BREAKTHROUGH OF THE YEAR:
The Runners-Up

2 DIGGING OUT FOSSIL DNA

Family feud. DNA confirms that Neandertals split from modern humans 450,000 years ago. FRANK FRANKLIN II/AP

In January 2006, researchers combined metagenomics with a new rapid sequencing technique called pyrosequencing, which uses pulses of light to read the sequence of thousands of bases at once, to get a whopping 13 million bases from a 27,000-year-old mammoth. The same sample also yielded another 15 million bases from bacteria, fungi, viruses, soil microbes, and plants--DNA that will provide clues about this giant mammal's environment. With those two advances, ancient DNA sequencing is off and running.

See Web links on paleogenomics

Bye-bye. The great ice sheets are losing ice to melting and icebergs faster than it forms. CREDIT: RICHARD ALLEY/PENN STATE UNIVERSITY

Current ice sheet losses aren't raising sea level faster than 0.1 meter per century, but researchers fear that the rate could rise to a meter per century or more in the near future. As recently as 5 years ago, they assumed that global warming would simply melt more and more ice from the ice sheets, as it is melting mountain glaciers. But it turns out the ice isn't just melting faster, it is moving faster. Radar mapping shows that in recent years, glaciers carrying ice away from the sheets have sped up by as much as 100%. In West Antarctica, warming ocean waters seem to have attacked the floating tongues of ice that hold back the ice sheet's outlet glaciers. Around southern Greenland, something else seems to be quickening the pace of outlet glaciers, perhaps lubrication by increasing amounts of surface meltwater seeping to a glacier's base.

Now glaciologists are wondering how the next chapter will play out. Will the relatively strong warming around the ice continue, or will it be weakened by natural variations of climate? Will the ice sheets adjust to the new warmth by eventually slowing their ice loss? And will more glaciers succumb to the spreading warmth? A few more breakthroughs are definitely in order.

See Web links on shrinking ice

Transitional. Odd fossil fish bears features of amphibians. CREDIT: KALLIOPI MONOYIOS

Three specimens were found during a 2004 field expedition to Ellesmere Island in the far north of Nunavut, Canada. They were named Tiktaalik roseae for "large freshwater fish" in the Inuktitut language and a donor who helped fund the expedition, respectively. With fins and scales, the 3-meter-long Tiktaalik is clearly a fish. It had a flat head with eyes on top and lived in shallow streams.

What makes Tiktaalik unique among fish is that each of the front fins has a wrist and elbow, providing flexible motion. Also unlike other fish, Tiktaalik sported a neck--the oldest one known in the fossil record--and could move its head. Achieving that flexibility required losing a bone called the operculum, which modern fish use to pump water over their gills. Tiktaalik still had well-developed gills, and it probably used its neck and stout limbs to push its head above water to inhale.

Another feature that makes Tiktaalik close kin to tetrapods is its robust, overlapping ribs. Although their function isn't completely clear, researchers think they could have helped support its body out of water and aided in breathing. Forays onto land would have offered an escape from sharks and other predators, as well as insects to eat. Tiktaalik isn't a perfect tetrapod, of course--among other traits, it lacks fingers and toes--but it was certainly a big step in the right direction.

See Web links on Tiktaalik

The disappearing act began in May, when two independent analyses predicted that it should be possible to ferry electromagnetic waves around an object to hide it. All that was needed was a properly designed shell of "metamaterial," an assemblage of tiny metallic rods and c-shaped rings. The waves churn the electrons in the rods and rings, and the sloshing affects the propagation of the waves. Both analyses specified how to sculpt the properties of the metamaterial and left it to experimenters to design the materials to meet those specs.

Outta sight. Although not as fashionable as this electronic garment, a cloak unveiled this year is a step toward true invisibility. CREDIT: SHIZUO KAMBAYASHI/AP

The real breakthrough may lie in the theoretical tools used to make the cloak. In such "transformation optics," researchers imagine--à la Einstein--warping empty space to bend the path of electromagnetic waves. A mathematical transformation then tells them how to mimic the bending by filling unwarped space with a material whose optical properties vary from point to point. The technique could be used to design antennas, shields, and myriad other devices. Any way you look at it, the ideas behind invisibility are likely to cast a long shadow.

See Web links on cloaking technology

CREDITS: GREGORY HAGEMAN; NATIONAL EYE INSTITUTE, NATIONAL INSTITUTES OF HEALTH

AMD researchers are making progress on another front as well. Over the past year and a half, they have uncovered several genes that influence an individual's susceptibility to the eye disease. One of them is the gene for VEGF itself, and another makes a protein that might also help regulate blood vessel growth. In addition, several groups have zeroed in on genes encoding proteins involved in inflammation, which can damage tissues if not controlled properly. Identifying those genes could help physicians determine whether a person is at high risk for AMD and thus should take preventive steps such as consuming more antioxidants and not smoking. And by shedding light on the causes of AMD, genetic studies should also provide targets for devising even better therapies.

