It's our last dive, and Dr. Craig Cary and Ky Hacker are taking the plunge with Pilot Bruce Strickrott. Ho hum. Not! The word from the bottom is surprise! They've come down into a snowstorm the likes of which neither Bruce nor Craig has ever seen -- and they've logged a lot of dives between them. To Ky, it's all new, but it's new to Bruce and Craig, too.
Expedition Leader Pat Hickey gives the credit to Frosty, the Styrofoam snowman who's riding Alvin today for shrinking purposes. "Frosty brought the snow," says Pat.
In the evening, everyone gathers around the video screen in the computer lab to see what they're talking about. It's marine snow, of course -- not the flaky crystals they're getting back home in Connecticut, the frosty kind. Marine snow is a host of organisms, dead and alive, floating through the water. Because they are mostly the same color, they dot the water like snowflakes dot the sky.
"So it was really coming down?" I comment to Bruce that night at the post-dive meeting.
"No," he says. "It was really coming up."
While snow above the surface comes down by force of gravity, snow at the vents gets thrown up by the force of the flow coming out of the vents. The snow made it hard to see -- like passing through the blast from a snowblower -- but, amid it, the observers could see giant Riftia
pachyptila and gathered sulfide from the chimneys nearby.
Unexpected discoveries are all part of the exploration process for the Extreme 2004 scientists. Over and over we are reminded how little we know, how unknown the ocean is, and how unpredictable the vents are. Areas that were enormously active a year or two ago (during other Extreme dives) have quieted down or nearly died out now. New vents have opened up and are spewing out the chemicals that give rise to new life.
While Craig was down below checking out what was new at 13º north, I was on Atlantis talking to other people in the Biocomplexity Group in an effort to understand the work they're doing and how the Extreme 2004 cruise fits into their process.
"Can you give me a timeline?" I asked Co-Principal Investigator Alison Murray.
She did. It's a complex one. The Metagenome Project has been in the works for years.
The plan began to become reality in 2002, when the Extreme 2002 dives brought up Alvinella samples from the area where we are now. Craig Cary and Barbara Campbell extracted DNA from the cells of those worms.
Barbara began to make a library of the DNA fragments. Once the procedure was in place, robots were "hired" and programmed to do the library-making work.
Dr. Joe Grzymski explains what happens next: "The whole pool of DNA is chopped up. It's like putting it in a shotgun and shooting it out." (In fact, it's called a shotgun library.)
The shotgun is cloned into E. coli bacteria, which allows the DNA to grow into colonies. Colonies of a certain size are picked by the robots. The number of colonies picked is the number of DNA sequences that will be performed.
These colonies were BLASTed. This means that they were compared with all of the data that had already been sequenced and placed in the public domain by anyone.
This step is the first one in the bioinformatics aspect of the project, in which computer programming is written that helps biologists sort and group their data. It is the creation of Alison Murray and Mihailo Kaplarevic, along with Dr. Guang Gao, another co-principal investigator who is not on this cruise. A total of 210,000 clones were picked in this gene-finding step.
"The computer links DNA, joining like and like sequences," Alison explains.
After the BLAST, the computer tells whether or not the gene fragment has the predicted protein in it. "An assemblage of predicted proteins give us how the organisms deal with their environments," says Joe.
"We have organisms. We know their environment. So we compare them to lots of other organisms and what they do, to figure out what this one is doing," adds Joe.
The result is a hypothetical organism (one that represents a group, something like the "typical American teen") that might metabolize (convert energy) in one of three possible ways. We put all these possibilities on a microarray, which shows us which way it uses. There could be ten ways of dealing with sulfur, for example, but only one at a time is working. The microarray can tell us which one it is.
The next step, then, is to design the right sort of microarray to produce the information desired. These microarrays produce different colors based on what's showing up, or, as the scientists say, "lighting up." What lights up is what's active in the gene under a given circumstance. And it is these lit up circles -- gene fragments -- that will provide new information about Alvinella and the vent environment.