You would think that with the diving complete and the samples all stowed, the scientists and crew of R/V Atlantis would be aimlessly waiting for the ship to reach the dock. Well, you'd be wrong. The pace of life onboard not only has quickened but also is rapidly approaching a speed I cannot keep up with.

As I write this, the engine room is carefully adjusting the ship's ballast. This is an interesting physics problem for all you scholars out there. As we burn fuel, we transform the heavy liquid into a gas exhaust that leaves the confines of the ship. Therefore, we're getting lighter.

As we get lighter, we sit higher in the water, losing some stability. How do you correct for that? Can you think of a way to do it? Well, this is actually a topic I overheard Captain George Silva discussing with Chief Engineer Jeff Little and First Engineer Jim Schubert.

If you guessed that the best way to offset the weight of the fuel lost is to replace it with salt water, you're right! Underneath the lowest decks of the ship are the fuel containers and ballast containers. They run all the way from the bow to the stern and all the way from port to starboard. As you may imagine, it pays to have many tanks of different sizes in many locations. But how do you know when to fill certain tanks?

"Well, there's actually a stability program, that takes into account different factors associated with the stability of the ship," said Jim. There are many things to consider, including how far the ship could tip before it would roll over, bow vs. stern trim, port vs. starboard list, and the comfort of passengers (to prevent seasickness).

In addition to all those, this program is designed specifically for Atlantis. It factors in the location and weight of critical equipment such as the cranes, A-frame, and Alvin. That's why it's also important for scientists to provide weights and locations of any significant equipment they add to the ship. As fuel is burned, the computer program factors in all of these issues and decides which ballast tanks to fill.

"Tanks are either completely filled or empty so as to prevent the water from sloshing and upsetting the balance," Jim continued. As we've been traveling and burning fuel, we've been filling the ballast tanks. So now, we have a fair amount of water and less fuel.

How do you keep the tanks from corroding in the salt water? "The ballast tanks are concrete-lined and they have sacrificial zincs," explained Jeff. These zincs are common on ships in places that come in contact with salt water. The idea is that the corrosion takes place on the zinc instead of on the steel.

"It's also important to remember that the fuel and water are in separate tanks, so there is no mixing of fuel and water."

When we come into San Diego, the first order of business will be refueling at a fuel dock. This is an island-like platform with large containers of diesel fuel.

"We can take on 20,000 to 30,000 gallons of fuel per hour comfortably," said Jeff. "So, it'll take us about 4 to 5 hours to completely fill up."

This is no small task, because as the fuel is being added, the ballast tanks must be carefully pumped out. In this way, the ship will remain in the same position in the water. The ballast water has an interesting history.

"We need to exchange our ballast water in the open ocean, outside of 200 nautical miles, according to maritime regulations," explained Jeff.

Can you think why it is not permissible to dump water from one port (say Manzanillo, Mexico) into another port (like San Diego, California)? This is not an easy question, but the answer lies in the microscopic organisms living in the water. Atlantis and other ships that travel between ports could potentially carry organisms to new locations, introducing them to environments where they didn't exist before.

These organisms could potentially thrive in their new environment and take over and become invasive and out-compete the organisms that lived there (we call these native species). Since ballast water is one of the primary ways that this could happen, Atlantis and other ships are required to empty their ballast tanks and take on new water in the open ocean, which is believed to contain relatively few numbers of potentially invasive organisms. There are several other ways to minimize introducing new organisms, but this one seems to work well.

Isn't that fuel just going to sit in the tanks in Atlantis on the dock for a while?

"Right," said Jeff. "We add two things to the fuel. One is a treatment for the reduction of smoke when we burn it. The other is to control biological growth. If you let it sit for too long, this fungus will begin to grow."

Where will this fuel be taking Atlantis? Well, after we are unloaded, safely back ashore, Atlantis will begin preparing for its next adventure to Easter Island, off the coast of South America.

