Diving for Microbes

Sixteen panels of four different clumps of marine microorganisms collected from a methane seep off the coast of northern California. Each clump, called an aggregate, is about 10 microns (millionths of a meter) across. The microbes have been tagged with fluorescent markers. DNA glows blue.

On the ocean floor, a thousand meters under the sea, there's no light and little oxygen. Without conventional sources of food, a group of mysterious microbes have evolved to eat methane, forming the base of an ecosystem that abounds with crabs, tube worms, and shrimp. By consuming this greenhouse gas, these bugs prevent further warming of the planet, showing that despite their itty-bitty size, their importance to the world is not to be overlooked. "They are an integral part of almost every facet of our planet," says Assistant Professor of Geobiology Victoria Orphan, whose team of researchers dive into the ocean to uncover whatever secrets these critters may hold. This group of bugs consists of bacteria and archaea—another type of microscopic life—and Orphan's lab is learning how these two types of microbes work together to harness the energy locked in methane.

Orphan's team explores the sea floor in the waters off the coasts of such places as Costa Rica and the Eel River Basin in northern California, steering robotic submarines equipped with arms that dig for gray mud teeming with the microbes. Sometimes the researchers venture into the murky deep themselves, aboard the Alvin, the sub famous for exploring the wreck of the Titanic.

Back at the lab, they analyze the mud samples with a series of techniques pulled from geochemistry and microbiology. Applying a method called magneto fluorescence in situ hybridization (magnetoFISH), Orphan and her colleagues can pick out the bugs and identify them. The bacteria glow green, while the archaea glow red. The team also uses another technique called nanoscale secondary ion mass spectrometry (nanoSIMS), blasting the microbial cells with a beam of cesium ions and analyzing whatever particles ricochet back out. With nanoSIMS, the researchers discovered that the microbes play a surprisingly big role in the world's nitrogen cycle. Besides eating methane, the bugs apparently can break down gaseous nitrogen into forms that they—and other organisms—can use. Nitrogen is an essential nutrient that makes up 78 percent of our atmosphere, but in its gaseous state it assumes a chemical form that life cannot use.

These bacteria and archaea flourish in harsh, oxygenless environments akin to those on Earth during the first couple billion years of the planet's existence. As organisms that also share DNA with the first-known lifeforms, these methane-munching microbes are living fossils, telling us something about our planet's history. And if life can take hold in such unforgiving conditions on Earth, perhaps it can take hold in extraterrestrial environments. These underwater bugs, then, may be our connection to life in the distant past and on other worlds.

At the very least, these microbes are crucial for life on this planet. "If all bacteria and archaea just stopped functioning, life on Earth would come to an abrupt halt," says Anne Dekas, one of Orphan's graduate students. "I can't think of anything as important as that."

To read more and watch videos from the dives, see the E&S Zmag. Or listen to our audio podcast.

Marcus Woo

Elementary School Students Tour Caltech's Tectonics Observatory and Seismo Lab

Sixty sixth graders from Hamilton Elementary School in Pasadena recently visited campus to tour Caltech's Tectonics Observatory and Seismological Laboratory. Their first stop was the lab of grad student Willy Amidon (right), who showed them his collection of geologic specimens and asked, "How old are these rocks?" He then showed them how to answer that question by demonstrating the methods scientists use in the cosmogenic dating of rocks, from grinding the samples to extracting microscopic zirconium crystals and then baking them in a mass spectrometer to drive off and measure helium-3.

Amidon explained that when the sun's cosmic rays hit a rock, He-3 is produced and then trapped in zirconium crystals. The He-3 only starts to build up when the rock reaches Earth's surface and is exposed to the rays—so the more He-3 present, the longer the rock has been at the surface, and the older it is.

The sixth graders next visited Caltech postdoc Itai Haviv (right), who gave a presentation on the rise of the Himalayas. He explained how the world's highest mountain range was born and how scientists conduct geologic field work in remote areas with no roads. He also showed how scientists separate the rate of mountain building from the rate of erosion by examining the different minerals in Himalayan rocks to estimate the age of the rocks, and hence the mountains' growth rate.

The students' final stop was with Tectonics Observatory research seismologist Anthony Sladen (below), who discussed the two recent earthquakes in Chile and Haiti. He showed them how to use Google Earth to locate the fault responsible for the Haitian quake, and how to find the epicenters of the two earthquakes and the locations of their numerous aftershocks. Sladen explained that the images of Haiti on  Google Earth are so detailed that rescue teams were able to use the application to locate people after the disaster.

The students also created their own earthquakes using "earthquake machines" built with blocks, sandpaper, and springs. The resulting seismic waves were then detected and displayed on a laptop using the Mac OS X application SeisMac. Through this simple model, they learned firsthand why it is not possible for seismologists to predict the next earthquake.

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Caltech Receives More than $33 Million from American Recovery and Reinvestment Act

Neuroeconomics and the fundamentals of jet noise just some of the many projects supported

PASADENA, Calif.-Research in genomic sciences, astronomy, seismology, and neuroeconomics are some of the many projects being funded at the California Institute of Technology (Caltech) by the American Recovery and Reinvestment Act (ARRA).

As part of the federal government program of stimulating the economy, ARRA is providing approximately $21 billion for research and development. The goal is for the funding to lead to new scientific discoveries and to support jobs.

ARRA provides the funds to federal research agencies such as the National Institutes of Health, the National Science Foundation, and the Department of Energy, which then support proposals submitted by universities and other research institutions from across the country.

Caltech has received 82 awards to date, totaling more than $33 million. Spending from the grants began in the spring of 2009 and thus far has led to the support of 93 jobs at the Institute.

"This funding will help lead to substantive and important work here at Caltech," says Caltech president Jean-Lou Chameau. "We're grateful to have this opportunity to advance research designed to benefit the entire country."

