Encyclopedia of Life Blog

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.)

EOL Bioinfomatics Team just finished the three-days ‘Nomina 2′ workshop. More than 15 developers from all around the world assembled together and, finally, created the Global Names Index — tool and database which holds most of living things’ names, authorized by name specialists (nomenclators).
Cathy Norton (BHL Project) kindly provided us with some photos:

and video:

Not an octopus, not a squid…what is a cuttlefish?

For one, it’s a cephalopod, that means “head foot” in Greek (☺), and in fact, all of the above are also cephalopods and are basically just giant mushy heads attached to various numbers of long suction-cup covered feet. Delicious.

These creatures, which also include the much stranger looking nautilus, are known for being the camouflage wizards of the world. If Gandalf was a sea creature, this would be it. Also, if you thought chameleons were cool, its time to get with it and realize who’s really got it going on. They are able to look like a nasty lumpy clump of brown seaweed one second and then be covered in moving iridescent rainbows the next. The species page had some excellent video of this happening. They also can squirt some seriously black ink at you if you scare them and have an attitude if that doesn’t work. Here is a video of a baby one hunting like a fiend:

The EOL species page for this particular cuttlefish was curated by scientist Roger Hanlon, who has been studying cuttlefish for almost three decades. His work was featured in a New York Times article in February. The article and accompanying video describe Hanlon’s theory on how their skin and brains work to help them change shape and color in seconds. Here is another short video of him explaining a bit about his work and about the magical camo abilities of cuttlefish in under three minutes:

The Australian Giant Cuttlefish, Sepia apama, is the largest cuttlefish on earth. That means that this gem is in fact, bigger than a bread box, but not by much; reaching just above ~20 inches long. They are world famous for of all things, their mating habits. Every year during the austral fall (May - July) in northern Spencer Gulf, northwest of Adelaide (they are found all along the southern coast of Australia normally), they gather to spawn by the hundreds. This is the only place on earth where cuttlefish have been observed to gather en mass to mate, and it has received great attention, starting out as an easy catch for fisherman and then morphing into a mecca for diving ecotourists. As a result of this the area is now mostly protected from overfishing and the cuttlefish are free to love and make wild colorchanging babies. (My advice, GO THERE! What better excuse to go to Australia! Here are some stories from tourists in the area.)

The species page features several awesome videos of them mating fighting, changing color and also laying their eggs, which look like gooey lychee nuts that they stick to the undersides of rocks.

A second reason to go check them out is that during this mating event they exhibit a fascinating example of what some eco-tourists like to call “crossdressing” something that was noticed by Hanlon during his observations of them there. This is the phenomena of small males using their camouflage to disguise themselves as females in order to sneak under the eyes of protective and violent larger males and sneakily mate with the females they are guarding. I like to call this “The Woody Allen” maneuver (brains outwits brawn and wins the girl) and it’s pretty genius. Also great fodder for pondering the different ways that organisms connive to pass on their genes in the struggle for survival.

Cuttlefish may sound familiar for a couple of reasons, their bones, cuttlebones (which are inside their heads and one of the things that distinguishes them from squid and octopi) are sold in pet stores to provide calcium and sharpen the beaks of domestic birds. The word “Sepia” comes from the Persian word for cuttlefish, artists used to use cuttlefish and squid ink to paint with and tone things, hence the setting on your digital camera that makes pictures look all old. People love to eat cuttlefish, two fun examples of this are in Italy where they make a dish called Risotto al Nero di Seppie, a tar-looking risotto dish made with cuttlefish ink, as well as dried cuttlefish which is a popular snack in Asia.

Streetside snack of dried cuttlefish in Asia

Finally in the popular novel Twenty Thousand Leagues Under the Sea by Jules Verne, Captain Nemo and his companions battle with a group of giant cuttlefish. While the cuttlefish loose, they do manage to kill one of the crew members. Jules Vernes’ description of the cuttlefish in the book is not completely scientifically accurate, but here is a video of our friend Sepia apama attacking a scuba diver (not very scary, but will give you an idea of  Vernes imaginative capabilities):

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!

