Technology-dependent emissions of gas extraction in the US

The KIT measurement instrument on board of a minivan directly measures atmospheric emissions on site with a high temporal resolution. -  Photo: F. Geiger/KIT
The KIT measurement instrument on board of a minivan directly measures atmospheric emissions on site with a high temporal resolution. – Photo: F. Geiger/KIT

Not all boreholes are the same. Scientists of the Karlsruhe Institute of Technology (KIT) used mobile measurement equipment to analyze gaseous compounds emitted by the extraction of oil and natural gas in the USA. For the first time, organic pollutants emitted during a fracking process were measured at a high temporal resolution. The highest values measured exceeded typical mean values in urban air by a factor of one thousand, as was reported in ACP journal. (DOI 10.5194/acp-14-10977-2014)

Emission of trace gases by oil and gas fields was studied by the KIT researchers in the USA (Utah and Colorado) together with US institutes. Background concentrations and the waste gas plumes of single extraction plants and fracking facilities were analyzed. The air quality measurements of several weeks duration took place under the “Uintah Basin Winter Ozone Study” coordinated by the National Oceanic and Atmospheric Administration (NOAA).

The KIT measurements focused on health-damaging aromatic hydrocarbons in air, such as carcinogenic benzene. Maximum concentrations were determined in the waste gas plumes of boreholes. Some extraction plants emitted up to about a hundred times more benzene than others. The highest values of some milligrams of benzene per cubic meter air were measured downstream of an open fracking facility, where returning drilling fluid is stored in open tanks and basins. Much better results were reached by oil and gas extraction plants and plants with closed production processes. In Germany, benzene concentration at the workplace is subject to strict limits: The Federal Emission Control Ordinance gives an annual benzene limit of five micrograms per cubic meter for the protection of human health, which is smaller than the values now measured at the open fracking facility in the US by a factor of about one thousand. The researchers published the results measured in the journal Atmospheric Chemistry and Physics ACP.

“Characteristic emissions of trace gases are encountered everywhere. These are symptomatic of gas and gas extraction. But the values measured for different technologies differ considerably,” Felix Geiger of the Institute of Meteorology and Climate Research (IMK) of KIT explains. He is one of the first authors of the study. By means of closed collection tanks and so-called vapor capture systems, for instance, the gases released during operation can be collected and reduced significantly.

“The gas fields in the sparsely populated areas of North America are a good showcase for estimating the range of impacts of different extraction and fracking technologies,” explains Professor Johannes Orphal, Head of IMK. “In the densely populated Germany, framework conditions are much stricter and much more attention is paid to reducing and monitoring emissions.”

Fracking is increasingly discussed as a technology to extract fossil resources from unconventional deposits. Hydraulic breaking of suitable shale stone layers opens up the fossil fuels stored there and makes them accessible for economically efficient use. For this purpose, boreholes are drilled into these rock formations. Then, they are subjected to high pressure using large amounts of water and auxiliary materials, such as sand, cement, and chemicals. The oil or gas can flow to the surface through the opened microstructures in the rock. Typically, the return flow of the aqueous fracking liquid with the dissolved oil and gas constituents to the surface lasts several days until the production phase proper of purer oil or natural gas. This return flow is collected and then reused until it finally has to be disposed of. Air pollution mainly depends on the treatment of this return flow at the extraction plant. In this respect, currently practiced fracking technologies differ considerably. For the first time now, the resulting local atmospheric emissions were studied at a high temporary resolution. Based on the results, emissions can be assigned directly to the different plant sections of an extraction plant. For measurement, the newly developed, compact, and highly sensitive instrument, a so-called proton transfer reaction mass spectrometer (PTR-MS), of KIT was installed on board of a minivan and driven closer to the different extraction points, the distances being a few tens of meters. In this way, the waste gas plumes of individual extraction sources and fracking processes were studied in detail.

Warneke, C., Geiger, F., Edwards, P. M., Dube, W., Pétron, G., Kofler, J., Zahn, A., Brown, S. S., Graus, M., Gilman, J. B., Lerner, B. M., Peischl, J., Ryerson, T. B., de Gouw, J. A., and Roberts, J. M.: Volatile organic compound emissions from the oil and natural gas industry in the Uintah Basin, Utah: oil and gas well pad emissions compared to ambient air composition, Atmos. Chem. Phys., 14, 10977-10988, doi:10.5194/acp-14-10977-2014, 2014.

Technology-dependent emissions of gas extraction in the US

The KIT measurement instrument on board of a minivan directly measures atmospheric emissions on site with a high temporal resolution. -  Photo: F. Geiger/KIT
The KIT measurement instrument on board of a minivan directly measures atmospheric emissions on site with a high temporal resolution. – Photo: F. Geiger/KIT

Not all boreholes are the same. Scientists of the Karlsruhe Institute of Technology (KIT) used mobile measurement equipment to analyze gaseous compounds emitted by the extraction of oil and natural gas in the USA. For the first time, organic pollutants emitted during a fracking process were measured at a high temporal resolution. The highest values measured exceeded typical mean values in urban air by a factor of one thousand, as was reported in ACP journal. (DOI 10.5194/acp-14-10977-2014)

Emission of trace gases by oil and gas fields was studied by the KIT researchers in the USA (Utah and Colorado) together with US institutes. Background concentrations and the waste gas plumes of single extraction plants and fracking facilities were analyzed. The air quality measurements of several weeks duration took place under the “Uintah Basin Winter Ozone Study” coordinated by the National Oceanic and Atmospheric Administration (NOAA).

The KIT measurements focused on health-damaging aromatic hydrocarbons in air, such as carcinogenic benzene. Maximum concentrations were determined in the waste gas plumes of boreholes. Some extraction plants emitted up to about a hundred times more benzene than others. The highest values of some milligrams of benzene per cubic meter air were measured downstream of an open fracking facility, where returning drilling fluid is stored in open tanks and basins. Much better results were reached by oil and gas extraction plants and plants with closed production processes. In Germany, benzene concentration at the workplace is subject to strict limits: The Federal Emission Control Ordinance gives an annual benzene limit of five micrograms per cubic meter for the protection of human health, which is smaller than the values now measured at the open fracking facility in the US by a factor of about one thousand. The researchers published the results measured in the journal Atmospheric Chemistry and Physics ACP.

“Characteristic emissions of trace gases are encountered everywhere. These are symptomatic of gas and gas extraction. But the values measured for different technologies differ considerably,” Felix Geiger of the Institute of Meteorology and Climate Research (IMK) of KIT explains. He is one of the first authors of the study. By means of closed collection tanks and so-called vapor capture systems, for instance, the gases released during operation can be collected and reduced significantly.

“The gas fields in the sparsely populated areas of North America are a good showcase for estimating the range of impacts of different extraction and fracking technologies,” explains Professor Johannes Orphal, Head of IMK. “In the densely populated Germany, framework conditions are much stricter and much more attention is paid to reducing and monitoring emissions.”

