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Analytical Chemistry

Isotope Clumping Reveals Details Of Ancient Earth

Expanding field answers questions about formation temperatures of geological features and plant and animal matter

by Elizabeth K. Wilson
June 15, 2015 | A version of this story appeared in Volume 93, Issue 24

Hyacinth in the lab, A snail shell, A dinosaur tooth.
Credit: Jeanine Ash (left), Michael Hren(center), John Eiler(right)
Isotope clumping has been used to study photosynthesis in plants (left), carbonate formation (center), and dinosaur teeth (right).

Like many good scientific ideas conceived long ago, isotope clumping just needed technology to make its study a reality.

With the advent of a new breed of mass spectrometers, isotope chemists can finally make use of the powerful information stored in isotope clumps: molecules containing not just one but two or more heavy isotopes. With this new method, researchers have been able to pin down climate conditions and geological features that existed on ancient Earth and trace the origins of atmospheric gases with a certainty only dreamed of just a decade ago.

Isotope clumping is a rare but significant phenomenon that had been theorized as far back as the 1930s. For instance, carbon dioxide normally exists in the form 16O=12C=16O or 16O=13C=16O. But occasionally, clumped-isotope versions of the molecule, such as 18O=13C=18O, can form. The relative abundance of isotope clumps in a substance provides a record of the temperature at which that substance was formed. And, as scientists are discovering, biological processes such as photosynthesis can affect the abundances and configurations of isotopic clumps.

Isotope clumping differs from the well-established, highly successful field of isotope chemistry, where scientists study geological, astronomical, and biological processes by measuring bulk enrichments or depletions of isotopes.

Clumped-isotope chemistry, with its ability to deliver information about formation temperatures, promises to both augment traditional isotope chemistry and take the field in completely new directions.

In the past five years, isotope clumping has made headlines as the method used to estimate the altitude of ancient mountains from soil samples, dinosaur body temperatures from teeth, and the long-disputed formation temperature of carbonates in the famous martian meteorite ALH84001. Scientists are already speculating about its ability to determine the origin of methane on Mars.

Beginning in the late 1990s, the acknowledged father of the field of isotope clumping, California Institute of Technology geological and planetary sciences professor John M. Eiler, had been pondering the concept while poring over scientific literature from the 1930s and ’40s. A single paragraph in one paper stood out: It described the possibility of using multiply substituted isotopes to do thermometry. The implications of such a technique were huge, Eiler realized.

What was required, however, was a mass spectrometer sensitive enough to detect the rare clumps. Such a machine would require more powerful magnets and better detector sensitivity, mass resolution, and stability. In the early 2000s, Eiler realized that the design of such an instrument should be possible. He approached numerous manufacturers, asking them to build a prototype.

“Nobody would do it because it’s a big investment,” Eiler says. He eventually convinced Thermo Fisher Scientific. The instrument produced by the firm gave the Caltech group the boost it needed to begin studying isotope clumping.

Soon after, they published studies of the existence of clumped isotopes in CO2, both in the air and in solid carbonate. “That’s when the field really blew up,” Eiler says.

Numerous other groups around the world, from Europe to Japan, are now jumping on the isotope clumping bandwagon, using the technique to study numerous systems, including living corals and nanoscopic fossils. The number of papers on the topic has grown from a handful in 2010 to several dozen in 2014.

Until recently, most isotope clumping research projects have focused on carbonate. It’s common in rocks and animal shells, substances that make up a large part of Earth’s paleorecord. And it’s usually formed under equilibrium conditions, in which isotopes freely change places between molecules without outside influence. Being formed under equilibrium conditions is a prerequisite for being able to deduce temperatures from isotope clumping information.

One of the major complications for this new field, however, is that few systems are truly in equilibrium. Methane, for example, is a powerful greenhouse gas produced both thermally and biologically. The production of methane by microbes, in particular, involves nonequilibrium processes and has led to wildly inaccurate formation temperature estimates from clumping studies. Groups led by Shuhei Ono, biogeochemistry professor at Massachusetts Institute of Technology, and by Eiler and his postdoc Daniel A. Stolper have recently published papers proposing new models for microbial methane production that lead to more accurate predictions (Science 2015, DOI:10.1126/science.aaa4326; Geochim. Cosmochim. Acta 2015, DOI: 10.1016/j.gca.2015.04.015).

