Twice a day, seven days a week, from February to November for the past four years, two researchers have layered themselves with thermal underwear and outerwear, with fleece, flannel, double gloves, double socks, padded overalls and puffy red parkas, mummifying themselves until they look like twin Michelin Men. Then they step outside, trading the warmth and modern conveniences of a science station (foosball, fitness center, 24-hour cafeteria) for a minus-100-degree Fahrenheit featureless landscape, flatter than Kansas and one of the coldest places on the planet. They trudge in darkness nearly a mile, across a plateau of snow and ice, until they discern, against the backdrop of more stars than any hands-in-pocket backyard observer has ever seen, the silhouette of the giant disk of the South Pole Telescope, where they join a global effort to solve possibly the greatest riddle in the universe: what most of it is made of.

For thousands of years our species has studied the night sky and wondered if anything else is out there. Last year we celebrated the 400th anniversary of Galileo’s answer: Yes. Galileo trained a new instrument, the telescope, on the heavens and saw objects that no other person had ever seen: hundreds of stars, mountains on the Moon, satellites of Jupiter. Since then we have found more than 400 planets around other stars, 100 billion stars in our galaxy, hundreds of billions of galaxies beyond our own, even the faint radiation that is the echo of the Big Bang.

Now scientists think that even this extravagant census of the universe might be as out-of-date as the five-planet cosmos that Galileo inherited from the ancients. Astronomers have compiled evidence that what we’ve always thought of as the actual universe—me, you, this magazine, planets, stars, galaxies, all the matter in space—represents a mere 4 percent of what’s actually out there. The rest they call, for want of a better word, dark: 23 percent is something they call dark matter, and 73 percent is something even more mysterious, which they call dark energy.

“We have a complete inventory of the universe,” Sean Carroll, a California Institute of Technology cosmologist, has said, “and it makes no sense.”

Scientists have some ideas about what dark matter might be—exotic and still hypothetical particles—but they have hardly a clue about dark energy. In 2003, the National Research Council listed “What Is the Nature of Dark Energy?” as one of the most pressing scientific problems of the coming decades. The head of the committee that wrote the report, University of Chicago cosmologist Michael S. Turner, goes further and ranks dark energy as “the most profound mystery in all of science.”

The effort to solve it has mobilized a generation of astronomers in a rethinking of physics and cosmology to rival and perhaps surpass the revolution Galileo inaugurated on an autumn evening in Padua. They are coming to terms with a deep irony: it is sight itself that has blinded us to nearly the entire universe. And the recognition of this blindness, in turn, has inspired us to ask, as if for the first time: What is this cosmos we call home?

Scientists reached a consensus in the 1970s that there was more to the universe than meets the eye. In computer simulations of our galaxy, the Milky Way, theorists found that the center would not hold—based on what we can see of it, our galaxy doesn’t have enough mass to keep everything in place. As it rotates, it should disintegrate, shedding stars and gas in every direction. Either a spiral galaxy such as the Milky Way violates the laws of gravity, or the light emanating from it—from the vast glowing clouds of gas and the myriad stars—is an inaccurate indication of the galaxy’s mass.

But what if some portion of a galaxy’s mass didn’t radiate light? If spiral galaxies contained enough of such mystery mass, then they might well be obeying the laws of gravity. Astronomers dubbed the invisible mass “dark matter.”

“Nobody ever told us that all matter radiated,”Vera Rubin, an astronomer whose observations of galaxy rotations provided evidence for dark matter, has said. “We just assumed that it did.”

The effort to understand dark matter defined much of astronomy for the next two decades. Astronomers may not know what dark matter is, but inferring its presence allowed them to pursue in a new way an eternal question: What is the fate of the universe?

They already knew that the universe is expanding. In 1929, the astronomer Edwin Hubble had discovered that distant galaxies were moving away from us and that the farther away they got, the faster they seemed to be receding.

This was a radical idea. Instead of the stately, eternally unchanging still life that the universe once appeared to be, it was actually alive in time, like a movie. Rewind the film of the expansion and the universe would eventually reach a state of infinite density and energy—what astronomers call the Big Bang. But what if you hit fast-forward? How would the story end?

The universe is full of matter, and matter attracts other matter through gravity. Astronomers reasoned that the mutual attraction among all that matter must be slowing down the expansion of the universe. But they didn’t know what the ultimate outcome would be. Would the gravitational effect be so forceful that the universe would ultimately stretch a certain distance, stop and reverse itself, like a ball tossed into the air? Or would it be so slight that the universe would escape its grasp and never stop expanding, like a rocket leaving Earth’s atmosphere? Or did we live in an exquisitely balanced universe, in which gravity ensures a Goldilocks rate of expansion neither too fast nor too slow—so the universe would eventually come to a virtual standstill?