For biologist Paul Sternberg, the Thomas Hunt Morgan Professor of Biology at Caltech and a Howard Hughes Medical Institute investigator, the ARRA funds mean an opportunity to improve upon WormBase, an ongoing multi-institutional effort to make genetic information on the experimental animal C. elegans freely available to the world.

"All biological and biomedical researchers rely on publicly available databases of genetic information," says Sternberg. "But it has been expensive and difficult to extract information from scientific research articles. We have developed some tools to make it less expensive and less tedious to get the job done, for WormBase and many other groups."

Sternberg's ARRA funds-$989,492-will go towards developing a more efficient approach to extracting key facts from published biological-science papers.

Among the other diverse Caltech projects receiving ARRA funds are:

  • a catalog of jellyfish DNA;
  • improving the speed of data collection at Caltech's Center of Excellence in Genomic Science;
  • studies into the fundamentals of particle physics;
  • the California High School Cosmic Ray Observatory (CHICOS) program, which provides high school students access to cosmic ray research;
  • the search for new astronomical objects such as flare stars and gamma-ray bursts, and the means to make those discoveries accessible to the public; and
  • a $1 million upgrade of the Southern California Seismic Network.

Caltech Professor of Mechanical Engineering Tim Colonius received ARRA funds for research into better understanding how noise is created by turbulence in the exhaust of turbofan aircraft engines and what might be done to mitigate it. Jet noise is an environmental problem subject to increasingly severe regulation throughout the world.

"To meet the ambitious noise-reduction goals under discussion, a greatly enhanced understanding of the basic physics is needed," says Colonius. "Very large-scale computer simulations and follow-up analyses will bring us much closer to the goal of discovering the subtle physical mechanisms responsible for the radiation of jet noise and allow us to develop methods for suppressing it."

Colonius received $987,032 in ARRA funds from the National Science Foundation.

Colin Camerer, the Robert Kirby Professor of Behavioral Economics, received his ARRA funds to explore the application of neurotechnologies to solving real-life economic problems.

"Our project, with my Caltech colleague Antonio Rangel, will explore the psychological and neural correlates of value and decision-making and their use in improving the efficiency of social allocations," says Camerer.

Camerer and his colleagues previously found that they could use information obtained through functional magnetic resonance imaging measurements to develop solutions to economic challenges.

Rangel, an associate professor of economics, has a second ARRA-funded project to analyze the neuroeconomics of self-control in dieting populations.

"Funding of this nature is critical to much of the work we do here at Caltech," adds Chameau. "And with ARRA support, dramatic discoveries may be just around the corner."

For a complete list of ARRA projects, visit: http://www.recovery.gov

# # #

About Caltech:

Caltech is recognized for its highly select student body of 900 undergraduates and 1,200 graduate students, and for its outstanding faculty. Since 1923, Caltech faculty and alumni have garnered 32 Nobel Prizes and five Crafoord Prizes.

In addition to its prestigious on-campus research programs, Caltech operates the Jet Propulsion Laboratory (JPL), the W. M. Keck Observatory in Mauna Kea, the Palomar Observatory, and the Laser Interferometer Gravitational-Wave Observatory (LIGO). Caltech is a private university in Pasadena, California. For more information, visit http://www.caltech.edu.

Jon Weiner
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Caltech Scientists Discover Fog on Titan

PASADENA, Calif.—Saturn's largest moon, Titan, looks to be the only place in the solar system—aside from our home planet, Earth—with copious quantities of liquid (largely, liquid methane and ethane) sitting on its surface. According to planetary astronomer Mike Brown of the California Institute of Technology (Caltech), Earth and Titan share yet another feature, which is inextricably linked with that surface liquid: common fog. 

The presence of fog provides the first direct evidence for the exchange of material between the surface and the atmosphere, and thus of an active hydrological cycle, which previously had only been known to exist on Earth. 

In a talk to be delivered December 18 at the American Geophysical Union's 2009 Fall Meeting in San Francisco, Brown, the Richard and Barbara Rosenberg Professor and professor of planetary astronomy, details evidence that Titan's south pole is spotted "more or less everywhere" with puddles of methane that give rise to sporadic layers of fog. (Technically, fog is just a cloud or bank of clouds that touch the ground). 

Brown and his colleagues also describe their findings in a recent paper published in The Astrophysical Journal Letters. 

The researchers made their discovery using data from the Visual and Infrared Mapping Spectrometer (VIMS) onboard the Cassini spacecraft, which has been observing Saturn's system for the past five years. 

The VIMS instrument provides "hyperspectral" imaging, covering a large swath of the visible and infrared spectrum. Brown and his colleagues—including Caltech undergraduate students Alex Smith and Clare Chen, who were working with Brown as part of a Summer Undergraduate Research Fellowship (SURF) project—searched public online archives to find all Cassini data collected over the moon's south pole from October 2006 through March 2007. They filtered the data to separate out features occurring at different depths in the atmosphere, ranging from 20 kilometers (12.4 miles) to .25 kilometers (820 feet) above the surface. Using other filters, they homed in on "bright" features caused by the scattering of light off small particles—such as the methane droplets present in clouds. 

In this way, they isolated clouds located about 750 meters (less than a half-mile) above the ground. These clouds did not extend into the higher altitudes—into the moon's troposphere, where regular clouds form. In other words, says Brown, they had found fog. 

"Fog—or clouds, or dew, or condensation in general—can form whenever air reaches about 100 percent humidity," Brown says. "There are two ways to get there. The first is obvious: add water (on Earth) or methane (on Titan) to the surrounding air. The second is much more common: make the air colder so it can hold less water (or liquid methane), and all of that excess needs to condense." 

This, he explains, is the same process that causes water droplets to form on the outside of a cool glass.