Fracking is increasingly discussed as a technology to extract fossil resources from unconventional deposits. Hydraulic breaking of suitable shale stone layers opens up the fossil fuels stored there and makes them accessible for economically efficient use. For this purpose, boreholes are drilled into these rock formations. Then, they are subjected to high pressure using large amounts of water and auxiliary materials, such as sand, cement, and chemicals. The oil or gas can flow to the surface through the opened microstructures in the rock. Typically, the return flow of the aqueous fracking liquid with the dissolved oil and gas constituents to the surface lasts several days until the production phase proper of purer oil or natural gas. This return flow is collected and then reused until it finally has to be disposed of. Air pollution mainly depends on the treatment of this return flow at the extraction plant. In this respect, currently practiced fracking technologies differ considerably. For the first time now, the resulting local atmospheric emissions were studied at a high temporary resolution. Based on the results, emissions can be assigned directly to the different plant sections of an extraction plant. For measurement, the newly developed, compact, and highly sensitive instrument, a so-called proton transfer reaction mass spectrometer (PTR-MS), of KIT was installed on board of a minivan and driven closer to the different extraction points, the distances being a few tens of meters. In this way, the waste gas plumes of individual extraction sources and fracking processes were studied in detail.

Warneke, C., Geiger, F., Edwards, P. M., Dube, W., Pétron, G., Kofler, J., Zahn, A., Brown, S. S., Graus, M., Gilman, J. B., Lerner, B. M., Peischl, J., Ryerson, T. B., de Gouw, J. A., and Roberts, J. M.: Volatile organic compound emissions from the oil and natural gas industry in the Uintah Basin, Utah: oil and gas well pad emissions compared to ambient air composition, Atmos. Chem. Phys., 14, 10977-10988, doi:10.5194/acp-14-10977-2014, 2014.

Fountain of youth underlies Antarctic Mountains

Images of the ice-covered Gamburtsev Mountains revealed water-filled valleys, as seen by the cluster of vertical lines in this image. -  Tim Creyts
Images of the ice-covered Gamburtsev Mountains revealed water-filled valleys, as seen by the cluster of vertical lines in this image. – Tim Creyts

Time ravages mountains, as it does people. Sharp features soften, and bodies grow shorter and rounder. But under the right conditions, some mountains refuse to age. In a new study, scientists explain why the ice-covered Gamburtsev Mountains in the middle of Antarctica looks as young as they do.

The Gamburtsevs were discovered in the 1950s, but remained unexplored until scientists flew ice-penetrating instruments over the mountains 60 years later. As this ancient hidden landscape came into focus, scientists were stunned to see the saw-toothed and towering crags of much younger mountains. Though the Gamburtsevs are contemporaries of the largely worn-down Appalachians, they looked more like the Rockies, which are nearly 200 million years younger.

More surprising still, the scientists discovered a vast network of lakes and rivers at the mountains’ base. Though water usually speeds erosion, here it seems to have kept erosion at bay. The reason, researchers now say, has to do with the thick ice that has entombed the Gamburtsevs since Antarctica went into a deep freeze 35 million years ago.

“The ice sheet acts like an anti-aging cream,” said the study’s lead author, Timothy Creyts, a geophysicist at Columbia University’s Lamont-Doherty Earth Observatory. “It triggers a series of thermodynamic processes that have almost perfectly preserved the Gamburtsevs since ice began spreading across the continent.”

The study, which appears in the latest issue of the journal Geophysical Research Letters, explains how the blanket of ice covering the Gamburtsevs has preserved its rugged ridgelines.

Snow falling at the surface of the ice sheet draws colder temperatures down, closer to protruding peaks in a process called divergent cooling. At the same time, heat radiating from bedrock beneath the ice sheet melts ice in the deep valleys to form rivers and lakes. As rivers course along the base of the ice sheet, high pressures from the overlying ice sheet push water up valleys in reverse. This uphill flow refreezes as it meets colder temperature from above. Thus, ridgelines are cryogenically preserved.

The oldest rocks in the Gamburtsevs formed more than a billion years ago, in the collision of several continents. Though these prototype mountains eroded away, a lingering crustal root became reactivated when the supercontinent Gondwana ripped apart, starting about 200 million years ago. Tectonic forces pushed the land up again to form the modern Gamburtsevs, which range across an area the size of the Alps. Erosion again chewed away at the mountains until earth entered a cooling phase 35 million years ago. Expanding outward from the Gamburtsevs, a growing layer of ice joined several other nucleation points to cover the entire continent in ice.

The researchers say that the mechanism that stalled aging of the Gamburtsevs at higher elevations may explain why some ridgelines in the Torngat Mountains on Canada’s Labrador Peninsula and the Scandinavian Mountains running through Norway, Sweden and Finland appear strikingly untouched. Massive ice sheets covered both landscapes during the last ice age, which peaked about 20,000 years ago, but many high-altitude features bear little trace of this event.

“The authors identify a mechanism whereby larger parts of mountains ranges in glaciated regions–not just Antarctica–could be spared from erosion,” said Stewart Jamieson, a glaciologist at Durham University who was not involved in the study. “This is important because these uplands are nucleation centers for ice sheets. If they were to gradually erode during glacial cycles, they would become less effective as nucleation points during later ice ages.”

Ice sheet behavior, then, may influence climate change in ways that scientists and computer models have yet to appreciate. As study coauthor Fausto Ferraccioli, head of the British Antarctic Survey’s airborne geophysics group, put it: “If these mountains in interior East Antarctica had been more significantly eroded then the ice sheet itself
may have had a different history.”

Other Authors


Hugh Carr and Tom Jordan of the British Antarctic Survey; Robin Bell, Michael Wolovick and Nicholas Frearson of Lamont-Doherty; Kathryn Rose of University of Bristol; Detlef Damaske of Germany’s Federal Institute for Geosciences and Natural Resources; David Braaten of Kansas University; and Carol Finn of the U.S. Geological Survey.

Copies of the paper, “Freezing of ridges and water networks preserves the Gamburtsev Subglacial Mountains for millions of years,” are available from the authors.

Scientist Contact


Tim Creyts

845-365-8368

tcreyts@ldeo.columbia.edu

Fountain of youth underlies Antarctic Mountains

Images of the ice-covered Gamburtsev Mountains revealed water-filled valleys, as seen by the cluster of vertical lines in this image. -  Tim Creyts
Images of the ice-covered Gamburtsev Mountains revealed water-filled valleys, as seen by the cluster of vertical lines in this image. – Tim Creyts

Time ravages mountains, as it does people. Sharp features soften, and bodies grow shorter and rounder. But under the right conditions, some mountains refuse to age. In a new study, scientists explain why the ice-covered Gamburtsev Mountains in the middle of Antarctica looks as young as they do.

The Gamburtsevs were discovered in the 1950s, but remained unexplored until scientists flew ice-penetrating instruments over the mountains 60 years later. As this ancient hidden landscape came into focus, scientists were stunned to see the saw-toothed and towering crags of much younger mountains. Though the Gamburtsevs are contemporaries of the largely worn-down Appalachians, they looked more like the Rockies, which are nearly 200 million years younger.

More surprising still, the scientists discovered a vast network of lakes and rivers at the mountains’ base. Though water usually speeds erosion, here it seems to have kept erosion at bay. The reason, researchers now say, has to do with the thick ice that has entombed the Gamburtsevs since Antarctica went into a deep freeze 35 million years ago.

“The ice sheet acts like an anti-aging cream,” said the study’s lead author, Timothy Creyts, a geophysicist at Columbia University’s Lamont-Doherty Earth Observatory. “It triggers a series of thermodynamic processes that have almost perfectly preserved the Gamburtsevs since ice began spreading across the continent.”

