SCIENCE at work Just another IU News Blog Wed, 15 Mar 2017 18:07:59 +0000 en-US hourly 1 Ecologist to present public lecture on mountaintop removal mining Wed, 15 Mar 2017 18:07:32 +0000 An expert in ecosystem ecology and biogeochemistry will discuss the impact of mountaintop removal mining on the environment March 22 at Indiana University Bloomington.

Emily Bernhardt. Courtesy Duke University

Emily Bernhardt. Courtesy Duke University

Emily Bernhardt of Duke University will deliver the 36th Joan Wood Lecture from 4 to 5 p.m. in Myers Hall, Room 130. Her lecture is titled “The remaking of Appalachian ecosystems by mountaintop removal coal mining.”

The talk, hosted by the IU Bloomington College of Arts and Sciences’ Department of Biology, is free and open to the public.

Over the past several decades, mountaintop removal practices have affected an estimated 10 percent of the Central Appalachian forests, an approximately 800-mile range that encompasses regions such as the Blue Ridge Mountains of West Virginia and the Great Smoky Mountains of North Carolina and Tennessee.

“The associated impacts of surface coal mining on air, water and wildlife resources in this region have been profound and extend well beyond the permit boundaries of individual mines,” Bernhardt said. “This talk will explore a decade-long effort to answer a series of basic questions about the individual and aggregate effects of mountaintop mines on Appalachian rivers and watersheds.”

The lecture will also address the connection between environmental research and policy.

“Emily is one of the leading experts on how human impacts like climate change, chemical pollution and land cover change are affecting the way ecosystems work,” said Richard Phillips, associate professor in the IU Bloomington Department of Biology. “She’s also an exceptionally broad thinker whose willingness to tackle environmental problems that cross disciplinary boundaries have allowed her to become one of the most accomplished biogeochemists of her generation.”

Bernhardt’s lab conducts research on topics such as soil priming, nanomaterial toxicity, ecosystem development, wetland restoration, stream restoration, urban thermal pollution, saltwater incursion and watershed nitrogen cycling. She is president of the Society for Freshwater Science and holds a bachelor’s degree in biology from the University of North Carolina at Chapel Hill and a doctorate in ecology and evolutionary biology from Cornell University.

Established in 1990, the Joan Wood Lecture Series was created to highlight women in science-related careers and encourage undergraduate women to pursue advanced degrees in science. It is named in honor of IU Bloomington Department of Biology alum and medical geneticist Joan Wood.

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Places & Spaces: Mapping Science exhibition to debut new ‘macroscopes’ at Vanderbilt University Fri, 20 Jan 2017 01:47:18 +0000 Post by IU Newsroom intern Laura Ellsworth:

Places & Spaces: Mapping Science, a traveling exhibition founded and curated by IU professor Katy Bӧrner, will debut its 2017 iteration at Vanderbilt University on Jan. 23.

This international collection of world-class data visualizations will be on display in conjunction with the theme “Our Lives Online.”

Bӧrner is an IU Distinguished Professor of Information Science and Intelligent Systems Engineering in the IU School of Informatics and Computing. She will also deliver a keynote lecture at Vanderbilt on Jan. 27.


An visitor explores a macroscope during an exhibition of Places & Spaces at the IU Art Museum in September 2016.

The Places & Spaces exhibit, established at IU in 2005, showcases the visualization of complex data in innovative formats, helping many to make sense of large streams of data. Each year, new visualizations are added, selected from international and interdisciplinary submissions.

The current exhibition includes 100 science maps, sculptures, hands-on activities and interactive visualizations called macroscopes. The macroscopes — accessed via a 46-inch touchscreen display introduced into the exhibit upon its 10th anniversary two years ago — present data visually to make new perspectives possible. Visitors are encouraged to “touch the data” and engage with the macroscopes on a touchscreen kiosk. Three to five new macroscopes are expected to be added to the exhibit each year through 2024.

“In the information age, being able to ‘read and write’ data visualization is becoming as important as being able to read and write text,” Bӧrner said. “The visualizations displayed in this exhibition showcase the power of data visualizations to save lives, to make decisions informed by high-quality data, and to communicate the beauty and value of science to a general audience.”

Bӧrner is also the founding director of the IU Cyberinfrastructure for Network Science Center, which serves as home base for the exhibit.

Four new macroscopes will debut at the exhibition at Vanderbilt University. They are:

  • Smelly Maps: Features a “smellscape” of 12 cities mapped by smell using social media
  • HathiTrust: Highlights the diversity of publications collected in digital form by HathiTrust.
  • Excellence Networks: Compares how research institutions, such as Indiana and Vanderbilt universities, collaborate with one another.
  • FleetMon Explorer: Shows how the amount of shipping traffic that navigates the Strait of Malacca compared to other major shipping lanes of the world.
Places & Spaces at the David J. Sencer Center for Disease Control and Prevention Museum in Washington, D.C., which hosted an exhibit in 2016.

Places & Spaces at the David J. Sencer Centers for Disease Control and Prevention Museum in Washington, D.C., which hosted an exhibit in 2016.

The HathiTrust macroscope was a project of David Reagan, a senior analyst and programmer at University Information Technology Services; Lisel Record, curator of Places & Spaces; and Bӧrner. A collaboration between IU and the University of Illinois, the HathiTrust Research Center at HathiTrust Digital Repository leverages these institution’s powerful data storage infrastructures to house and provide open access to over 8 million volumes and 2 billion pages of archived material from major research institutions and libraries worldwide.

For over a decade, Places & Spaces has collected science maps and visualization tools from leading experts in the natural, physical and social sciences, as well as from industry and government experts. The collections’ data visualizations cover topics as diverse as the settings of Victorian poems and maps showing the national mood through tweets over the course of the day.

By helping visitors grasp the abstract concepts, relationships and dynamism of complex systems, the exhibition promotes more informed, effective decision-making on the part of private individuals, industry practitioners, public policymakers and others. The exhibition has traveled to 28 countries on six continents and showcases the work of 235 mapmakers that hail from 68 cities in 16 different countries.

Many of the science maps in the exhibit are viewable online, along with further information about the Vanderbilt

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IU scientist joins mentor and collaborator for Nobel Prize events in Sweden Mon, 09 Jan 2017 17:35:13 +0000 Amar Flood studied under 2016 Nobel Laureate J. Fraser Stoddart as a postdoctoral scholar at UCLA

Last month, members of the Royal Swedish Academy of Sciences — the organization that awards the Nobel Prize — honored three experts in the field of molecular machines with one of the highest honors in the field of science and research during a ceremony Dec. 10 in Stockholm, Sweden.

Amar Flood, left, with his wife, Michiko Owaki, and Fraser Stoddart. Credit: Nobel Foundation.

Amar Flood, left, with his wife, Michiko Owaki, and Fraser Stoddart. Credit: Nobel Foundation.

Joining those scientists for a week of scientific talks, formal events and intellectual stimulation were dozens of close collaborators, colleagues and friends, among whom could be found Amar Flood, a professor in the Indiana University Bloomington College of Arts and Sciences’ Department of Chemistry, who attended the activities with his wife and children at the invitation of J. Fraser Stoddart, one of the 2016 Nobel Laureates and a mentor to Flood during his time as a postdoctoral scholar at the University of California at Los Angeles.

“It was extremely rewarding to see a mentor and colleague get this tremendous honor… tears of joy came in the place of words,” said Flood, who joined 15 invited guests of Stoddart and their families in Stockholm from Dec. 5 to 13. “This award raises the profile and credibility of the whole field of molecular machines.”

Stoddart was honored for the design and synthesis of molecular machines, which are nanoscopically small groups of precisely designed molecules that can perform specific tasks when energy is added. Flood’s own work focuses on the creation of highly specialized molecular structures, or “supramolecules,” with industrial and environmental applications. Recently, for instance, his lab reported the first evidence for a new molecule with potential applications in the safe storage of nuclear waste and reduction of chemicals that contaminate water and trigger large fish kills.

As a postdoctoral scholar studying molecular electronics and molecular machines under Stoddart from 2002 to 2005, Flood said the senior scientists’ influence sparked a lifelong interest in molecular machines, as well as taught him other critical skills as a researcher, such as how to write strong research papers, engage in productive collaborations and lead research groups.

More broadly, Flood said Stoddart’s influence taught him to “pursue high standards of research, to collaborate with the best people, and to win over the hearts and minds of your colleagues.”

As a guest of Stoddart, Flood and his family had the opportunity to attend a white-tie banquet beneath the opulent golden arches of the Stockholm’s City Hall Cellar, which was held in conjunction with the official award ceremony, after which the attendees joined the smaller ceremony group for a nightcap. They also attended Stoddart’s reception at the U.S. Embassy, the Nobel Lectures in Chemistry, and the filming of the BBC News series, Nobel Minds. He also attended gatherings of the Stoddart group every night at Stockholm’s historic Grand Hôtel. Joining him on the trip were his wife, Michiko Owaki, and sons, Benjamin, 8, and Sean, 6.

In one of the most popular photos from coverage of the Nobel Prize, Stoddart poses with the children who accompanied him as guests at Nobel Week. Flood’s son Sean stands to the left, making a peace sign atop of Stoddart’s head. Benjamin wears a black-and-blue shirt. Credit: Nobel Foundation.

Stoddart poses with the children of his guests at Nobel Week. Flood’s son Sean stands to the left, making a peace sign atop of Stoddart’s head. Benjamin wears a black-and-blue shirt. The photo was one of the most popular to emerge from coverage of the prize. Credit: Nobel Foundation.

“The whole experience was amazing,” Flood said. “It was incredible to see scientists treated like superstars. They had paparazzi and photo shoots; winners were stopped on the streets to sign autographs. The highlight was a standing ovation at the end of the Nobel lectures.”

Currently, Stoddart and Flood’s collaborations focus on advancing research opportunities in supramolecular chemistry and molecular machines, such as organizing conferences and supporting each other’s advocacy for more support for these research topics. Flood also helped proofread several sections of Stoddart’s latest book, “The Nature of the Mechanical Bond,” and is co-author on multiple papers with Stoddart.

“All of us in Stockholm who were a part of Fraser’s group of 15 guests and their families were extremely appreciative of the invitation, and his generosity during the Nobel week,” Flood said. “My academic brothers and sisters are spread all over the world. While I see them once or twice a year, we never get to meet each other’s families. For this reason, this gathering was particularly special for allowing my family to meet and connect with that of my academic family.”

Flood also noted that Stoddart “paid special attention to extending the invitation to all our families. He felt that the children could gain a lot from the experience by being introduced to science at the highest level, and to see that they too could have this level of impact in the future.”

The other winners of the 2016 Nobel Prize in Chemistry were Jean-Pierre Sauvage of University of Strasbourg, France, and Bernard “Ben” L. Feringa of the University of Groningen, the Netherlands. Stoddart is a professor at Northwestern University.

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Indiana University scientist named American Physical Society fellow Fri, 06 Jan 2017 15:33:45 +0000 Indiana University professor J. Timothy Londergan has been elected as a fellow in the Division of Nuclear Physics of the American Physical Society, the pre-eminent organization of physicists in the United States.

Timothy J. Lundergan

J. Timothy Londergan

An emeritus professor in the IU Bloomington College of Arts and Sciences’ Department of Physics, Londergan was honored for his “work on approximate parton of symmetries, such as charge and flavor symmetry, and for models of the scattering behavior of quarks and hadrons.”

A symmetry is a physical or mathematical feature that remains unchanged or preserved throughout a transformation. Quarks are subatomic particles that come in a number of types, or “flavors,” and combinations, including hadrons, which are composed of three quarks. Scattering refers to particle-particle collisions between these objects.

As a physicist, Londergan is particularly interested in “broken symmetries” of quarks, which provide direct evidence for “non-perturbative” quark effects, or effects that cannot be understood with standard mathematical methods. Broken symmetries are significant since they can reveal new insights about the nature of these subatomic particles.

A former Rhodes Scholar, Londergan holds a bachelor’s degree from the University of Rochester and a Ph.D. from Oxford University. He served as chair of the IU Bloomington Department of Physics from 1990 to 1997 and director of the Herman B Wells Scholars Program from 2003 to 2013. He also served three terms as a director of the IU Nuclear Theory Center.

Londergan’s research was supported by the National Science Foundation from 1976 to 2016. He was also involved for nearly 30 years in NSF-sponsored summer research designed to provide undergraduates experience analyzing data from facilities such as Brookhaven National Laboratory in New York and Jefferson National Laboratory in Virginia.

No more than one-half of 1 percent of American Physical Society members are elected fellows each year. New fellows are nominated by their peers for outstanding contributions to the field, including original research and publication, innovative applications to science and technology, exceptional teaching and outreach, or esteemed leadership and service to the society.

A complete list of the 2016 fellows is available in the November issue of APS News.


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IU scientists earn ‘BioArt’ award for image of beetle brain on cusp of metamorphosis Tue, 06 Dec 2016 15:36:07 +0000 Work to be displayed at the National Institutes of Health in early 2017

A stunning image of an insect’s brain and nerve cord captured by three Indiana University scientists will be on display at the National Institutes of Health early next year.

The winning image shows the central nervous system in a species of horned dung beetle.

The winning image shows the central nervous system in a species of horned dung beetle.

Eduardo Zattara, Armin Moczek and Jim Powers of the IU Bloomington College of Arts and Sciences’ Department of Biology are among the winners of the Federation of American Societies for Experimental Biology’s 2016 BioArt competition, an annual contest to share the beauty and breadth of biological research.

Zattara is a postdoctoral researcher in the lab of Moczek, a professor in the department. Powers is an assistant research scientist and manager of the IU Light Microscopy Imaging Center, where the image was generated.

The winning image from IU shows a highly detailed picture of the central nervous system in a species of horned dung beetle, Onthophagus sagittarius. The image was captured close to the insect’s emergence from the pupal to adult stage.

Visible in the image are the beetle’s optic lobes, which are in the process of growing and extending toward the outer surface of the head to form a pair of compound eyes. The colors are the result of different fluorescent labels used to highlight physical structures and chemical processes involved in the transformation. Structural proteins appear in red; serotonin, a neurotransmitter, in green; and genetic material in blue.

The image was captured at the Light Microscopy Imaging Center using an LSM880 laser-scanning confocal microscope from Zeiss Microscopy, one of several highly advanced imaging devices made available to IU scientists during summer 2015. Capturing and rendering the complete 50-gigabyte dataset required over 14 hours and the full processing power of the microscope’s computer, according to Zattara, who had to leave the machine running overnight to get the image.

Although the image is beautiful, Zattara said the “gorgeous dataset” isn’t purely aesthetic. It also played a critical role in the discovery, reported earlier this year, that switching off select head patterning genes in Onthophagus resulted in the loss of the beetles’ horns and appearance of a third eye structure in the center of the head. That study was part of a larger project to investigate the evolution of novel complex traits in Moczek’s lab funded by the National Science Foundation.

“After we got the first preliminary results suggesting the central nervous system could play a role in patterning these strange structures in Onthophagus, I decided to investigate the brain and nerve cord of a developing beetle using immunofluorescence and confocal microscopy, since these technologies allow us to obtain highly detailed three-dimensional images of tiny structures,” Zattara said. “Ultimately, the image helped put us on the right track by showing that the brain did not seem to be the cause for losing horns and gaining a third eye.

Winners included Eduardo Zattara and Armin Moczek. (Jim Powers not pictured.)

Winners included Eduardo Zattara and Armin Moczek. (Not pictured: Jim Powers.)

“This is an image whose creation was driven at least as much by the challenge and fun of trying out a new technology as the collection of data,” he added. “Oftentimes, you don’t really know what an image will look like until you are done acquiring and processing the data. After leaving the microscope running all night, we arrived the next morning to find this huge data file. It took a few more hours for the high-end computer to crunch through the data before we could see the final render. But the wait was totally worthwhile, as the resulting image was crisp, highly detailed and very aesthetically pleasing. It was perfect for a contest like FASEB BioArt, and I’m honored to be named one of this year’s winners.”

The nation’s largest coalition of biomedical researchers, the Federation of American Societies for Experimental Biology represents 30 scientific societies and over 125,000 researchers from around the world. The organization aims to advance health and welfare by promoting progress and education in biological and biomedical sciences through service to member societies and collaborative advocacy.

The IU scientists’ image is one of 10 selected as winners in the 2016 competition. Also credited for their role in the image are Jonathan Cherry and Matthew Curtis of Zeiss Microscopy, which will feature the image in the company’s promotional materials.

The winning entries were unveiled Nov. 23 on the federation’s website. The art exhibit at NIH is expected to go live in late January or early February. The exact date is to be determined.

The original, 50GB dataset is available to researchers. For more information, contact Eduardo Zattara at

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IU scientists to participate in Ask Me Anything session on Reddit Mon, 05 Dec 2016 18:39:05 +0000 On Dec. 7, three IU scientists will invite the public to “Ask Me Anything.”

Hui-Chen Lu, Yousuf Ali and Hunter Allen will participate in a Q-and-A session from 1 to 2 p.m. EST on r/Science, the science message board of Reddit.

Yu and colleagues will participate in PLOS Science Wednesdays AMA Series on Dec. 7.

Lu and colleagues will participate in PLOS Science Wednesdays AMA Series on Dec. 7.

The massively popular social media platform, which hosts daily Ask Me Anything sessions, or “AMAs,” regularly attracts an audience of over 10,000 people to these online events.

The session is organized by the online peer reviewed journal PLOS as part of the PLOS Science Wednesdays AMA Series.