See Web links on macular degeneration

For Florida beach mice, a single base difference in the melanocortin-1 receptor gene accounts for up to 36% of the lighter coat color that distinguishes the beach mice, evolutionary biologists reported in July. For cactus finches, the activity of the calmodulin gene is upregulated, causing their relatively long beaks, researchers reported in August.

Genes help drive speciation in other ways as well. Since the late 1930s, researchers have realized that as two incipient species diverge, the sequences of two or more interacting genes can evolve along different paths until the proteins they encode no longer work together in any crossbred offspring. Working with Drosophila melanogaster and a sister species, D. simulans, evolutionary geneticists have pinpointed the first such pair of incompatible genes, demonstrating in transgenic flies the genes'killing effects in hybrids of the two species. In October, a separate team found another fast-evolving gene and is homing in on its partner. They both seem to be nuclear pore proteins that are no longer compatible in fruit-fly hybrids. In September, fruit-fly researchers found that hybrids had problems because a particular gene was in a different place in the two species, likely because of duplication and loss of the original copy in one of them.

CREDIT: MAURICIO LINARES

See Web links on speciation

An ordinary microscope cannot resolve features smaller than half the wavelength of the light used to illuminate an object--about 200 nanometers for visible light. For years, physicists and engineers have devised schemes to get around the "diffraction limit," and this year, researchers used those techniques to do some real biology.

Clearly. New microscopy techniques resolve nanometer-sized features of proteins. CREDIT: E. BETZIG ET AL./SCIENCE (2006)

In August, another team imaged proteins within cells using a simpler technique known as photoactivated localization microscopy (PALM). The researchers used a fluorescent tag that had to be turned on with a pulse of light of one wavelength before it could be excited to fluoresce by light of another wavelength. By applying the first laser at a very low level, the researchers could turn on one tag molecule at a time. The molecule still produced a blurry spot when viewed through the microscope, but the researchers could nail down its position very precisely by finding the center of the blob. Repeating the process over and over, the team mapped proteins in cells with nanometer resolution. Two other groups introduced similar techniques this year.

Just how widely the techniques will be used remains to be seen. PALM is too slow to track dynamic processes, and STED requires fluorescent tags that can withstand intense excitation. Still, researchers are optimistic that more applications will follow, now that the diffraction limit is no longer a limit.

See Web links on sub-diffraction-limit microscopy

Record keeper. Learning and LTP go hand in hand in the rodent hippocampus. CREDIT: BRAINMAPS.ORG

But some predictions of the LTP-memory hypothesis have been harder to test. One is that it should be possible to observe LTP in the hippocampus when an animal learns something. In January, Spanish scientists reported just such an observation in mice conditioned to blink upon hearing a tone. In August, another research team described LTP in the hippocampus of rats that had learned to avoid an area where they'd previously received a shock.

A study published in August addressed another prediction: that abolishing LTP after learning should erase what was learned. Researchers injected a compound that blocks an enzyme needed to sustain LTP into the hippocampus of rats after they'd been trained to avoid a "shock zone" in their enclosure. The treatment eradicated both LTP and the memory of the shock zone's location.

Although the new results add to evidence that LTP is a molecular mechanism of memory, much work remains. For example, researchers still haven't figured out how the many forms of LTP identified in brain tissue relate to different kinds of memory. And they may have a while to wait for the ultimate test, which some call the "Marilyn Monroe criterion": inducing LTP at select synapses to create the vivid memory of an event, such as an evening with the voluptuous movie star, that never happened.

See Web links on LTP

PiRNAs made their grand entrance last summer, when four independent groups released a burst of papers describing them. In a sense, their sudden prominence is not surprising. The Piwi genes to which piRNAs bind belong to a gene family called Argonaute, other members of which help control small RNAs known as microRNAs (miRNAs) and small interfering RNAs (siRNAs). Scientists already believed that the Piwi genes regulate the development and maintenance of sperm cells in many species. With the discovery of piRNAs, they may be close to figuring out how that happens.

Particularly intriguing to biologists is the appearance of piRNAs: Many measure about 30 RNA bases in length, compared with about 22 nucleotides for miRNAs and siRNAs. Although that may not sound like much of a difference, it has gripped biologists and convinced them that piRNAs are another class of small RNAs altogether. Also striking is the molecules' abundance and variety. One group of scientists found nearly 62,000 piRNAs in rat testes; nearly 50,000 of those appeared just once.

CREDIT: BERNARD HOFFMAN/TIME LIFE PICTURES/GETTY IMAGES

See Web links on piRNAs