The study, which appears in the latest issue of the journal Geophysical Research Letters, explains how the blanket of ice covering the Gamburtsevs has preserved its rugged ridgelines.

Snow falling at the surface of the ice sheet draws colder temperatures down, closer to protruding peaks in a process called divergent cooling. At the same time, heat radiating from bedrock beneath the ice sheet melts ice in the deep valleys to form rivers and lakes. As rivers course along the base of the ice sheet, high pressures from the overlying ice sheet push water up valleys in reverse. This uphill flow refreezes as it meets colder temperature from above. Thus, ridgelines are cryogenically preserved.

The oldest rocks in the Gamburtsevs formed more than a billion years ago, in the collision of several continents. Though these prototype mountains eroded away, a lingering crustal root became reactivated when the supercontinent Gondwana ripped apart, starting about 200 million years ago. Tectonic forces pushed the land up again to form the modern Gamburtsevs, which range across an area the size of the Alps. Erosion again chewed away at the mountains until earth entered a cooling phase 35 million years ago. Expanding outward from the Gamburtsevs, a growing layer of ice joined several other nucleation points to cover the entire continent in ice.

The researchers say that the mechanism that stalled aging of the Gamburtsevs at higher elevations may explain why some ridgelines in the Torngat Mountains on Canada’s Labrador Peninsula and the Scandinavian Mountains running through Norway, Sweden and Finland appear strikingly untouched. Massive ice sheets covered both landscapes during the last ice age, which peaked about 20,000 years ago, but many high-altitude features bear little trace of this event.

“The authors identify a mechanism whereby larger parts of mountains ranges in glaciated regions–not just Antarctica–could be spared from erosion,” said Stewart Jamieson, a glaciologist at Durham University who was not involved in the study. “This is important because these uplands are nucleation centers for ice sheets. If they were to gradually erode during glacial cycles, they would become less effective as nucleation points during later ice ages.”

Ice sheet behavior, then, may influence climate change in ways that scientists and computer models have yet to appreciate. As study coauthor Fausto Ferraccioli, head of the British Antarctic Survey’s airborne geophysics group, put it: “If these mountains in interior East Antarctica had been more significantly eroded then the ice sheet itself
may have had a different history.”

Other Authors


Hugh Carr and Tom Jordan of the British Antarctic Survey; Robin Bell, Michael Wolovick and Nicholas Frearson of Lamont-Doherty; Kathryn Rose of University of Bristol; Detlef Damaske of Germany’s Federal Institute for Geosciences and Natural Resources; David Braaten of Kansas University; and Carol Finn of the U.S. Geological Survey.

Copies of the paper, “Freezing of ridges and water networks preserves the Gamburtsev Subglacial Mountains for millions of years,” are available from the authors.

Scientist Contact


Tim Creyts

845-365-8368

tcreyts@ldeo.columbia.edu

Re-learning how to read a genome

New research has revealed that the initial steps of reading DNA are actually remarkably similar at both the genes that encode proteins (here, on the right) and regulatory elements (on the left). The main differences seem to occur after this initial step. Gene messages are long and stable enough to ensure that genes become proteins, whereas regulatory messages are short and unstable, and are rapidly 'cleaned up' by the cell. -  Adam Siepel, Cold Spring Harbor Laboratory
New research has revealed that the initial steps of reading DNA are actually remarkably similar at both the genes that encode proteins (here, on the right) and regulatory elements (on the left). The main differences seem to occur after this initial step. Gene messages are long and stable enough to ensure that genes become proteins, whereas regulatory messages are short and unstable, and are rapidly ‘cleaned up’ by the cell. – Adam Siepel, Cold Spring Harbor Laboratory

There are roughly 20,000 genes and thousands of other regulatory “elements” stored within the three billion letters of the human genome. Genes encode information that is used to create proteins, while other genomic elements help regulate the activation of genes, among other tasks. Somehow all of this coded information within our DNA needs to be read by complex molecular machinery and transcribed into messages that can be used by our cells.

Usually, reading a gene is thought to be a lot like reading a sentence. The reading machinery is guided to the start of the gene by various sequences in the DNA – the equivalent of a capital letter – and proceeds from left to right, DNA letter by DNA letter, until it reaches a sequence that forms a punctuation mark at the end. The capital letter and punctuation marks that tell the cell where, when, and how to read a gene are known as regulatory elements.

But scientists have recently discovered that genes aren’t the only messages read by the cell. In fact, many regulatory elements themselves are also read and transcribed into messages, the equivalent of pronouncing the words “capital letter,” “comma,” or “period.” Even more surprising, genes are read bi-directionally from so-called “start sites” – in effect, generating messages in both forward and backward directions.

With all these messages, how does the cell know which one encodes the information needed to make a protein? Is there something different about the reading process at genes and regulatory elements that helps avoid confusion? New research, published today in Nature Genetics, has revealed that the initial steps of the reading process itself are actually remarkably similar at both genes and regulatory elements. The main differences seem to occur after this initial step, in the length and stability of the messages. Gene messages are long and stable enough to ensure that genes becomes proteins, whereas regulatory messages are short and unstable, and are rapidly “cleaned up” by the cell.

To make the distinction, the team, which was co-led by CSHL Professor Adam Siepel and Cornell University Professor John Lis, looked for differences between the initial reading processes at genes and a set of regulatory elements called enhancers. “We took advantage of highly sensitive experimental techniques developed in the Lis lab to measure newly made messages in the cell,” says Siepel. “It’s like having a new, more powerful microscope for observing the process of transcription as it occurs in living cells.”

Remarkably, the team found that the reading patterns for enhancer and gene messages are highly similar in many respects, sharing a common architecture. “Our data suggests that the same basic reading process is happening at genes and these non-genic regulatory elements,” explains Siepel. “This points to a unified model for how DNA transcription is initiated throughout the genome.”

Working together, the biochemists from Lis’s laboratory and the computer jockeys from Siepel’s group carefully compared the patterns at enhancers and genes, combining their own data with vast public data sets from the NIH’s Encyclopedia of DNA Elements (ENCODE) project. “By many different measures, we found that the patterns of transcription initiation are essentially the same at enhancers and genes,” says Siepel. “Most RNA messages are rapidly targeted for destruction, but the messages at genes that are read in the right direction – those destined to be a protein – are spared from destruction.” The team was able to devise a model to mathematically explain the difference between stable and unstable transcripts, offering insight into what defines a gene. According to Siepel, “Our analysis shows that the ‘code’ for stability is, in large part, written in the DNA, at enhancers and genes alike.”

This work has important implications for the evolutionary origins of new genes, according to Siepel. “Because DNA is read in both directions from any start site, every one of these sites has the potential to generate two protein-coding genes with just a few subtle changes. The genome is full of potential new genes.”

This work was supported by the National Institutes of Health.