Earlier this year, Lu and colleagues published a paper in PLOS reporting evidence that the enzyme NMNAT2 appears to exert a protective effect on memory.

The study is significant since the research could affect how scientists understand the mechanisms behind a range of neurodegenerative diseases known as “proteinopathies,” which include Alzheimer’s, Parkinson’s and Huntington’s diseases, as well as amyotrophic lateral sclerosis, also known as ALS or Lou Gehrig’s disease.

These diseases are called as proteinopathies because they occur when proteins “misfold,” causing them to grow “sticky” and clump up in the brain. These clumps of proteins are often referred to as “plaques,” or “tangles.”

A Gill Professor in the Linda and Jack Gill Center for Biomolecular Science and Department of Psychological and Brain Sciences in the IU Bloomington College of Arts and Sciences, Lu is lead author on the study. Ali and Hunter are co-authors and members of Lu’s lab at IU.

The IU scientists and colleagues’ study found that NMNAT2, or nicotinamide mononucleotide adenylyl transferase 2, appears to prevent or repair the errors that cause these clumps by binding to misfolded proteins. The enzyme also appears to help protect neurons from stress caused by over-excitation.

Hui-Chen Lu is the lead author on the study that is the subject of the AMA.

Hui-Chen Lu is the lead author on the study that is the subject of the AMA.

As part of the study reported in PLOS, the scientists observed that increasing levels of NMNAT2 in mice whose brains had been damaged by Tau — a protein that correlates with neurodegenerative disease progression — reduced levels of the toxic protein. Significantly, the scientists increased NMNAT2 levels in the hippocampus, a regain of the brain related to learning and memory.

A fourth author of the paper will also join the AMA: Hugo Bellen, a professor at the Baylor College of Medicine and an investigator with the Howard Hughes Medical Institute.

To submit a question for the AMA, visit r/Science starting at 9 a.m. EST Dec. 7. Audience members are also invited to join the conversation during the AMA on Twitter using the hashtag #PLOSredditAMA.

A downloadable app is available from Reddit to ask questions or submit comments during the AMA.

This page will be updated with a direct link to the session after it goes live.

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Virtual liver model could help reduce overdose risk from acetaminophen, other drugs Tue, 29 Nov 2016 16:40:28 +0000 Biocomplexity Institute researchers at IU Bloomington create computer simulation to analyze drug absorption at the cellular to whole-body level

Researchers at Indiana University’s Biocomplexity Institute have developed a virtual model of the human liver to better understand how the organ metabolizes acetaminophen, a common non-prescription painkiller and fever-reducer used in over-the-counter drugs such as Tylenol.

The study, reported in the peer-reviewed online journal PLOS ONE, suggests that virtual tissues models could play an important role in modern pharmacokinetics, the branch of pharmacology concerned with the movement of drugs within the body.

“This image shows an overview of the multi-scale computer model for drug metabolism. The images on the left show the three biological scales in the model – the whole-body level, the liver organ level and the cellular level.”

An overview of the multi-scale computer model for drug metabolism. The images on the left show the three biological scales in the model: the whole-body level, the organ level and the cellular level.

Specifically, the study employs “virtual tissue” technology developed at the institute to model the distribution of drugs in the human body at multiple scales — time and location in the body — an ability that could help contribute to more personalized prescription guidelines that reduce the risk of overdose.

Acetaminophen metabolism is significant because poisoning from a liver metabolite of acetaminophen is the leading cause of acute liver failure in the United States, resulting in over 33,000 hospital admissions and 500 deaths each year. Acute liver failure can lead to death since the liver is the primary organ responsible for the metabolism and clearance of toxins, including drugs, from the body.

“Although this model of acetaminophen toxicity isn’t currently directed at developing interventions to accidental overdoses, it suggests a surprisingly large degree of difference in sensitivity to the drug across large populations,” said James Sluka, a research scientist at the Biocomplexity Institute, who is a co-lead author on the paper. “According to our model, as many as one in a thousand people may be unusually sensitive to the drug’s toxicity.”

The other co-lead author on the work is Xiao Fu, a graduate student at the Biocomplexity Institute. Other authors are Julio Belmonte, also a graduate student; Sherry Clendenon, a research associate; and Maciej Swat, an associate scientist, all of the Biocomplexity Institute. John Wambaugh, a computational toxicologist with the U.S. Environmental Protection Agency, also contributed to the study.

The senior author on the paper is James A. Glazier, director of the Biocomplexity Institute and a professor in the Department of Intelligent Systems Engineering in the School of Informatics and Computing at IU Bloomington.

The liver acts as a blood flow gateway between the gut and the rest of the body due to the organ’s position between the gastro-intestinal tract and the systematic circulation part of the cardiovascular system. It also plays a key role in preventing nutrient imbalance, which can contribute to high cholesterol, obesity and Type II diabetes.

To construct a virtual liver model that took into account “multiple scales” of time and location in the body, Sluka and colleagues used publically available data on acetaminophen distribution and metabolism that reflected the drug’s uptake in the gastrointestinal tract, distribution throughout the body and uptake and metabolism in the liver, and the clearance of the drug and metabolites from the body.

“The lack of significant data in humans beyond models of drug concentration in the blood stream was a major challenge,” Sluka said. “We had to not only depend upon human data but also information from animal- and cell-based studies to create a highly accurate virtual liver.”

At the whole-body level, Sluka and colleagues’ model simulates a drug’s absorption from the gastro-intestinal tract, distribution by the blood to the tissues and organs, and removal by the liver and kidneys.

James Glazier is director of the Biocomplexity Institute

James Glazier is director of the Biocomplexity Institute

At the organ level, the model simulates how compounds carried by the blood enter the liver through the hepatic artery and portal vein; flow through the network of sinusoids, which are liver capillary blood vessels; and exit though the organ’s hepatic central vein.

At the subcellular level, the model takes into account how metabolic pathways inside the liver convert chemical compounds into metabolites, which are either transported back into the blood or into the gastrointestinal tract through the bile duct.

Metabolites can also be toxic to liver cells and, in the case of overdose, irreversibly damage the liver. Generally, gene expression patterns within the liver determine which of the organ’s multiple pathway are used to metabolize a chemical.

Using this system, Sluka and colleagues were able to model an oral dose of acetaminophen’s concentration at various points in time in various tissues in the body, especially the liver. IU’s supercomputing resources were then used to simulate the process in thousands of virtual patients over the course of several days — an experiment that would have otherwise required several years to complete.

“These three submodels can also be run independently, which greatly simplifies the calibration of the model as well as the ability to connect the model’s predictions to clinically accessible measurements from real patients,” Sluka said. “So we can directly connect measurements from the clinic or the lab to the measurements predicted by our mathematical and computational models.”

Moreover, Sluka pointed out that the team’s virtual liver model was built using open source software, including technology developed by the Biocomplexity Institute called CompuCell3D, so other researchers can reuse all or part of the software without restriction; modify it to examine the toxic risk of different drugs or environmental toxins; or use it to study the toxicity of these compounds in nonhuman species.

This study was supported by the U.S. Environmental Protection Agency and the National Institutes of Health’s National Institute of General Medical Sciences, National Institute of Environmental Health Science and National Institute of Biomedical Imaging and Bioengineering.

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IU informatics researcher earns three federal patents to strengthen user control in the ‘app economy’ Tue, 15 Nov 2016 15:45:25 +0000 “The future is apps” is a phrase commonly uttered by technology experts. Anyone who has ever struggled to find the right app at the right time might not share that opinion, however.


Sameer Patil

Sameer Patil‘s efforts to strike at the heart of this modern dilemma — and also strengthen user privacy in the “app economy” — was recently recognized by the U.S. Patent and Trademark Office, which has issued three patents to the assistant professor in the IU School of Informatics and Computing for his efforts on app search and discovery.

The work that led to the patents was conducted in 2014 at Quixey, a Mountain View, California-based company that aims to connect people with apps. A research scientist at Finland’s Helsinki Institute for Information Technology at the time, Patil spent four weeks during the summer of 2014 as a consultant at Quixey. He jokingly calls the job his “summer vacation” that year.

“The two major U.S. players in app search — Google’s Play Store and the Apple App Store — need improvement on two major fronts: relevance and accuracy, and search,” said Patil, who joined IU in August. “There currently isn’t a good way to sort or filter or find apps, and both services are overly focused on precise queries. If you don’t know an app happens to be called ‘Yelp,’ for example, you might not be able to find it. A search for ‘app for finding places to eat’ doesn’t cut it.”

His work at Quixey, which involved designing and conducting focus groups with users to understand their practices and preferences regarding finding and using mobile apps, generated insight that resulted in eight patent applications, three of which have been granted within the past couple of months. The common thread connecting the patents is their focus on protecting individual privacy while also opening up the convenience of social app search to a wider audience.

Patil’s first patent describes how to automatically infer who is currently using a shared device. The techniques use device usage patterns and contextual information, such as sensor data, which can indicate how the user is holding the device, or how the device is being used. A child might be more likely to play games aimed at children, for example, while a parent is more likely to use a banking application or use the device late at night.

“The ability to automatically detect who is using a device is enormously useful, since most devices like iPads are used by multiple people in the same family,” Patil said. “There is often information that parents want to keep private from children, or vice versa. This system could also be used to avoid showing adult content, like violent video games, to children who might be using the device.”

Patil’s second patent describes a technique to preserve privacy while also opening  up information about people’s apps to provide suggestions based upon apps used by a user’s friends, or other users with the same tastes — similar to Amazon’s “other people also search for” function.


Patil’s patents help people find new apps while protecting their privacy.

“Collective discovery is a powerful way to learn about new products, but not everyone is comfortable with other people knowing all of their information, since people use apps to track everything, including personal information like their medical history,” Patil said. “This patent describes a technique by which a user can indicate specific apps they’re OK with sharing and those they want to keep private.”

The third patent addresses another challenge in the world of apps: mobile devices that constantly run out of storage space due to unused and forgotten applications. This patent lays out a method to recommend apps for deletion based upon factors such as the amount of memory required, frequency of use and even physical location.

Although smartphones and tablets are the products most clearly targeted by the methods described in the patents, Patil points out that many other consumer electronic devices are now using “apps,” including GPS devices, smart TVs, smartwatches and even home appliances like refrigerators.

Patil is a member of the security group in the IU School of Informatics and Computing. His efforts at Quixey relate to his broader academic interests through a focus on providing individuals control over their data.

The research is also emblematic of the school’s strong connections with the industrial sector, including the fast-paced world of Silicon Valley. Many IU students have found internships and employment in the region after graduation, and several faculty have served as visiting scientists at companies such as LinkedIn and Yahoo. The dean’s advisory council at the school is also composed of prominent businesspeople and entrepreneurs who have made their careers in software and technology.

Patil is the principal investigator on a National Science Foundation grant to promote privacy compliance in software design in collaboration with Cisco and Microsoft. He is also the recipient of a 2016 Faculty Research Award from Google. Before joining IU as a faculty member, Patil spent 2011 to 2012 as a postdoctoral researcher in the lab of Apu Kapadia, an associate professor in the IU School of Informatics and Computing. He has also served as an assistant research professor at New York University and a research scientist in the mobile technologies research group at Yahoo Labs.

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Philosopher Dennett to lecture at IU Bloomington Tue, 08 Nov 2016 18:43:31 +0000 Post by IU News and Media Specialist Steve Hinnefeld who normally writes for the Policy Briefings blog:

Daniel Dennett has been called “one of our most important living philosophers,” a “Darwinian fundamentalist” and quite a few other things, positive and negative. As Julian Baggini observed in a profile for the Guardian, big thinkers make big targets, and they don’t come much bigger than Dennett.

Dan C. Dennett

Daniel C. Dennett | Tufts University

Expect thought-provoking analysis and lively discussion this week when Dennett presents two lectures at IU Bloomington as the inaugural event in the Department of Philosophy distinguished speaker series.

Dennett will speak Nov. 10 on “From Bacteria to Bach and Back: The Evolution of Minds” and Nov. 11 on “A Magician’s View of Consciousness.” Both lectures will be from 4 to 6 p.m. in Whittenberger Auditorium of the Indiana Memorial Union. They are free and open to the public.

“For almost five decades now, Daniel Dennett has been a powerful and influential advocate for explaining minds and behavior in scientific terms,” said Gary Ebbs, professor and chair of the philosophy department. “He draws on results from biology, psychology and neuroscience to demystify the mind.  His writings and lectures weave together vivid, thought-provoking examples, informed expositions of scientific results and high-level clarifications of key concepts and experiences of our mental life.”

Dennett is co-director of the Center for Cognitive Studies at Tufts University, where he is also University Professor and Austin B. Fletcher Professor of Philosophy. He is the author of “Breaking the Spell,” “Freedom Evolves”, “Darwin’s Dangerous Idea” and other books. He co-edited “The Mind’s I,” published in 1981, with IU College of Arts and Sciences Distinguished Professor Douglas Hofstadter.

His most recent books include “Intuition Pumps and Other Tools for Thinking” and “Caught in the Pulpit: Leaving Belief Behind.” His latest, “From Bacteria to Bach and Back,” is in press. His TED Talks, including “The Illusion of Consciousness” and “Dangerous Memes,” have been viewed millions of times.

The author of over 400 scholarly articles, Dennett has received two Guggenheim Fellowships, a Fulbright Fellowship and a Fellowship at the Center for Advanced Studies in Behavioral Science. He was elected to the American Academy of Arts and Sciences in 1987. He was an Indiana University William T. Patten Lecturer in 2006.

For more on Dennett and his IU lectures, see Hussain Ather’s article in the Indiana Daily Student.

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Robots invade and volcanos erupt on campus at third annual Science Fest Tue, 25 Oct 2016 21:24:50 +0000 Post by IU Newsroom intern Sheila Raghavendran

On Saturday, Oct. 22, IU was overrun with robots.

These robots — machines such as PARO, the therapeutic robotic seal — were on site for holding and petting as part of the School of Informatics and Computing’s activities at the IU Bloomington College of Arts and Sciences’ third annual Science Fest.

Parents and youngsters examine rocks during Science Fest outside Owen Hall on Saturday, Oct. 22, 2016.

Parents and children explore rocks outside Owen Hall at IU’s third annual Science Fest.

Many science departments in the college, including chemistry, astronomy, physics and psychological and brain sciences, also hosted activities for students and the general public.

When Science Fest started in 2014, it was the first time these departments and other groups were brought together to hold an event to share science with the public all on one day, according to Tina Gilliland, outreach liaison for the College of Arts and Sciences’ Office of Science Outreach.

This year there were 15 departments and groups holding activities — the highest number Science Fest has seen.

Along with PARO, Science Fest also offered a station for people to try their hand at designing 3D models with the help of Matt Francisco, a visiting lecturer at the School of Informatics and Computing, and his students.

“The kids learn that they need to provide us with enough information to create a 3D model,” Francisco said. “They’re often very good at drawing one perspective, but it’s not enough information to do 3D modeling, so I have my assistants, who are getting them to do at least two views.”

Aside from robot interactions, other activities included an explosive volcanic eruption simulation using water and liquid nitrogen hosted by the Department of Geological Sciences and an earthquake simulation that could be cranked up to a magnitude of 7.0 hosted by the Indiana Geological Survey.

Lauren Reynolds, 10, of Bloomington, smiles as she pets, PARO, an advanced interactive therapeutic baby seal, during Science Fest in Lindley Hall on Saturday, Oct. 22, 2016.

Lauren Reynolds, 10, of Bloomington learned about PARO, a therapeutic robot baby seal, during a hands-on event in Lindley Hall.

According to Teddie Phillipson-Mower, associate director for the Office of Science Outreach, these and other Science Fest activities are meant to be fun yet informative.

“It’s not just activity after activity,” she said. “The people running these … they’re explaining the science behind everything that’s happening.”

The volcanic eruption simulation took place outside the Student Building in a large trash can. When activated with liquid nitrogen, the trash can launched several feet into the air, erupting with water and golf balls.

Ian Wang, a Ph.D. student in geological sciences, broke down the volcanic simulation process.

“This whole trash can will be simulating the magma chamber,” Wang said. “If we put liquid nitrogen in it — because liquid nitrogen is so cold when it is put in the water — it will turn into gas… [and] expand. This expansion is really fast and eventually it will actually explode and blow water out. That’s like what happens in the real volcanic eruption.”

Bloomington High School South freshman Tabby Duvall said she did not know much about earthquakes before Science Fest, but that experiencing the simulation at the Indiana Geological Survey “Quake Cottage” gave her some insight on how to prepare.

Water erupts out of a trash can as part of a volcanic eruption demonstration during Science Fest outside the Student Building on Saturday, Oct. 22, 2016.

A trash can spews water and golf balls as part of a volcano demonstration outside the Student Building.

“It’d be kind of scary to be in a 7.0,” Duvall said. “I just learned what to do in an earthquake — you have to cover your head and grab onto something; go into storage and bring food and water in case of [emergency].”

Bloomington resident Michael Cole said he brings his kids to Science Fest every year to encourage their exploration of sciences.

“Each year it seems like there are better events and more and more people, which is fantastic,” Cole said. “One thing I noticed this year specifically is that it seems like there’s more and more women in the sciences, which for my daughter is very inspirational.”

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IU physicist played early role in history of Nobel Prize-winning theory Tue, 04 Oct 2016 20:27:25 +0000 A physicist at Indiana University played an important role in the history of the work of two scientists honored by today’s Nobel Prize in Physics.