Well, here we sit, at 31º08' north, 116º56' west, going nowhere fast. Seas have been so calm, and we've made such good time, that we're pausing here for an hour or two, 90 nautical miles from San Diego, to test R/V Atlantis's dynamic positioning system.

The dynamic positioning system is what allows Atlantis to stay in place without an anchor, regardless of wind or currents. The wind is coming from about 300º and the current from the north. The combination, says Second Mate Craig Dickson, creates a rate called drift, which indicates how much these factors can push Atlantis off-course. Atlantis is a tall ship, he says, so wind is more of a factor than current in our drift.

What's so important about dynamic positioning, and why test it? Craig tells me that Atlantis's next cruise will involve Jason II, the remotely operated vehicle (ROV) that will be diving in the areas of Tahiti and Easter Island. Expedition Leader Pat Hickey showed me a copy of the cruise prospectus so I could see what Jason would be up to:

"Near-bottom mapping and sampling of major tectonic escarpments at Pito Deep that expose the internal structure of oceanic crust created at super-fast spreading rates at the East Pacific Rise about three million years ago. Operations include imaging and sampling of three study areas with DSL-120 side-scan sonar, Jason II, and Alvin. Limited nighttime dredging and Sea Beam mapping will also be done."

Big sigh: don't you wish that cruise was going to be as watchable as this one was? I do.

To deploy Jason II, an acoustic wire is dropped into the ocean from Atlantis's action winch on the fantail and will stay down for a few days to help track and guide Jason II. Being able to maintain position becomes crucial in this situation and knowing that the dynamic positioning system was working was important.

The system measures the rate of drift and "tells" Atlantis's thrusters to adjust the ship's position to counteract the drift. "There are two stern thrusters and one bow thruster," Craig tells me. "The stern thrusters can't overpower the bow thruster, though."

Ordinary Seaman Jennifer Hickey steps up to the bridge to help run the test, and Craig walks over to the chart table in front of the big bridge windows to show me our position along the coast of Baja California. On the distant horizon, a container ship is moving along.

From the bridge, Able-Bodied Seaman Raul Martinez has told me, the horizon is 12 miles away. That means that on a clear day, Atlantis sits in the middle of a circle with a 24-mile diameter. From the fantail, though, the horizon is only five miles away, and the circle shrinks to ten miles across. I use my vantage point to spy for whales, but still don't see so much as a spout. I'm still hopeful I'll encounter some of the gray whales that migrate south to breed and give birth.

"Maybe," says Craig. He hasn't seen any this trip, but Jennifer saw a big one cross the bow yesterday.

Our plan for the rest of the trip is as follows (once the dynamic positioning test is finished):

We'll set a course for one more waypoint, just inside Isla Los Coronados. After that, our next goal is the sea buoy outside San Diego harbor. There, we'll take on a harbor pilot and customs officials. I look forward to another mini tugboat like the one in Manzanillo, but Craig says the harbor pilots here arrive on a catamaran that used to be involved in races. That ought to be worth seeing.

I'll have to set my alarm pretty early, because we're due to arrive at the sea buoy at 6 a.m. tomorrow. The customs officials have to clear all that we're bringing into the United States, including things we bought in Manzanillo (I have vanilla and chocolate for Christmas presents), science equipment, and substances of all kinds.

Once we're done with these processes, we arrive at a fuel island in San Diego harbor. How long does it take to fill the tanks on this ship? Well, Atlantis has a fuel capacity of 296,470 gallons of diesel fuel. Shipboard Science Support Group Technician Dave Sims tells me we'll only take on 85 percent of our fuel capacity, and estimates this will take four or five hours. We're expecting to dock in the midafternoon.

The principal investigators of the Biocomplexity Project are giving a party for the scientists, Alvin Group, and crew tomorrow night in San Diego, and in the early hours of Tuesday morning, a few other East coasters and I will walk down Atlantis's gangplank for the last time and head for the airport.