“Analysis of transcription start sites from nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers.” appears online in Nature Genetics on November 10, 2014. The authors are: Leighton Core, André Martins, Charles Danko, Colin Waters, Adam Siepel, and John Lis. The paper can be obtained online at: http://dx.doi.org/10.1038/ng.3142

About Cold Spring Harbor Laboratory

Founded in 1890, Cold Spring Harbor Laboratory (CSHL) has shaped contemporary biomedical research and education with programs in cancer, neuroscience, plant biology and quantitative biology. CSHL is ranked number one in the world by Thomson Reuters for the impact of its research in molecular biology and genetics. The Laboratory has been home to eight Nobel Prize winners. Today, CSHL’s multidisciplinary scientific community is more than 600 researchers and technicians strong and its Meetings & Courses program hosts more than 12,000 scientists from around the world each year to its Long Island campus and its China center. For more information, visit http://www.cshl.edu.

Re-learning how to read a genome

New research has revealed that the initial steps of reading DNA are actually remarkably similar at both the genes that encode proteins (here, on the right) and regulatory elements (on the left). The main differences seem to occur after this initial step. Gene messages are long and stable enough to ensure that genes become proteins, whereas regulatory messages are short and unstable, and are rapidly 'cleaned up' by the cell. -  Adam Siepel, Cold Spring Harbor Laboratory
New research has revealed that the initial steps of reading DNA are actually remarkably similar at both the genes that encode proteins (here, on the right) and regulatory elements (on the left). The main differences seem to occur after this initial step. Gene messages are long and stable enough to ensure that genes become proteins, whereas regulatory messages are short and unstable, and are rapidly ‘cleaned up’ by the cell. – Adam Siepel, Cold Spring Harbor Laboratory

There are roughly 20,000 genes and thousands of other regulatory “elements” stored within the three billion letters of the human genome. Genes encode information that is used to create proteins, while other genomic elements help regulate the activation of genes, among other tasks. Somehow all of this coded information within our DNA needs to be read by complex molecular machinery and transcribed into messages that can be used by our cells.

Usually, reading a gene is thought to be a lot like reading a sentence. The reading machinery is guided to the start of the gene by various sequences in the DNA – the equivalent of a capital letter – and proceeds from left to right, DNA letter by DNA letter, until it reaches a sequence that forms a punctuation mark at the end. The capital letter and punctuation marks that tell the cell where, when, and how to read a gene are known as regulatory elements.

But scientists have recently discovered that genes aren’t the only messages read by the cell. In fact, many regulatory elements themselves are also read and transcribed into messages, the equivalent of pronouncing the words “capital letter,” “comma,” or “period.” Even more surprising, genes are read bi-directionally from so-called “start sites” – in effect, generating messages in both forward and backward directions.

With all these messages, how does the cell know which one encodes the information needed to make a protein? Is there something different about the reading process at genes and regulatory elements that helps avoid confusion? New research, published today in Nature Genetics, has revealed that the initial steps of the reading process itself are actually remarkably similar at both genes and regulatory elements. The main differences seem to occur after this initial step, in the length and stability of the messages. Gene messages are long and stable enough to ensure that genes becomes proteins, whereas regulatory messages are short and unstable, and are rapidly “cleaned up” by the cell.

To make the distinction, the team, which was co-led by CSHL Professor Adam Siepel and Cornell University Professor John Lis, looked for differences between the initial reading processes at genes and a set of regulatory elements called enhancers. “We took advantage of highly sensitive experimental techniques developed in the Lis lab to measure newly made messages in the cell,” says Siepel. “It’s like having a new, more powerful microscope for observing the process of transcription as it occurs in living cells.”

Remarkably, the team found that the reading patterns for enhancer and gene messages are highly similar in many respects, sharing a common architecture. “Our data suggests that the same basic reading process is happening at genes and these non-genic regulatory elements,” explains Siepel. “This points to a unified model for how DNA transcription is initiated throughout the genome.”

Working together, the biochemists from Lis’s laboratory and the computer jockeys from Siepel’s group carefully compared the patterns at enhancers and genes, combining their own data with vast public data sets from the NIH’s Encyclopedia of DNA Elements (ENCODE) project. “By many different measures, we found that the patterns of transcription initiation are essentially the same at enhancers and genes,” says Siepel. “Most RNA messages are rapidly targeted for destruction, but the messages at genes that are read in the right direction – those destined to be a protein – are spared from destruction.” The team was able to devise a model to mathematically explain the difference between stable and unstable transcripts, offering insight into what defines a gene. According to Siepel, “Our analysis shows that the ‘code’ for stability is, in large part, written in the DNA, at enhancers and genes alike.”

This work has important implications for the evolutionary origins of new genes, according to Siepel. “Because DNA is read in both directions from any start site, every one of these sites has the potential to generate two protein-coding genes with just a few subtle changes. The genome is full of potential new genes.”

This work was supported by the National Institutes of Health.

“Analysis of transcription start sites from nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers.” appears online in Nature Genetics on November 10, 2014. The authors are: Leighton Core, André Martins, Charles Danko, Colin Waters, Adam Siepel, and John Lis. The paper can be obtained online at: http://dx.doi.org/10.1038/ng.3142

About Cold Spring Harbor Laboratory

Founded in 1890, Cold Spring Harbor Laboratory (CSHL) has shaped contemporary biomedical research and education with programs in cancer, neuroscience, plant biology and quantitative biology. CSHL is ranked number one in the world by Thomson Reuters for the impact of its research in molecular biology and genetics. The Laboratory has been home to eight Nobel Prize winners. Today, CSHL’s multidisciplinary scientific community is more than 600 researchers and technicians strong and its Meetings & Courses program hosts more than 12,000 scientists from around the world each year to its Long Island campus and its China center. For more information, visit http://www.cshl.edu.

Offshore islands amplify, rather than dissipate, a tsunami’s power

This model shows the impact of coastal islands on a tsunami's height. -  Courtesy of Jose Borrero/eCoast/USC
This model shows the impact of coastal islands on a tsunami’s height. – Courtesy of Jose Borrero/eCoast/USC

A long-held belief that offshore islands protect the mainland from tsunamis turns out to be the exact opposite of the truth, according to a new study.

Common wisdom — from Southern California to the South Pacific — for coastal residents and scientists alike has long been that offshore islands would create a buffer that blocked the power of a tsunami. In fact, computer modeling of tsunamis striking a wide variety of different offshore island geometries yielded no situation in which the mainland behind them fared better.

Instead, islands focused the energy of the tsunami, increasing flooding on the mainland by up to 70 percent.

“This is where many fishing villages are located, behind offshore islands, in the belief that they will be protected from wind waves. Even Southern California residents believe that the Channel Islands and Catalina will protect them,” said Costas Synolakis of the USC Viterbi School of Engineering, a member of the multinational team that conducted the research.

The research was inspired by a field survey of the impact of the 2010 tsunami on the Mentawai Islands off of Sumatra. The survey data showed that villages located in the shadow of small offshore islets suffered some of the strongest tsunami impacts, worse than villages located along open coasts.

Subsequent computer modeling by Jose Borrero, adjunct assistant research professor at the USC Viterbi Tsunami Research Center, showed that the offshore islands had actually contributed to — not diminished — the tsunami’s impact.

Synolakis then teamed up with researchers Emile Contal and Nicolas Vayatis of Ecoles Normales de Cachan in Paris; and Themistoklis S. Stefanakis and Frederic Dias, who both have joint appointments at Ecoles Normales de Cachan and University College Dublin to determine whether that was a one-of-a-kind situation, or the norm.