The winners of the 2016 Nobel Prize in Physics are David J. Thouless, Michael Kosterlitz and F. Duncan M. Haldane, who were recognized Oct. 4 for theoretical discoveries of topological phase transitions and topological phases of matter.

Jorge V. José

Jorge V. José

Topology is a branch of mathematics that describes objects with special geometric properties. Thouless and Kosterlitz’s ideas were first described in 1971 as a novel phase transition of topological objects called vortices under the name Berezinskii-Kosterlitz-Thouless Theory.

A professor of physics in the IU Bloomington College of Arts and Sciences’ Department of Physics, Jorge V. José led theoretical work in the late 1970s that helped spur wider scientific acceptance of BKT theory, which has since been used to advance mathematical methods to study unusual phases of matter such as those found in superconductors, superfluids and ultra-thin magnetic films.

More recently, in recognition for this role in the early history of the theory, José was selected to edit a 40th anniversary book on the subject whose first chapter is authored by Thouless and Kosterlitz.

José’s role in the history of BKT theory began shortly after the first description of the theory. A postdoctoral researcher at the time at Brown University, José approached Leo Kadanoff — his colleague and a world-renowned physicist who previously served as his Ph.D. thesis advisor — with some thoughts on BKT theory, which had started to cause a stir in the world of physics, despite some colleagues who called into question some of the claims of BKT theory about the behavior of matter under extreme conditions.

The germ of that conversation went on to blossom into a new theoretical way to validate many of these predictions of BKT theory.

“We were able to provide a new layer of mathematical proof to some of the BKT ideas that had been previously presented intuitively,” said José, who explained the work they conducted applied certain developments in theoretical physics that had arisen in the years since the original formulation of BKT — such as renormalization and gauge theory – to BKT theory in order to strengthen evidence for its assertions about the ways in which matter behaves under extreme conditions.


José was selected to edit a 40th anniversary book on Berezinskii-Kosterlitz-Touless Theory.

The work — authored by José, Kadanoff and collaborators at Harvard and IBM — was first reported in the journal Physical Review B of the American Physical Society in 1977. Soon after, in 1978, the methods described in that paper played an important role in the design of physical experiments conducted on thin layers of helium at Cornell University.

“That was really the key moment,” José added. “Everything really took off after that. Everyone found new ways to apply the BKT theory to their own areas.”

The experiments constituted the first physical evidence for the phase transitions predicted by BKT theory — and kicked off decades of expansion and elaboration upon the theory that has touched nearly every field of physics. Since its inception, BKT theory has been actively applied to condensed matter physics, high energy physics, atomic physics, nuclear physics, statistical physics and nonlinear systems, among other fields.

Industrial and commercial applications of the BKT theory include everything from the design of next generation electronics and quantum computers to describing the behavior of ultra-cold atomic gases trapped under quasi-two-dimensional conditions.

The third scientist who lent his name to BKT theory was Vadim Berezinskii, who died in 1980.

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IU study reveals rats have greater episodic memory than previously thought Thu, 29 Sep 2016 16:18:34 +0000 Anyone who has ever spotted a familiar face at a party but been unable to place where or when they last met that person knows the difference between episodic memory and familiarity.

Familiarity is mere recognition. Episodic memory is the ability to recall a memory’s context — to remember where and when you saw that familiar face. It’s also the difference between sputtering your way through a reintroduction or smoothly referring back to details about the last time you talked to your acquaintance.

A rat in the center of eight spices. IU scientists used over 30 spices in two mazes with different circular patterns on the floor to gauge rat’s ability to remember information in specific contexts.

A rat in the center of eight spices. IU scientists used over 00 spices in two circular “arenas” with different black-and-white patterns on the floor to gauge rat’s ability to remember information in specific contexts.

Although it’s easy to grasp the difference in these types of memory in ourselves, it’s not easy to know how animals see the world. Do their memories also take context into account?

A new study by Indiana University researchers that appears online today in the journal Current Biology suggests that rats exhibit much stronger episodic memory than previously thought. It is the first study to show that these animals can remember more than 30 events in context.

The lead author on the study is Danielle Panoz-Brown, a graduate student in the lab of Jonathon Crystal, a professor in the IU Department of Psychological and Brain Sciences, who is also an author on the paper.

“Most work shows that rats, and other animals, remember one, two or perhaps three events,” Crystal said. “This new work shows that rats remember many events — over 30 — and are likely able to remember many more using episodic memory.”

He added that the existence of episodic memory in lower animals has implications for research on human diseases that affect memory, including Alzheimer’s, Parkinson’s and Huntington’s diseases, since the majority of research on the brain — and the drugs used to treat memory diseases and dementia — start out based on insights into how the brain works in rats.

So, if a pharmaceutical company creates an Alzheimer’s drug to target memory based on research into one type of memory — the part of the brain responsible for finding missing objects, for example — but doesn’t also have data on the type of memory that helps individuals remember the important people, places and things in their life, it runs the risk of producing a product that helps a person remember where they put the car keys, but not how they met their spouse.

That risk is the impetus behind several other studies published by Crystal over the past several years. In January, Crystal’s lab reported evidence that animals also possess independent working memory systems by showing that rats could remember a longer list of items when asked to recall a combination of physical locations and smells versus when they used only a single category of information. And prior to that, they found that rats also possess “source memory,” which is the ability to recall where a new piece of information was acquired.

Jonathon Crystal

Jonathon Crystal

To conduct the new study, Panoz-Brown and Crystal developed a series of challenges in which rats were asked to recall up to 30 different scents — basil, strawberry and banana, among many others — to earn a treat. However, they only earned the reward when they chose the correct scent in a certain context — one of two circular “arenas” with different black-and-white patterns on the floor.

The rats were exposed to a series of many odors and then taught to associate “new” odors — ones to which they had not been previously exposed — with food. After learning this “rule,” they were put into one arena and exposed to an odor (for example, a strawberry). They were then put into a second arena and exposed to two odors (such as blueberry and strawberry). Finally, they were placed back into the first arena and presented with two odors. They correctly chose blueberry as the “new” odor, despite their previous exposure in the other context.

The results suggest the rats realized the second odor counted as “new” since they had not yet encountered it in the second context. Moreover, the rats performed similarly on several other challenges, including a test designed to challenge their ability to recall these “rules” over time and an attempt to confuse them through rapidly switching the contexts.

“Our findings suggest that the ability to represent numerous episodic memories is quite old in the evolutionary timescale,” Crystal said. “More broadly, our work supports the view that rats may be used to model fundamental aspects of human memory.”

Unfortunately, not many researchers study these more-complex areas of memory. One major reason is that it’s just easier to target the parts of the brain that remember location. Automated technology used by many labs makes it easier to simply track a rat as it runs through a maze — a test of location-based memory — as opposed to studying more-sophisticated forms of memory.

For that, Crystal’s lab relies on a large team of undergraduate students who can prepare more-complex tests and closely monitor the results. IU undergraduate researchers who worked on this study were Hannah E. Corbin, Stefan J. Dalecki, Meredith Gentry, Sydney Brotheridge and Christina M. Sluka, who are all also authors on the paper. Also an author is Jie-En Wu, a member of Crystal’s lab who was a high school student at the time of the research reported in the paper.

This research was supported by the National Institutes of Health’s National Institute on Aging and the National Institute of Mental Health.

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IU part of $1 million grant from NSF to create country’s first big data “spoke” focused on neuroscience Wed, 28 Sep 2016 15:36:13 +0000 “The field of neuroscience is transforming,” wrote IU neuroscientist Franco Pestilli in a commentary published last year in the journal Nature Scientific Data. “Brain data from people and institutions around the world are being openly shared — moving from office desks and personal storage devices to institutionally supported cloud systems and public repositories.”

This process of openly sharing brain data — a part of the larger movement toward “open science” — is ushering in the era of “big data neuroscience.”

An environmental portrait of Franco Pestilli.

IU neuroscientist Franco Pestilli is principal investigator on the NSF grant funding the Neuroscience Spoke of the Midwest Big Data Hub.

And now, as part of the team named recipient on a $1 million grant, IU will play a role on the forefront of this era by contributing to the establishment of the Neuroscience Spoke in the Midwest Big Data Hub. The principal investigator on the award is Pestilli, an assistant professor in the IU Bloomington College of Arts and Sciences’ Department of Psychological and Brain Sciences.

The award — a part of a major new initiative from the National Science Foundation and White House to “create a national ecosystem for Big Data and Data Science” — is a symbol of IU’s progression toward leadership in the field of both neuroscience and big data science. It is also part of $11 million in federal grants announced today to advance research and create infrastructure designed to ensure data acquired by publicly funded basic research is effectively shared and used.

“This award will help put IU on the map as a leader in the big data neuroscience,” Pestilli said. “We will contribute to moving neuroscience research beyond a cottage industry model, where independent labs generate data that remains unshared, by establishing a regional and national network of professionals and scientists who are proficient in data science and who possess the assets necessary to share data, software and computing resources that contribute to the impact of the scientific enterprise and the reproducibility of results.”

Pestilli’s co-investigators on the Neuroscience Spoke are Olaf Sporns, IU Distinguished Professor in Psychological and Brain Sciences, and Andrew Saykin, Raymond C. Beeler Professor of Radiology and Imaging Sciences at the IU School of Medicine.

The term “spoke” refers to IU’s position as part of the Midwest Big Data Hub, one of four regional “hubs” across the country funded under the NSF’s Big Data Hub program. The award makes IU part of the only spoke in the United States focused on neuroscience.

Big data hubs are administrative entities that facilitate research and coordination across regions composed of spokes with specific areas of interest. Members of the Midwest Hub are IU, University of Michigan, Iowa State University, the University of North Dakota and the University of Illinois at Urbana-Champaign.

The Neuroscience Spoke will facilitate the sharing of data such as this visualization of two brain connectomes. The image, which uses two different methods for mapping human white matter, is based upon a scan of Pestilli's own brain.

The Neuroscience Spoke will facilitate the sharing of data such as this visualization of two brain connectomes. The image, which uses two different methods for mapping human white matter, is based upon a scan of Pestilli’s brain.

The Neuroscience Spoke is made up of IU, the University of Michigan, Case Western University, The Ohio State University, Northwestern University and the University of Washington St. Louis.

A major part of the new spoke’s effort to improve neuroscience data sharing will be a series of Big Data Neuroscience workshops designed to create closer ties between the research labs, neuroimaging centers and hospitals affiliated with the members of the Midwestern Big Data Hub.

The first of these workshops, organized by Pestilli, will be held in the third quarter of 2017 at IU Bloomington, after which they will move to Ohio State in 2018 and the University of Michigan in 2019.

Each workshop will host everyone from leaders to trainees in the field of neurosciences to learn and discuss best practices around big data. Planning for the workshops has already begun, with the preparations for the first event kicking off at the University of Michigan on Sept. 21 to 22.

Beyond its leading position in the new Neuroscience Spoke, IU is also playing other leading roles in the NSF’s Big Data Hub initiative. Beth Plale, professor in the IU School of Computing and Informatics and science director of the IU Pervasive Technology Institute, is a co-primary investigator on the Midwest Big Data Hub, and Bernice Pescosolido, IU Distinguished Professor of Sociology, is leader of the Midwest Big Data Hub’s Network Science Spoke.

Pescosolido and Sporns are also scientific co-directors of the IU Network Science Institute, or IUNI. Saykin is a member of the scientific leadership team at IUNI.

“This is, effectively, a ‘collaborative IUNI grant,'” said Pestilli, who is also an affiliate of IUNI. “The institute’s leadership has been incredibly helpful to me in clarifying the requirements of this new NSF program.”

Other co-investigators on IU’s portion of the Neuroscience Spoke grant are Lei Wang of Northwestern University and Daniel Marcus of Washington University in St. Louis. Wang will be contributing expertise on Mediator software technology. Marcus will serve as a consultant on the grant due to his expertise in neuroscience data management.

“I look forward to reaching out to the extended IU campus for contributions to these efforts,” added Pestilli. “IU expertise in high-performance computing, infrastructure engineering and big data projects will naturally extend to these new efforts in the neurosciences.”

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IU graduate students share passion for science and conversation with ‘ScIU’ Thu, 18 Aug 2016 21:35:50 +0000 A committed team of graduate students from across the sciences at IU are banding together to provide a glimpse inside the world of Bloomington’s research labs through a new effort that seeks inform, entertain and spark conversations about science.

ScIU: Conversations in Science,” which officially launches Aug. 22, is a new blog that seeks to foster discussion and awareness about science across the university and the community.

ScIU students

Among the writers and editors of ScIU are Lana Ruck, Ed Basom, Nichole Nagoette, Victoria Kohout, Noah Zarr, Daniel Bullock and Benjamin Draper (left to right, back row) and Maria Tiongco, Amrita Bhattacharya, Josey Topolski, Mark Juers, Anna Jessee, Clara Boothby and Fabio Mendes (left to right, front row). Photo by Mike Jackson.

“We’re taking the time to do this because we love the discovery, the questions and the excitement of science – of trying to work and understand, and to build upon the knowledge of those who came before us,” said Briana K. Whitaker, a graduate student in the IU College of Arts and Sciences’ Department of Biology and a member of the blog’s editorial team. “With ScIU, we’re hoping to foster conversations between scientists and non-scientists and to start a dialogue about IU science that helps connect different people on and around campus.”

The graduate student editors and writers at ScIU represent a wide swath of science departments at IU Bloomington, all of whom have been collaborating on the project since last spring. Together, they’ve brainstormed topics, discussed the challenges of science writing and worked to raise excitement about the blog among their peers and research mentors.

The project was originally proposed and remains supported by the IU Bloomington College of Arts and Sciences’ Research Office and Office of Science Outreach, whose mission includes the promotion of diversity, awareness and accessibility of science to everyone.

“This project is all about public engagement with the sciences and focusing a two-way dialogue that not only communicates IU’s cutting-edge research to the public but is responsive to the public about what they need from science to make informed decisions in their lives,” said Jo Anne Tracy, director of the Office of Science Outreach and assistant dean for research in the College of Arts and Sciences.

“When we put out the call, our graduate students showed up with not only the same expectations, but also a highly nuanced understanding about how to make it work. I can’t say enough about how impressed I am with their enthusiasm and work ethic,” she added.

The blog’s target audience is everyone from faculty and staff to postdoctoral researchers, graduate students and undergrads who may be considering careers in science – as well as IU parents, nonscientists and other members of the public. The blog’s mission statement asserts that “scientists have an active role to play in communities” and that “open communication about science is everyone’s responsibility.”

The first post to kick off the blog will be a thoughtful meditation upon the larger purpose of science, written by Fábio Mendes, a graduate student in the lab of Matthew Hahn, professor of biology and informatics. Mendes’ entry explores the many advances that science has brought humanity — medical, technological, societal — as well as the importance of basic science and reward in pursuing answers for their own sake.

ScIU homepage

The ScIU homepage prior to “launch” on Aug. 22.

Other entries coming right out the gate will explore such subjects as “superhybrids,” or those special species that demonstrate how the “Tree of Life” is actually a tangled shrub; the “secret life of fungus” as revealed through an analysis of switchgrass; and how an on-campus language lab is working to address the many challenges faced by bilingual language speakers in over-the-phone conversations.

Of course, Whitaker notes that blogging is a big commitment, especially for busy graduate students. So she and her fellow students have developed a deep stable of contributing writers, not to mention a highly involved team of editors.

The editorial team for ScIU includes Whitaker; Maria Tiongco of the Department of Astronomy; Ed Basom, Benjamin Draper and Josey Topolski of the Department of Chemistry; Clara Boothby of the Department of English; Anna Jessee of the Department of Geological Sciences; Emily Byers of the Department of Speech and Hearing Sciences; and Rachel Skipper and Noah Zarr of the Department of Psychological and Brain Sciences. The blog’s writers and editors include graduate students in the School of Informatics and Computing and the College of Arts and Sciences’ departments of Astronomy, Biology, Chemistry, Physics, Psychological and Brain Sciences, and Speech and Hearing Sciences.

Additional editorial support is provided by Katie Van Loo, a recent Ph.D. graduate of the Department of Psychological and Brain Sciences, and Elizabeth Rosdeitcher, science writer in the Department of Psychological and Brain Sciences.

To check out the blog and join the conversation, visit the ScIU webpage.

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IU physicist presents new evidence about nature of the third mass state in neutrinos Mon, 08 Aug 2016 15:11:29 +0000 A year and a day after delivering the first results from a multi-million-dollar detector built to shed light on the nature of neutrinos, IU physicist Mark Messier announced the project had produced new evidence about the nature of the “third mass state” of these mysterious subatomic particles.

An illustration of the three neutrino mass states and the three flavors that make them up (electron, muon and tau), as they were previously though to mix. NOvA’s new result shows that the third mass state may not have equal amounts of muon (yellow jellybeans) and tau (blue jellybeans) flavors. Image by Fermilab/Sandbox Studios.

The results were presented at the 2016 International Conference of High-Energy Physics in Chicago.

“Neutrinos are always surprising us,” said Messier, who is co-spokesperson for the NOvA experiment, the project that generated the results. “This result is a fresh look into one of the major unknowns in neutrino physics.”

A $278 million international collaboration of nearly 230 scientists and engineers from 41 institutions across the globe, the NOvA experiment is headquartered at the U.S. Department of Energy’s Fermi National Accelerator Laboratory

Neutrinos have previously been detected in three types, called flavors – muon, tau and electron. They also exist in three mass states, but those states don’t necessarily correspond directly to the three flavors.

