As we transit from the 13° north site to San Diego, I've been thinking a lot about how far we've been away from the land. In truth, though, the ocean is a well-connected place, and I don't just mean by satellite phones and e-mail. No, I'm talking about how despite the fact that we were about 1,500 nautical miles from shore, there is still a direct connection between the open ocean community and the coastal community.

Alvin Pilot-in-Training Noel Masias asked me last night, "Mike, what do you normally do?"

I responded that normally I work far away from our current location, in the salt marshes on the East Coast of the United States.

"Oh," he said, "I remember awhile back some ideas circulated about how open-ocean organisms spent some of their lives in coastal estuaries."

He's right. Many pelagic (open ocean) organisms spend part of their life cycles (often juvenile stages) in areas like coastal estuaries.

Well, that got me to thinking that if we have this connection to the shore then human impacts on the shore can affect the open ocean, way out here. No sooner did I ponder these thoughts than Dr. Craig Cary walked in with his digital camera.

"Mike, can you take a look at these on your laptop?" As I loaded the pictures, he began to tell Karen and I what we'd be seeing.

"There's a beautiful bird I saw from the deck," he said, as Karen and I began to look forward to some great shots! "Unfortunately, it looks like the bird is tangled in monofilament line."

Lo and behold, the pictures showed that in fact the bird was trailing fishing line from its legs. This served as a serious reminder that human activities on the coast have big impacts, even way out here.

Well, needless to say, this reminder about how humans can have negative impacts on the environment saddened us all. However, this raised some interesting questions in my mind about how Atlantis minimized its impact on the environment.

First, I looked to our garbage. With 55 people aboard, there is going to be trash. If you look at any of the trash containers on Atlantis, you'll realize that there's never a single barrel standing alone, there are always two together. When we received our orientation briefing, we were told that one of these cans is for the biodegradable trash. The other is for non-biodegradable. Biodegradable trash is mostly paper products, leftover food, and most metals including aluminum and steel.

The big "no-no" that you never throw in the biodegradable barrel is plastics. Plastics go in the other barrel, along with other non-biodegradable items, such as Styrofoam. This includes all types of plastic and any items that you aren't sure about. We never take chances ...

After the trash has been sorted in this way, the two barrels are emptied and have very different fates. If we are farther than 12 nautical miles from land, the biodegradable trash is sent overboard. These items are quickly saturated with water and begin to break down. Plastics, as we saw in the pictures that Craig took, don't break down easily and so they are obviously not sent overboard. Instead, these items are sent to Atlantis' incinerator, located just aft (towards the stern) of the galley. Here, they are burned in the same way that trash on the land is burned. In this way, trash does not build up on the ship.

"What about when we're closer to shore than 12 nautical miles?" I asked.

"Inside 12 nautical miles, we store everything on the ship and dispose of it when we dock using land-based facilities," said First Engineer Jim Schubert.

Now that you know how our trash is handled, I am sure that you're wondering (as I was) about where the sinks and toilets drain. It turns out that Atlantis has its own sewage processing plant, just like a small town. The toilets work on a vacuum system, very different from land-based bathrooms. This system conserves lots of water.

It's very important to conserve water, because even though we're surrounded by water, we need to actually make every drop that we use. You see, human beings can't drink salt water; our kidneys weren't designed to handle all that salt. So, the Second Engineer Marcel Vieira heads up Atlantis' fresh water–making department, taking in saltwater from the ocean and producing fresh water for us to drink.

Atlantis is equipped with an evaporator and a reverse osmosis machine. You can probably guess how the evaporator works, but maybe you don't know about reverse osmosis. Reverse osmosis uses pressure to push water through a membrane. The membrane is designed to let water pass through, but not salts.

Marcel runs the machines about every other night to help fill up the water holding tank, which can hold 6,000 gallons of fresh water.

A student asked me, "How much fresh water do you use in a day?"

I didn't know, so I asked Jim again. "We use about 3,000 gallons of fresh water every day. That includes everything -- from brushing your teeth to the ultra-pure deionized water used to clean the scientific equipment."

Well, after all my research into how Atlantis minimizes the footprint it leaves behind, I am convinced that the crew does a superb job of handling the waste that is produced by those living aboard. Everyone I've talked to aboard is extremely conscious of the impact they could have on this beautiful environment, and do their best to make sure that we leave nothing behind but ripples in the water.

We have reached the end of the dives. Alvin is up on deck, being stripped down, in a process that will take several days of continuous maintenance. Alvin won't be needed again until a few months from now, when another expedition will take it to Easter Island and Tahiti, in the South Pacific. Oh, I'd be happy to make that trip, too!

We are underway again, steaming north at about 12 knots speed over ground (SOG) running northward. Our dives took place west of Costa Rica, and now we move along over the ocean toward the corner or elbow of Mexico once again. It will take us six days to reach our final destination, San Diego.

