Encyclopedia of Life Blog

From August 17^th through August 22^nd I attended the 6^th World Congress of Herpetology in Manaus, Brazil organized by Richard Vogt from the Instituto Nacional de Pesquisas da Amazônia. The congress proved to be an excellent opportunity for me to meet colleagues I had previously just known from publications and emails. Several interesting symposia and talks provided a great environment to discuss the goals of BioSynC and the EOL as well as to develop ideas and enthusiasm for synthesis meeting proposals.

I was invited to the World Congress of Herpetology to give a plenary lecture entitled “Human impacts on the diversity, distribution, and systematics of turtles.” My talk summarized the many ways that humans impact turtles and how this modifies natural patterns. These impacts include cultural uses, habitat destruction and modification, the pet trade, and, most importantly, the direct harvest of turtles for food. One of my main themes was that while humans have been showing an increased curiosity about and ability to understand biodiversity over the past 300 years, during this time human population has exploded from just over half a billion to almost 7 billion. Anthropogenic impacts on biodiversity have grown accordingly and a combination of ethnographic, historical, and paleontological evidence demonstrate a shifting baseline in our understanding of turtle diversity, distribution, and abundance. In addition to harvesting wild turtles for food, one of the main ways that humans alter natural patterns of turtle diversity is through the industrial-scale farming of turtles. I discussed how this has led to genetic pollution, feral populations, and examples of confused taxonomy. My talk concluded with three recommendations for overcoming these distortions of natural patterns: 1) fieldwork; 2) museum-based research; 3) the development of rapidly accessible biodiversity databases such as the EOL.

After the congress, I participated in a week fieldtrip up the Rio Negro on a boat called the Enigma. This excursion was aimed at giving herpetologists an introduction into Amazonian biota, with an emphasis on turtles. During my week on the Rio Negro I saw many new (to me) species of amphibians and reptiles as well as macaws and river dolphins. I also observed that many of the human impacts on turtles that I had discussed in my talk also occur in the Amazon Basin. For example, in a small village one day’s boat ride northwest of Barcelos we found villagers butchering and eating rare big-headed turtles (Peltocephalus dumerilianus). While netting two species of Podocnemis (P. erythrocephala and P. sextuberculata), we noticed a highly skewed sex ration of ~90% males that might be evidence of the unsustainable harvesting of females at their nesting sites. Finally, we also visited a small, but developing, farm that is trying to raise Amazon giant river turtles (Podocnemis expansa) for profit.

Left: A local prepares a meal of a freshly-butchered Amazon big-headed turtle (Peltocephalus dumerilianus). Center: Me in my goofy congress hat with a boatload of six-tubercled Amazon river turtles (Podocnemis sextuberculata [lower inset]). We also netted red-headed Amazon river turtles (P. erythrocephala [upper inset]). Right: A turtle farmer with a giant Amazon river turtle (Podocnemis expansa).

Clearly, the dynamic interaction between populations of humans and turtles in the Amazon requires careful multi-faceted investigations including fieldwork and trade surveys. One of my goals as a postdoctoral researcher at BioSynC is to use the EOL to collate such relevant data on the biology and conservation of endangered turtles worldwide. Hopefully by making data on these species and problems rapidly accessible, the scientific community will better understand turtle diversity and therefore be better equipped to guide conservation efforts.

The countryside in Taiwan, the city of Taichung and Dr. Shao.

From August 11-17th I traveled to Taichung, Taiwan to attend the TaiBNet (Taiwan Biodiversity National Information Network) 2008 Workshop on the status of Taiwan species diversity, organized by Dr. Shao Kwang-Tsao and hosted at the National Museum of Natural Sciences. This conference was held to address the Convention on Biological Diversity’s (CBD) mandate to “achieve by 2010 a significant reduction of the current rate of biodiversity loss at the global, regional and national level as a contribution to poverty alleviation and to the benefit of all life on Earth.” This conference was an opportunity for Taiwan to evaluate the current situation of its biodiversity and map out some estimated future trends.

At the meeting over 200 researchers and students from all over Taiwan each made presentations on the status of the major organismal groups in Taiwan, including mosses, insects, mammals, worms, molluscs, flowering plants, fungi, and reptiles.  I was one of 6 invited international participants and gave the opening lecture titled “The Encyclopedia of Life; an open access resource for information on all species living on earth”, which was very well received. It was a rare chance to meet  with people from many of the leading Southeast Asian database partners including “Species 2000 China Node” and Fishbase, digital learning and communication are extremely popular in Taiwan, so there was great interest in EOL. I expect at least 3 synthesis meeting proposals to come out of the meeting and possibly many more.

Dr. Chen Tien Hsi measuring a turtle

Also on my trip I was lucky enough to be able to assist Dr. Chen Tien-Hsi for a half day before flying back to the US. Dr. Chen, a conservation biologist in northern Taiwan, and former student of Dr. Shao, traps native turtles in ponds and forests in Taiwan to monitor the size and condition of local populations. He checks his traps every 2-3 days, so it’s a continuous cycle of wading through ponds and hiking through dense jungle. We found three IUCN endangered turtle species while checking the traps in a small protected area near Keelung; Ocadia sinensis, Cuora flavomarginata, and Mauremys mutica. Cuora, the Chinese box turtle, is extremely rare and is interesting because it evolved the ability to seal itself into its shell separately from the more common North American box turtles. Mauremys mutica, the Asian yellow pond turtle, was very active in this area and is known for its ability to hybridize with other turtle species. Ocadia sinesis, the Chinese stripe-necked turtle, is rarely seen in the wild in Taiwan, where it is threatened by habitat destruction. We released one of these after measuring and photographing it, and it kept running back into the turtle trap! He ran back into the trap three times before finally making it back to the pond, here he on try number two:

I would like to say a special thanks to Professor Shao and to his students, particularly Ching, Burke, Seven, Lee-Sea, and Jin Hua.  They were excellent hosts and I would have been lost without their translation skills.

On July 25-26, The BioSynC hosted an educational workshop called “I Dig Tanzania!”

The two day event was the culmination of a new learning initiative in which groups of teens in New York City and Chicago teamed up with a group of paleontologists headed up by The Field Museum’s Assistant Curator Ken Angielczyk (Geology) and Collections Manager Bill Simpson (also Geology) to learn about evolution, paleontology, Tanzanian culture, and what field work is like for scientists. While the scientists were conducting their work in southwestern Tanzania in late June, the kids performed a virtual fossil excavation of their own in the virtual world Teen Second Life. The teens were in regular communication with the scientists by satellite phone and also watched videos the team uploaded from the field each day. At the workshop, the teens from Chicago and New York got to meet each other, as well as four members of the scientific team, for the first time in person. They also made presentations about their learning experiences to the public, watched two documentary videos about their work and the scientists’ work in the field, participated in behind the scenes tours of the Geology Department and the Evolving Planet exhibit, discussed fieldwork and careers in science with the team members, and learned about Tanzanian music in a drumming workshop that took place in the Hall of African Mammals. “I Dig Tanzania!” was a collaboration between BioSync, The Field Museum’s Education and Geology departments, and the New York-based Global Kids. Funding for the project was generously provided by the John D. and Catherine T. MacArthur Foundation and The Grainger Foundation.

Here is the link to some pictures posted by Rik Panganiban from Global Kids, click here, as well as the blog that all the kids contributed to during the event.

Finally here is a short documentary video about the scientists expedition, enjoy!

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”.