Their study, of which Dias was the corresponding author, was published in Proceedings of the Royal Society A on Nov. 5.

The team designed a computer model that took into consideration various island slopes, beach slopes, water depths, distance between the island and the beach, and wavelength of the incoming tsunami.

“Even a casual analysis of these factors would have required hundreds of thousands of computations, each of which could take up to half a day,” Synolakis said. “So instead, we used machine learning.”

Machine learning is a mathematical process that makes it easier to identify the maximum values of interdependent processes with multiple parameters by allowing the computer to “learn” from previous results.

The computer starts to understand how various tweaks to the parameters affect the overall outcome and finds the best answer quicker. As such, results that traditionally could have taken hundreds of thousands of models to uncover were found with 200 models.

“This work is applicable to some of our tsunami study sites in New Zealand,” said Borrero, who is producing tsunami hazard maps for regions of the New Zealand coast. “The northeast coast of New Zealand has many small islands offshore, similar to those in Indonesia, and our modeling suggests that this results in areas of enhanced tsunami heights.”

“Substantial public education efforts are needed to help better explain to coastal residents tsunami hazards, and whenever they need to be extra cautious and responsive with evacuations during actual emergencies,” Synolakis said.

###

The research was funded by EDSP of ENS-Cachan; the Cultural Service of the French Embassy in Dublin; the ERC; SFI; University College Dublin; and the EU FP7 program ASTARTE. The study can be found online at http://rspa.royalsocietypublishing.org/content/470/2172/20140575.

Offshore islands amplify, rather than dissipate, a tsunami’s power

This model shows the impact of coastal islands on a tsunami's height. -  Courtesy of Jose Borrero/eCoast/USC
This model shows the impact of coastal islands on a tsunami’s height. – Courtesy of Jose Borrero/eCoast/USC

A long-held belief that offshore islands protect the mainland from tsunamis turns out to be the exact opposite of the truth, according to a new study.

Common wisdom — from Southern California to the South Pacific — for coastal residents and scientists alike has long been that offshore islands would create a buffer that blocked the power of a tsunami. In fact, computer modeling of tsunamis striking a wide variety of different offshore island geometries yielded no situation in which the mainland behind them fared better.

Instead, islands focused the energy of the tsunami, increasing flooding on the mainland by up to 70 percent.

“This is where many fishing villages are located, behind offshore islands, in the belief that they will be protected from wind waves. Even Southern California residents believe that the Channel Islands and Catalina will protect them,” said Costas Synolakis of the USC Viterbi School of Engineering, a member of the multinational team that conducted the research.

The research was inspired by a field survey of the impact of the 2010 tsunami on the Mentawai Islands off of Sumatra. The survey data showed that villages located in the shadow of small offshore islets suffered some of the strongest tsunami impacts, worse than villages located along open coasts.

Subsequent computer modeling by Jose Borrero, adjunct assistant research professor at the USC Viterbi Tsunami Research Center, showed that the offshore islands had actually contributed to — not diminished — the tsunami’s impact.

Synolakis then teamed up with researchers Emile Contal and Nicolas Vayatis of Ecoles Normales de Cachan in Paris; and Themistoklis S. Stefanakis and Frederic Dias, who both have joint appointments at Ecoles Normales de Cachan and University College Dublin to determine whether that was a one-of-a-kind situation, or the norm.

Their study, of which Dias was the corresponding author, was published in Proceedings of the Royal Society A on Nov. 5.

The team designed a computer model that took into consideration various island slopes, beach slopes, water depths, distance between the island and the beach, and wavelength of the incoming tsunami.

“Even a casual analysis of these factors would have required hundreds of thousands of computations, each of which could take up to half a day,” Synolakis said. “So instead, we used machine learning.”

Machine learning is a mathematical process that makes it easier to identify the maximum values of interdependent processes with multiple parameters by allowing the computer to “learn” from previous results.

The computer starts to understand how various tweaks to the parameters affect the overall outcome and finds the best answer quicker. As such, results that traditionally could have taken hundreds of thousands of models to uncover were found with 200 models.

“This work is applicable to some of our tsunami study sites in New Zealand,” said Borrero, who is producing tsunami hazard maps for regions of the New Zealand coast. “The northeast coast of New Zealand has many small islands offshore, similar to those in Indonesia, and our modeling suggests that this results in areas of enhanced tsunami heights.”

“Substantial public education efforts are needed to help better explain to coastal residents tsunami hazards, and whenever they need to be extra cautious and responsive with evacuations during actual emergencies,” Synolakis said.

###

The research was funded by EDSP of ENS-Cachan; the Cultural Service of the French Embassy in Dublin; the ERC; SFI; University College Dublin; and the EU FP7 program ASTARTE. The study can be found online at http://rspa.royalsocietypublishing.org/content/470/2172/20140575.

Geologists dig into science around the globe, on land and at sea

University of Cincinnati geologists will be well represented among geoscientists from around the world at The Geological Society of America’s Annual Meeting and Exposition. The meeting takes place Oct. 19-22, in Vancouver, Canada, and will feature geoscientists representing more than 40 different disciplines. The meeting will feature highlights of UC’s geological research that is taking place globally, from Chile to Costa Rica, Belize, Bulgaria, Scotland, Trinidad and a new project under development in the Canary Islands.

UC faculty and graduate students are lead or supporting authors on more than two dozen Earth Sciences-related research papers and/or PowerPoint and poster exhibitions at the GSA meeting.

The presentations also cover UC’s longtime and extensive exploration and findings in the Cincinnati Arch of the Ohio Valley, world-renowned for its treasure trove of paleontology – plant and animal fossils that were preserved when a shallow sea covered the region 450 million years ago during the Paleozoic Era.

Furthermore, in an effort to diversify the field of researchers in the Earth Sciences, a UC assistant professor of science education and geology, Christopher Atchison, was awarded funding from the National Science Foundation and the Society of Exploration Geophysics to lead a research field trip in Vancouver for students with disabilities. Graduate and undergraduate student participants will conduct the research on Oct. 18 and then join events at the GSA meeting. They’ll be guided by geoscience researchers representing the United Kingdom, New Zealand, Canada and the U.S. Those guides include Atchison and Julie Hendricks, a UC special education major from Batavia, Ohio, who will be using her expertise in American Sign Language (ASL) to assist student researchers representing Deaf and Hard of Hearing communities.

The meeting will also formally introduce Arnold Miller, UC professor of geology, as the new president-elect of the national Paleontological Society Thomas Lowell, professor of geology, is a recently elected Fellow of the Geological Society of America – a recognition for producing a substantial body of research. Lowell joins colleagues Warren Huff, professor of geology, and Lewis Owen, professor and head of the Department of Geology, as GSA Fellows.

Here are highlights of the UC research to be presented at the GSA meeting Oct. 19-22:

Staying Put or Moving On? Researchers Develop Model to Identify Migrating Patterns of Different Species

Are plant and animal species what you might call lifelong residents – they never budge from the same place? That’s a relatively common belief in ecology and paleoecology – that classes of organisms tend to stay put over millions of years and either evolve or go extinct as the environment changes. UC researchers developed a series of numerical models simulating shifting habitats in fossil regions to compare whether species changed environments when factoring geological and other changes in the fossil record. They found that geologically driven changes in the quality of the fossil record did not distort the real ecological signal, and that most species maintained their particular habitat preferences through time. They did not evolve to adapt to changing environments, but rather, they migrated, following their preferred environments. That is to say, they did not stay in place geographically but by moving, they were able to track their favored habitats. Field research for the project was conducted in New York state as well as the paleontological-rich region of Cincinnati; Dayton, Ohio, Lexington, Ky.; and Indiana. Funding for the project was supported by The Paleontological Society; The Geological Society of America; The American Museum of Natural History and the UC Geology Department’s Kenneth E. Caster Memorial Fund.