On Earth, this is the most common method of making fog, Brown says. "That fog you often see at sunrise hugging the ground is caused by ground-level air cooling overnight, to the point where it cannot hang onto its water. As the sun rises and the air heats, the fog goes away." 

Similarly, fog can form when wet air passes over cold ground; as the air cools, the water condenses. And mountain fog occurs when air gets pushed up the side of a mountain and cools, causing the water to condense. 

However, none of these mechanisms work on Titan. 

The reason is that Titan's muggy atmosphere takes a notoriously long time to cool (or warm). "If you were to turn the sun totally off, Titan's atmosphere would still take something like 100 years to cool down," Brown says. "Even the coldest parts of the surface are much too warm to ever cause fog to condense." 

Mountain fog is also out of the question, he adds. "A Titanian mountain would have to be about 15,000 feet high before the air would get cold enough to condense," he says. And yet the tallest mountains the moon could possibly carry (because of its fragile, icy crust) would be no more than 3000 feet high. 

The only possible way to make Titanian fog, then, is to add humidity to the air. And the only way to do that, Brown says, is by evaporating liquid—in this case, methane, the most common hydrocarbon on the moon, which exists in solid, liquid, and gaseous forms. 

Brown notes that evaporating methane on Titan "means it must have rained, and rain means streams and pools and erosion and geology. The presence of fog on Titan proves, for the first time, that the moon has a currently active methane hydrological cycle." 

The presence of fog also proves that the moon must be dotted with methane pools, Brown says. That's because any ground-level air, after becoming 100 percent humid and turning into fog, would instantly rise up into the atmosphere like a giant cumulus cloud. "The only way to make the fog stick around on the ground is to both add humidity and cool the air just a little," he explains. "The way to cool the air just a little is to have it in contact with something cold, like a pool of evaporating liquid methane." 

In addition to Smith and Chen, The Astrophysical Journal Letters paper, "Discovery of Fog at the South Pole of Titan," was coauthored by Máté Ádámkovics from the University of California, Berkeley. The work was funded by a grant from the National Science Foundation's Planetary Astronomy program. 

For more information about the discovery, go to Brown's blog at http://www.mikebrownsplanets.com/2009/08/fog-titan-titan-fog-and-peer-review.html.

Kathy Svitil

Caltech Scientists Explain Puzzling Lake Asymmetry on Titan

PASADENA, Calif.—Researchers at the California Institute of Technology (Caltech) suggest that the eccentricity of Saturn's orbit around the sun may be responsible for the unusually uneven distribution of lakes over the northern and southern polar regions of the planet’s largest moon, Titan. A paper describing the theory appears in the November 29th advance online edition of Nature Geoscience.

Saturn's oblong orbit around the sun exposes different parts of Titan to different amounts of sunlight, which affect the cycles of precipitation and evaporation in those areas. Similar variations in Earth's orbit also drive long-term ice-age cycles on our planet.

As revealed by Synthetic Aperture Radar (SAR) imaging data obtained by NASA's Cassini spacecraft, liquid methane and ethane lakes in Titan's northern high latitudes cover 20 times more area than lakes in the southern high latitudes. The Cassini data also show there are significantly more partially filled and now-empty lakes in the north. (In the radar data, smooth features—like the surfaces of lakes—appear as dark areas, while rougher features—such as the bottom of an empty lake—appear bright.) The asymmetry is not likely to be a statistical fluke because of the large amount of data collected by Cassini in its five years surveying Saturn and its moons.

Scientists initially considered the idea that "there is something inherently different about the northern polar region versus the south in terms of topography, such that liquid rains, drains, or infiltrates the ground more in one hemisphere," says Oded Aharonson, associate professor of planetary science at Caltech and lead author of the Nature Geoscience paper. However, Aharonson notes that there are no substantial known differences between the north and south regions to support this possibility.

Alternatively, the mechanism responsible for this regional dichotomy may be seasonal. One year on Titan lasts 29.5 Earth years. Every 15 Earth years, the seasons of Titan reverse, so that it becomes summer in one hemisphere and winter in the other. According to this seasonal variation hypothesis, methane rainfall and evaporation vary in different seasons—recently filling lakes in the north while drying lakes in the south.

The problem with this idea, Aharonson says, is that it accounts for decreases of about one meter per year in the depths of lakes in the summer hemisphere. But Titan's lakes are a few hundred meters deep on average, and wouldn't drain (or fill) in just 15 years.

In addition, seasonal variation can't account for the disparity between the hemispheres in the number of empty lakes. The north polar region has roughly three times as many dried-up lake basins as the south and seven times as many partially filled ones.

"How do you move the hole in the ground?" Aharonson asks. "The seasonal mechanism may be responsible for part of the global transport of liquid methane, but it's not the whole story."

A more plausible explanation, say Aharonson and his colleagues, is related to the eccentricity of the orbit of Saturn—and hence of Titan, its satellite—around the sun.

"We propose that, in this orbital configuration, the difference between evaporation and precipitation is not equal in opposite seasons, which means there is a net transport of methane from south to north," says Aharonson. This imbalance would lead to an accumulation of methane—and hence the formation of many more lakes—in the northern hemisphere.

This situation is only true right now, however. Over very long time scales of tens of thousands of years, Saturn's orbital parameters vary, at times causing Titan to be closer to the sun during its northern summer and farther away in southern summers, and producing a reverse in the net transport of methane. This should lead to a buildup of the hydrocarbon—and an abundance of lakes—in the southern hemisphere.

"Like Earth, Titan has tens-of-thousands-of-year variations in climate driven by orbital motions," Aharonson says. On Earth, these variations, known as Milankovitch cycles, are linked to changes in solar radiation, which affect the global redistribution of water in the form of glaciers, and are believed to be responsible for ice-age cycles.