The results of the experiment announced Aug. 8 suggest that one of the three neutrino mass states might not include equal parts of muon and tau flavor, as previously thought. Scientists refer to this as “non-maximal mixing,” and NOvA’s result is the first hint that this may be the case for the third mass state.

“In physics, symmetries are often important clues about what’s going on behind the scenes,” Messier said. “In this case we’ve seen a symmetry break, and exactly how and in which direction can tell us more about how neutrinos relate to each other and the other fundamental particles.”

The experiment data was collected from the NuMI Off-Axis Electron Neutrino Appearance far detector building, a 14,000-ton, multi-story structure in Ash River, Minn. The neutrinos created for the experiment are generated at Fermilab, located in Batavia, Ill., and then beamed through the Earth to the detector over 500 miles to the northwest.

Mark Messier, professor of physics, is co-spokesperson for the NOvA Experiment. He is shown here seen here during the construction of the NOvA detector in 2012.

Mark Messier, IU professor of physics, is co-spokesperson for the NOvA Experiment. He is seen here during the construction of the NOvA detector in 2012. Photo by Fermilab.

The Minnesota facility has been collecting this data since February 2014. But IU’s role in the experiment began a decade ago, during the facility’s construction. IU scientists played a key role in the design and construction of the facility’s three-million-gallon “liquid scintillator,” the main component used to detect the neutrinos from Fermilab. The scintillator glows softly in response to ion radiation.

Other IU scientists who played a role in NOvA are Stuart Mufson, professor in the Department of Astronomy; Jim Musser, professor in the Department of Physics; John Karty, associate scientist in the Department of Chemistry; Mark Gebhard, a master technician; and Jon Urheim, professor of physics. The group has six students and three post-doctoral researchers working on NOvA analysis.

The NOvA experiment is funded by the U.S. Department of Energy Office of Science, the National Science Foundation and other institutions worldwide.

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IU, Bloomington rally around Wally the corpse flower Wed, 03 Aug 2016 20:32:05 +0000 “Bloomington loves Wally.”

So read a handmade sign tacked to the window of IU’s Jordan Hall Greenhouse on East Third Street, where a giant, odoriferous corpse flower named after a former IU staffer recently grew to a height of 6 feet 3 inches.

Over 5,000 people came to witness the corpse flower at IU Jordan Hall Greenhouse.

Over 5,000 people came to witness the corpse flower at IU Jordan Hall Greenhouse. Photo by IU Communications.

Scientifically named Amorphophallus titanum, or a titan arum, the enormous bloom unfurled the evening of Friday, July 29, revealing a deep crimson interior for about 36 hours, after which the plant’s leaves drew closed and the spadix — a large stem-like structure — sagged like a balloon after a party.

But during the short period from Friday evening to Sunday morning, Wally drew about 5,000 visitors to the greenhouse, including IU President Michael A. McRobbie. At the height of the bloom, the wait to visit the plant climbed over 90 minutes, with a line snaking through the greenhouse and into the main academic building.

“It’s a pretty impressive number when you add in the people who came on Friday afternoon and the people on Sunday to the crazy crowds on Saturday,” said Jean-François Gout, a research associate in the IU Bloomington Department of Biology, who produced a time-lapse video of the bloom (see below). “I myself saw the line extend to the end of the hallway in Jordan Hall.”

After laying dormant for nine years, the plant grew over 6 feet tall in three weeks.

After nine years, IU’s corpse flower (or “titan arum”) grew over six feet tall in three weeks to produce its first bloom. Photo by IU Communications.

The majority of visitors hailed from Bloomington, but some arrived from farther afield. IU gardener John Leichter reported meeting several “flower groupies” who said they had traveled from New York City, where they recently saw another corpse flower bloom. The Herald-Times also reported visitors from Ohio and Oklahoma.

Many others simply peered through greenhouse windows from the sidewalk, or tuned into the live-stream. IU Collaborative Technologies estimates the live-stream player page was loaded 115,585 times during the bloom, with views reported from 96 different countries.

The size of the corpse flower attracted onlookers; so did the odor: a fetid smell produced by a cluster of small flowers — or “unbranched inflorescence” — at the base of the spadix to attract insect pollinators who normally feed on dead animals.

One visitor to the greenhouse described the smell on Twitter as “between a litterbox and the New York City subway.” The Department of Biology’s Facebook page said the scent was detectable outside the greenhouse on Friday night.

In addition to kicking off a weeklong vigil across Bloomington — with several updates on WFIU, a front page and follow up article in the Herald-Times and multiple reports on television and print news sites in Indianapolis — the IU corpse flower’s impending bloom drew national attention, with references to the flower on National Public Radio, the Wall Street Journal and Smithsonian Magazine.

Jordan Hall Greenhouse Supervisor John Lemon removes pollen from Wally's "splathe" for shopping to the

Jordan Hall Greenhouse Supervisor John Lemon removes pollen through Wally’s “spathe” for shipping to the U.S. Botanic Garden in Washington, D.C., where it will fertilize the corpse flower in bloom at the national greenhouse. Photo by IU Bloomington Department of Biology.

The plant even got an unofficial celebrity endorsement, with actor and comedian Andy Richter posting a link to the livestream to 775,000 followers on Twitter. Two posts about the flower on IU’s Facebook page reached over 150,000 unique users and were shared over 375 times. Many others visited the Department of Biology’s Facebook page for daily updates.

The national attention stemmed in part from the unusually large number of other corpse flowers blooming at the same time around the country. The bloom at the New York Botanical Gardens beat out IU’s flower by a day, opening on Thursday, July 28; another corpse flower at the U.S. Botanic Garden in Washington, D.C., opened Aug. 1.

Beyond similar bloom dates, IU’s plant has an even closer connection with the plant in the nation’s capital: the two could soon produce offspring.

Since corpse flowers bloom so rarely, IU gardeners explain it’s hard to produce new plants, especially since the male and female parts of the plant don’t bloom at the same time, making self-fertilization difficult. The U.S. Botanic Garden’s bloom presented a unique opportunity.

On Aug. 1, IU greenhouse supervisor John Lemon harvested pollen from Wally’s spathe, or outer leaf, cutting a small window in the structure to collect the pale yellow pollen, after which the small motes were shipped via express mail to the national greenhouse.

IU President Michael A. McRobbie, right, examines the flower with Clay Fuqua, chair of the IU Bloomington Department of Biology.

IU President Michael A. McRobbie, right, examines the flower with Clay Fuqua, chair of the IU Bloomington Department of Biology. Photo by IU Bloomington Department of Biology.

Staffers at the Washington, D.C. facility will use the pollen to fertilize their plant. If all goes according to plan, Wally will soon be a proud papa, with some of the seeds from the “union” returning to Bloomington to create Wally Jr.

In addition, IU greenhouse staff are preparing the current plant for the next bloom, which should arrive in three years now that a flower has appeared for the first time. IU gardeners will soon relocate Wally’s “corm” — the basketball-sized, bulb-like structure from which the flower or leaf springs — to a larger pot, which should encourage the next bloom to grow even bigger. In between blooms, the plant also generates a single leaf, which can reach 20 feet tall, that nourishes the corm in order to produce another leaf or bloom.

But Wally’s most lasting legacy may be the awareness raised about the IU Jordan Hall Greenhouse, a unique research facility constructed in the 1950s, which is free and open to the public. Wally’s nickname even highlights the greenhouse’s long history, referring to Hugh “Wally” Scales, who retired in the early 1970s after many years as the chief botanical gardener in the Department of Biology.

To support upgrades to the greenhouse through the unofficially named “Wally Fund,” visit the Biology Enrichment Fund and note “Jordan Hall Greenhouse” in the “In honor of” field.

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Enormous, rare ‘corpse flower’ about to make pungent debut at IU’s Jordan Hall Greenhouse Tue, 19 Jul 2016 19:21:34 +0000 If houseplants, like houseguests, start to stink after three days, then an extremely rare plant that hasn’t bloomed in nine years at IU’s Jordan Hall Greenhouse is due to create a stench for the ages.

One of the world’s largest species of flower, the Amorphophallus titanum or titan arum, is expected to put forth its first bloom any day now. Known as the “corpse flower” for its overpoweringly foul odor, the bloom of this plant is an extremely rare sight.

Corpse flower with Adam Fudickar

The corpse plant at IU’s Jordan Greenhouse on July 14. Adam Fudickar, a postdoctoral researcher in the Department of Biology, gives a sense of scale. Photo by Terri Greene, Indiana University.

As of July 19, the plant’s stem had reached a height of 3 feet, with several more feet expected. Interested individuals can follow the flower’s progress in real time via a live webstream, or visit the IU Bloomington Department of Biology’s Facebook page and a special Web page for updates on the expected bloom date.

A native to western Sumatra, the corpse flower takes eight to 20 years to bloom for the first time. After that, the flower appears every three years, and each bloom lasts only 24 to 36 hours. This is the first bloom of IU’s flower, and only five corpse flower blooms have been publicly recorded worldwide in the past year.

“With all of its size and fragrance, the flowering of this plant is not to be missed,” said paleobotanist David Dilcher, professor emeritus in the IU Bloomington College of Arts and Sciences’ Department of Biology and Department of Geology. “Although it’s related to the calla lily, a common sight in gardens across Indiana, the titan arum is tropical, with an enormous flower that is deep red in color and smells like rotten meat. The bloom of this plant is a spectacular sight rarely seen outside of major botanical gardens.”

The flower will be open for public viewing from 7:30 a.m. to 3:45 p.m. Monday to Friday and 9 a.m. to 3 p.m. Saturday and Sunday at IU’s Jordan Hall Greenhouse, at the corner of Third Street and South Hawthorne Drive in Bloomington, Ind. Parking is available at the Atwater Garage on Faculty Drive, between Third Street and Atwater Avenue.

The powerful scent of the corpse flower is designed to attract pollinators, such as sweat bees, beetles and carrion flies, which normally feed on dead animals. Because the flower blooms so rarely and lasts for so few hours, it requires an extremely strong odor to attract these insects quickly over a large area.

Corpse flower

The corpse flower had reached a height of 3 feet by July 19. Photo by Eric Rudd, Indiana University.

The corpse flower itself is technically made up of a cluster of small flowers arranged at the base of the stem, a structure known as an “unbranched inflorescence.” Normally the stems, which can weigh 110 pounds, grow about 3 to 5 feet tall, after which a taller leaf replaces the bloom.

Some plants grow much larger, however, with flowers of 10 feet tall recorded and leaves that span 20 feet tall and 16 feet wide. The heaviest stem ever recorded – 258 pounds – was documented at the Botanical Garden of Bonn, Germany, in 2006.

Despite its size, the titan arum doesn’t possess the largest unbranched inflorescence in the world – that title goes to the Lobelia rhynchopetalum, or giant lobelia, which only blooms every 50 years, according to Eric Knox, director of the IU Herbarium. But the titan arum is unquestionably the largest species cultivated in a greenhouse environment.

And while IU’s greenhouse staff cannot predict the final size of this particular bloom, IU gardener John Leichter said the plant is once again “about to outgrow its pants,” having been repotted every other year for the past nine years because of its rapidly increasing size.

The titan arum also requires specialized care, Leichter added, including the right temperature, humidity and watering. Too much water, for example, rots the plant’s bulb; too little and it will never bloom.

A corpse plant in bloom. Photo by Kew Royal Botanical Gardens.

A corpse plant in bloom. Photo by Kew Royal Botanical Gardens.

Creating a new plant from a single flower is a challenge since the male and female parts of the plant mature at different rates. After the plant blooms, department gardeners hope to save the pollen until the next flower’s appearance in three years to create a second plant through self-fertilization.

In addition, the Jordan Hall Greenhouse hosts two smaller plant species whose flowers also produce an extremely pungent smell: a voodoo lily, which smells like horse manure, and a “devil’s tongue,” which smells “like three-day-old roadkill,” according to Leichter.

The late Greg Speichert, former director of the Hilltop Garden and Nature Center at IU, donated the titan arum to IU in December 2007.

“These are rare plants,” Dilcher said. “It is a true credit to the IU greenhouse staff that they have been able to grow a bulb into a flower of this size in Bloomington.”

Members of the public and the media are welcome to view the flower. For more information, contact Terri Greene at 812-856-1476 or or the Jordan Hall Greenhouse at 812-855-7717 or

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High school students get crash course in science with latest addition to Biology Department’s summer research programs Tue, 12 Jul 2016 18:09:08 +0000 Post by Lauren Bryant, associate director for research development communications, Office of the Vice Provost for Research:

When Mary Ann Tellas was a freshman at Indiana University Bloomington, she had the good fortune to encounter the late Jim Holland, a professor of biology at IU Bloomington known for his tireless recruiting and mentoring of students, particularly students underrepresented on campus.


RISE participants Sammy Cheng, left, and Cristen Lee, right, carry out an experiment in the lab of Tuli Mukhopadhyay, an associate professor in the IU Bloomington College of Arts and Sciences’ Department of Biology. Photo by Terri Greene.

“His biology course was packed with students, and I could see why. His teaching inspired students. He got me to really enjoy biology,” says Tellas, who went on to earn a degree in biology and teach high school biology in the Indianapolis area.

“Years later, Dr. Holland sought me out to work with a program he developed to address the racial disparities that exist in STEM,” Tellas adds. “I never knew how he found me, but I was honored to be a part of the initiative.”

Tellas now co-directs the program founded by Holland and has developed two additional related programs with Armin Moczek, professor of biology at IU Bloomington. The three STEM (science, technology, engineering and math) programs for underrepresented students are offered through the Department of Biology at IU Bloomington.

The first two programs are the Jim Holland Summer Enrichment Program, enabling eighth- to 10th-grade students to spend a week on campus, and the Jim Holland Summer Science Research Program, during which a subset of first-year students from the summer enrichment program return to campus to spend a week conducting research with an IU Bloomington faculty member.

The newest of the programs is the Jim Holland Research Initiative in STEM Education, or RISE, a two-week summer program that just finished its inaugural year this summer at IU Bloomington.

“What has been missing at IU, but also broadly across the underrepresented minority-STEM landscape, is a program that connects these types of early high school initiatives to college and beyond,” says Moczek.

“RISE is such a program,” he continues. “It completes a big part of the STEM pipeline vision we hold.”


RISE participants Isis Smith, left, and Kat Gilmer, right, examine a sample beneath a microscope. Photo by Mary Ann Tellas.

In June, RISE brought 10 top-performing students, all about to be seniors in their respective schools, to the Bloomington campus. They were exposed to eight scientific disciplines, from atmospheric sciences to mathematics and statistics to virology, in classes and hands-on activities taught by more than 40 IU faculty members and graduate students. Along the way, the students were also given tours of campus and loads of information about campus programs regarding college readiness, scholarships, service learning, undergraduate research opportunities and more.

Moczek calls RISE a “huge deal.” RISE participants Isis Smith and Kathryn Gilmer agree. On a hot summer afternoon, Smith and Gilmer donned white lab coats over their T-shirts and carried out plaque assays — a common scientific procedure for determining the quantity of infectious virus particles in a sample — in the basement laboratory of Tuli Mukhopadhyay, an associate professor of biology at IU Bloomington.

“The experience and exposure of this program are amazing,” says Smith, who is from Hammond, Ind., and aims to pursue biochemistry in college. “Plus it’s an excuse to come to this campus. Being at IU excites me.”

“This is such a unique opportunity,” adds Gilmer, from Carmel, Ind. “It’s just so interesting to learn about all the different types of science, and it helps me figure out what kind of science I want to pursue.”

Both Smith and Gilmer plan to apply to IU, which Moczek and Tellas say is one of two main goals of the RISE program. “We want them to stay in STEM, and we want them to come here,” says Moczek.

If the first- and second-year Holland programs are any indication, RISE will accomplish those goals. So far, Moczek and Tellas note, 100 percent of the students who’ve been through earlier Holland programs have enrolled in a postsecondary institution, 37 percent of them at IU Bloomington or another IU campus. More than 68 percent of all the participants report majoring in a STEM discipline.


Mukhopadhyay provides instructions to RISE participants Khant Min Soe, center, and Denis Joseph, right. Photo by Terri Greene.

Denis Joseph, a student from Bloomington, doesn’t plan to do lab research when he gets to IU. His sights are set on being a direct admit to the Kelley School of Business, but RISE has been no less valuable, he says.

“The Holland programs have been super rewarding and valuable,” says Joseph. “I’ve learned the skills to be able to think critically and observe what others don’t. I think the exposure and engagement with leaders in their fields of study we get puts us years ahead.”

Davis Joseph, another RISE student and Denis’s twin brother, is serious about pursuing premed in college and says the opportunities to practice “hands-on stuff” have been a high point of the program for him. At another lab station, Christen Lee, from the Chicago area, shares his view.

“We’re hands-on in the lab almost every day, and I really enjoy it,” Lee says. “I can see and understand all at the same time.”

As she pauses between working with student pairs, Tuli Mukhopadhyay notes that the high schoolers around her lab are doing hands-on work typical of a 400-level college course in virology.

“I’m super impressed with this group,” Mukhopadhyay says. “They’re not afraid to ask questions.”

During a break in the afternoon’s experimental procedure, the RISE students question third-year biology graduate student Tamanash Bhattacharya about his experiences. Bhattacharya attests to his love for viruses (“viruses shape the tree of life”) and to the open and collaborative nature of the Department of Biology (“you can follow your own questions”).

“Cool,” say the students, nodding their heads before turning back to their microscopes. “Very cool.”