Presenter: Andrew Zaffos, UC geology doctoral student

Co-authors: Arnold Miller, Carlton Brett

Pioneering Study Provides a Better Understanding of What Southern Ohio and Central Kentucky Looked Like Hundreds of Millions of Years Ago

The end of the Ordovician period resulted in one of the largest mass extinction events in the Earth’s history. T.J. Malgieri, a UC master’s student in geology, led this study examining the limestone and shales of the Upper Ordovician Period – the geologic Grant Lake Formation covering southern Ohio and central Kentucky – to recreate how the shoreline looked some 445 million years ago. In this pioneering study of mud cracks and deposits in the rocks, the researchers discovered that the shoreline existed to the south and that the water became deeper toward the north. By determining these ecological parameters, the ramp study provides a better understanding of environments during a time of significant ecological change. Malgieri says the approach can be applied to other basins throughout the world to create depth indicators in paeloenvironments.

Presenter: T.J. Malgieri, UC geology master’s student

Co-authors: Carlton Brett, Cameron Schalbach, Christopher Aucoin, UC; James Thomka (UC, University of Akron); Benjamin Dattilo, Indiana University Purdue University Ft. Wayne

UC Researchers Take a Unique Approach to Monitoring Groundwater Supplies Near Ohio Fracking Sites

A collaborative research project out of UC is examining effects of fracking on groundwater in the Utica Shale region of eastern Ohio. First launched in Carroll County in 2012, the team of researchers is examining methane levels and origins of methane in private wells and springs before, during and after the onset of fracking. The team travels to the region to take water samples four times a year.

Presenter: Claire Botner, a UC geology master’s student

Co-author: Amy Townsend-Small, UC assistant professor of geology

Sawing Through Seagrass to Reveal Clues to the Past

Kelsy Feser, a UC doctoral student in geology, is working at several sites around St. Croix in the Virgin Islands to see if human developments impact marine life. The research focuses on shells of snails and clams that have piled up on the sea floor for thousands of years. Digging through layers of thick seagrass beds on the ocean floor, Feser can examine deeper shells that were abundant thousands of years ago and compare them to shallower layers that include living clams and snails. Early analysis indicates a greater population of potentially pollution-tolerant mussels in an area near a landfill on the island, compared with shells from much earlier time periods. Feser is doing this sea grass analysis around additional sites including tourist resorts, an oil refinery, a power plant and a marina. Funding for the research is provided by the Paleontological Society, the GSA, the American Museum of Natural History and the UC Geology Department.

Presenter: Kelsy Feser, UC geology doctoral student

Co-authors: Arnold Miller

Turning to the Present to Understand the Past

In order to properly interpret changes in climate, vegetation, or animal populations over time, it is necessary to establish a comparative baseline. Stella Mosher, a UC geology master’s student, is studying stable carbon, nitrogen, sulfur and strontium isotopes in modern vegetation from the Canary Islands in order to quantify modern climatic and environmental patterns. Her findings will provide a crucial foundation for future UC research on regional paleoclimatic and paleoenvironmental shifts.

Presenter: Stella Mosher, graduate student in geology

Co-authors: Brooke Crowley, assistant professor of geology; Yurena Yanes, research assistant professor of geology

A Study on the Impact of Sea Spray

Sulfur is an element of interest in both geology and archaeology, because it can reveal information about the diets of ancient cultures. This study takes a novel approach to studying how sea spray can affect the sulfur isotope values in plants on a small island, focusing on the island of Trinidad. Researchers collected leaves from different plant species to get their sulfur isotope value, exploring whether wind direction played a role in how plants were influenced by the marine water from sea spray. Vegetation was collected from the edges of the island to the deeply forested areas. The study found that sulfur isotope values deeper inland and on the calmer west coast were dramatically lower in indicating marine water than vegetation along the edges and the east coast. The findings can help indicate the foraging activities of humans and animals. Funding for the study was supported by the Geological Society of America, the UC Graduate Student Association and the UC Department of Geology.

Presenter: Janine Sparks, UC geology doctoral student

Co-authors: Brooke Crowley, UC assistant professor, geology/anthropology; William Gilhooly III, assistant professor, Earth Sciences, Indiana University-Purdue University Indianapolis

Proxy Wars – The Paleobiology Data Debate

For the past several decades, paleobiologists have built large databases containing information on fossil plants and animals of all geological ages to investigate the timing and extent of major changes in biodiversity – changes such as mass extinctions that have taken place throughout the history of life. Biodiversity researcher Arnold Miller says that in building these databases, it can be a challenge to accurately identify species in the geological record, so it has been common for researchers to instead study biodiversity trends using data compiled at broader levels of biological classification, including the genus level, under the assumption that these patterns are effective proxies for what would be observed among species if the data were available. Miller has been involved in construction of The Paleobiology Database, an extensive public online resource that contains global genus- and species-level data, now permitting a direct, novel look at the similarities and differences between patterns at these two levels. Miller’s discussion aims to set the record straight as to when researchers can effectively use a genus as a proxy for a species and also when it’s inappropriate. This research is funded by the NASA Astrobiology Program.

Presenter: Arnold Miller, UC professor of geology

A Novel New Method for Examining the Distribution of Pores in Rocks

Oil and gas companies take an interest in the porosity of sedimentary rocks because those open spaces can be filled with fuel resources. Companies involved with hydraulic fracturing (“fracking”) are also interested in porosity because it could be a source for storing wastewater as a result of fracking. In this unique study, UC researchers made pore-size measurements similar to those used in crystal size distribution (CSD) theory to determine distribution of pores as a function of their sizes, using thin sections of rock. In addition to providing accurate porosity distribution at a given depth, their approach can be extended to evaluate variation of pore spaces as a function of depth in a drill core, percent of pores in each size range, and pore types and pore geometry. The Texas Bureau of Economic Geology provided the rock samples used in the study. Funding for the study was supported by the Turkish Petroleum Corporation.

Presenter: Ugurlu Ibrahim, master’s student in geology

Co-author: Attila Kilinc, professor of geology

Researchers Turn to 3-D Technology to Examine the Formation of Cliffband Landscapes

A blend of photos and technology takes a new twist on studying cliff landscapes and how they were formed. The method called Structure-From-Motion Photogrammetry – computational photo image processing techniques – is used to study the formation of cliff landscapes in Colorado and Utah and to understand how the layered rock formations in the cliffs are affected by erosion.