"On Titan, there are long-term climate cycles in the global movement of methane that make lakes and carve lake basins. In both cases we find a record of the process embedded in the geology," he adds.

"We may have found an example of long-term climate change, analogous to Milankovitch climate cycles on Earth, on another object in the solar system," he says.

The paper, "Titan's Asymmetric Lake Distribution and its Potential Astronomical Evolution," was coauthored by Caltech graduate student Alexander G. Hayes; Jonathan I. Lunine of the Lunar and Planetary Laboratory; Ralph D. Lorenz of the Applied Physics Laboratory at the Johns Hopkins University; Michael D. Allison of the NASA Goddard Institute for Space Studies; and Charles Elachi, director of the Jet Propulsion Laboratory. The work was partially funded by the Cassini Project.

For more information, visit http://www.gps.caltech.edu/~oa/titanlakes.shtml.


Kathy Svitil

Caltech Researchers Reveal Unexpected Sources of Nitrogen Fixation

High-resolution chemical imaging of deep-sea microorganisms may help explain lingering nitrogen mystery

Pasadena, Calif.—Researchers at the California Institute of Technology (Caltech) have identified an unexpected metabolic ability within a symbiotic community of microorganisms that may help solve a lingering mystery about the world's nitrogen-cycling budget. A paper about their work appears in the October 16 issue of the journal Science.

The element nitrogen is a critical part of amino acids, the building blocks of proteins, and therefore essential to all life. Although nitrogen is plentiful on Earth—it comprises 78 percent of the atmosphere, by volume—the element is usually found strongly bonded to itself, in the form of the diatomic gas N2. To be biologically useful, a nitrogen atom must be released from this coupling and converted to a reduced, or "fixed," state; reduced nitrogen atoms gain an electron, which makes them chemically reactive.

Although lightning, combustion, and other nonbiological processes can reduce nitrogen, far more is generated by nitrogen-fixing microorganisms such as bacteria—in particular, photosynthetic cyanobacteria. These organisms produce the bulk of the nitrogen available to living things in the ocean. 

Still, when researchers add up all of the known sources of fixed nitrogen (biological and otherwise) in the global nitrogen cycle and compare it to the sinks—where nitrogen is taken up for growth and energy—they come up short. It appears that more nitrogen is being used than is being made. The apparent nitrogen budget, in effect, does not balance. This discrepancy had led scientists to question whether the nitrogen cycle is truly out of balance, or whether the known inventories of sources and sinks are misleadingly incomplete. 

Victoria J. Orphan, an assistant professor of geobiology at Caltech, along with graduate student Anne E. Dekas and postdoctoral research scholar Rachel S. Poretsky, suggest the answer is, at least in part, an incomplete catalog of the sources of fixed nitrogen. 

The team studied ocean sediment samples obtained in methane cold seeps located at a depth of about 1,800 feet. The area, known as the Eel River Basin, is located approximately 20 miles off the coast of the northern California town of Eureka, on a continental margin in a region supporting high levels of natural methane seepage at the seabed. 

In the laboratory, the researchers examined the methane-rich sediment and the tiny microbial conglomerations that live within. These spherical cell conglomerates, averaging about 500 cells each, consist of two types of anaerobic microorganisms living in a unique symbiotic relationship fueled by methane. The first microorganism is a bacterium that reduces the chemical sulfate into sulfide (via a process that produces the rotten-egg odor of salt marshes and mud flats) to generate energy. The second is a methane-oxidizing archaeon (the archaea are a group of nonbacterial single-celled microorganisms). Working together, these two symbionts are responsible for consuming the majority of the naturally released methane in the deep sea. 

Although these symbiotic associations themselves are not new—these conglomerations were discovered about a decade ago and are found on continental margins worldwide—the Caltech scientists discovered something unexpected: the methane-consuming archaea were actively fixing nitrogen, and sharing it with their bacterial neighbors. 

"This is the first time that nitrogen fixation has been documented within methane-oxidizing archaea," Dekas says.

Interestingly, although these organisms have a nitrogen-poor diet of methane gas, they live in an environment that contains reduced nitrogen—in the form of ammonium and other chemicals—which means they shouldn't need to create their own. "It's possible that they do need to because they are living in a crowded community—a tightly packed ball—that prevents some organisms from having access to the nitrogen," she says. Another possibility is that these environments do not have as much biologically available reduced nitrogen as had been thought. 

To determine that the archaea were indeed fixing nitrogen, the researchers first incubated the archaeal-bacterial assemblages with a dinitrogen gas, N2, that was composed of two atoms of nitrogen-15. Nitrogen-15 is a nonradioactive isotope of nitrogen that contains one more neutron than regular nitrogen (nitrogen-14) and can be used as a tracer for the incorporation of the element. 

The researchers then used a technique called fluorescent in situ hybridization (FISH) to stain the two types of organisms in the sediment, and analyzed these cells for their nitrogen-15 content using a state-of-the-art instrument called a nanometer secondary ion mass spectrometer, or nanoSIMS. The nanoSIMS, which is housed at the Caltech Center for Microanalysis, is capable of collecting chemical and isotopic data at a spatial scale of 50 to 100 nanometers, or around five to 10 times smaller than the size of a single microbial cell. 

Both the archaea and, to a lesser extent, their bacterial neighbors had incorporated the nitrogen-15, which could have happened only if the N2 had been fixed by the archaea—and then shared. 

"The high spatial resolution of the nanoSIMS instrument—which produces a focused beam of ions that is smaller than a single cell—allowed us to directly pinpoint which of the symbiotic cells in the consortia had assimilated the nitrogen-15–labeled N2 into their biomass," Orphan notes.