The Holland programs receive support from the IU Bloomington College of Arts & Sciences, the IU Office of the Vice President for Diversity, Equity, and Multicultural Affairs, and IU’s School of Public and Environmental Affairs. For more information about these pre-college programs, visit their page on the IU Bloomington Department of Biology website. To learn more about Moczek’s outreach projects, visit his lab’s website.

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Indiana University physicists playing key roles in quest for new particles Fri, 01 Jul 2016 19:21:16 +0000 The building blocks that make up the elements on the periodic table are straightforward. Atoms are composed of protons, neutrons and electrons.

But two of those particles – neutrons and protons – haven’t been considered elementary particles since the 1960s. They’re hadrons, composed of three quarks: subatomic particles that come in six “flavors,” up, down, top, bottom, charm and strange. There are also anti-quarks, which have similar properties but possess equal and opposite charges.

Large Hadron Collider

The Large Hadron Collider is the largest and most powerful collider in the world used in the search for subatomic particles. Photo courtesy CERN.

Quark combinations include baryons, which contain three quarks, and mesons, which contain a single quark and an anti-quark. More recently four- and five-quark particles have been detected. This ever-growing menagerie of quark types and combinations is sometimes referred to by physicists as the “particle zoo.”

In the June 23 issue of the journal Nature, Matthew Shepherd, associate professor, and Ryan Mitchell, associate scientist, of the IU Bloomington College of Arts and Sciences’ Department of Physics, along with Jozef Dudek of Old Dominion University, attempt to wrangle this unruly group together in a review paper that explores the current state of knowledge about these fundamental particles, as well as what physicists know about forces that guide their existence and formation, described in part by the theory of quantum chromodynamics.

The colleagues were invited to write the piece after Shepherd delivered a talk on exotic mesons at the 12th Conference on the Intersections of Particle and Nuclear Physics in May 2015.

In the paper, he and the other authors observe that physicists’ knowledge of the behavior and structure of hadrons is currently limited, in part, by the lack of any simple relationship between the quarks described by quantum chromodynamics and the properties of hadrons detected experimentally.

Due to the complexity of this relationship between theory and practice, physicists have turned computer-based simulations to try and predict what kinds of particles may exist — simulations whose results have developed to the point where they’re starting to match up with the results observed in the “wild” at major particle research facilities. These experiment sites range from the Large Hadron Collider in Switzerland to the U.S. Department of Energy’s Fermilab, located near Chicago, and Thomas Jefferson National Accelerator Facility in Newport News, Va. The result is a recent, precipitous rise in contenders for new types of hadrons.

A review of the quest for new types of hadrons is also peppered by IU physicists playing key roles. The GlueX Experiment, for example, which is pioneering the search for exotic mesons, is led in part by Shepherd, who is deputy spokesperson for the project. The first experiments officially began data collection in February after the completion of a seven-year, $339 million facilities expansion at the Jefferson Lab.

Also contributing to GlueX is IU Physics Professor Adam Szczepaniak, who is leading a collaboration between IU and the Jefferson Lab to develop the theoretical tools needed to interpret data from the facility — as well as other experiments — as the director of the Joint Physics Analysis Center at IU. The founding spokesperson for the experiment was IU Physics Professor Emeritus Alex Dzierba, who originally led IU’s involvement in the project.

Jefferson Lab groundbreaking

IU physicist Matthew Shepherd, fourth from right, breaks ground on an expansion to the U.S. Department of Energy’s Thomas Jefferson National Accelerator Facility in 2009. Photo courtesy U.S. Department of Energy.

In terms of four-quark particles, or “tetraquarks,” IU physicist Daria Zieminska was the lead member of the team that recently announced the detection of the first “four-flavored” tetraquark — the first particle determined to contain four different quark flavors: up, down, strange and bottom. As the leader of the “heavy flavor” group of the DZero Experiment at Fermilab, Zieminska plays a lead role on research into all of the larger quark particles detected by the project.

Mitchell also had a role in the search for tetraquarks as a key player in the BESIII Experiment in Beijing, China, which reported other tetraquark candidates in 2013. Those results were noted as a highlight of the year by the American Physical Society.

And beyond the world of quarks, IU scientists are pioneering research on a very different type of subatomic particle, neutrinos, which, unlike quarks, are not governed by the strong force, one of the four fundamental forces. Last August, IU Physics Professor Mark Messier announced the first results of the NOvA Experiment, another experiment in collaboration with FermiLab designed to detect oscillating neutrinos, one of three forms of the subatomic particle. Messier has been a leader on the experiment since the project broke ground on a $278 million neutrino detector located in northern Minnesota.

To learn more about the current state of research on quarks, check out Shepherd’s interview on the June 23 episode of the Nature Podcast.

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Study finds that plant growth responses to high carbon dioxide depend on symbiotic fungi Thu, 30 Jun 2016 18:19:38 +0000 Research by an international team of environmental scientists from the United Kingdom, Belgium and United States, including Indiana University, has found that plants that associate with one type of symbiotic fungi grow bigger in response to high levels of carbon dioxide, or CO2, in the atmosphere, but plants that associate with the other major type of symbiotic fungi do not.

Ectomycorrhizal versus Arbuscular mycorrhizal fungi

Ectomycorrhizal fungi (shown as mushrooms connected to the roots of the tree) increase the uptake of nitrogen by the plant. Arbuscular mycorrhizal fungi (show as grass roots on the left) do not provide that advantage to their host. Image by Victor O. Leshyk

The study, which appears online today in the journal Science, calls into question whether the “greening of the Earth” that results from carbon dioxide stimulation of plant growth — often called the “CO2 fertilization effect” — will persist as fossil fuel emissions continue to rise globally.

“Pumping extra carbon dioxide into a greenhouse is a common tactic to stimulate plant growth, but nature is much more complex than a greenhouse,” said Richard Phillips, associate professor in the IU College of Arts and Sciences’ Department of Biology, who is a co-author on the study. “So, there is great debate about whether pumping carbon dioxide into the atmosphere through fossil fuel combustion stimulates plant growth in nature, where soil nutrient levels are typically much lower than in a greenhouse.”

Fungi that form symbiotic relationships with plants are called mycorrhizal fungi. Over 90 percent of all plant life on Earth associates with mycorrhizal fungi, which provide plants with soil nutrients in exchange for plant carbohydrates.

“While researchers have long known that mycorrhizal fungi play an essential role in the growth and health of plants, their role in helping ecosystems store carbon has never been investigated on such a broad scale — until now,” said second-year PhD student César Terrer of Imperial College London, who is first author on the paper. “Our analysis is the first to demonstrate that only plants that associate with a certain type of fungal partner – one that helps them acquire nitrogen from soil – are likely to grow bigger as carbon dioxide levels rise.”

Other authors are on the study are Colin Prentice of Imperial College London; Sara Vicca of the University of Antwerp, Belgium; and Bruce A. Hungate of the Northern Arizona University.

The research team examined 83 experimental studies of plant responses to CO2 levels equivalent to those expected by the year 2050, assuming an increase of about 2 percent each year globally.

They found a marked difference in the ability of certain plants to take advantage of increased CO2 levels. Plants that grew in nitrogen-rich soils were able to grow bigger and sustain high levels of growth throughout the experiment, following expectations. In nitrogen-poor soils, however, only plants that associate with a certain type of symbiotic fungi were able to keep growing larger.

The group of fungi that enabled plants to grow bigger under high CO2 levels is ectomycorrhizal fungi – a type of fungi that helps plants access soil nutrients by decomposing organic matter, such as the remains of dead plants and microbes.

Richard Phillips

Richard Phillips

Plants that associate with the other major type of mycorrhizal fungi – arbuscular mycorrhizal fungi – were unable to maintain high levels of growth under elevated CO2. While these fungi also increase plant access to nutrients, they cannot access nutrients locked up in soil organic matter.

“Nearly all plants associate with only a single type of mycorrhizal fungi,” said Phillips. “And since the type of fungal associates are known for most plant species, we can begin to predict which ecosystems may respond favorably to high levels of CO2 and which ones will not.”

Ectomycorrhizal fungi associate only with woody plants, such as trees and shrubs, and tend to dominate in forests at high latitudes. Arbuscular mycorrhizal fungi associate with all forms of plant life and dominate in nearly all ecosystems, aside from the boreal forest. In temperate forests, about the half the tree species associate with each type of fungi.

About 30 percent of human CO2 emissions are currently absorbed by land-based ecosystems, without which climate change would be happening even faster than it is now.

The results of this study should enable climate scientists make more accurate predictions of the effects of CO2 in the future, Phillips said.

“In some ways, our research represents encouraging news in that many of our forests may continue to slow climate change by soaking up carbon dioxide,” he added. “On the other hand, it is sobering in that the CO2 fertilization effect may occur on a relatively small fraction of the Earth’s surface. And if climate change also increases the frequency and intensity of disturbances such as droughts and floods, the magnitude of the plant growth response to high carbon dioxide will be diminished.”

Research by Phillips was supported by the U.S. Department of Energy and the National Science Foundation.

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IU postdoctoral researcher named a Pew Latin American Fellow in the Biomedical Sciences Thu, 09 Jun 2016 17:49:57 +0000 A postdoctoral researcher in the IU Bloomington College of Arts and Sciences’ Department of Chemistry is one of only 10 scientists named to the 2016 class of Pew Latin American Fellows in the Biomedical Sciences, a program of the Pew Charitable Trusts.

Daiana Capdevila

A native of Argentina, Daiana A. Capdevila will receive support from the program to spend two years in the lab of Lilly Chemistry Alumni Professor David Giedroc, whose group conducts basic research into the fight against drug-resistant bacterial infection.

“My work at IU involves performing experiments with bacteria to explore the biological aspects of protein regulation,” Capdevila said. “This includes studying how sensor proteins from bacteria such as Streptococcus pneumoniae and Staphylococcus aureus cause molecular changes that allow them to bind to DNA and control the creation of proteins, evading the immune response.”

The research puts her in the middle of the “arms race” between the immune system and bacteria. The sensor proteins studied in Capdevila’s work are used by bacteria to trigger the activation of genes that allow these microbes to counteract the immune system’s efforts to either withhold or poison them with metal ions, a strategy evolved by the immune system to defeat bacterial infection.

Insights from the work could contribute to the development of a novel class of antibiotics able to fight bacteria such as multidrug-resistant Staphylococcus aureus, or MRSA. The primary bacterial strain in deadly hospital-acquired infections, MRSA was estimated by the Centers for Disease Control and Prevention to have infected over 72,000 people in the United States in 2014 alone.

The Pew fellowship officially begins Aug. 1, but Capdevila has been a part of Giedroc’s lab since April 2015. She said she was first drawn to studying in the United States — and Giedroc’s lab at IU specifically — for the opportunity to gain expertise in biomolecular nuclear magnetic resonance spectroscopy, an advanced technology not yet widely available in Argentina.

“Daiana’s receipt of this award really strengths our ties with a number of labs in South America that are very well regarded internationally,” said Giedroc, who praised the quality of the lab where Capdevila previously earned her doctorate.

Ultimately, Capdevila said she said she wants to use the skill she gains at IU to establish her own research lab in Argentina. In fact, nearly 70 percent of past fellows in the Pew Latin American Fellows program return to their home countries to build much-needed infrastructure for scientific exploration. Other Pew fellows from this year’s class hail from Brazil, Chile and Mexico.

“The individuals selected [for this fellowship] are just embarking on exciting careers that will expand frontiers in biomedical science, and joining a network of scientists whose work has the potential to improve human health and well-being around the world,” said Rebecca W. Rimel, Pew’s president and CEO. The program was originally established in 1990 to encourage knowledge exchange and collaboration across borders.

Hailing from the bustling capital city of Buenos Aires, with a population of nearly 3 million, Capdevila said life in Bloomington took some time to get used to. But she welcomes her sojourn as a Hoosier.

“Living here for the past year, I’ve definitely enjoyed the landscape and the surroundings of the town and the woods on campus,” she said. “Bloomington made me realize that I really like biking to the lab, buying local groceries and living in a college town.”

The Latin American fellows program is part of Pew’s strategy to invest in young scientists who are exploring questions fundamental to advancing human health. Other members of this year’s class are studying at the National Institutes of Health, Cold Spring Harbor Laboratory, Massachusetts General Hospital, Yale University, Columbia University, Tufts University, Rockefeller University and the University of Virginia.

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IU Bloomington researcher working to reveal genetic clues behind long-term survival in ovarian cancer Tue, 24 May 2016 15:33:53 +0000 Although not as common as some forms of cancer in the U.S., ovarian cancer ranks among the top causes of cancer death in women. It’s notoriously difficult to detect early, and most women who receive an advanced stage diagnosis do not survive more than five years.

Kenneth P. Nephew

Kenneth P. Nephew

But a small percentage of patients live far longer. To find out why, IU Bloomington researcher Kenneth P. Nephew is a part of the Ovarian Cancer Consortium for Long-Term Survival, which recently received “Phase II” funding from the Department of Defense Ovarian Cancer Research Program.

As a co-investigator in the consortium, Nephew is working to help more women join the ranks of these long-term survivors. He will investigate and describe the epigenome of tumors from ovarian cancer survivors who have survived 10 or more years following a diagnosis of advanced stage ovarian cancer.

“We’re working to reveal the secrets of these tumors to find out what makes these women genetically unique,” said Nephew, a professor of cellular and integrative physiology and obstetrics and gynecology in the Medical Sciences Program at the IU School of Medicine-Bloomington. “We want to identify these genetic differences, and build upon this knowledge to work toward improving the long-term survival and quality of life for all women impacted by this disease.”

This work will be accomplished through DNA methylation profiling and bioinformatics analysis. Data from Nephew’s lab will be integrated with other data collection projects within the consortium, which includes seven research sites across the United States and Europe as well as the active support from 11 patient advocates representing 11 partnering foundations that support patients. The ultimate goal of the consortium is to identify a biologic molecular and psychosocial pattern that can predict long-term survival.

The Ovarian Cancer Consortium for Long-Term Survival is led by Dr. Michael Birrer of the Massachusetts General Hospital Cancer Center (see video below). The consortium also leverages the resources of the Gynecologic Oncology Group from the NRG Oncology Foundation .

Nephew is also a fellow at the Indiana Molecular Biology Institute and a member of the IU Simon Cancer Center.

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IU sophomore on ‘front end’ of sustainability research on bird migration, climate Tue, 19 Apr 2016 19:23:35 +0000 “If there’s ever a fire, we’re supposed to grab that book first.”

That’s how one researcher describes the only copy of a binder containing nearly 50 years of painstakingly collected data on the migratory patterns of dark-eyed juncos in southern Indiana.

The person currently contributing new information to this priceless record is Lia Bobay, a sophomore environmental science major in the School of Public and Environmental Affairs who is collecting and analyzing data on the birds as a 2020 Sustainability Scholar.

Undergraduates in IU’s 2020 Sustainability Scholars Program participate in two semesters of sustainability research with access to world-class faculty on the IU Bloomington campus. Bobay’s research mentors are Ellen Ketterson, IU Distinguished Professor in the IU Bloomington College of Arts and Sciences’ Department of Biology, and Adam Fudickar, a postdoctoral researcher in Ketterson’s lab.

A renowned expert on birds, Ketterson started her research on dark-eyed juncos in the early 1960s in collaboration with the late Val Nolan Jr., IU professor of law and biology, and Ketterson’s husband. The junco data log sits on a shelf outside her office in Jordan Hall on the IU Bloomington campus.

Lia Bobay and Adam Fudickar

Lia Bobay and Adam Fudickar hold birds captured at the IU Research and Teaching Preserve. Birds are released after tagging. Photo by Eric Rudd

The logs contain hundreds of pages of measurements — times, temperatures, climate conditions, bird weight and sex — with each line representing a single junco captured and released in the field. Collecting data on a single bird can take hours.

Since the fall, Bobay has been working with Fudickar to determine whether climate change has altered the male-to-female ratio of dark-eyed juncos in southern Indiana. The birds, which breed in the boreal forests of northern Canada and Alaska, migrate to Indiana during the cold-weather months of November to April. Historically, males outnumber females in Indiana and females outnumber males in southern states.

If changes in temperature influence the birds’ migration distance, Bobay predicts that a shift in the sex ratio will correlate with temperature. The results could provide new insight into the impacts of broad-scale climate changes across North America over the past half-century.

Lia Bobay

Bobay’s research experience has given her new insight into the science that influences environmental policy. Photo by Eric Rudd

“When I first applied to this program, I never thought I would get the opportunity to do this sort of work,” said Bobay, who also has a minor in sustainability studies. “I’ve really gained a new appreciation for birds and all of their variety. Once it’s brought to your attention, you really can’t help but realize how amazing they are.”

It also helps to learn from mentors as passionate about birds as Fudickar and Ketterson, the latter of whom she jokes “has about 30 bird apps on her phone.”

Although they’re primarily focused on basic data collection and analysis, the work also has potential to make a real impact.

“The more we understand about how alterations to the environment impact plant and animal life, the more prepared we are to act in response,” Fudickar said.

Fieldwork for the study takes place on part of the IU Research and Teaching Preserve, a 1,600-acre area of protected natural resources used to support research, teaching and outreach at IU. To capture birds, Bobay and Fudickar arrive at the site, located about 10 miles outside of Bloomington, at sunrise to unfurl gossamer nets across a long, muddy stretch of land on the preserve, sprinkling birdseed beneath the traps, after which birds swooping down to eat get gently caught in the nets.

After carefully untangling the birds, Bobay grasps each delicate creature in the crook of her hand between thumb and forefinger — a trick learned as part of her field training. After applying a band across the birds’ legs and taking some measurements, including a small blood sample, the animals are released back into the wild.