Assuming the existence of dark matter and that the law of gravitation is universal, two teams of astrophysicists—one led by Saul Perlmutter, at the Lawrence Berkeley National Laboratory, the other by Brian Schmidt, at Australian National University—set out to determine the future of the universe. Throughout the 1990s the rival teams closely analyzed a number of exploding stars, or supernovas, using those unusually bright, short-lived distant objects to gauge the universe’s growth. They knew how bright the supernovas should appear at different points across the universe if the rate of expansion were uniform. By comparing how much brighter the supernovas actually did appear, astronomers figured they could determine how much the expansion of the universe was slowing down. But to the astronomers’ surprise, when they looked as far as halfway across the universe, six or seven billion light-years away, they found that the supernovas weren’t brighter—and therefore nearer—than expected. They were dimmer—that is, more distant. The two teams both concluded that the expansion of the universe isn’t slowing down. It’s speeding up.

The implication of that discovery was momentous: it meant that the dominant force in the evolution of the universe isn’t gravity. It is...something else. Both teams announced their findings in 1998. Turner gave the “something” a nickname: dark energy. It stuck. Since then, astronomers have pursued the mystery of dark energy to the ends of the Earth—literally.

“The South Pole has the harshest environment on Earth, but also the most benign,” says William Holzapfel, a University of California at Berkeley astrophysicist who was the on-site lead researcher at the South Pole Telescope (SPT) when I visited.

He wasn’t referring to the weather, though in the week between Christmas and New Year’s Day—early summer in the Southern Hemisphere—the Sun shone around the clock, the temperatures were barely in the minus single digits (and one day even broke zero), and the wind was mostly calm. Holzapfel made the walk from the National Science Foundation’s Amundsen-Scott South Pole Station (a snowball’s throw from the traditional site of the pole itself, which is marked with, yes, a pole) to the telescope wearing jeans and running shoes. One afternoon the telescope’s laboratory building got so warm the crew propped open a door.

But from an astronomer’s perspective, not until the Sun goes down and stays down—March through September— does the South Pole get “benign.”

“It’s six months of uninterrupted data,” says Holzapfel. During the 24-hour darkness of the austral autumn and winter, the telescope operates nonstop under impeccable conditions for astronomy. The atmosphere is thin (the pole is more than 9,300 feet above sea level, 9,000 of which are ice). The atmosphere is also stable, due to the absence of the heating and cooling effects of a rising and setting Sun; the pole has some of the calmest winds on Earth, and they almost always blow from the same direction.

Perhaps most important for the telescope, the air is exceptionally dry; technically, Antarctica is a desert. (Chapped hands can take weeks to heal, and perspiration isn’t really a hygiene issue, so the restriction to two showers a week to conserve water isn’t much of a problem. As one pole veteran told me, “The moment you go back through customs at Christchurch [New Zealand], that’s when you’ll need a shower.”) The SPT detects microwaves, a part of the electromagnetic spectrum that is particularly sensitive to water vapor. Humid air can absorb microwaves and prevent them from reaching the telescope, and moisture emits its own radiation, which could be misread as cosmic signals.

To minimize these problems, astronomers who analyze microwaves and submillimeter waves have made the South Pole a second home. Their instruments reside in the Dark Sector, a tight cluster of buildings where light and other sources of electromagnetic radiation are kept to a minimum. (Nearby are the Quiet Sector, for seismology research, and the Clean Air Sector, for climate projects.)

Astronomers like to say that for more pristine observing conditions, they would have to go into outer space—an exponentially more expensive proposition, and one that NASA generally doesn’t like to pursue unless the science can’t easily be done on Earth. (A dark energy satellite has been on and off the drawing board since 1999, and last year went “back to square one,” according to one NASA adviser.) At least on Earth, if something goes wrong with an instrument, you don’t need to commandeer a space shuttle to fix it.

The United States has maintained a year-round presence at the pole since 1956, and by now the National Science Foundation’s U.S. Antarctic Program has gotten life there down to, well, a science. Until 2008, the station was housed in a geodesic dome whose crown is still visible above the snow. The new base station resembles a small cruise ship more than a remote outpost and sleeps more than 150, all in private quarters. Through the portholes that line the two floors, you can contemplate a horizon as hypnotically level as any ocean’s. The new station rests on lifts that, as snow accumulates, allow it to be jacked up two full stories.