Scientists are also discovering that some biological processes can influence isotope clumping. Laurence Y. Yeung, earth sciences professor at Rice University, and coworkers have discovered that photosynthesis produces the isotope clump 18O18O far less often than what would be expected by chance (C&EN, April 27, 2015, page 26). This newly discovered signature will help scientists identify how and where oxygen circulates in Earth’s environment.

As with any new field that’s just starting to take off, there’s also a large focus on instrumentation and standardization. “The limitation of studying clumped isotopes is purely technical,” says Cedric John, head of the Carbonate Research Group at Imperial College London.

Credit: Edward Young
Young’s Panorama is the most powerful mass spectrometer designed to study isotope clumping.
A photo of a mass spec lab.
Credit: Edward Young
Young’s Panorama is the most powerful mass spectrometer designed to study isotope clumping.

In the lab of Edward D. Young, geochemistry and cosmochemistry professor at the University of California, Los Angeles, looms a behemoth mass spectrometer, called Panorama. Built by Wales-based Nu Instruments, Panorama is arguably the largest mass spectrometer designed for studying isotope clumping, with the highest resolving power. Panorama began operating in April, Young says, and should be able to detect clumps that no other machine can, such as doubly deuterated methane. He’s now soliciting samples for study from numerous colleagues.

John’s group is trying to help make the field more accessible by standardizing technology. “When we started, we relied on the goodwill of people in the community to help us make it work,” he says.

His group is commercializing a line of mass-spectrometer-based systems, called IBEX, which automates sample processing, removing a great deal of grunt work. They’re also developing open-source software for analyzing clumped-isotope data.

There are, of course, other ways to detect isotope clumps. Highly sensitive spectroscopy techniques have the potential to identify the unique signatures of molecules that contain isotope clumps. This has implications for extraterrestrial studies because spectrometers could be made small enough to fly on a spacecraft, unlike the large mass specs used to study isotope clumping on Earth.

Ono and his group at MIT are breaking ground in this area and have worked with Massachusetts-based Aerodyne Research to design and build an infrared spectrometer that they’ve used in their methane studies.

Meanwhile, Eiler continues to push the clumped-isotope envelope, setting his sights on complex molecules such as amino acids. His lab is now studying isotope clumping in alanine. “We’re simply trying to describe how its isotopic structure made in the lab is different from alanine made by life.”  


At low temperatures, molecules such as O2 form more clumps (18O18O) than at high temperatures.

That two or more heavy isotopes could wind up together in the same molecule isn’t unthinkable. In fact, scientists have long known that as atoms randomly change places with each other, there’s a calculable chance isotope clumps will occur, even if infrequently.

Bonds between heavy isotopes are stronger than bonds between lighter isotopes, or between one light and one heavy isotope, so they’re more likely to persist.

Because of complex thermodynamic factors, at equilibrium, heavy isotopes tend to clump more frequently than would be expected by chance.

This thermodynamic preference for clumping varies dramatically with temperature. As temperatures drop, molecular vibrations slow, and the abundance of strongly bonded clumps of heavy isotopes increases. As temperatures rise, however, the thermal energy of the system quickly overrides the relatively small differences in isotope bond strengths.

By comparing the abundance of isotope clumps in a sample with the amount that should form by chance, scientists get a remarkably precise measurement of the absolute temperature at which the material formed.

The technique solves a problem that’s hindered geochemists for decades. For example, in the case of ancient carbonate formation in seawater, the abundance of the heavy isotope 18O relative to 16O in carbonate is a marker of the formation temperature. However, this abundance ratio is also affected by the seawater’s isotopic composition. Because scientists don’t know the isotopic composition of the ancient seawater, they’re unable to determine absolute temperature.

Isotope clumps, however, carry all this vital information independently. It’s the distribution of isotopes in clumps relative to nonclumps that indicates the temperature at which the material formed. The absolute abundance of isotopes doesn’t matter.

And now that the degree to which isotopes clump can be measured, the gates to a new scientific landscape are wide open.


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