Lia Bobay and Adam Fudickar

Bobay and Fudickar review the original long-term dataset on dark-eyed junco migration in southern Indiana. Photo by Kevin Fryling

The measurements are made at the Kent Farm Banding Station, a recent addition to this part of the preserve that occupies a formerly abandoned building on the site. Also near the station is a small aviary that houses junco species from across North America. Fudickar is director of the banding station.

In addition to field research, Bobay’s work as a sustainability scholar has taught her advanced data management and analysis methods for seeking out correlations between the migration data and climate. She also played a role with Fudickar in working with the IU Libraries to digitize the information in Ketterson’s logs, which not only enabled the data analysis but also safely preserved the migration records in a modern digital format.

“This work really gives students the chance to experience a lot of different kinds of research, and Lia’s been very enthusiastic,” Fudickar said. “It’s great to work with young minds who can bring a fresh perspective and ask import questions.”

As a student at SPEA, Bobay said her main interests lean toward environmental policy, not necessarily hard science and fieldwork, but her experience as a sustainability scholar has given new insights into the role that environmental practitioners play in gathering and interpreting the data that informs long-term policy.


Ellen Ketterson, center, with Bobay, center left, and members of her lab. Photo courtesy Ketterson Lab.

The program will also provide her the opportunity to attend the 2016 North American Ornithological Conference in Washington, D.C., in August.

“This whole experience has helped me better understand a really important component of sustainability and sustainability practice: the actual scientific research,” she said.

“I feel like I’m really on the front end of this topic now, which isn’t necessarily somewhere I had thought I would be. And it’s really interesting.”

For more information about the 2020 Sustainability Scholars program, visit the IU Newsroom’s Student Experience Blog.

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White House highlights IU’s role in initiative to preserve water quality on Indiana farmlands Tue, 29 Mar 2016 21:23:46 +0000 A summit on water quality hosted by the Obama administration on March 22 highlighted a program to improve water quality in the nation’s heartland led in part by Indiana University.

Todd V. Royer

Todd V. Royer

The project is the Indiana Watershed Initiative, which uses watershed-scale conservation methods to reduce nutrient runoff from regional farms. Todd V. Royer, an associate professor in the IU School of Public and Environmental Affairs, is a member of the project led by University of Notre Dame’s Environmental Change Initiative.

“It is an honor for our work to be recognized by the White House during this period of increased concern about water quality in the United States,” said Royer, who also chairs the Illinois Environmental Protection Agency’s Nutrient Science Advisory Committee. “We’re confident that our research will provide information that can be used throughout the Midwest to improve water quality while maintaining productive farmland.”

An expert on the ecological and biogeochemical processes that affect water quality in streams and rivers, Royer’s work has a strong focus on Indiana farms. In his laboratory at IU, he and his students conduct work to identify and reduce the sources of pollution to water, such as nitrogen and phosphorus in agricultural regions, and road salt and pharmaceutical compounds in urban settings.

The Indiana Watershed Initiative, a part of Notre Dame’s Environmental Change Initiative supported by the U.S. Department of Agriculture’s Regional Conservation Partnership Program, combines two practical conservation methods that prevent nutrient and sediment loss from cropland. These are the planting of winter cover crops and the restoration of floodplains.

Winter cover crops are typically grasses or small grains grown between regular crop production seasons to prevent nutrient runoff and improve the soil. The restoration of floodplains is accomplished by re-engineering drainage ditches and small streams.

The initiative, which will pay farmers in two Indiana watersheds located in Kosciusko and Jasper counties to implement these practices, aims to affect 85 percent of the croplands under the project over the next four years, during which researchers will measure the resulting benefits to the area’s soil and water quality.

The initiative was highlighted the 2016 White House World Water Summit as part of the country’s efforts to successfully meet a national goal of reducing farm nutrient runoff by 40 percent. The summit was designed to bring together thought leaders, scientists and legislators working on innovative solutions to water problems as well as highlight current and future strategies for the use, conservation and protection of water.

An expansion of the Indiana Watershed Initiative was also announced at the summit. With farmer cooperation, Royer and collaborators at Notre Dame will grow the project to encompass economic valuation, working to quantify the economic and environmental benefits of conservation on farms. Results from the analysis could help promote implementation of these practices across the 11 million corn and soybean acres in Indiana.

Support for the expansion is made possible with support the USDA Natural Resources Conservation Service, U.S. Geological Survey, The Nature Conservancy, Walton Family Foundation, Indiana Soybean Alliance and Indiana Corn Marketing Council as well as collaboration with Iowa State University.

The White House summit also coincided with the United Nation’s World Water Day, which has been celebrated on March 22 for more than 20 years as a day to focus attention on the importance of fresh water and advocates for the sustainable management of freshwater resources. The summit was made particularly urgent this year due to a record-breaking drought in the West, severe flooding in the Southeast and the water-quality crisis in Flint, Mich.

The director of the Environmental Change Initiative is Jennifer Tank, Galla Professor in the Department of Biological Sciences at Notre Dame.

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IU to host Society for Ecological Restoration annual chapter meeting Tue, 29 Mar 2016 17:09:35 +0000 Over 200 individuals from 13 U.S. states and Colombia are expected to arrive at Indiana University April 1 to 3 for the annual meeting of the Midwest-Great Lakes Chapter of the Society for Ecological Restoration.

The event, “Overcoming Challenges to Ecological Restoration in the 21st Century,” will be held in the Indiana University Memorial Union on the IU Bloomington campus.

A keynote presentation by Douglas Ladd, director of conservation for the Nature Conservancy in Missouri, will take place as part of the event from 1:45 to 2:45 p.m. on April 2 in the IMU. The title of his talk is “Does Ecological Restoration Need a Rethink?”

Midwest-Great Lakes Chapter of the Society for Ecological Restoration logo

The Midwest-Great Lakes Chapter of the Society for Ecological Restoration promotes the science and practice of ecological restoration across seven states, including Indiana.

Registration is open to the public. Registration is $170 ($95 for students) for all three days or $100 ($50 for students) for one day. On-site registration is available at the IMU East Lounge from 9:30 a.m. to 6:30 p.m. April 1 and from 7 to 11 a.m. April 2.

“This event is an opportunity to share information on the science and practice of the ecological restoration of forests, grasslands, urban areas, wetlands, streams and rivers,” said Mary Damm, a graduate student in the IU Bloomington College of Arts and Sciences’ Department of Biology and a member of the organizing committee for the meeting. “Restoring land includes not only planting native trees and herbs, but also re-establishing ecosystem processes such as ground water storage for wetlands and controlled burns to oak forests, savannas and prairies.”

The Midwest-Great Lakes Society for Ecological Restoration Chapter, which serves a seven-state region of Ohio, Indiana, Michigan, Illinois, Wisconsin, Minnesota and Iowa, is one of the society’s largest regional chapters in the world. The chapter promotes the science and practice of ecological restoration to assist with the recovery and management of degraded ecosystems throughout the Midwest and Great Lakes region of the U.S.

The chapter’s annual meeting brings together scientists and restoration practitioners from federal agencies, state agencies, nonprofit groups, environmental consulting companies and academia to share their perspectives on future challenges to ecological restoration — such as climate change, invasive species and overconsumption of native plants by deer and other herbivores — as well as topics such as civic engagement and environmental monitoring. Participants will also discuss potential strategies for overcoming these challenges to ensure success of restoration efforts in the Midwest.

The visitors from Colombia will represent the Estacion Biologica Guayacanal Foundation in Bogota; they will present two sessions on their organization’s restoration work in that country. U.S. presenters will hail from the chapter’s Midwest affiliates and beyond.

“In the United States, the restoration movement has its roots in Indianapolis with natural landscaping by Jens Jensen in the early 20th century at the Riverdale Estate — now Marian University — as well as prairie plantings initiative by Aldo Leopold at the University of Wisconsin-Madison Arboretum.” Damm said. “Restoration has increased in relevance and importance since, and thousands of acres of land have been restored across the Midwest, United States and the globe.”

Jordan River at IU Bloomington

The Jordan River on the IU Bloomington campus.

The meeting will also emphasize campus-community partnerships for restoration research and education with tours that highlight wetland and forest restoration efforts along the Jordan River east of the Jordan Avenue parking garage and at the IU Research and Teaching Preserve, a resource established in 2001 to enhance the research, teaching and service missions of the university by providing natural field settings for research and teaching that complement existing facilities and infrastructure at IU.

Biologists and restoration practitioners from IU and Eco Logic LLC will also give presentations on their collaborative work and lead field trips to the campus restoration sites during the meeting. A Bloomington, Ind.-based company founded in 1999, Eco Logic provides customers with ecological consulting, invasive plant management, reforestation, prairie installation, and stream and riparian habitat restoration. The organization’s mission is to establish and restore native ecosystems and communities and the ecological processes they support through planning, implementation and monitoring.

The meeting will conclude April 3 with guided trips to the Goose Pond Fish and Wildlife Area in Greene County, Ind., and the Hitz-Rhodehamel Woods Nature Preserve in Brown County, Ind., where attendees can learn more about the restoration projects undertaken at these two sites.

For more information, contact Mary Damm,; Heather Reynolds,; or Spencer Goehl,

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Craft brewing is a passion and a business for IU biochemist and cancer researcher Matt Bochman Mon, 21 Mar 2016 15:27:27 +0000 When Matt Bochman arrived at Indiana University Bloomington three years ago as an assistant professor of molecular and cellular biochemistry — fresh off a postdoctoral fellowship at Princeton University — one of the first things he did was pay a visit to some of the craft breweries throughout the region.

But this tour of the local watering holes was as much business as pleasure.

“I wanted to get my name out there as the local ‘yeast guy,'” he said.

IU assistant professor Matthew Bochman, center, with graduate student Cody Rogers, left, and Caleb Staton, director of sour operations at Upland Brewing Co. The trio hold glasses of the brew recovered based upon research in Bochman’s lab and conducted in collaboration with the local brewery.

Although his primary work involves conducting basic research with applications to cancer, Bochman also has a passion for the science of craft brewing, including the microscopic organisms that are key to the brewing process.

Shortly after making the rounds of local breweries, Bochman struck up a fruitful partnership with Flat 12 Bierwerks, a craft brewery in downtown Indianapolis just a mile east of Monument Circle. The owners reached out because they wanted to create “an all-Indiana beer.”

“They peppered me with all sorts of questions — about quality control, setting up a lab, experimenting with yeast — but what they really wanted to do was create a whole new brew,” Bochman said. “They had Indiana water, they had Indiana hops, they had barley that was grown and malted in the state, but they needed the yeast.”

Fortunately, brewer’s yeast grows on trees — literally. Tree bark is one of the best sources for the tiny microbes. So are flowers, fruits, berries and many other natural resources across the state. Soon Bochman had helped Flat 12 identify a strain of yeast for their project.

He has also consulted with breweries and craft distilleries such as Cardinal Spirits and Upland Brewing Co. in Bloomington; Sun King Brewery and Central State Brewing in Indianapolis; and the Maui Brewing Co., based in Hawaii.

But collaboration with Flat 12 also sparked an idea for a business. In 2015, Bochman successfully applied for a $13,000 translational research pilot grant from the Johnson Center for Innovation and Translational Research, an IU Bloomington-based organization in Simon Hall that works with faculty throughout the campus to identify current and new research programs that hold commercial potential and to protect intellectual property.

Bochman’s company, called Wild Pitch Yeast LLC, provides home and craft brewers kits with instructions for “bio-prospecting” yeast in their own backyards, after which the samples are sent to the lab to test for strains of brewer’s yeast and enriched for ethanol-tolerant cultures. The company then returns the isolated yeast strains to the brewers, along with a scientific breakdown of the yeast’s properties and the option to buy larger amounts of the cultures, typically enough to create a five-gallon test batch of beer. Quantities for up to 30-barrel batches are also available.

The company also retains the right to “bank” a strain of the yeast for future use, and Bochman has filed intellectual property disclosures on a number of the strains for potential licensing to larger craft breweries. His partners in the company are Rob Caputo, executive director of the Brewers of Indiana Guild, and Justin Miller of Black Acre Brewing in Indianapolis.

Upland Brewing Company

Upland Brewing Co. in Bloomington, Ind.

“We’ve had people send in stuff from everywhere,” Bochman said. “The home brewers are especially creative … we’ve had people send in their hair, the soupy contents of puddles from beer spills, the spent grains left over after brewing that typically sit outside in dumpsters after they’re used in the brewing process … plus of course plenty of samples from more traditional sources.”

And the yeasts can make a big difference in the brews. “In beers that aren’t heavily hopped, the yeast is responsible for 50 percent or more of the flavor,” he said. The same batch of wort, for example, can be transformed into six distinctly different flavored beers with six different types of yeast.

In less than a year, Wild Pitch Yeast has banked about 300 strains of brewer’s yeast, primarily from Midwestern states such as Indiana, Ohio, Kentucky and Pennsylvania — but they’ve also got strains from New York, Texas and California and European countries such as Belgium and Italy.

In addition to an inspiration for a business, Bochman’s interest in craft brewing has recently become a path to publication. His most recent consultation with Upland Brewing — to help troubleshoot bottling complications on a batch of sour beer called “Cauldron” — is the basis of a paper out this month in the academic journal Food Microbiology.

It’s also a source for bonding with friends and family outside the world of academia. “Even though my main job is working on basic questions in biochemistry related to cancer, it’s my work with yeasts and craft beers that everyone always wants to talk about when I’m home for the holidays,” he said.

The Johnson Center grant ends in April, but Bochman’s eager to find more funding to continue the project.

“Ideally, I would like to have a graduate student working on this full time,” he said. “The hard part is funding.”

What isn’t the hard part? Finding interested graduate students.

“They’re knocking down the doors,” he said with a laugh.

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Nobel Laureate and IU professor’s seminal paper highlighted in journal Genetics Tue, 01 Mar 2016 16:37:12 +0000 Anyone perusing the 100th anniversary issue of the journal Genetics will be treated to a spotlight on a seminal paper from 1943 by a former Indiana University faculty member and Nobel Prize winner.

Salvador Luria in 1948

Salvador Luria at work at IU Bloomington in 1948. Photo courtesy IU Archives.

Salvador E. Luria, a member of the IU faculty from 1942 to 1950, conducted an experiment in Bloomington that went on to inform a revolutionary article titled, “Mutations of bacteria from virus sensitivity to virus resistance,” which contributed to his winning the 1969 Nobel Prize in Physiology or Medicine.

Born in Italy, Luria fled to the United States from France during the Nazi invasion in the spring of 1940. He soon became an instructor, then assistant professor, then associate professor of bacteriology at IU, where he developed an experiment — in collaboration with Vanderbuilt University’s Max Delbruck — that shed important new light on the ways in which certain bacterial cultures rapidly develop resistance to viral infection.

Luria and colleagues’ experiment explained previously mysterious inconsistent mutation rates in bacteria. They found that bacterial mutations arising quickly after viral infection resulted in descendants with mutations present in many cells, whereas descendants whose mutations occurred in later generations had mutations present in only a few cells. The experiment became known as the “fluctuation test.”

The idea for the experiment struck at a strange moment – watching a colleague win $3 in dimes from a slot machine during a Saturday night faculty dance. The moment inspired Luria to examine the role of random spontaneous mutation in bacterial response to infection, with bacteria mutating shortly after viral infection effectively “winning the jackpot.”

The experiment is also regarded as an important early demonstration that statistical analysis can shed light on biological processes inaccessible through direction observation.

In addition to his Nobel Prize, Luria has a connection to another famous Nobel Laureate who taught at IU. His first graduate student at IU Bloomington was James D. Watson, who just three years after earning his doctorate under Luria’s direction co-discovered the structure of DNA with Francis Crick.

Luria received an IU honorary doctor of science degree in 1970.

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Meet Lekeah Durden, NSF Research Fellow and IU Ph.D. student in biology Fri, 26 Feb 2016 15:06:49 +0000 Lekeah Durden, a Ph.D. student in the IU Bloomington College of Arts and Sciences’ Department of Biology, was recently featured by the National Science Foundation during Black History Month as an NSF Research Fellow.

Photo of Lekeah Durden, a PhD student in Biology who is participating in the National Science Foundation social media campaign for Black History Month.

Lekeah Durden, an IU Ph.D. student in biology

“My involvement in eco-evolutionary research allows me to be the positive change I want to see in the world because seeing other underrepresented groups in graduate studies helps create a diverse student body and future faculty that is more inclusive and representative of our community,” she said on the site.

Durden was also named a James P. Holland Fellow in the IU Bloomington Department of Biology in 2014-15. Her work in the lab of Keith Clay, IU Distinguished Professor of Biology, investigates host-microbe interactions in a fungus found in plants.

What first interested you in pursuing a career in biology?

I was always an inquisitive young kid; I loved being outside and observing the world around me. I think a fascination for the natural world got my attention and never let go.

Why did you choose IU to pursue your Ph.D. degree?

I chose to pursue my Ph.D. at IU because the Evolution, Ecology and Behavior Graduate Program was highly rated and had several professors studying host-microbial interactions and performing research that I found interesting. The Department of Biology has so many great scientific minds that I get to interact with on a daily basis, I find it really easy to get engaged with the research going on here.

What is your research interest?

My research interest revolves around host-microbe interactions. I mainly ask questions about the spectrum of mutualisms and pathogens and how their dynamics impact disease spread for their co-evolved host.

What do you enjoy most about this subject?

