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


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. 


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



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












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







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About Palomar Transient Factory:



Palomar Observatory:
Scott Kardel
(760) 742-2111

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

Linda Vu

Jon Weiner

Caltech Scientists Predict Greater Longevity for Planets with Life

Billion-year life extension for Earth also doubles the odds that advanced life will be found elsewhere in the universe

PASADENA, Calif.- Roughly a billion years from now, the ever-increasing radiation from the sun will have heated Earth into uninhabitability; the carbon dioxide in the atmosphere that serves as food for plant life will disappear, pulled out by the weathering of rocks; the oceans will evaporate; and all living things will disappear.

Or maybe not quite so soon, say researchers from the California Institute of Technology (Caltech), who have come up with a mechanism that doubles the future lifespan of the biosphere—while also increasing the chance that advanced life will be found elsewhere in the universe.


Earth maintains its surface temperatures through the greenhouse effect. Although the planet's greenhouse gases—chiefly water vapor, carbon dioxide, and methane-have become the villain in global warming scenarios, they're crucial for a habitable world, because they act as an insulating blanket in the atmosphere that absorbs and radiates thermal radiation, keeping the surface comfortably warm.














The work described in the paper, "Atmospheric Pressure as a Natural Regulator of the Climate of a Terrestrial Planet with Biosphere," was funded by NASA and the Virtual Planetary Laboratory at Caltech.

Kathy Svitil












Lori Oliwenstein

Caltech Scientists Lead Deep-Sea Discovery Voyage

Research mission uncovers several new species and thousands of fossilized coral samples.

PASADENA, Calif.--Scientists from the California Institute of Technology (Caltech) and an international team of collaborators have returned from a month-long deep-sea voyage to a marine reserve near Tasmania, Australia, that not only netted coral-reef samples likely to provide insight into the impact of climate change on the world's oceans, but also brought to light at least three never-before-seen species of sea life.

"It was truly one of those transcendent moments," says Caltech's Jess Adkins of the descents made by the remotely operated submersible Jason. Adkins was the cruise's lead scientist and is an associate professor of geochemistry and global environmental science at Caltech. "We were flying--literally flying--over these deep-sea structures that look like English gardens, but are actually filled with all of these carnivorous, Seuss-like creatures that no one else has ever seen."

The voyage on the research vessel RV Thompson explored the Tasman Fracture Commonwealth Marine Reserve, southwest of Tasmania. The voyage was funded by the National Science Foundation and was the second of two cruises taken by the team, which included researchers from the United States--including scientists from Caltech and the Woods Hole Oceanographic Institution in Massachusetts, which owns and operates the submersible Jason--and Australia's Commonwealth Scientific and Industrial Research Organisation (CSIRO). The first of those voyages was taken in January 2008, with this most recent one spanning 33 days from mid-December 2008 through mid-January 2009.

Up until now, the area of the reef the scientists were exploring--called the Tasman Fracture Zone--had only been explored to a depth of 1,800 meters (more than 5,900 feet). Using Jason, the researchers on this trip were able to reach as far down as 4,000 meters (well over 13,000 feet).

"We set out to search for life deeper than any previous voyage in Australian waters," notes scientist Ron Thresher from CSIRO's Climate Adaptation and Wealth from Oceans Flagships.

The cruise had two main goals, says Adkins. One was to try to use deep-sea corals to reconstruct the paleoclimate--with an emphasis on the changes in climate over the last 100,000 years--and to understand the fluctuations in CO2 found in the ice-core records. Investigators also wanted to look at changes in the ocean over a much smaller slice of time--the past few hundred to one thousand or so years. "We want to see what's happened to the corals over the Industrial Revolution timescale," says Adkins. "And we want to see if we can document those changes."

The second goal? "Simply to document what's down there," says Adkins.

"In one sense, the deep ocean is less explored than Mars," he adds. "So every time you go to look down there you see new things, magical things."

Among the "magical things" seen on this trip were

  • a new species of carnivorous sea squirt that "looks and behaves like a Venus fly trap," says Adkins;
  • new species of barnacles (some of which Adkins says may even belong to an entirely new family); and
  • a new species of sea anemone that Adkins calls "the bane of our existence," because it looks just like the coral they were trying to collect.

The sea anemone was particularly vexing for the researchers, because they were hoping to find deep-sea (or abyssal) samples of the fossilized coral, but were unable to find the coral much below 2,400 meters (nearly 7,800 feet). The look-alike sea anemone, on the other hand, kept popping up all over the place on the deep-sea floor, raising--and then dashing--the scientists' hopes.

