In my mind, there are really two organisms that don't get a lot of attention as they come up in Alvin's scientific basket: the vent mussels and giant clams. However, there are two scientists aboard who make sure that they're not completely overlooked. When Alvin returns to the surface, having sent the message ahead that there are molluscs aboard, Frank Stewart and Dr. Eric DeChaine prepare for a busy night. First, they arrive on deck with cool, filtered seawater and transfer the mussels and clams from Alvin's bioboxes. Then, the mussels and clams are brought to the lab and carefully dissected.

But before we look at what takes place in their lab, you'll need a little background information. Eric and Frank are fascinated not just by the vent mussel and giant clam, but more importantly by those organisms' partnership with bacteria. You can sort of think of this like the idea of 'sharing.'

The bacteria live inside the vent mussel or the giant clam and provide food to the clam or mussel in exchange for a place to live and access to an energy source. The organism that houses the bacteria is called 'the host,' and the bacteria are called 'symbiotic bacteria' or just 'symbionts.' Sometimes an organism would not be able to survive without these symbionts (like the clam, who depends entirely on the bacteria for food). Other organisms depend on the bacteria to a large degree (like the mussel, who can feed a little on its own, but not a lot).

"We're primarily interested in understanding the relationship between these organisms and their bacterial symbionts," explains Eric. But what does this activity look like on the ship? On the ship, Eric and Frank are in sample collection mode. During the course of Extreme 2004, they'll gather everything from the organisms themselves to pieces of the environment such as basalt (rock) and sulfide chimneys. Once the samples are on board, Frank and Eric's primary mission is to preserve them for future work at their laboratory at Harvard University in Cambridge, Massachusetts.

"In total, we'll probably collect about 150 mussels, 10 clams, and 30 Riftia samples," Eric explains. "From those, we take a piece of the organism (the host) and a collection of the bacteria that live inside cells in the gills. That's about 300 samples, and that doesn't include the environment samples or water samples."

What do they do with all these samples? Once the molluscs have been dissected, the process of gathering the exact material necessary for their work begins. The first tissue samples need to be collected from the host organism, either the vent mussel (Bathymodiolus thermophilus) or the giant clam (Calyptogena magnifica).

"We usually take tissue samples from the adductor muscles, the ones that hold the shell closed," Eric explains. "That way we know that we're getting pure host tissue (mussel or clam) and very little contamination from bacteria."

The second sample that contains the symbiotic bacteria living in specialized cells in the breathing apparatus (gills) of the molluscs is harder to obtain. "The bacteria live inside the host's gill tissue, so it's tough to get just the bacteria's DNA and not the host's," says Frank. "We try to separate them by grinding up the tissue and filtering it, but there still could be some mollusc material in our sample."

Eric, Frank, and I had a great discussion about the question, "Why is it important to do this work?" Eric and Frank explained that they are basically interested in the foundation, or the base of the food web, at these sites.

By understanding more about the diversity of these symbionts, scientists can learn a lot about the evolution of the symbionts and how these symbiotic relationships began. They also can learn a lot about how these vents are connected to each other. For example, by looking at the similarities and differences in the DNA of these symbiotic bacteria at different vent sites, they can hypothesize about ocean current patterns around the vents.

There are other applications as well. "Understanding bacterial symbiosis helps us to understand the way bacteria work," said Frank. "This can help scientists working in the medical field understand how bacteria infect human beings."

While a lot of the concepts that Frank and Eric were talking about are very complicated and sometimes difficult to understand, they did a great job of helping me to understand why their work is so important.

In other news, Kevin Portune and Dr. Joe Grzymski accompanied Alvin Pilot Bruce Strickrott to the seafloor as observers in Alvin, and they returned from the vents with great samples and excellent photographs. In addition to collecting samples and taking photographs, they were extremely busy answering questions during our Phone Call to the Deep.