The snowfall in this ultra-arid region may be minimal, but that which blows in from the continent’s edges can still make a mess, creating one of the more mundane tasks for the SPT’s winter-over crew. Once a week during the dark months, when the station population shrinks to around 50, the two on-site SPT researchers have to climb into the telescope’s 33-foot-wide microwave dish and sweep it clean. The telescope gathers data and sends it to the desktops of distant researchers. The two “winter-overs” spend their days working on the data, too, analyzing it as if they were back home. But when the telescope hits a glitch and an alarm on their laptops sounds, they have to figure out what the problem is—fast.

“An hour of down time is thousands of dollars of lost observing time,” says Keith Vanderlinde, one of 2008’s two winter-overs. “There are always little things. A fan will break because it’s so dry down there, all the lubrication goes away. And then the computer will overheat and turn itself off, and suddenly we’re down and we have no idea why.” At that point, the environment might not seem so “benign” after all. No flights go to or from the South Pole from March to October (a plane’s engine oil would gelatinize), so if the winter-overs can’t fix whatever is broken, it stays broken—which hasn’t yet happened.

More than most sciences, astronomy depends on the sense of sight; before astronomers can reimagine the universe as a whole, they first have to figure out how to perceive the dark parts. Knowing what dark matter is would help scientists think about how the structure of the universe forms. Knowing what dark energy does would help scientists think about how that structure has evolved over time—and how it will continue to evolve.

Scientists have a couple of candidates for the composition of dark matter—hypothetical particles called neutralinos and axions. For dark energy, however, the challenge is to figure out not what it is but what it’s like. In particular, astronomers want to know if dark energy changes over space and time, or whether it’s constant. One way to study it is to measure so-called baryon acoustic oscillations. When the universe was still in its infancy, a mere 379,000 years old, it cooled sufficiently for baryons (particles made from protons and neutrons) to separate from photons (packets of light). This separation left behind an imprint—called the cosmic microwave background—that can still be detected today. It includes sound waves (“acoustic oscillations”) that coursed through the infant universe. The peaks of those oscillations represent regions that were slightly denser than the rest of the universe. And because matter attracts matter through gravity, those regions grew even denser as the universe aged, coalescing first into galaxies and then into clusters of galaxies. If astronomers compare the original cosmic microwave background oscillations with the distribution of galaxies at different stages of the universe’s history, they can measure the rate of the universe’s expansion.

Another approach to defining dark energy involves a method called gravitational lensing. According to Albert Einstein’s theory of general relativity, a beam of light traveling through space appears to bend because of the gravitational pull of matter. (Actually, it’s space itself that bends, and light just goes along for the ride.) If two clusters of galaxies lie along a single line of sight, the foreground cluster will act as a lens that distorts light coming from the background cluster. This distortion can tell astronomers the mass of the foreground cluster. By sampling millions of galaxies in different parts of the universe, astronomers should be able to estimate the rate at which galaxies have clumped into clusters over time, and that rate in turn will tell them how fast the universe expanded at different points in its history.

The South Pole Telescope uses a third technique, called the Sunyaev-Zel’dovich effect, named for two Soviet physicists, which draws on the cosmic microwave background. If a photon from the latter interacts with hot gas in a cluster, it experiences a slight increase in energy. Detecting this energy allows astronomers to map those clusters and measure the influence of dark energy on their growth throughout the history of the universe. That, at least, is the hope. “A lot of people in the community have developed what I think is a healthy skepticism. They say, ‘That’s great, but show us the money,’” says Holzapfel. “And I think within a year or two, we’ll be in a position to be able to do that.”

The SPT team focuses on galaxy clusters because they are the largest structures in the universe, often consisting of hundreds of galaxies—they are one million billion times the mass of the Sun. As dark energy pushes the universe to expand, galaxy clusters will have a harder time growing. They will become more distant from one another, and the universe will become colder and lonelier.

Galaxy clusters “are sort of like canaries in a coal mine in terms of structure formation,” Holzapfel says. If the density of dark matter or the properties of dark energy were to change, the abundance of clusters “would be the first thing to be altered.” The South Pole Telescope should be able to track galaxy clusters over time. “You can say, ‘At so many billion years ago, how many clusters were there, and how many are there now?’” says Holzapfel. “And then compare them to your predictions.”

Yet all these methods come with a caveat. They assume that we sufficiently understand gravity, which is not only the force opposing dark energy but has been the very foundation of physics for the past four centuries.