The fixation process, say the scientists, is painfully slow; the organisms themselves have ultraslow growth rates, doubling once every three to six months. "But they are passing on some nitrogen to their neighbors, which means they are producing more than they need," despite the energy cost of doing so, Dekas says. "We don't know what benefit the archaeal organisms get from sharing it, but we do know they need the bacterial symbiont to stay alive," she adds.

"Previously, assumptions about when and where nitrogen fixation takes place made it seem unlikely that nitrogen fixation would occur in this environment, or within such energetically starved organisms," Dekas says. "These results suggest that these assumptions may need to be reevaluated, and that there could be more nitrogen-fixing organisms in other unexpected environments. Together, these previously overlooked sources of nitrogen may be an important component in the marine nitrogen inventory."

The research in the paper, "Deep-Sea Archaea Fix and Share Nitrogen in Methane-Consuming Microbial Consortia," was supported by the National Science Foundation and the Gordon and Betty Moore Foundation.

Kathy Svitil

Caltech Scientists Discover Storms in the Tropics of Titan

Pasadena, Calif.—For all its similarities to Earth—clouds that pour rain (albeit liquid methane not liquid water) onto the surface producing lakes and rivers, vast dune fields in desert-like regions, plus a smoggy orange atmosphere that looks like Los Angeles's during fire season—Saturn's largest moon, Titan, is generally "a very bland place, weatherwise," says Mike Brown of the California Institute of Technology (Caltech).

"We can watch for years and see almost nothing happen. This is bad news for people trying to understand Titan's meteorological cycle, as not only do things happen infrequently, but we tend to miss them when they DO happen, because nobody wants to waste time on big telescopes—which you need to study where the clouds are and what is happening to them—looking at things that don't happen," explains Brown, the Richard and Barbara Rosenberg Professor of Planetary Astronomy.

However, just because weather occurs "infrequently" doesn't mean it never occurs, nor does it mean that astronomers, in the right place at the right time, can't catch it in the act.

That's just what Emily Schaller—then a graduate student of Brown's—and colleagues accomplished when they observed, in April 2008, a large system of storm clouds appear in the apparently dry mid-latitudes and then spread in a southeastward direction across the moon. Eventually, the storm generated a number of bright but transient clouds over Titan's tropical latitudes, a region where clouds had never been seen—and, indeed, where it was thought they were extremely unlikely to form.

Schaller, now a Hubble Postdoctoral Fellow at the University of Arizona, Brown, and their colleages; Henry Roe, a former Caltech postdoctoral scholar in Brown’s group, now at the Lowell Observatory in Flagstaff; and Tapio Schneider, a professor of environmental science and engineering at Caltech, describe their work, and its implications for climate on Titan, in the August 13 issue of Nature.

"A couple of years ago, we set up a highly efficient system on a smaller telescope to figure out when to use the biggest telescopes," Brown says. The first telescope, NASA's Infrared Telescope Facility, on Mauna Kea, takes a spectrum of Titan almost every single night. "From that we can't tell much, but we can say 'no clouds,' 'a few clouds,' or, if we get lucky 'monster clouds,'" he explains.

Schaller explains, "The period during which I was collecting data for my thesis, sadly, corresponded entirely to an extended period of essentially no clouds, so we never really got to show the full power of the combined telescopes. But then, after finishing and turning in my thesis, I walked back across campus to my office to look at the data from the previous night to find that Titan suddenly had the biggest clouds ever. I like to think it was Titan’s graduation gift to me. Or perhaps a bad joke."

A major storm erupts in the desert tropics of Titan.
Credit: Emily Schaller et al./Gemini Observatory

The day after the telescope's big find (and Schaller’s thesis submission), Schaller, Brown, and Roe began tracking the clouds with the large Gemini telescope on Mauna Kea and watched this system evolve for a month. "And what a cool show it was," Brown says.

"The first cloud was seen near the tropics and was caused by a still-mysterious process, but it behaved almost like an explosion in the atmosphere, setting off waves that traveled around the planet, triggering their own clouds. Within days a huge cloud system had covered the south pole, and sporadic clouds were seen all the way up to the equator."

Schneider, an expert on atmospheric circulations, was instrumental in helping to sort out the complicated chain of events that followed the initial outburst of cloud activity.

"The monthlong event has many important implications for understanding the hydrological cycle on Titan," says Brown, "but one of the reasons I am most excited about it is that it shows clouds near the equator—where the [European Space Agency's] Huygens probe landed—for the first time. For a while now, people have speculated that the equatorial regions are simply too dry to ever have significant clouds."

And yet, the images snapped by the Huygens probe in January 2005, as it descended through Titan's soupy atmosphere and toward the surface, revealed small-scale channels and streams, which looked just like features created by fluids—by water, here on Earth, and on Titan, probably by liquid methane.

Experts had speculated for years on how there could be streams and channels in a region with no rain. The new results suggest those speculations may prove unneccessary. "No one considered how storms in one location can trigger them in many other locations," says Brown.

The paper, "Storms in the tropics of Titan," appears in the August 13 issue of Nature. The research was supported by a Hubble Postdoctoral Fellowship (to Schaller), the NASA Planetary Astronomy Program, and a Planetary Astronomy Grant from the National Science Foundation.

For more information about the discovery, go to http://www.mikebrownsplanets.com.

View a video of astronomers Henry Roe and Mike Brown discussing recently announced observations of storm clouds in the tropics of Titan.

Kathy Svitil

Caltech Researchers Show How Organic Carbon Compounds Emitted by Trees Affect Air Quality

Research provides first-ever glimpse of role of epoxides in atmospheric chemistry

PASADENA, Calif.—A previously unrecognized player in the process by which gases produced by trees and other plants become aerosols—microscopically small particles in the atmosphere—has been discovered by a research team led by scientists at the California Institute of Technology (Caltech).