I've always liked being on a boat that's moving, up until the other night when I got a taste of seasickness. So I'm really relieved that tonight the sea seems calmer, and we're moving along with a gentle rhythm. Midway through the evening, I take a break from putting together Neat Stuff and walk out to the fantail to see if there are any stars out.

There are -- but not just in the sky. In the wake billowing out from the stern of the boat, I see sprays of sparkles, some the size of dimes, some as small as glitter. I look and look and look. They gleam coming up from the thrusters and fade as the boat moves away.

After a bit, I climb the stairs to the 01 deck and walk up to the bow. Eric DeChaine and Frank Stewart are sitting on the benches there (which have been considerately cleared of booby poop by the firehose drill we had yesterday -- yay, fire hose drill!), talking and looking at the stars.

I lean over the bow and comment, "The water's all twinkly again tonight."

The guys look over the rail. "Dinoflagellates!" exclaims Eric.

Well, he took the word right out of my mouth. By now you know me better than to believe this, although, let me tell you, my knowledge grows in leaps and bounds.

"What are they doing?" I ask.

"Just getting excited," says Eric. "They get stirred up in the water." That makes their lights go on.

It reminds me of a moment in one of my favorite movies, Local Hero, when the marine biologist gives a scientific explanation for the Northern Lights, and the hero says, "You say the darndest things."

I've thought that comment so many times on this trip, while talking to just about every one of the scientists! I think back to a couple of days ago, when some of us were talking about submarines and how they navigate. Astrid Schnetzer told a story about the first "super-silent" submarines, with engines designed to be so quiet in the water that the subs could not be detected.

Were their designers ever surprised when they realized that, although the subs couldn't be heard, they could be seen. The waters around them were full of bioluminescent creatures -- fish, krill, jellies, copepods -- with the result that the subs stood out like ink blots on paper. They were perfectly outlined by the glowing water.

I go back to Astrid today to find out more about bioluminescence. Not only am I fascinated by the critters in the wake and the bow wave, I have been down deep to see the show of lit-up beings when I dove in Alvin.

"Ninety percent of mesopelagic and bathypelagic organisms bioluminesce," says Astrid. "It's the rule, rather than the exception." Bioluminescent creatures include bacteria, dinoflagellates, invertebrates, and fish, she says. Only one freshwater organism is known to bioluminesce, an invertebrate.

There are two known ways that bioluminescers bioluminesce (oh come on, you know you love these words as much as I do!) One is to produce an enzyme-protein complex. Both come together to make light. The protein group needed is called luciferin. The enzyme needed is luciferase.

(SAT word check: Who was Lucifer? The Bringer of Light in the Bible. The suffix -in is associated with proteins and -ase is the suffix associated with enzymes.) Two-thirds of bioluminescent animals do it this way; they pretty much stay lit.

"They set forth energy in light," Astrid explains, "the way we set forth energy in heat."

The other third use photoproteins, which can create a one-time sparkle that can be an instant long or can go on for a while.

Bioluminescers have photophores, organs that do nothing else but light. Astrid shows me a photograph of a fish with photophores that look like rows of dots along the center lines of its belly and back. On the back, photophores work at one level, so that the fish looks black from above. On the belly, they produce more light, so that from below, the fish blends in with its surroundings.

Astrid told me about a few cool bioluminescers. Jellyfish light their tentacles, attracting prey right toward the spot that kills. The flashlight fish can shine their 'flashlights' -- light-producing organs near their eyes.

But why do they need to light up? There are many possible reasons, some more entertaining than others:

· to lure,

· to search,

· to recognize fellow members of their species,

· to swim around in schools without crashing into each other or losing orientation,

· as camouflage,

· as a warning against toxic substances, and

· as a burglar alarm.

Astrid tells me a story to explain the burglar alarm idea: "Little dinoflagellates are being chased by a larger copepod. They light up so that everything sparkles, except the copepod. This puts the copepod into a kind of reverse spotlight [like the submarine] to attract bigger fish. So the bigger fish comes and eats the copepod. And the dinoflagellates get away."

I've been writing about the ocean for a long time, about how it fills enormous basins on the Earth, and how the swirl of currents and rivers within it affect everything that happens all over the planet. But for the first time, on this trip, I really begin to have an inkling (a tiny glimmer of an idea) of how massively huge and deep -- ridiculously huge and deep -- the oceans are.

Our ship barely breaks the surface as it goes thumping along. The wake is big and wide, but its effects disappear from the surface long before the horizon. And down there, all these light-up things are, brilliant in their undersea world, completely invisible except for the moment that Atlantis comes along to kick them up and get them excited. I could get excited enough to light up myself. Maybe I already have.

P.S. When I showed this story to Astrid to make sure I had my facts straight, she told me about flushing the toilet in Bermuda. (Please see Mike's journal today for toilet flushing on Atlantis!) In Bermuda, where they must conserve fresh water, toilets use seawater to flush. When Astrid first arrived there from her native Austria, people told her she should turn out the lights and check out the toilet. She didn't know if they were putting her on, but she tried it. Lights out, flush, and -- sparkles!