Twenty times a second, a laser high in the Sacramento Mountains of New Mexico aims a pulse of light at the Moon, 239,000 miles away. The beam’s target is one of three suitcase-size reflectors that Apollo astronauts planted on the lunar surface four decades ago. Photons from the beam bounce off the mirror and return to New Mexico. Total round-trip travel time: 2.5 seconds, more or less.

That “more or less” makes all the difference. By timing the speed-of-light journey, researchers at the Apache Point Observatory Lunar Laser-ranging Operation (APOLLO) can measure the Earth-Moon distance moment to moment and map the Moon’s orbit with exquisite precision. As in the apocryphal story of Galileo dropping balls from the Leaning Tower of Pisa to test the universality of free fall, APOLLO treats the Earth and Moon like two balls dropping in the gravitational field of the Sun. Mario Livio, an astrophysicist at the Space Telescope Science Institute in Baltimore, calls it an “absolutely incredible experiment.” If the orbit of the Moon exhibits even the slightest deviation from Einstein’s predictions, scientists might have to rethink his equations—and perhaps even the existence of dark matter and dark energy.

“So far, Einstein is holding,” says one of APOLLO’s lead observers, astronomer Russet McMillan, as her five-year project passes the halfway point.

Even if Einstein weren’t holding, researchers would first have to eliminate other possibilities, such as an error in the measure of the mass of the Earth, Moon or Sun, before conceding that general relativity requires a corrective. Even so, astronomers know that they take gravity for granted at their own peril. They have inferred the existence of dark matter due to its gravitational effects on galaxies, and the existence of dark energy due to its anti-gravitational effects on the expansion of the universe. What if the assumption underlying these twin inferences—that we know how gravity works—is wrong? Can a theory of the universe even more outlandish than one positing dark matter and dark energy account for the evidence? To find out, scientists are testing gravity not only across the universe but across the tabletop. Until recently, physicists hadn’t measured gravity at extremely close ranges.

“Astonishing, isn’t it?” says Eric Adelberger, the coordinator of several gravity experiments taking place in a laboratory at the University of Washington, Seattle. “But it wouldn’t be astonishing if you tried to do it”—if you tried to test gravity at distances shorter than a millimeter. Testing gravity isn’t simply a matter of putting two objects close to each other and measuring the attraction between them. All sorts of other things may be exerting a gravitational influence.

“There’s metal here,” Adelberger says, pointing to a nearby instrument. “There’s a hillside over here”—waving toward some point past the concrete wall that encircles the laboratory. “There’s a lake over there.” There’s also the groundwater level in the soil, which changes every time it rains. Then there’s the rotation of the Earth, the position of the Sun, the dark matter at the heart of our galaxy.

Over the past decade the Seattle team has measured the gravitational attraction between two objects at smaller and smaller distances, down to 56 microns (or 1/500 of an inch), just to make sure that Einstein’s equations for gravity hold true at the shortest distances, too. So far, they do.

But even Einstein recognized that his theory of general relativity didn’t entirely explain the universe. He spent the last 30 years of his life trying to reconcile his physics of the very big with the physics of the very small—quantum mechanics. He failed.

Theorists have come up with all sorts of possibilities in an attempt to reconcile general relativity with quantum mechanics: parallel universes, colliding universes, bubble universes, universes with extra dimensions, universes that eternally reproduce, universes that bounce from Big Bang to Big Crunch to Big Bang.

Adam Riess, an astronomer who collaborated with Brian Schmidt on the discovery of dark energy, says he looks every day at an Internet site (xxx.lanl.gov/archive/astro-ph) where scientists post their analyses to see what new ideas are out there. “Most of them are pretty kooky,” he says. “But it’s possible that somebody will come out with a deep theory.”

For all its advances, astronomy turns out to have been laboring under an incorrect, if reasonable, assumption: what you see is what you get. Now astronomers have to adapt to the idea that the universe is not the stuff of us—in the grand scheme of things, our species and our planet and our galaxy and everything we have ever seen are, as theoretical physicist Lawrence Krauss of Arizona State University has said, “a bit of pollution.”

Yet cosmologists tend not to be discouraged. “The really hard problems are great,” says Michael Turner, “because we know they’ll require a crazy new idea.” As Andreas Albrecht, a cosmologist at the University of California at Davis, said at a recent conference on dark energy: “If you put the timeline of the history of science before me and I could choose any time and field, this is where I’d want to be.”

Richard Panek wrote about Einstein for Smithsonian in 2005. His book on dark matter and dark energy will appear in 2011.