Besides the real-world application of understanding disease spread throughout populations, I really enjoy investigating how some microbes can be beneficial, yet variation in environmental conditions or hosts can lead it to act as a pathogen.

Durban potting plants

Durden’s research investigates fungal symbionts that live within a plant hosts, including varieties of morning glories.

What does your lab work involve at IU, and whose lab are you working in?

I am a member of the lab of Keith Clay, IU Distinguished Professor of Biology. One major project in the Clay lab pertains to fungal symbionts that live within a plant host. These close associations are formed for many reasons; one of my projects focuses on varieties of morning glories that have an endophytic fungi that produces toxic alkaloids. I am investigating the maintenance of the co-evolved fungal endophyte since it is transmitted from parent to offspring each generation.

Why do you support programs that support women and underrepresented minorities in science?

As a woman and a minority, I participated in programs that supported underrepresented groups in STEM that helped nurture my interests. During my undergraduate work at New Mexico State University, I was a Minority Access to Research Career scholar. This initiative was designed to prepare students for doctoral programs. It gave me a great opportunity to get bench work experience, meet speakers from graduate programs across the U.S., present at a national conference and participate in an internship at UW-Madison.

Morning glories at the IU Biology greenhouse

Durden conducts much of her work in the Jordan Hall Greenhouse at IU Bloomington.

At IU, I have participated in science outreach at local elementary schools in Bloomington and volunteered at Science Fest and Science Olympiad. I also taught high school students through Foundations in Science and Math, a summer program that graduate students in the STEM disciplines organize every summer for high school students in order for them to develop key foundational skills they need for future coursework in high school science and math classes. I had great mentors, and I find that science is more enjoyable when I can share with others and help spark that interest. For me, participating in outreach helps bring a familiar face to science.

Anything else you would like to add?

I’d like to encourage students of all ages, especially at the high school and undergraduate level, that if you have an inkling that you like science, find ways to explore it. You never know what you’ll find if you don’t take the time to search.

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IU paleobotanist plays role in discovery of ‘Jurassic butterflies’ Wed, 03 Feb 2016 16:16:30 +0000 What looks like a butterfly, acts like a butterfly, but isn’t a butterfly?

A study out today in the Proceedings of the Royal Society: B that features IU paleobotanist David Dilcher as a co-author identifies a Jurassic-age insect whose behavior and appearance closely mimic a butterfly — but whose emergence on Earth predates the butterfly by about 40 million years.

Dilcher — who made international headlines last year for his role in discovering the mythical “first flower” — said these proverbial “first butterflies” survived in a similar manner as their modern sister insects by visiting plants with “flower-like” reproductive organs producing nectar and pollen.


An artist’s rendering of Oregramma illecebrosa consuming pollen drops from bennettitales, an extinct order of plant from the Triassic period. Image by Vichai Malikul, scientific illustrator, Smithsonian Institution

The butterfly-like insects, which went on to evolve into a different form of insect from the modern butterfly, is an extinct “lacewing” of the genus kalligrammatid called Oregramma illecebrosa. Another genus of this insect — of the order Neuroptera — survives into our modern era, and are commonly known as fishflies, owlflies or snakeflies.

The discovery of this insect was made possible by the examination of well-preserved fossils recently recovered from ancient lake deposits in northeastern China and eastern Kazakhstan. The study was led by Conrad Labandeira, a curator at the Smithsonian Institution’s National Museum of Natural History, and Dong Ren of Capital Normal University in Beijing, China, where the fossils are housed. Dilcher is an emeritus professor in the IU Bloomington College of Arts and Sciences’ Department of Geological Sciences.

“Poor preservation of lacewing fossils had always stymied attempts to conduct a detailed morphological and ecological examination of the kalligrammatid,” Dilcher said. “Upon examining these new fossils, however, we’ve unraveled a surprisingly wide array of physical and ecological similarities between the fossil species and modern butterflies, which shared a common ancestor 320 million years ago.”

The species are an example of convergent evolution, Dilcher explains, where two distantly related animals develop similar characteristics independently.

As a paleobotanist, Dilcher contributed to the study by describing these ecological similarities, including the insect’s relationship to a type of fossilized plant found in the same region of China as the insect fossils. An extinct order of seed plants called bennettitales, these plants first appeared about 250 million years ago during the Triassic period, surviving for nearly 200 million years until the end of the late Cretaceous period.

An image of the fossilized lacewing Oregramma illecebrosa, left, and the modern owl butterfly Calico Memnon, right. Images courtesy Conrad C. Labandeira and Jorge Santiago-Blay, left, and Jim DiLoretto, right.

Based on their examination, which drew in part upon microscopically small clues such as the fossilized remains of food and pollen trapped in the mouthparts of the insects, Dilcher and colleagues concluded kalligrammatid fed upon bennettitales using a long tongue to probe nectar deep within the plant. The insects also possessed hairy legs that allowed for carrying pollen from the male flower-like reproductive organs of one plant to the female flower-like reproductive organs of another.

Eventually, this system of pollination by long-tongued lacewings traveling between plants with exposed reproductive parts — called gymnosperms — gave way to the more familiar system of insect pollinators and modern flowers, or angiosperms, in which the reproductive parts of the plants are contained with a protective seed.

However, another evolutionary innovation found in the ancient lacewing fossils’ wings remained remarkably unchanged over the course of millennia: so-called “eye spots.”

This unique pattern on the wings, arising over 200 million years ago, is nearly identical to markings on the modern owl butterfly. To this day, owl butterflies use these circular marks as a defense mechanism against predators, which mistake the spots as the eyes of a larger, more threatening animal.

Evolution is a great innovator, Dilcher said. But at the same time: “if it worked once, why not try it again.”

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Confocal microscope acquisition opens new possibilities at IU Light Microscopy Imaging Center Tue, 02 Feb 2016 17:36:23 +0000 Down the stairs near the first floor entrance of Myers Hall on the IU Bloomington campus, IU scientists are peering beyond what’s visible to the naked eye to reveal the complex hidden mechanisms that drive biology, chemistry and other processes in the natural world.

The IU Light Microscopy Imaging Center is home to nearly a dozen extremely powerful instruments capable of, among other things, tracing the delicate contours of the brain, mapping a chemical’s path though cellular channels or capturing the smallest details of an iridescent insect’s wing.


A 3-D image of a cladoceran, or water flea, created using the new instrument. Image courtesy Eduardo Zattara

Recently, the center acquired the latest in its collection of ultra-advanced imaging technology: a Leica TCS SP8 spectral confocal microscope system.

A confocal microscope uses a combination of intense laser illumination and ultra-sensitive light detectors to capture the interior details of microscopically small objects layer by layer, after which the images are automatically reconstructed to create a 3-D picture.

The high-powered instrument, which was acquired with support from the IU Bloomington College of Arts and Sciences and Office of the Vice President for Research, is the first upgrade of this particular technology at the Light Microscopy Imaging Center since 2007 – a significant leap in power and capability, including the ability to capture near-real-time images.

“Up until recently, the majority of imaging technology has only been able to provide scientists with structural information; the real cutting-edge is real-time imaging,” said Jeff Zaleski, a professor in the College’s Department of Chemistry and associate vice provost for sciences at IU Bloomington. “Today, our researchers need the ability to see changes in structural events in real time and watch processes as they happen — to view not just biological structures but also the actual physical processes that occur during those events. This new instrument moves us significantly further in that direction.”

The brand name of the new instrument may be familiar to photography enthusiasts, but the Leica TCS SP8 isn’t merely a high-powered camera – or even a typical confocal microscope. The instrument boasts myriad detectors and electronics not found in “off-the-shelf” systems.


A cutaway reconstruction of a growing beetle horn. Image courtesy Eduardo Zattara

Instead, IU’s custom-built system was designed to accommodate the advanced capabilities required by investigators at a major research university, said Sid Shaw, associate professor in the College of Arts and Sciences’ Department of Biology and technical director at the imaging center, who expects the new technology to provide services to IU departments beyond biology, such as chemistry and biochemistry.

“These commercial systems are sort of like cars; there is a base model that you configure for your particular needs,” Shaw added. “In our case, it’s more Ferrari, less Yugo.”

Since the instrument can capture near-real-time images, the Leica TCS SP8 is also better suited to research that uses live samples, said Jim Powers, an assistant research scientist in the Department of Biology, who serves as imaging center manager.

He also highlighted the instrument’s white light laser, which makes the system compatible with any fluorescent probe — the technology used to differentiate biological structures under investigation (a specific protein, for example) from the surrounding matter by causing them to light up, or “excite,” under laser light.

This feature is significant for the center because its earlier confocal microscope was limited to only seven probes. If a researcher came to the center with a painstakingly prepared sample — but neglected to use one of the correct probes — they simply could not image it. “Now, it’s pretty much unlimited,” Powers said.

LMIC Manager Jim Powers uses the Leica TCS SP8 spectral confocal microscope system. Image by Kevin Fryling

Among the first images captured using the new instrument are two beautiful, highly detailed pictures of insect structures created by Eduardo Zattara, a postdoctoral research fellow in the lab of Armin Moczek, a professor in the Department of Biology whose work concerns the evolution and development of beetle horns.

One image shows a cutaway reconstruction of a growing horn, a test image for an experiment investigating specific aspects of the horn’s development. The other shows a cladoceran, or water flea, collected from the lily pond by the Herman B Wells Library. The natural “auto-fluorescent” properties of the arthropods’ shell provides dramatic contours to the creature’s image as it rotates in 360 degrees.

It’s these sorts of capabilities that helped the Leica TCS SP8 win out over other similar instruments, four of which were physically transported to campus over the summer for interested researchers to “test run” the new technology.

The current system was officially installed at the Light Microscopy Imaging Center near the end of the fall semester. After a long wait, Powers is pleased to finally offer training sessions on the instrument. These personal sessions, which began recently, will extend through this semester and beyond.

Researchers interesting in training on the Leica SP8 can set up an appointment by emailing

Video by Eduardo Zattara

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Science the Second Time Around: Plenitude Today Fri, 08 Jan 2016 20:08:15 +0000 Editor’s note: In this ongoing series, “Science the Second Time Around,” IU author and mythologist Gregory Schrempp is sharing his experience going “back to school” in science with support from a New Frontiers Experimentation grant from the IU Office of the Vice President for Research.

The astronomy course I recently finished auditing changed direction at mid-term. The first half had emphasized our solar system and the great paradigms brought to it: Ptolemaic, Copernican, Universal Gravitation, Electromagnetism, Relativity.

But the second half surveyed the known contents of the universe. I started to tell a friend about the new direction. “A zoo?” he asked. Yes, the second half was an organized display of “cosmic species.”

I was initially concerned that the “zoo” would be less interesting than the great paradigms, but the feeling did not last. Popular science writers constantly claim that if you are into wonder, there is more of it to be found in reality than in fantasy. I got a taste of what they mean. The array of cosmic things leaves me in sheer, speechless amazement.



My personal favorite had always been Saturn, with its intricate, perfect rings. But now I have others — including a scrappy little moon of Saturn called Enceladus, which shoots out the most impressive plumes of water vapor. The moon and its plumes looked so much like a little satellite with a retro-pack that I couldn’t help but wonder if those eruptions could ever alter the little guy’s orbit.

We love lists. Many of the artistic genres studied by folklorists and ethnomusicologist suggest that enumeration is a basic source of artistic and intellectual pleasure. There are long mythic-cosmogonic genealogies that go on interminably naming the things found on earth, in the sea, and in the sky.

Musicians use the term “list-song” to describe a popular format: “A, you’re adorable; B, you’re so beautiful…” Religious litanies follow the same principle: “Saint Benedict, pray for us; Saint Luke, pray for us…”

A parade is a list that marches past you. A clear night sky gives us a cosmic parade, one that telescopes and space-probes now allow us to check out up-close.

But in addition to the amazing things, I think I caught glimmers, in the textbook and lectures, of something older and deeper. Specifically, the idea of plenitude celebrated in Arthur O. Lovejoy’s classic “The Great Chain of Being.”

Plenitude is the principle, found already in Plato, that there are no gaps in nature, no possibilities untried. When, on the fly, I asked Professor Deliyannis about plenitude, he replied thoughtfully, “I think a lot of astronomers believe that.” I hope to resume the conversation.

I’ve encountered versions of multiverse theory which treat plenitude as a hypothesis, predicting that all possibilities will be actualized, like the proverbial monkeys with typewriters eventually writing all of Shakespeare.

Might not the idea of plenitude be built into the very structure of our intellect? Given even a small set of diverse things, there is an impulse to ask how far the series extends — and to wonder whether it might go on until all possibilities offered by the cosmos are used up.

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Science the second time around: Anthropomorphic complexity Tue, 08 Dec 2015 19:19:32 +0000 Editor’s note: In this ongoing series, “Science the Second Time Around,” IU author and mythologist Gregory Schrempp is sharing his experience going “back to school” in science with support from a New Frontiers Experimentation grant from the IU Office of the Vice President for Research.

Gregory Schrempp

Gregory Schrempp

Mythologists are used to the claim that myths are unscientific because they are relentlessly anthropomorphic — the idea that the archaic creators of the world’s mythologies projected parochial, local scenes from human life onto the cosmos to explain its workings.

An Enlightenment philosopher and author of “Of the Origin of Fables,” Bernard Fontanelle, once famously described ancient humans explaining rain as the gods pouring out pitchers of water:

“These poor savages…could only explain the effects of nature by grosser and more palpable things with which they were familiar.”

While Fontenelle’s account illustrates the process and problem of anthropomorphism, the matter is really more complex.

One complication lies in the history of the critique. You might suppose from Fontenelle’s comments that the charge of anthropomorphic distortion arose as a confrontation between science and religion — but in fact it first appeared as a self-critique in religious thought. It was the pre-Socratic philosopher Xenophanes who first declared “if horses and lions had gods, they would look like horses and lions.” Others like Plato followed, insisting that we purge our theology of anthropomorphic content.

In the general astronomy course I am attending with support from IU’s New Frontiers in the Arts and Humanities grant program, I encountered a brilliant example of another type of complication: the possibility that knowledge of the universe can be inhibited not just by parochialism but also by the opposite: our not being parochial enough.

Specifically, professor Constantine Deliyannis laid out a detailed mathematical progression that calculated the acceleration, due to earth’s gravity, of an apple falling to the ground, and then showed that the same formula precisely describes the centripetal acceleration, again due to earth’s gravity, of the moon orbiting earth.

This was not a surprise, but it’s one thing to know something generally and another to work through the math.

Had our archaic ancestors really followed the route that Fontanelle imagined for them, they might have hit on the moon as an apple early on, and spared us the long detour through metaphysical constructs such as Aristotle’s celestial spheres, which, while fascinating, had the effect of disconnecting celestial from terrestrial motion.

We should not entirely dismiss Fontenelle’s view of the origin of mythology, but his portrayal of our anthropomorphic impulse is far too simplistic to account for the ways our human desires abet or impede science.

Even the mathematical lesson retained an allusion to myth with the anecdote of Isaac Newton and the falling apple — not the first time in Western mythology that an apple has changed our fate.


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IU scientists, alumni among winners of 2016 Breakthrough Prize in Physics Thu, 03 Dec 2015 18:02:01 +0000 Facebook founder Mark Zuckerberg has been in the news this week for the announcement that he and his wife will give 99 percent of their wealth to charity over the course of their lives.

But this isn’t the tech entrepreneur’s first foray into philanthropy. He and other leaders at tech giants such as Google and Alibaba are the main investors in the Breakthrough Prize, a new award that seeks to generate excitement about science — and that recently awarded $22 million to science researchers across the globe.


This year’s Breakthrough Prize ceremony aired live on the National Geographic Channel Nov. 8, and Sunday, Nov. 29, on FOX.

Among the winners of the 2016 Breakthrough Prize in Fundamental Physics was Takaaki Kajita of the University of Tokyo, who shared the award with four colleagues for their contributions to the “fundamental discovery and exploration of neutrino oscillations, revealing a new frontier beyond, and possibly far beyond, the standard model of particle physics.”

Also sharing the award with Kajita are other scientists whose work contributes to breakthroughs in the understanding of neutrinos, the mysterious subatomic particles which some speculate could comprise half the mass of the known universe. These researchers include IU physicist Mark Messier, a professor in the IU Bloomington College of Arts and Sciences’ Department of Physics; Masaki Ishitsuka, a former postdoctoral researcher in Messier’s research group; and Alec Habig and Chang Kee Jung, both former graduate students at IU.

Each of the researchers with connections to IU on the prize can cite associations to Kajita’s role as a leader of the Super-Kamiokande Collaboration, the world’s largest underground neutrino detector located under Mount Ikenoyama near the city of Hida in Japan. Jung, a professor of physics at the State University of New York at Stony Brook, has led the international T2K Collaboration, also cited in the prize for breakthroughs in neutrino research; Habig leads a world-wide effort to detect supernova explosions in our galaxy using neutrinos as a professor of physics at the University of Minnesota; and Ishitsuka is a faculty member at the University of Tokyo, where he also continues to study neutrinos.

Mark Messier, center, with the Deputy U.S. Secretary of Energy, left, in 2014.

Mark Messier, center, with the Deputy U.S. Secretary of Energy, left, in 2014. Courtesy Fermilab.

Messier, who now serves from IU as a leader on the NOvA experiment, a $278-million neutrino detector located in northern Minnesota, was cited on the prize in relation to this doctoral thesis, which concerned a breakthrough experiment from the Super-Kamiokande that earned Kajita the 2015 Nobel Prize in Physics earlier this year, along with the Canadian physicist Arthur McDonald.