Their research on the creation and effects of these chemicals, called epoxides, is being featured in this week's issue of the journal Science.

Paul Wennberg, the R. Stanton Avery Professor of Atmospheric Chemistry and Environmental Science and Engineering and director of the Ronald and Maxine Linde Center for Global Environmental Science at Caltech, and John Seinfeld, the Louis E. Nohl Professor and professor of chemical engineering, have been studying the role of biogenic emissions—organic carbon compounds given off by plants and trees—in the atmospheric chemical reactions that result in the creation of aerosols.

"If you mix emissions from the city with emissions from plants, they interact to alter the chemistry of the atmosphere," Wennberg notes.

While there's been plenty of attention paid to the effect of emissions from cars and manufacturing, less is understood about what happens to biogenic emissions, especially in places where there are relatively few man-made emissions. That situation is the focus of the research that led to this Science paper. "What we're interested in," Wennberg explains, "is what happens to the chemicals produced by trees once they are emitted into the atmosphere."

In these studies, the research team focused on a chemical called isoprene, which is given off by many deciduous trees. "The king emitters are oaks," Wennberg says. "And the isoprene they emit is one of the reasons that the Smoky Mountains appear smoky."

Isoprene is no minor player in atmospheric chemistry, Wennberg notes. "There is much more isoprene emitted to the atmosphere than all of the gases—gasoline, industrial chemicals—emitted by human activities, with the important exceptions of methane and carbon dioxide," he says. "And isoprene only comes from plants. They make hundreds of millions of tons of this chemical . . . for reasons that we still do not fully understand."

"Much of the emission of isoprene occurs where anthropogenic emissions are limited," adds Caltech graduate student Fabien Paulot, the paper's first author. "The chemistry is very poorly understood."

Once released into the atmosphere, isoprene gets "oxidized or chewed on" by free-radical oxidants such as OH, explains Wennberg. It is this chemistry that is the focus of this new study. In particular, the research was initiated to understand how the oxidation of isoprene can lead to formation of atmospheric particulate matter, so-called secondary organic aerosol. "A small fraction of the isoprene becomes secondary organic aerosol," Seinfeld notes, "but because isoprene emissions are so large, even this small fraction is important."

Up until now, the chemical pathways from isoprene to aerosol were not known. Wennberg, Seinfeld, and their colleagues discovered that this aerosol likely forms from chemicals known as epoxides.

The name is apt. "These epoxides are nature's glue," says Wennberg. And, much like the epoxy you buy in a hardware store—which requires the addition of an acid for the compound to turn into glue—the epoxides found in the atmosphere also need an acidic kick in order to become sticky.

"When these epoxides bump into particles that are acidic, they make glue," Wennberg explains. "The epoxides precipitate out of the atmosphere and stick to the particles, growing them and resulting in lowered visibility in the atmosphere." Because the acidity of the aerosols is generally higher in the presence of anthropogenic activities, the efficiency of converting the epoxides to aerosol is likely higher in polluted environments, illustrating yet another complex interaction between emissions from the biosphere and from humans. 

"Particles in the atmosphere have been shown to impact human health, as they are small enough to penetrate deep into the lungs of people. Also, aerosols impact Earth's climate through the scattering and absorption of solar radiation and through serving as the nuclei on which clouds form. So it is important to know where particles come from," notes Seinfeld.

The research team was able to make this scientific leap forward thanks to their development of a new type of chemical ionization mass spectrometry (CIMS), led by coauthor and Caltech graduate student John Crounse. "These new CIMS methods open up a very wide range of possibilities for the study of new sets of compounds that scientists have been largely unable to measure previously, mainly because they decompose when analyzed with traditional techniques."

In general, molecules identified and quantified using mass spectroscopy must first be converted to charged ions. They are then directed into an electric field, where the ions are sorted by mass. The problem with traditional ionization techniques is that delicate molecules, such as those produced in the oxidation of isoprene, generally fragment during the ionization process, making their identification difficult or impossible. "This new method was originally developed in order to allow scientists to make atmospheric measurements from airplanes. It is able to ionize gases, even fragile peroxide compounds, while still preserving information about the size or mass of the original molecule," says Wennberg.

That makes determining the individual gases in a complex mixture much easier—especially when, as it turned out, you're looking at a chemical you weren't expecting to find.

Wennberg and colleagues also used oxygen isotopes—oxygen atoms with different numbers of neutrons in their nucleus, and thus different masses—to gain insight into the chemical mechanism yielding epoxides. Epoxides have remained unindentified so far because they have the same mass as another chemical that had been anticipated to form in isoprene oxidation, peroxide. "The oxygen isotopes separated the peroxides from epoxides and further showed that as the epoxides form, OH is recycled to the atmosphere," comments Paulot. "Since OH is the atmosphere detergent, cleaning the atmosphere of many chemicals, the recycling has important implications for the overall oxidizing capacity of the atmosphere."

The identification of a major photochemical pathway to formation of epoxides helps to explain just how tree emissions of organic carbon compounds influence the air in both city and rural settings. While trees aren't exactly the "killers" that Ronald Reagan was once so famously derided for calling them, their isoprene emission levels can—and often probably should—"be a part of the criteria we use when buying and planting trees in a polluted urban setting," notes Wennberg. In fact, he points out, the South Coast Air Quality Management District in Southern California already does this with its list of "approved" trees that don't emit large amounts of organic carbon compounds into the atmosphere.

In addition to Wennberg, Paulot, Crounse, and Seinfeld, other authors on the Science paper, "Unexpected epoxide formation in the gas-phase photooxidation of isoprene," are Henrik Kjaergaard of the University of Otago in New Zealand and the University of Copenhagen in Denmark; former Caltech postdoctoral scholar Andreas Kürten, now at Goethe University in Germany; and Caltech postdoctoral scholar Jason St. Clair.