Presenter: Dylan Ward, UC assistant professor of geology

Testing the Links Between Climate and Sedimentation in the Atacama Desert, Northern Chile

The Atacama Desert is used as an analog for understanding the surface of Mars. In some localities, there has been no activity for millions of years. UC researchers have been working along the flank of the Andes Mountains in northern Chile, and this particular examination focuses on the large deposits of sediment that are transported down the plateau and gather at the base. The researchers are finding that their samples are not reflecting the million-year-old relics previously found on such expeditions, but may indicate more youthful activity possibly resulting from climatic events. The research is supported by a $273,634 grant from the National Science Foundation to explore glacio-geomorphic constraints on the climate history of subtropical northern Chile.

Presenter: Jason Cesta, UC geology master’s student

Co-author: Dylan Ward, UC assistant professor of geology

Uncovering the Explosive Mysteries Surrounding the Manganese of Northeast Bulgaria

UC’s geology collections hold minerals from field expeditions around the world, including manganese from the Obrochishte mines of northeastern Bulgaria. Found in the region’s sedimentary rock, manganese can be added to metals such as steel to improve strength. It’s widely believed that these manganese formations were the result of ocean water composition at the time the sediments were deposited in the ocean. In this presentation, UC researchers present new information on why they believe the manganese formations resulted from volcanic eruptions, perhaps during the Rupelian stage of the geologic time scale, when bentonite clay minerals were formed. The presentation evolved from an advance class project last spring under the direction of Warren Huff, a UC professor of geology.

Presenter: Jason Cesta, UC geology master’s student

Co-authors: Warren Huff, UC professor of geology; Christopher Aucoin; Michael Harrell; Thomas Malgieri; Barry Maynard; Cameron Schwalbach; Ibrahim Ugurlu; Antony Winrod

Two UC researchers will chair sessions at the GSA meeting: Doctoral student Gary Motz will chair the session, “Topics in Paleoecology: Modern Analogues and Ancient Systems,” on Oct. 19. Matt Vrazo, also a doctoral student in geology, is chairing “Paleontology: Trace Fossils, Taphonomy and Exceptional Preservation” on Oct. 21, and will present, “Taphonomic and Ecological Controls on Eurypterid Lagerstäten: A Model for Preservation in the Mid-Paleozoic.”

###

UC’s nationally ranked Department of Geology conducts field research around the world in areas spanning paleontology, quaternary geology, geomorphology, sedimentology, stratigraphy, tectonics, environmental geology and biogeochemistry.

The Geological Society of America, founded in 1888, is a scientific society with more than 26,500 members from academia, government, and industry in more than 100 countries. Through its meetings, publications, and programs, GSA enhances the professional growth of its members and promotes the geosciences in the service of humankind.

Geologists dig into science around the globe, on land and at sea

University of Cincinnati geologists will be well represented among geoscientists from around the world at The Geological Society of America’s Annual Meeting and Exposition. The meeting takes place Oct. 19-22, in Vancouver, Canada, and will feature geoscientists representing more than 40 different disciplines. The meeting will feature highlights of UC’s geological research that is taking place globally, from Chile to Costa Rica, Belize, Bulgaria, Scotland, Trinidad and a new project under development in the Canary Islands.

UC faculty and graduate students are lead or supporting authors on more than two dozen Earth Sciences-related research papers and/or PowerPoint and poster exhibitions at the GSA meeting.

The presentations also cover UC’s longtime and extensive exploration and findings in the Cincinnati Arch of the Ohio Valley, world-renowned for its treasure trove of paleontology – plant and animal fossils that were preserved when a shallow sea covered the region 450 million years ago during the Paleozoic Era.

Furthermore, in an effort to diversify the field of researchers in the Earth Sciences, a UC assistant professor of science education and geology, Christopher Atchison, was awarded funding from the National Science Foundation and the Society of Exploration Geophysics to lead a research field trip in Vancouver for students with disabilities. Graduate and undergraduate student participants will conduct the research on Oct. 18 and then join events at the GSA meeting. They’ll be guided by geoscience researchers representing the United Kingdom, New Zealand, Canada and the U.S. Those guides include Atchison and Julie Hendricks, a UC special education major from Batavia, Ohio, who will be using her expertise in American Sign Language (ASL) to assist student researchers representing Deaf and Hard of Hearing communities.

The meeting will also formally introduce Arnold Miller, UC professor of geology, as the new president-elect of the national Paleontological Society Thomas Lowell, professor of geology, is a recently elected Fellow of the Geological Society of America – a recognition for producing a substantial body of research. Lowell joins colleagues Warren Huff, professor of geology, and Lewis Owen, professor and head of the Department of Geology, as GSA Fellows.

Here are highlights of the UC research to be presented at the GSA meeting Oct. 19-22:

Staying Put or Moving On? Researchers Develop Model to Identify Migrating Patterns of Different Species

Are plant and animal species what you might call lifelong residents – they never budge from the same place? That’s a relatively common belief in ecology and paleoecology – that classes of organisms tend to stay put over millions of years and either evolve or go extinct as the environment changes. UC researchers developed a series of numerical models simulating shifting habitats in fossil regions to compare whether species changed environments when factoring geological and other changes in the fossil record. They found that geologically driven changes in the quality of the fossil record did not distort the real ecological signal, and that most species maintained their particular habitat preferences through time. They did not evolve to adapt to changing environments, but rather, they migrated, following their preferred environments. That is to say, they did not stay in place geographically but by moving, they were able to track their favored habitats. Field research for the project was conducted in New York state as well as the paleontological-rich region of Cincinnati; Dayton, Ohio, Lexington, Ky.; and Indiana. Funding for the project was supported by The Paleontological Society; The Geological Society of America; The American Museum of Natural History and the UC Geology Department’s Kenneth E. Caster Memorial Fund.

Presenter: Andrew Zaffos, UC geology doctoral student

Co-authors: Arnold Miller, Carlton Brett

Pioneering Study Provides a Better Understanding of What Southern Ohio and Central Kentucky Looked Like Hundreds of Millions of Years Ago

The end of the Ordovician period resulted in one of the largest mass extinction events in the Earth’s history. T.J. Malgieri, a UC master’s student in geology, led this study examining the limestone and shales of the Upper Ordovician Period – the geologic Grant Lake Formation covering southern Ohio and central Kentucky – to recreate how the shoreline looked some 445 million years ago. In this pioneering study of mud cracks and deposits in the rocks, the researchers discovered that the shoreline existed to the south and that the water became deeper toward the north. By determining these ecological parameters, the ramp study provides a better understanding of environments during a time of significant ecological change. Malgieri says the approach can be applied to other basins throughout the world to create depth indicators in paeloenvironments.

Presenter: T.J. Malgieri, UC geology master’s student

Co-authors: Carlton Brett, Cameron Schalbach, Christopher Aucoin, UC; James Thomka (UC, University of Akron); Benjamin Dattilo, Indiana University Purdue University Ft. Wayne

UC Researchers Take a Unique Approach to Monitoring Groundwater Supplies Near Ohio Fracking Sites

A collaborative research project out of UC is examining effects of fracking on groundwater in the Utica Shale region of eastern Ohio. First launched in Carroll County in 2012, the team of researchers is examining methane levels and origins of methane in private wells and springs before, during and after the onset of fracking. The team travels to the region to take water samples four times a year.