Here are some of the highlights of the press coverage surrounding the recent launch. Most of the major news media addressed it in various degrees of thoroughness and each article has its own tone, some are very encouraging while others take a more cautionary stance. Check them out and form your own opinions. Here is the New York Times, The BBC, The Boston Globe and Nature News. There is also a site that has links to much of the press coverage of the EOL in the past year, but is also updated daily and includes major news sources as well as blogs and online columns. There are articles ranging all the way back to the first mini-launch in May 2007 posted and more appear daily. Enjoy!

Also, not listed in the site above, or anywhere online, the EoL was described in the latest issue of the Bulletin of the Royal Entomological Society, Antenna (Winter 2008 Volume 32 (1)) on p. 68) in the section called “Embiopteran Tools”. It is exciting to know that the word is being spread about the potential of the EOL to be useful in numerous fields of biology.

Here at the Encyclopedia of Life, we are on constant lookout for cool technologies and user groups. One that we have had our eye on for a long time is Drupal, a content management system that uses PHP and MySQL as the backend database. Drupal has an immensely active fanbase and an increasing number of installations throughout the world. DrupalCon was held March 3-6, 2008 at the Boston, Massachusetts Convention & Expo Center. If you’re interested in how the conference was organized and what sessions were held, take a peek at the program (PDF).

Peter Mangiafico and I attended DrupalCon and were floored by the enthusiasm. I was particularly interested in the jQuery and GIS/Mapping sessions. Brian Aker’s (MySQL) plenary was also very helpful. And, this from Peter:

I was at DrupalCon on Thursday, March 6 and the first thing I noticed was that this seemed to be the highest concentrations of laptops per square inch I have ever seen, with a higher percentage of glowing Apple symbols on the back of them than the population in general. You could tell you were in the right rooms just by glancing around and noticing folks coding in the audience in real-time. The sessions I went to were well-attended, with the “Using Drupal with External Data Sources” session spilling out of the room. It was great to see how many folks are using Drupal to solve their specific needs across different domains, from education to business.

Thanks to amazing efforts by many of the biodiversity informatics group staff (especially Pam who’s basically not slept since we went live very early Tuesday morning), we’re back up and running again. We’ve been stable since yesterday afternoon, but we’re still dealing with many more hits than we ever expected - we’re now listed on over 400 press websites in 10 different languages!  So please bear with us if things are a bit slow or we need to take the site down to try to make additional upgrades to improve the performance. We’re currently working on ways to address this going forward so everyone can experience the Encyclopedia of Life. Thanks for your patience!

Many impatient visitors to The Encyclopedia of Life are no doubt clamoring for a look inside. So you can at least have a glimpse, here are two videos we just posted to YouTube:

Homepage:

Species Pages:

You may have noticed that the EOL site has been flaky at best since approximately 12 EST this afternoon. Although we are serving the site from a load balanced cluster of several machines, we are experiencing phenomenal loads.

I just churned through the web logs from web machines in this cluster and there were 5.8M hits in the span of 3 hours. Most of these happened within 1 hour. We were down (and continue to experience intermittent access) for a few hours, then flipped the machines back on. Since then, there were an additional 5.7M hits, totaling 11.5M hits since 9AM this morning and it is now 2:45PM here. Wow!

We are working hard to resolve the issue so stay tuned and please have patience! I’ll post updates here as the day progresses.

Update Feb 27 @ 11:45AM EST:

In the first 24 hours (minus the approx. 3-4 hours we were completely down) there were:
18.5M hits, 13.3M page views, and 940GB of data transferred.

The Encyclopedia of Life was officially launched and we are tracking progress and responses. Please be sure to complete the survey accessible on the homepage and to also participate in our forum. We haven’t said much yet about what’s going on behind the scenes, so here’s a quick glimpse into the gadgetry whirring away and the people keeping it all working well at the Marine Biological Laboratory in Woods Hole, MA:

The EOL Biodiversity Informatics Launch Team

Pam Fournier, keeps the rack-mounted servers (one of three cabinets shown) working well

We’ll have plenty more to write about the infrastructure and informatics behind EOL. That is, when we stop to take a breath.