Purchase of the mass spectrometer used in this study was funded by a Major Research Instrumentation Award from the National Science Foundation. Additional support for the work described in the Science article came from Caltech trustee William Davidow and by grants from the Office of Science, the U.S. Department of Energy, the U.S. Environmental Protection Agency, the Royal Society of New Zealand, and NASA.

Lori Oliwenstein
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Caltech, JPL Scientists Say that Microbial Mats Built 3.4-Billion-Year-Old Stromatolites

Findings may provide insight into the origins of life on Earth, and even the search for life on Mars

PASADENA, Calif.-Stromatolites are dome- or column-like sedimentary rock structures that are formed in shallow water, layer by layer, over long periods of geologic time. Now, researchers from the California Institute of Technology (Caltech) and the Jet Propulsion Laboratory (JPL) have provided evidence that some of the most ancient stromatolites on our planet were built with the help of communities of equally ancient microorganisms, a finding that "adds unexpected depth to our understanding of the earliest record of life on Earth," notes JPL astrobiologist Abigail Allwood, a visitor in geology at Caltech.

Their research, published in a recent issue of the Proceedings of the National Academy of Sciences (PNAS), might also provide a new avenue for exploration in the search for signs of life on Mars.

"Stromatolites grow by accreting sediment in shallow water," says John Grotzinger, the Fletcher Jones Professor of Geology at Caltech. "They get molded into these wave forms and, over time, the waves turn into discrete columns that propagate upward, like little knobs sticking up."

Geologists have long known that the large majority of the relatively young stromatolites they study-those half a billion years old or so-have a biological origin; they're formed with the help of layers of microbes that grow in a thin film on the seafloor.

How? The microbes' surface is coated in a mucilaginous substance to which sediment particles rolling past get stuck. "It has a strong flypaper effect," says Grotzinger. In addition, the microbes sprout a tangle of filaments that almost seem to grab the particles as they move along.

"The end result," says Grotzinger, "is that wherever the mat is, sediment gets trapped."

Thus it has become accepted that a dark band in a young stromatolite is indicative of organic material, he adds. "It's matter left behind where there once was a mat."

But when you look back 3.45 billion years, to the early Archean period of geologic history, things aren't quite so simple.

"Because stromatolites from this period of time have been around longer, more geologic processing has happened," Grotzinger says. Pushed deeper toward the center of Earth as time went by, these stromatolites were exposed to increasing, unrelenting heat. This is a problem when it comes to examining the stromatolites' potential biological beginnings, he explains, because heat degrades organic matter. "The hydrocarbons are driven off," he says. "What's left behind is a residue of nothing but carbon."

This is why there has been an ongoing debate among geologists as to whether or not the carbon found in these ancient rocks is diagnostic of life or not.

Proving the existence of life in younger rocks is fairly simple-all you have to do is extract the organic matter, and show that it came from the microorganisms. But there's no such cut-and-dried method for analyzing the older stromatolites. "When the rocks are old and have been heated up and beaten up," says Grotzinger, "all you have to look at is their texture and morphology."

Which is exactly what Allwood and Grotzinger did with samples gathered at the Strelley Pool stromatolite formation in Western Australia. The samples, says Grotzinger, were "incredibly well preserved." Dark lines of what was potentially organic matter were "clearly associated with the lamination, just like we see in younger rocks. That sort of relationship would be hard to explain without a biological mechanism."

A rare paelosurface view of what the conical stromatolites would have looked like if you snorkeled in the shallows of the reef.
Credit: Abigail Allwood

"We already knew from our earlier work that we had an assemblage of stromatolites that was most plausibly interpreted as a microbial reef built by Early Archean microorganisms," adds Allwood, "but direct evidence of actual microorganisms was lacking in these ancient, altered rocks. There were no microfossils, no organic material, not even any of the microtextural hallmarks typically associated with microbially mediated sedimentary rocks."

So Allwood set about trying to find other types of evidence to test the biological hypothesis. To do so, she looked at what she calls the "microscale textures and fabrics in the rocks, patterns of textural variation through the stromatolites and-importantly-organic layers that looked like actual fossilized organic remnants of microbial mats within the stromatolites."

What she saw were "discrete, matlike layers of organic material that contoured the stromatolites from edge to edge, following steep slopes and continuing along low areas without thickening." She also found pieces of microbial mat incorporated into storm deposits, which disproved the idea that the organic material had been introduced into the rock more recently, rather than being laid down with the original sediment. "In addition," Allwood notes, "Raman spectroscopy showed that the organics had been 'cooked' to the same burial temperature as the host rock, again indicating the organics are not young contaminants."

Allwood says she, Grotzinger, and their team have collected enough evidence that it's no longer any "great leap" to accept these stromatolites as biological in origin. "I think the more we dig at these stromatolites, the more evidence we'll find of Early Archean life and the nature of Earth's early ecosystems," she says.

That's no small feat, since it's been difficult to prove that life existed at all that far back in the geologic record. "Recently there has been increasing but still indirect evidence suggesting life existed back then, but direct evidence of microorganisms, at the microscale, remained elusive due to poor preservation of the rocks," Allwood notes. "I think most people probably thought that these Early Archean rocks were too poorly preserved to yield such information."

The implications of the findings don't stop at life on Earth.

"One of my motivations for understanding stromatolites," Allwood says, "is the knowledge that if microbial communities once flourished on Mars, of all the traces they might leave in the rock record for us to discover, stromatolite and microbial reefs are arguably the most easily preserved and readily detected. Moreover, they're particularly likely to form in evaporative, mineral-precipitating settings such as those that have been identified on Mars. But to be able to interpret stromatolitic structures, we need a much more detailed understanding of how they form."