Presenter: Claire Botner, a UC geology master’s student

Co-author: Amy Townsend-Small, UC assistant professor of geology

Sawing Through Seagrass to Reveal Clues to the Past

Kelsy Feser, a UC doctoral student in geology, is working at several sites around St. Croix in the Virgin Islands to see if human developments impact marine life. The research focuses on shells of snails and clams that have piled up on the sea floor for thousands of years. Digging through layers of thick seagrass beds on the ocean floor, Feser can examine deeper shells that were abundant thousands of years ago and compare them to shallower layers that include living clams and snails. Early analysis indicates a greater population of potentially pollution-tolerant mussels in an area near a landfill on the island, compared with shells from much earlier time periods. Feser is doing this sea grass analysis around additional sites including tourist resorts, an oil refinery, a power plant and a marina. Funding for the research is provided by the Paleontological Society, the GSA, the American Museum of Natural History and the UC Geology Department.

Presenter: Kelsy Feser, UC geology doctoral student

Co-authors: Arnold Miller

Turning to the Present to Understand the Past

In order to properly interpret changes in climate, vegetation, or animal populations over time, it is necessary to establish a comparative baseline. Stella Mosher, a UC geology master’s student, is studying stable carbon, nitrogen, sulfur and strontium isotopes in modern vegetation from the Canary Islands in order to quantify modern climatic and environmental patterns. Her findings will provide a crucial foundation for future UC research on regional paleoclimatic and paleoenvironmental shifts.

Presenter: Stella Mosher, graduate student in geology

Co-authors: Brooke Crowley, assistant professor of geology; Yurena Yanes, research assistant professor of geology

A Study on the Impact of Sea Spray

Sulfur is an element of interest in both geology and archaeology, because it can reveal information about the diets of ancient cultures. This study takes a novel approach to studying how sea spray can affect the sulfur isotope values in plants on a small island, focusing on the island of Trinidad. Researchers collected leaves from different plant species to get their sulfur isotope value, exploring whether wind direction played a role in how plants were influenced by the marine water from sea spray. Vegetation was collected from the edges of the island to the deeply forested areas. The study found that sulfur isotope values deeper inland and on the calmer west coast were dramatically lower in indicating marine water than vegetation along the edges and the east coast. The findings can help indicate the foraging activities of humans and animals. Funding for the study was supported by the Geological Society of America, the UC Graduate Student Association and the UC Department of Geology.

Presenter: Janine Sparks, UC geology doctoral student

Co-authors: Brooke Crowley, UC assistant professor, geology/anthropology; William Gilhooly III, assistant professor, Earth Sciences, Indiana University-Purdue University Indianapolis

Proxy Wars – The Paleobiology Data Debate

For the past several decades, paleobiologists have built large databases containing information on fossil plants and animals of all geological ages to investigate the timing and extent of major changes in biodiversity – changes such as mass extinctions that have taken place throughout the history of life. Biodiversity researcher Arnold Miller says that in building these databases, it can be a challenge to accurately identify species in the geological record, so it has been common for researchers to instead study biodiversity trends using data compiled at broader levels of biological classification, including the genus level, under the assumption that these patterns are effective proxies for what would be observed among species if the data were available. Miller has been involved in construction of The Paleobiology Database, an extensive public online resource that contains global genus- and species-level data, now permitting a direct, novel look at the similarities and differences between patterns at these two levels. Miller’s discussion aims to set the record straight as to when researchers can effectively use a genus as a proxy for a species and also when it’s inappropriate. This research is funded by the NASA Astrobiology Program.

Presenter: Arnold Miller, UC professor of geology

A Novel New Method for Examining the Distribution of Pores in Rocks

Oil and gas companies take an interest in the porosity of sedimentary rocks because those open spaces can be filled with fuel resources. Companies involved with hydraulic fracturing (“fracking”) are also interested in porosity because it could be a source for storing wastewater as a result of fracking. In this unique study, UC researchers made pore-size measurements similar to those used in crystal size distribution (CSD) theory to determine distribution of pores as a function of their sizes, using thin sections of rock. In addition to providing accurate porosity distribution at a given depth, their approach can be extended to evaluate variation of pore spaces as a function of depth in a drill core, percent of pores in each size range, and pore types and pore geometry. The Texas Bureau of Economic Geology provided the rock samples used in the study. Funding for the study was supported by the Turkish Petroleum Corporation.

Presenter: Ugurlu Ibrahim, master’s student in geology

Co-author: Attila Kilinc, professor of geology

Researchers Turn to 3-D Technology to Examine the Formation of Cliffband Landscapes

A blend of photos and technology takes a new twist on studying cliff landscapes and how they were formed. The method called Structure-From-Motion Photogrammetry – computational photo image processing techniques – is used to study the formation of cliff landscapes in Colorado and Utah and to understand how the layered rock formations in the cliffs are affected by erosion.

Presenter: Dylan Ward, UC assistant professor of geology

Testing the Links Between Climate and Sedimentation in the Atacama Desert, Northern Chile

The Atacama Desert is used as an analog for understanding the surface of Mars. In some localities, there has been no activity for millions of years. UC researchers have been working along the flank of the Andes Mountains in northern Chile, and this particular examination focuses on the large deposits of sediment that are transported down the plateau and gather at the base. The researchers are finding that their samples are not reflecting the million-year-old relics previously found on such expeditions, but may indicate more youthful activity possibly resulting from climatic events. The research is supported by a $273,634 grant from the National Science Foundation to explore glacio-geomorphic constraints on the climate history of subtropical northern Chile.

Presenter: Jason Cesta, UC geology master’s student

Co-author: Dylan Ward, UC assistant professor of geology

Uncovering the Explosive Mysteries Surrounding the Manganese of Northeast Bulgaria

UC’s geology collections hold minerals from field expeditions around the world, including manganese from the Obrochishte mines of northeastern Bulgaria. Found in the region’s sedimentary rock, manganese can be added to metals such as steel to improve strength. It’s widely believed that these manganese formations were the result of ocean water composition at the time the sediments were deposited in the ocean. In this presentation, UC researchers present new information on why they believe the manganese formations resulted from volcanic eruptions, perhaps during the Rupelian stage of the geologic time scale, when bentonite clay minerals were formed. The presentation evolved from an advance class project last spring under the direction of Warren Huff, a UC professor of geology.

Presenter: Jason Cesta, UC geology master’s student

Co-authors: Warren Huff, UC professor of geology; Christopher Aucoin; Michael Harrell; Thomas Malgieri; Barry Maynard; Cameron Schwalbach; Ibrahim Ugurlu; Antony Winrod

Two UC researchers will chair sessions at the GSA meeting: Doctoral student Gary Motz will chair the session, “Topics in Paleoecology: Modern Analogues and Ancient Systems,” on Oct. 19. Matt Vrazo, also a doctoral student in geology, is chairing “Paleontology: Trace Fossils, Taphonomy and Exceptional Preservation” on Oct. 21, and will present, “Taphonomic and Ecological Controls on Eurypterid Lagerstäten: A Model for Preservation in the Mid-Paleozoic.”

###

UC’s nationally ranked Department of Geology conducts field research around the world in areas spanning paleontology, quaternary geology, geomorphology, sedimentology, stratigraphy, tectonics, environmental geology and biogeochemistry.

The Geological Society of America, founded in 1888, is a scientific society with more than 26,500 members from academia, government, and industry in more than 100 countries. Through its meetings, publications, and programs, GSA enhances the professional growth of its members and promotes the geosciences in the service of humankind.