You can check out the call on our Web site. Bruce also has been busy answering your questions in our Write the Scientists section. Be sure to check out his answers!

Alvin rises to the surface, and the A-frame hoists it up on deck. A few feet over the tracks, and it enters the hangar. Among the first to the basket is Dr. Horst Felbeck. He whips open a biobox (container) and removes the tubeworms packed carefully inside. He pops them into a bucket and whisks them into the hydro lab. It's the end of the day for Alvin, but it's the start of work for Horst and for Steffi Markert, who works with him.

They study Riftia pachyptila, giant tubeworms that live at the hydrothermal vents on the ocean floor. Here at the East Pacific Rise, they hope to gather enough samples to add to their understanding of the proteome of Riftia. The proteome is all the proteins that combine in the bacteria that live in and depend on Riftia. It's a symbiotic relationship, which means that they can't live without Riftia and Riftia can't live without them. This makes the bacteria symbionts.

So that's the vocabulary. And here on the ship R/V Atlantis, the study begins with the sample of Riftia brought up by Alvin. Horst and Steffi bring their samples to the hydro lab. Although they try to work on them right away, they also have a high-pressure tank where the Riftia can be kept alive until it is time to begin studying them. On the day that I visit the lab, a vent crab brought up accidentally by Alvin also is living in the tank. Here's what Horst and Steffi do with the worms:

1. Horst or Steffi removes the tubeworms from the tubes that they live in. The tube is made of a tough, natural material called chitin (pronounced "kite-in").

2. Steffi splits the worms open lengthwise, dissecting them to remove the trophosomes. This is what is inside the worm. For the most part, trophosomes are dark purplish-red, globby strands. The trophosomes have a distinctive color depending on what element they were most exposed to: black indicates a lack of hydrogen sulfide. Yellow indicates lots of hydrogen sulfide. Green is somewhere in between.

3. The trophosomes are moved to homogenizing vials to separate out large blood vessels and to give the substance a smoother consistency. Horst fills the vials with argon gas to prevent too much air from getting in. These vials have a liquid in the bottom that Steffi tells me is a homogenizing agent called Percoll, designed to keep the liquid from separating. Next the trophosome fluid is mashed in the tube with a glass pestle. This destroys the host cells but leaves the bacteria intact.

4. The homogenized material, a mashy liquid, is strained through a screen to remove solids and any remaining blood vessels.

5. Steffi places the closed vials in a centrifuge and spins them for 10 minutes to separate the bacteria from the host cells.

6. The bacteria can now be sucked out with a syringe.

7. Finally, the bacteria are extracted, washed, and counted under a microscope.

"This is the easiest place to screw up," says Steffi.

Horst replies, "You can screw up anyplace in the process, but it's pretty easy to do here."

After all this? Yes, they tell me. It's easy to count wrong, and that throws off your research. What they're hoping to learn is exactly what proteins -- and how many of them -- are found inside Riftia.

Horst and Steffi's work is just one example of research begun on the ship that will carry on long after the scientists go home. The goal for many is to gather enough samples -- enough vials, enough slides, enough data -- to work with once they get back to their labs.

As for me, I'm gathering material of my own: experiences that transfer into words and pictures for me to include in future books. I'm also getting tons of new understanding of the scientific process, of course, but something else, too. The more I sit with, observe, or chase around the scientists working to understand the vents, the better I understand the vents myself.

But I also understand, more and more, what it is like to study one aspect of the vents while others around you study theirs. It's interesting to see how it all adds up. How does it get divided, this big subject, among lots of people? Dr. Craig Cary tells me there are 20 to 30 groups like ours researching 9º North, plus others studying vent areas elsewhere, and still more studying extremophiles in places like Antarctica.

Horst Felbeck and Dr. Eric DeChaine are among the scientists on this ship whose research isn't focused only here. Eric's work on extreme environments has taken him to the tops of the Rocky Mountains. You can find out more about his work in Mike's journal today.