This carnivorous sea squirt was one of the new species seen during the voyage of the RV Thompson.
Credit: Advanced Imaging and Visualization Laboratory, WHOI/Jess Adkins, Caltech

"Not being able to find the coral down deeper was our single biggest disappointment on the trip," says Adkins.

Still, the 10,000-plus samples collected will help the researchers begin their work of deciphering just what has been happening to the ocean throughout the centuries of climate change, and during and between glacial cycles. First up: dating the fossils collected on this trip in order to determine which slice of history they came from.

"The deep ocean is part and parcel of these rapid climate changes," says Adkins. "These corals will be our window into what their impact is on climate, and how they have that impact. The info is there; now we just have to unpack it."

Further funding for the research came from CSIRO, the Commonwealth Environmental Research Facilities' Marine Biodiversity Hub, and the Australian Department of the Environment, Water, Heritage and the Arts.

Lori Oliwenstein

Caltech Researchers Find Ancient Climate Cycles Recorded in Mars Rocks

PASADENA, Calif.-- Researchers at the California Institute of Technology (Caltech) and their colleagues have found evidence of ancient climate change on Mars caused by regular variation in the planet's tilt, or obliquity. On Earth, similar "astronomical forcing" of climate drives ice-age cycles.

Using stereo topographic maps obtained by processing data from the high-resolution camera onboard NASA's Mars Reconnaissance Orbiter, the Caltech scientists, led by graduate student Kevin Lewis and Oded Aharonson, associate professor of planetary science, along with John Grotzinger, the Fletcher Jones Professor of Geology, identified and measured layered rock outcrops within four craters in the planet's Arabia Terra region. The layering in different outcrops occurs at scales ranging from a few meters to tens of meters, but at each location the layers all have similar thicknesses and exhibit similar features.

Based on a pattern of layers within layers measured at one location, known as Becquerel crater, the scientists propose that each layer was formed over a period of about 100,000 years and that these layers were produced by the same cyclical climate changes.

In addition, every 10 layers were bundled together into larger units, which were laid down over an approximately one-million-year period; in the Becquerel crater, the 10-layer pattern is repeated at least 10 times. This one-million-year cycle corresponds to a known pattern of change in Mars's obliquity caused by the dynamics of the solar system.

"Due to the scale of the layers, small variations in Mars's orbit are the best candidate for the implied climate changes. These are the very same changes that have been shown to set the pacing of ice ages on the Earth and can also lead to cyclic layering of sediments," says Lewis, the first author of a paper about the work published in this week's issue of Science.

Sequences of cyclic sedimentary rock layers exposed in an unnamed crater in Arabia Terra, Mars.
Credit: Topograpy, Caltech; HiRISE Images, NASA/JPL/University of Arizona

The tilt of Earth on its axis varies between 22.1 and 24.5 degrees over a 41,000-year period. The tilt itself is responsible for seasonal variation in climate, because the portion of the Earth that is tipped toward the sun--and that receives more sunlight hours during a day--gradually changes throughout the year. During phases of lower obliquity, polar regions are less subject to seasonal variations, leading to periods of glaciation.

Mars's tilt varies by tens of degrees over a 100,000-year cycle, producing even more dramatic variation. When the obliquity is low, the poles are the coldest places on the planet, while the sun is located near the equator all the time. This could cause volatiles in the atmosphere, like water and carbon dioxide, to migrate poleward, where they'd be locked up as ice.

When the obliquity is higher, the poles get relatively more sunlight, and those materials would migrate away. "That affects the volatiles budget. If you move carbon dioxide away from the poles, the atmospheric pressure would increase, which may cause a difference in the ability of winds to transport and deposit sand," Aharonson says. This is one effect that could change the rate of deposition of layers such as those seen by the researchers in the four craters.


"The whole climate system would be different," Aharonson says.

However, such large changes in climate would influence a variety of geologic processes on the surface. While the researchers cannot tie the formation of the rhythmic bedding on Mars to any particular geologic process, "a strength of the paper is that we can draw conclusions without having to specify the precise depositional process," Aharonson says.

"This study gives us a hint of how the ancient climate of Mars operated, and shows a much more predictable and regular environment than you would guess from other geologic features that indicate catastrophic floods, volcanic eruptions, and impact events," Lewis adds. "More work will be required to understand the full extent of the information contained within these natural geologic archives," he says.


