ABOARD THE R/V THOMAS G. THOMPSON—Challenger Deep is the deepest spot in the ocean—that we know of, at least. The seafloor is so poorly mapped that there could easily be something deeper out there, but that's not all that important to us. It's been visited many times by both human-occupied and remotely operated vehicles, including the National Science Foundation-funded Nereus.

Now it's time to look more broadly at the deep ocean, including the Mariana Trench, which is where Challenger Deep is located, especially if we want to learn something about the structure and function of hadal ecosystems. And for that, Challenger Deep may very well be one of the least interesting places to go.

For one thing the Mariana Trench is almost certainly not indicative of all trenches, and it may even be an outlier based on what little life has been found there. Much of the Mariana Trench sits beneath a naturally nutrient-poor "oligotrophic" part of the Pacific Ocean. Low nutrients means little phytoplankton. Little phytoplankton means few animals to live there and, more importantly, to die there and sink down through the water column to provide food for organisms at the bottom.

There was microbial life in the cores that James Cameron took when he visited with DEEPSEA CHALLENGER and that Nereus collected in 2009. Nereus also observed a few sea cucumbers, but, as hypothesized by the HADES program, Challenger Deep is essentially a flat, sediment-filled desert. Those same cores and ones collected by Nereus contained no larger animals like annelid worms that are common in the seafloor of other trenches. The same goes for free-swimming organisms like amphipods that are common at all depths of the ocean, including other trenches, but are noticeably missing at Challenger.

To borrow an analogy from Alan Jamieson of Aberdeen University, basing our assumptions of hadal ecology on observations from Challenger Deep would be like forming all our theories about mountain ecology based on what can be found at the top of Mt. Everest. Not during the climb, mind you, just what's at the summit.

What we're after is a foundation from which to form the basic precepts of hadal ecology. This will require answers to some questions that would be fairly straightforward to answer if we were studying a patch of forest or an alpine meadow: What lives where, in what numbers and with whom else nearby? How long do different species live and how do they change over their lifetime? How much food is there and form does it take? Who eats whom? What adaptations are necessary for life to survive in the deep?

When you think about it, it is astounding that there's a place on Earth we still know so little about. Beginning to answer these and many other questions, some of which we don't even know to ask yet, takes careful planning, precise measurement, and consistent observation and sampling. The problem is, there's all that water in the way, more than six miles of it, which is why we need the tools I described in the last two posts.

The depth of the seawater and its accumulated weight not only makes exploration physically challenging—we need specialized equipment that can operate for extended periods and withstand the pressure, cold and salt water—but it also limits us in how far through the darkness our instruments will let us observe and communicate. The marine environment also makes what we're doing an extremely delicate operation on the surface. For one thing, we have to do all of our heavy lifting and maneuvering of equipment from the relatively confined and constantly moving deck of a ship and do it far from shore with a small group of people.

Which is why things can sometimes go wrong. The other day, we were recovering Nereus from an aborted dive after the hair-thin optical fiber portion of its tether parted just 200 meters from the bottom, when the heavy umbilical between the float pack and the vehicle got caught up in one of the ship's propellers. The drive shaft was not engaged, but the Kevlar-reinforced umbilical managed to wrap around the base of the propeller. Some quick-thinking by members of the ship's crew and Nereus team prevented any serious damage, but we still had to return to the Northeast coast of New Zealand to wait for some commercial divers to come out, cut the fouled line, and inspect the propulsion unit.

Then on the way back out a seal failed on the crane that lifts Nereus' 6,700-pound bulk in and out of the water. So now we're back in Auckland waiting for repairs that we couldn't do at sea. If everything checks out, we'll be back over the trench soon. Because nobody on this ship can abide having a blank spot on the map of Earth or a blind spot in our knowledge of what shares the planet with us.