In the sub today with Pilot Anthony Tarantino are Frank Stewart, who is on his second dive, and Shellie Bench, who will be diving for the first time. Everyone is a little nervous. It's a little like driving around doing errands before a party, with just a little time to spare, and a definite deadline. This time, if power runs out, a job left off the list can't be done tomorrow; it just won't get done.
There are sample-gathering instruments -- prototraps, frying pans, and fries -- to recover as well as Alvinella to be collected along with the water-sampling sips from their tubes. These sips provide information such as the temperature and chemistry of the water that are required to understand the environment that the Alvinella are living in.
While Alvin is down there working, Dr. Craig Cary gives an hour-long seminar on his research and explains in detail why studying the hydrothermal vents is important in his work. This is the first in a series of seminars on subjects in the scientists' areas of expertise. We'll be hearing from many of them in the week to come.
Not all of the seminars will involve the primary area of study; Dr. Joe Grzymski is going to speak on coffee roasting, an activity that we've all enjoyed the fruits of. It's about time we learned to do it ourselves!
Along with his scientific equipment (Joe works with Dr. Alison Murray at the Desert Research Institute), Joe brought along a stereo system, an extensive collection of music arranged alphabetically (from Abba to the Zambonis), and some cuddly toys in odd shapes. It turns out that the toys are in the shape of famous microbes -- including Porphorymonas
gingivalis, the bacteria that causes bad breath, and Helicobacter
pylori, the one that causes ulcers. They are surprisingly cute.
Today is the day I've decided to begin wrapping my head around the work being done by the group led by Craig Cary and Alison Murray. They are studying the metagenome of the epibiont symbiosis of Alvinella
pompejana. Say what? I decided that this would be a test for my SAT vocabulary skills. How are you doing on the etymology (to throw you another fifty-cent word) on those?
Let's start with the easy words -- Alvinella
pompejana. You've seen them all over this Web site, the same way they're all over the hydrothermal vents. It's a toss-up which word origin is easier to determine.
Alvinella: Hey, where do you think that word came from? You're right. These worms were named after the sub that helped find them. (For a clue about where the name of Alvin came from, check out Mike's journal and the Alvin section of the Web site.)
Pompejana: Sounds like ... ? Pompeii. Pompejana is a Latin word that means 'of Pompeii.'
Organisms of any sort are known by the name of their genus and species. Alvinella is the genus, and pompejana is the species.
Now, take a deep breath and attempt two more words: epibiont symbiosis. Can you see a relationship between them? I see bio right in the middle; as in biology, which means the study of life. Its meaning is easy enough to figure out: bio means life. So how come there are different endings?
If you've been reading this Web site closely, you've probably seen the word symbiont too. Biont means, more or less, 'something that lives.' Something that lives how? Something that lives where? That information is in the other part of the word.
Mike League tells me that epi means on the outside, or on the back. When I think of other words that start with epi, the one that comes to me most quickly is epilogue. In a book, the epilogue is an afterword, something that adds a point or two to the end of a book. So it makes sense to me that thing Craig, Alison, and company are studying is on the outside, or back, or behind, of an Alvinella. That's where the bacteria everybody is excited about live.
Symbiont comes more easily, too, if I think about other sym words in my non-science world: sympathy, which means "feeling with someone" and symphony, which means "sounds working together." Because I know a little bit about Alvinella by now, I realize that the symbionts are things living together with Alvinella -- and that they're the things living on their backs. But hey, the word is symbiosis, not symbiont. That's okay. I believe osis means the state of things -- as in diagnosis.
Okay, so we've got something living on the back of Pompeii worms in a state of togetherness. What on earth is the metagenome of this situation? I know what a genome is -- it's the picture of an organism's DNA. But a metagenome? I think I might start to hyperventilate at this point from all these words. I try thinking of other words I know that have the word meta in them. Metal. Metabolism. Metacognition. Metastasize. Never met a word I didn't like -- until now.
Excuse me while I go upstairs to the dictionary in the ship's library.
Oh. Well. Did someone say 'ground-breaking' science? The Oxford
Illustrated Dictionary doesn't include it, although it does have a picture of a mermaid playing a viola -- something else I haven't been able to find here at the East Pacific Rise. The word metagenome doesn't appear in any of the library's dictionaries or encyclopedias, even the Encyclopedia
of Ocean Sciences, which was published just three years ago, in 2001. Let me go investigate some more. (How cool is it for me to be on this boat with not only a library at my fingertips, but the actual scientists who coined phrases?)
Metagenomics is such a new field that the first paper published on it -- and there have only been three on this subject -- came out in February, 2004.
"It means many genomes," Alison Murray says, explaining, "Up to now we only looked at one genome. Now we're looking at many." She says that the term metagenome itself is somewhat misleading -- because it isn't just about a lot of metagenomes, it's about many genomes within one environment."
I asked how many they meant by "many genomes."
"About 20 genomes in all, "Alison said. "Three dominate."
Joe Grzymski adds, "It's about many genomes being sequenced simultaneously, with no clue what pieces go where." Normally you take one genome, divide it up, and try to put it back together in a logical way. Metagenomics is more challenging, because it involves chopping up an assortment and trying to put it back together.
Fully a third of the scientists on this ship are involved in research on the metagenome of the hydrothermal vent environment. Coming tomorrow: a scorecard of who does what.