staff at the Field Museum to plan a more detailed meeting. The second one: “Visualizing the Tree of Life II: Developing a Graphic Interface for the EOL” (December 3) was held at Adobe Corporation headquarters. Hosted by BioSynC Director Mark Westneat, Assistant Director Rick Ree and Gever Tulley (Adobe), the meeting focused on developing a visualization interface for the “Tree of Life” which may serve as a gateway to the EOL. Mark and Rick were joined by several of the premier thinkers in phylogeny visualization: David Maddison (Arizona), Mike Sanderson (Arizona), Bill Piel (Yale), and David Patterson (EOL at MBL). Adobe is lending some great minds to the effort, including Gever Tulley, Marcos Weskamp, Simon Smith, and Mike Sundermeyer.
Our third meeting “Planning BryoZone: A Unified Bryozoan Reference on the Web” (December 12-15) was the first of many organism-focused synthesis meetings, organized by Scott Lidgard. Taxonomic synthesis meetings bring together some of the world’s experts on a particular taxonomic group to set the agenda for future research in the field and organize the group for incorporation into the EOL. This meeting focused on the Bryozoa, a cosmopolitan group of aquatic invertebrates that are found in all water depths and salinities, including freshwater. Bryozoans are an important group of microscopic animals that band together to create large skeletonized colonies, similar to tiny coral animals forming coral heads. The synthesis meeting brought together 10 experts from all over the world including Australia, New Zealand, South Korea, Poland, Colombia, the United Kingdom, and the United States to plan future research for the group. The meeting goals included producing a large PBI grant proposal for the National Science Foundation, designing and testing internet data that will become part of the EOL, and organizing the large but disparate existing data on these animals.
All three meetings were very successful, Adobe continues to pursue the creation of a tree visualization, and will debut a tree browser at the upcoming TED conference (end February 2008), while the Bryozoan scientists submitted their proposal and also are preparing data on Bryozoans to enter into the EOL.

Presentations and Outreach
As well as hosting meetings, BioSynC has been busy spreading the word about the EOL. Recent efforts include a presentation by Mark Westneat, Jim Edwards, and David Patterson on the EOL and BioSynC at the National Evolutionary Synthesis Center (Duke University), a variety of presentations to the public and to group meetings such as the Bivalve and Liverwort ATOL groups. A BioSynC team (Mark Westneat, Audrey Aronowsky, and Alta Buden) traveled to San Antonio,TX for the annual SICB conference, where they hosted a booth representing the BioSynC and the EOL.

Building The Center
Construction of the new Synthesis Center on the ground floor officially began December 21, 2007. Plans for the 3500 sq ft space in Hall C include two 150 sq ft offices for administrative staff, three shared 150 sq ft offices for postdoctoral and academic staff, an office cubicle area for students and interns, a conference room (300 sq ft), a seminar room (600 sq ft), a reception and discussion area complete with coffee and refreshment bar as well as a Tech Center with EOL consoles. The conference and seminar rooms will be fully AV and internet equipped. Six weeks into construction things are looking good, and we look forward to hosting biodiversity groups in our new space as soon as possible.

I know Dolphins are a cheap shot and everybody already loves them, BUT, did you know they could do this!!

Dolphins+violins+bubbles 

BioSynC is populated by a happy team of individuals with a wide range of experience. All of us have a scientific background and contribute to organizing and running synthesis meetings. Our Director, Dr. Mark Westneat has been at the Field Museum for 15 years and is the Zoology Curator of Fishes. He brings to the table an immense pool of connections within the scientific community with some of his main interests being the biomechanics of fishes as well as marine ecology and the study of coral reef life in particular. He currently acts as the main public representative for our organization, giving talks and presentations about the EOL, and our part of it on a regular basis.

Dr. Richard Ree, our assistant director, has been at the Field Museum for 5 years and is a leading authority in the systematics, evolution and biogeography of flowering plants. He acts as a representative for us within the botanical community (no small group) as well as helping Mark with other connections within the museum and scientific community.

Dr. Audrey Aronowsky, our scientific program manager, specializes in the systematics and ecology of marine mollusks; both snails and clams. She is active in many scientific societies and has organized and chaired sessions in invertebrate zoology, paleontology, and marine ecology. She is in charge of organizing synthesis meetings, managing scientific interactions within the center, and managing the center’s relationship with the scientific and academic community. Her baked goods and LSU Tigers enthusiasm have become renowned throughout the museum.

Alta Buden, our biodiversity specialist, recently completed her Bachelors Degree at the University of Chicago. She double majored in History and Philosophy of Science as well as Visual Arts. Besides having a broad knowledge of biodiversity, she acts as our resident artist and web expert, helping out with PR by coordinating our website, blog, posters, brochures, and image library. She also brings a fresh perspective to our work, having had experience working in many different nonscientific fields, from the New York Gallery scene to the human rights situation on the Thai-Burma border. She also works hard to keep everyone up to date on the “hip” lingo spoken by America’s youth today.

Dr. Torsten Dikow, our first Postdoctoral research associate, is an expert in the taxonomy, phylogeny, and biodiversity of the Asiloidea (robber flies). He joined us after completing his Ph.D. in entomology at Cornell University, Ithaca, NY and the American Museum of Natural History in New York City followed by a short postdoc at the same museum. He is originally from Germany and has traveled the world to study and collect true flies in habitats ranging from hot deserts to temperate forests and subtropical grasslands to tropical rain-forests.

We have recently (yesterday!) been joined by a new Administrative Assistant, Darolyn Striley, who we have stolen from the Natural History Museum of LA County, where she worked as a curatorial assistant for five years at the Marine Biodiversity Processing Center. She has taken on our financial and Human resources coordination as well as contributing her knowledge of Decapod crustaceans to our team. Originally from Guatemala, Darolyn received her Bachelors from UCLA in Women’s Studies. She has traveled extensively and done field work in Fiji, Palau and Montana. We are very glad to have her here and hope she survives her first Chicago winter. (Please note that the predicted high temp. for saturday is 7 degrees Fahrenheit!!!)