The other authors on the paper, "Controls on development and diversity of Early Archean stromatolites," are Mark Anderson, Max Coleman, and Isik Kanik from JPL; Andrew Knoll, the Fisher Professor of Natural History at Harvard University; and Ian Burch from the University of New South Wales in Australia.

The research described was supported in part by the Agouron Institute; Allwood was supported by the National Aeronautics and Space Administration Postdoctoral Program. 

Lori Oliwenstein

Unique Sky Survey Brings New Objects into Focus

Partnership involves Caltech's Palomar Observatory and other world leaders in astronomy

San Diego, Calif.–An innovative sky survey has begun returning images that will be used to detect unprecedented numbers of powerful cosmic explosions–called supernovae–in distant galaxies, and variable brightness stars in our own Milky Way. The survey also may soon reveal new classes of astronomical objects.

All of these discoveries will stem from the Palomar Transient Factory (PTF) survey, which combines, in a new way, the power of a wide-field telescope, a high-resolution camera, and high-performance networking and computing, with rapid follow-up by telescopes around the globe, to open windows of discovery for astronomers. The survey has already found 40 supernovae and is gearing up to switch to a robotic mode of operation that will allow objects to be discovered nightly without the need for human intervention.

The Palomar Transient Factory is a collaboration of scientists and engineers from institutions around the world, including the California Institute of Technology (Caltech); the University of California, Berkeley, and the Lawrence Berkeley National Laboratory (LBNL); Columbia University; Las Cumbres Observatory; the Weizmann Institute of Science in Israel; and Oxford University.

During the PTF process, the automated wide-angle 48-inch Samuel Oschin Telescope at Caltech's Palomar Observatory scans the skies using a 100-megapixel camera.

The flood of images, more than 100 gigabytes every night, is then beamed off of the mountain via the High Performance Wireless Research and Education Network–a high-speed microwave data connection to the Internet–and then to the LBNL's National Energy Scientific Computing Center. There, computers analyze the data and compare it to images previously obtained at Palomar. More computers using a type of artificial intelligence software sift through the results to identify the most interesting "transient" sources–those that vary in brightness or position.

Within minutes of a candidate transient's discovery, the system sends its coordinates and instructions for follow-up observations using the Palomar 60-inch telescope and other instruments.

Soon all of the steps in the process will be completely automated, including decisions about which transients merit a second look. When follow-up observations indicate that candidate transient detections show promise, a prioritized list of candidates is brought to the attention of astronomers from the PTF member institutions. Finally, an astronomer becomes personally involved, by performing detailed observations using telescopes such as Palomar's 200-inch Hale Telescope, a Keck Telescope in Hawaii, or other partner telescopes around the world.

The PTF is designed to search for a wide variety of transient sources with characteristic timescales ranging from minutes to months, giving astronomers one of their deepest and most comprehensive explorations of the universe in the time domain.

"By looking at the sky in a new way, we are ushering in a new era of astronomical discovery," says PTF principal investigator Shrinivas Kulkarni, MacArthur Professor of Astronomy and Planetary Science at Caltech and director of the Caltech Optical Observatories. "Nimble automated telescopes and impressive computing power make this possible."

"No one has looked on these timescales with this sensitivity before. It's entirely possible that we will find new astronomical objects never before seen by humans," says Nicholas Law of Caltech, the project scientist for PTF.

Because it looks for anything changing in the sky, the PTF survey covers a vast variety of different astronomical targets. The wide range of the survey extends across the entire universe. Astronomers expect to discover everything from stars exploding millions of light-years away to near-Earth asteroids that could someday impact our planet.

The 48-inch Samuel Oschin Telescope at Caltech's Palomar Observatory.

Much of the survey's time is spent searching for so-called Type Ia supernovae. These supernovae, formed from the explosion of a class of dead star known as a white dwarf, are very useful to astronomers because they can help determine the distance to galaxies located across the universe. Those distances allow astronomers to probe the origin, structure, and even the ultimate fate of the universe.

By operating more rapidly than previous surveys, PTF will also detect objects of a completely different nature, such as pulsating stars, different types of stellar explosions, and possibly planets around other stars.

PTF's innovative survey techniques also have raised astronomers' expectations of finding new, unexpected, astronomical objects.

The PTF already has found many new cosmic explosions, including 32 Type Ia supernovae, eight Type II supernovae, and four cataclysmic variable stars. Intriguingly, PTF also has found several objects with characteristics that do not exactly match any other objects that have been seen before. PTF astronomers are eagerly watching these objects to see how they change, and to determine what they might be.

The quantity and quality of incoming data have astonished astronomers working in the field. On one recent night, PTF patrolled a section of the sky about five times the size of the Big Dipper–and found 11 new objects. "Today I found five new supernovae before breakfast," says Caltech's Robert Quimby, a postdoctoral scholar and leader of the PTF software team. "In the previous survey I worked on, I found 30 in two years."

Images and more information on the PTF survey are available on the PTF website at http://www.astro.caltech.edu/ptf/.

# # #

About Palomar Transient Factory:

PTF is a five-year international collaboration of scientists and engineers from the California Institute of Technology, the National Energy Research Scientific Computing Center at Lawrence Berkeley National Laboratory, the Infrared Processing and Analysis Center, University of California at Berkeley, Las Cumbres Observatory Global Telescope Network, the University of Oxford, Columbia University, the Weizmann Institute of Science in Israel, and the Pennsylvania State University. The High Performance Wireless Research and Education Network (HPWREN) provides Palomar Observatory’s high-speed data connection.


Palomar Observatory:
Scott Kardel
(760) 742-2111

Jon Weiner
(626) 395-3226
Lawrence Berkeley National Lab:
Jon Bashor

Linda Vu

Jon Weiner


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