The paper, "Quasi-Periodic Bedding in the Sedimentary Rock Record of Mars," will be published in the December 5 issue of Science. The work was supported by NASA's Mars Data Analysis Program and the NASA Earth and Space Science Fellowship program.

Kathy Svitil

Potential for Large Earthquake Off the Coast of Sumatra Remains Large, Says Caltech-Led Team of Scientists





The devastating magnitude 9.2 earthquake that occurred off the western coast of Sumatra on December 26, 2004-the earthquake that spawned a lethal tsunami throughout the Indian Ocean-took place in a subduction zone, an area where one tectonic plate dips under another, forming a quake-prone region.










Other authors on the paper include Anthony Sladen, Aron J. Meltzner, John Galetzka, Jeff Genrich, and Don V. Helmberger from Caltech; Danny H. Natawidjaja from the Indonesian Institute of Science (LIPI); Peng Fang and Yehuda Bock from the Scripps Institution of Oceanography in La Jolla; Zhenhong Li from the University of Glasgow in Scotland; Mohamed Chlieh from the Université de Nice Sophia-Antipolis in France; Eric J. Fielding from the Jet Propulsion Laboratory; and Chen Ji from the University of California, Santa Barbara. The work detailed in the paper, "Partial rupture of a locked patch of the Sumatra megathrust during the 2007 earthquake sequence," was supported by funding from the National Science Foundation and the Gordon and Betty Moore Foundation.

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Lori Oliwenstein
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Caltech Geobiologists Discover Unique "Magnetic Death Star" Fossil

Fossil and other new forms date to ancient period of global warming














Kathy Svitil

Caltech Scientists Offer New Explanation for Monsoon Development

PASADENA, Calif.--Geoscientists at the California Institute of Technology have come up with a new explanation for the formation of monsoons, proposing an overhaul of a theory about the cause of the seasonal pattern of heavy winds and rainfall that essentially had held firm for more than 300 years.

The traditional idea of monsoon formation was developed in 1686 by English astronomer and mathematician Edmond Halley, namesake of Halley's Comet. In Halley's model, monsoons are viewed as giant sea-breeze circulations, driven by the differences in heat capacities between land and ocean surfaces that, upon heating by sunlight, lead to temperature differences between warmer land and cooler ocean surfaces--for example, between the Indian subcontinent and the oceans surrounding it.

"These circulations form overturning cells, with air flowing across the equator toward the warmer land surface in the summer hemisphere, rising there, flowing back toward and across the equator aloft, and sinking in the winter hemisphere," explains Tapio Schneider, associate professor of environmental science and engineering at Caltech.

A different explanation is offered by Schneider and Simona Bordoni of the National Center for Atmospheric Research in Boulder, Colorado. The duo used a computer-generated, water-covered, hypothetical earth (an "aquaplanet") to simulate monsoon formation and found that differences in heat capacities between land and sea were not necessary. Bordoni was a Moore Postdoctoral Scholar at Caltech and will return to Caltech as an assistant professor in 2009.

Monsoons arise instead because of an interaction between the tropical circulation and large-scale turbulent eddies generated in the atmosphere in middle latitudes. These eddies, which can span more than 300 miles across, form the familiar systems that govern the weather in middle latitudes.

The eddies, Schneider says, are "basically large waves, which crash into the tropical circulation. They 'break,' much like water waves on the beach, and modify the circulation as a result of the breaking. There are feedbacks between the circulation, the wind pattern associated with it in the upper atmosphere, and the propagation characteristics of the waves, which make it possible for the circulation to change rapidly." This can quickly generate the characteristic high surface winds and heavy rainfall of the monsoon.

Bordoni adds: "These feedbacks provide one possible explanation for the rapidity of monsoon onset, which had been a long-standing conundrum in the traditional view of monsoons," because substantial differences between land and sea temperatures can only develop slowly through heating by sunlight.

Although the results won't immediately produce better forecasts of impending monsoons, Schneider says, "in the long run, a better understanding of monsoons may lead to better predictions with semi-empirical models, but much more work needs to be done."

The paper, "Monsoons as eddy-mediated regime transitions of the tropical overturning circulation," appears in the advance online edition of Nature Geosciences. The work was supported by the Davidow Discovery Fund, a David and Lucile Packard Fellowship, a Moore Postdoctoral Fellowship, and the National Science Foundation. The National Center for Atmospheric Research is sponsored by the National Science Foundation. Any opinions, findings and conclusions or recommendations expressed in this publication are those of the author and do not necessarily reflect the views of the National Science Foundation.

Kathy Svitil


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