That discovery of neutrino mass through a quantum process called oscillations — by which neutrinos change identity in flight — is a phenomenon physicists across the globe continue to investigate at facilities such as NOvA, which recently reported its first measurements of oscillating neutrinos by intercepting a neutrinos beam generated over 500 miles south at Fermilab in Batavia, Ill. The mechanics behind the transformation of some of these neutrinos from one form to another during oscillation could shed light on the earliest origins of the universe.

The Breakthrough Prize is also unique for the glitz and glamour it brings to the world of science. The prizes were awarded during a ceremony on the National Geographic Channel Nov. 8 featuring performance by Pharrell Williams and presenters such as Russell Crowe, Hilary Swank and Kumail Nanjiani. On Nov. 29, the program re-broadcast on network television on FOX.

Although not everyone credited on the prize got the chance to strut their stuff on the red carpet, Messier said it’s notable that a number of Hoosiers — past and present — are among the scientists whose diligent work brings us just a little bit closer to uncovering the “big questions” every day.

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Science the second time around: Cosmology from within and without Tue, 17 Nov 2015 22:11:23 +0000 Editor’s Note: In this ongoing series, “Science the Second Time Around,” IU author and mythologist Gregory Schrempp is sharing his experience going “back to school” in science with support from a New Frontiers Experimentation grant from the IU Office of the Vice President for Research.

Gregory Schrempp

Gregory Schrempp

I recently had my first amazing experience in the class. It came not in the form of an entirely new idea, but rather as a series of historical examples from early astronomy that drove home an obvious but profound point: that the universe, for our species, had to be discovered from a moving point within.

The problems and mathematical descriptions that I’ve considered in class so far seem to fall into two broad categories: those formulated from an imagined vantage outside the solar system (the “god’s eye view”) and those formulated from a vantage point on earth (the “human’s eye view”).

The motives that originally gave rise to astronomy from a human’s eye view were no doubt quite practical — using the positions of stars and planets to time the agricultural cycle, for example. But it is also clear that at some point another motive arose: that of getting out of the human’s eye view and into the god’s eye view.

I’m tempted to think that the findings of astronomy could have been accomplished much more easily and quickly if we had been offered the god’s eye view first. Although the math connected with the human’s eye view perspective is not especially difficult, I still find it a challenge to “get my head around” human’s eye view formulations.

Recently, I even took a test that asked me to describe the attitude of an airplane based on a view of the horizon through the pilot’s window. If I had been an actual pilot, the plane would have gone down immediately.

That the distinction between the outside and inside view registered with such impact is probably due to my academic background. As a mythologist, I am acutely aware of the way in which these cosmoses were envisioned in mythology. The deity in the biblical story of Genesis 1, for example, is one of many creators based on the model of a craftsperson holding his or her work at arm’s length.

But not all cosmogonies adopt this model. I have never encountered a story in which the Greek god Zeus experiences a god’s eye view of the universe, for instance. Like many other deities in the Mediterranean, Asia and the Pacific, Zeus was born from descendants of Sky and Earth and seems never to have left this realm between these two borders.

You might wonder whether societies with the more distant creators would have had an advantage in escaping the parochialism of the human’s-eye view and inventing modern astronomy. It is not clear to me that they did, and there may be ways in which the impetus worked the opposite way.

For instance, Greek philosophy and early science emerged in a context that in many ways embodied skepticism toward parochial points of view, including their descriptions of the cosmos and of the gods.

The ancient Greeks had an impetus towards trying to see the cosmos from a higher point of view. The gods of the early philosophers were increasingly defined in opposition to human limitation, triviality and parochialism.

In sum, the complexity of Earth-bound view — figuring the system out from a moving point inside — was my first big revelation during class.

The first revelation, however, was not the biggest.

But that will have to wait until next time.

For more details about Schrempp’s project, see this article in Inside IU Bloomington.

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Fossilized embryo research garners career award for IU biologists Fri, 06 Nov 2015 20:18:17 +0000 Academic collaborations start out in a lot of ways, but sometimes the most fruitful research arises from opportunities in front of people the whole time.


Elizabeth and Rudolf Raff

That was certainly the case for two IU biologists recently honored as recipients of the 2015 Distinguished Career Award from the Geological Society of America during the organization’s annual meeting in Baltimore on Nov. 1 to 4.

Rudolf Raff, Distinguished Professor and James H. Rudy Professor of Biology, and Elizabeth Raff, professor of biology, both in the IU Bloomington College of Arts and Sciences’ Department of Biology, were presented the award from the Geobiology and Geomicrobiology Division of the organization in recognition of their outstanding contributions to geobiosciences.

“Although they already have each enjoyed distinguished and independent careers in other areas, it’s particularly striking they’ve garnered this award as a team,” said Clay Fuqua, professor and chair of the Department of Biology. “Beth and Rudy are a great example of a scientific couple who have combined forces to forge a fascinating new area of work.”

The Raffs’ research involves examining the remains of extremely fragile embryos preserved — almost miraculously — in the fossil record despite the passage of many geological ages. And they’ve discovered that a unique set of circumstances must occur to save these ancient signs of life at its earliest stages.

By studying the preserved embryos of the large sea urchin, Heliocidaris erythrogramma, the Raffs have found that two key events are required to cement the remains of embryos in the stone.

First, an embryo’s structure must be quickly stabilized by the inhibition of autolysis — the process by which cell cytoplasm is degraded by the release of destructive intracellular enzymes — immediately after death.


Fossilized embryos

The second event requires several “unexpected and remarkable” microbiological processes that result in the creation of a “pseudomorph,” a dense three-dimensional bacterial biofilm in which bacteria consume, but also replace, the embryo’s tissue.

Although many bacteria destroy soft tissue, the Raffs found that some bacteria actually preserve soft tissue by generating these pseudomorphs. Bacterial pseudomorphs are stable replicas of the embryos – “like sculptures of the original embryo constructed from bacteria.”

The Raffs are continuing their investigation into the mechanisms of blocking autolysis, as well as the actions and ecology of the diverse microbial players whose interactions lead to preservation or destruction of stabilized tissue. They are also working to identify and isolate bacterial species as potential “pseudomorphers” of embryos in various types of natural environments.

To learn more about the Raffs’ award-winning research, visit the Geological Society of America blog.

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Science the second time around: Problems with authority Tue, 03 Nov 2015 18:10:44 +0000 Editor’s Note: In this ongoing series, “Science the Second Time Around,” IU author and mythologist Gregory Schrempp is sharing his experience going “back to school” in science with support from a New Frontiers Experimentation grant from the IU Office of the Vice President for Research.

Gregory Schrempp

Gregory Schrempp

The first step in my four-year journey auditing science classes at IU was buying a textbook.

In general, I find the classic textbook in my general astronomy course very impressive, with one exception — an exception that triggered some ongoing thoughts about authority in studying science.

Specifically, I was surprised by the way an important equation — that of centripetal acceleration of objects in orbit — was introduced.

According to the text: “It can be shown from experiments that for a body of mass m to move in a circle with a radius r at speed v, it must be accelerated towards the center of the circle by a force: F = mv2/r.”

The equation is given little authority: no names, no description of the experiments — it’s even diminished by the use of the passive voice.

So, I went back a few pages and looked how the text had introduced Kepler’s laws of motions. Again, I found the reader was asked to put a significant amount of trust in the textbook’s authors since they only provided a bare-bones summary of the measurements used by Kepler to formulate his laws.

In fact, I found the overall presentation of Kepler’s findings depicted as a sort of “hero-story.” Formulas are more to be believed when they are shown to be hard-won.

(Even stories about great scientists’ quirks convey a similar message: that we should trust them due to some sort of other-worldly inspiration.)

However, I have found two sources of authority beyond the textbook: The first is experimental demonstration. Our professor, Constantine Deliyannis, provides these in abundance, and they generally work so well that one can chock up the flaws to imperfect experimental conditions — or, if you prefer, the charm of the universe.

The other is psychologically interesting: the idea that “deriving” an equation from another adds authority. The psychological appeal of a derived equation bears further inspection. It might seem deceptive since the situation can become that of symbolic logic — where one foregoes judgment of the major premise in favor of concern with the legitimacy of the derivational process itself.

I wonder whether my early Catholic upbringing increases the appeal of authority by derivation? As a religious tradition, it’s one in which all particular truths are supposed to emanate from absolute first principles.

While clearly there isn’t room for all of these considerations in every equation presented in a textbook, I would argue that the most important formulas should always include the following: an experimental demonstration, a description of methods, a diagram, some process of derivation — and, of course, a hero-story.

For more details about Schrempp’s project, see this article in Inside IU Bloomington.

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Science the second time around: Doing the math Fri, 23 Oct 2015 20:26:20 +0000 Editor’s Note: In this ongoing series, “Science the Second Time Around,” IU author and mythologist Gregory Schrempp is sharing his experience going “back to school” in science with support from a New Frontiers Experimentation grant from the IU Office of the Vice President for Research.

Gregory Schrempp

Gregory Schrempp

In my early career as a mythologist, I focused mostly on traditional world mythologies. Over the past 15 years, however, I’ve grown increasingly interested in the ways in which popular science writing borrows some of the same techniques as mythology.

I’m especially intrigued by the relationship between mythology and science. These two concepts are often cast as opposites — a characterization I’ve ultimately found to be inadequate.

Eventually, I started to wish that I could revive my knowledge of basic — not simply popular — science. In March, I was fortunate to receive a New Frontiers Experimentation grant to do just that – specifically, to audit one course a year for the next four years in basic science.

I am grateful to Constantine Deliyannis of IU’s Department of Astronomy for allowing me to audit his course A221 General Astronomy this semester — and for answering a number of questions that have arisen along the way. Deciding to audit a general intro course or a course requiring higher math skills designed for science majors was my first biggest decision in “going back to school,” and I’m very glad to have picked the latter path.

I find my math skills from high school and college have remained fairly strong. I loved the subject — especially branches such as probability theory that lead into philosophical quagmires — and find I can still follow most equations after putting myself through a math review this past summer.

It’s been a pleasant surprise to find my high-school physics class of more than 40 ago — and a number of the basic concepts like motion, waves, light, optics — stayed with me; that course must have been better than I remembered.

But I did encounter one problem: I couldn’t recall all the rules for manipulating equations (what cancels what, etc.), and found myself reconstructing the rules from the derivations presented in class or the textbook. There seem to be tons (or more precisely, newtons) of interesting stuff in the cosmos, but for me the feeling of “elegance” voiced by some astronomers and other scientists is pretty tightly bundled with the mathematics.

I also found that I remembered the basic trig functions, but not how to actually do the calculations. Thankfully, this is something that now can be performed by pushing a button.

Most of all, I’ve been intrigued to find the definition of energy — even beyond high school — remains “the ability to do work”; a term that even back then struck me as an inordinately anthropomorphic.

Perhaps, to be consistent, we should rank the energy-orbits of atoms on a scale of their relative enthusiasm or industriousness.

For more details about Schrempp’s project, see this article in Inside IU Bloomington.

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IU-built scintillator ‘in the game’ as NOvA experiment detects its first evidence of oscillating neutrinos Fri, 07 Aug 2015 13:44:26 +0000 An Indiana University professor who is co-lead scientist on a major, multi-institutional investigation into the mysterious behavior of the subatomic particles known as neutrinos recently announced the project’s first results before an international gathering of colleagues.


Mark Messier of IU, right, and Young-Kee Kim, former deputy director at Fermilab, during the construction of the NOvA detector in 2012.

Mark Messier, a professor in the IU Bloomington College of Arts and Sciences’ Department of Physics, delivered the address at the 2015 Meeting of the American Physical Society’s Division of Particles and Fields today in Ann Arbor, Mich.

The results are part of the $278-million NOvA project, an international collaboration of nearly 210 scientists and engineers from 39 universities, laboratories and institutions around the world. The experiments were conducted in partnership with Fermilab, a massive particle accelerator near Chicago funded by the U.S. Department of Energy.

“Scientists on the NOvA experiment saw their first evidence of oscillating neutrinos, confirming that the extraordinary detector built for the project not only functions as planned, but is also making great progress towards its goal of a major leap in our understanding of these ghostly particles,” said a statement released from the lab this morning.

Neutrinos come in three forms: muon neutrinos, electron neutrinos and tau neutrinos. The experiment whose first results were reported today seeks to answer a major mystery in modern physics: what causes neutrinos to transform – or “oscillate” – from one form to another? The principles that govern the oscillation of a muon neutrino into an electron neutrino, when solved, could hold new clues to the origins of the universe.


The far detector measures roughly 200 feet long, 50 feet high and 50 feet wide and is made of PVC filled with a scintillating oil. Photo courtesy Fermilab.

“IU’s involvement in the project has been extensive,” said Messier, who has worked on the project since it’s inception nine years ago. “IU’s major responsibility was to deliver three million gallons of the liquid scintillator that is the heart of the experiment.”

A material of mostly mineral oil and psuedocumene that becomes luminescent from ionized radiation, the scintillator fluid comprises an important part of NOvA – also known as the NuMI Off-Axis Electron Neutrino Appearance far detector building — whose physical structure and detection software were also partially designed by IU scientists.

A 14,000-ton, multi-story structure the size of several football fields, NOvA is located on a remote patch of land owned by the University of Minnesota in Ash River, Minn. The neutrinos created for the experiment are generated at Fermilab, located in Batavia, Ill., and then beamed instantly through the Earth to the detector over 500 miles to the northwest.

Neutrinos pass through matter as though it doesn’t exist. Although still poorly understood, neutrinos are the most abundant particles with mass in the universe.

“These results show that NOvA is ‘in the game,'” Messier said. “Even though we’re just getting started, we’re getting results of comparable quantity to other similar experiments around the world due to the excellent performance of the beam and detector.”


A pivoting machine used to move each block of the detector into place is now part of the completed structure. Photo courtesy Fermilab.

Other IU scientists playing an important part in NOvA are Stuart Mufson, professor in the Department of Astronomy; Jim Musser, professor in the Department of Physics; and John Karty, associate scientist in the Department of Chemistry, all of whom have served in a variety of roles related to the scintillator system. Mark Gebhard, a master technician, is responsible for coordinating efforts to monitor and test the system. Jon Urheim, professor of physics, has also contributed to the project.

Other IU contributors are Michael Baird, Gavin Davies, Hayes Meritt, Evan Niner and Denver Whittington, who are postdoctoral fellows, and Teresa Lackey, Ryan Murphy, Fernanda Psihas and Justin Vasel, who are graduate students.

In addition, Niner will join Fermilab as a postdoctoral fellow this fall. He and Baird will deliver thesis defenses based on their work on NOvA in IU’s Swain Hall on Monday, Aug. 10, and Friday, Aug. 14, respectively.

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A gut feeling that honey bee microbiome work at IU will be worth watching Thu, 31 Jul 2014 21:12:29 +0000 Although it has yet to become added fodder in the debate over if, how or when President Barack Obama has been over-stepping his authority, the White House did recently issue a Presidential Memorandum ordering relevant agencies and departments to create a federal strategy to promote the health of Apis mellifera – the western honey bee – a species that pollinates a third of what becomes the American diet.

If any of those task force representatives – nudge, nudge, National Science Foundation – are listening, Indiana University has a perfect designee for the effort to protect a pollinator worth $15 billion a year to the U.S. ag economy: IU biologist and assistant professor Irene L. G. Newton.

IU biologist Irene Newton

IU biologist Irene Newton

Not that Newton (Ph.D., Harvard, 2008) hasn’t had enough to do since coming to IU in 2011: Setting up a new lab, co-authoring a great paper on honey bee genetic diversity and its relationship to pathogenic bacteria, making herself available to the region’s beekeeping community, while forging ahead in another research interest area, the parasitic ‘male-killer’ bacteria Wolbachia pipientis. Oh, and she is also one of IU Biology’s junior faculty comfortable with blogging and tweeting, something we here at IU Communications love to see scientists doing.

But social media aside, we proffer Newton for a seat on the new Pollinator Health Task Force because, to put it bluntly, bacteria need a seat at the table. After all, they’ve been around for about 3.5 billion years, or four times longer than animals, and are partners in the working digestive systems of everything from honey bees to humans (we harbor about three pounds of microbes in our gut). They are literally etched into our genome, with about one-third of our genes originating from bacteria.

And when it comes to honey bees, and specifically the honey bee gut where sugar is metabolized, pollen turned into energy and toxins dismantled, bacteria are crucial players. That’s where Newton’s specialty lies: Understanding the diversity of microbial community types in the honey bee gut and the mechanisms that result in the species undergoing changes, healthy or not. Animal-bacteria relationships form essential partnerships in a myriad of species, including in the modulation of brain development and behavior in mammals, and Newton’s latest work, with her grad student Fredrick J. Lee as first author, underscores this partnership with the honey bee.

You can read more about their latest work in the IU press release here, and at Newton’s blog here, but in short the new research offers the first metatranscriptome sequencing of the honey bee gut and in turn offers fresh insights into the contribution that the microbial community plays in honey bees processing food.

In the new White House Presidential Memorandum, action steps include development of new public-private partnerships, increased citizen engagement, creation of a formal strategy to with explicit goals, milestones and measurement metrics, along with a call to increase and improve pollinator habitat. Indiana University already has a great advocate for these goals in Newton and as her lab’s work progresses in developing a better understanding of the molecular basis of interactions between bacteria and the honey bee, her stock is on course to rise.

Bee hives came to the White House in 2009 and in 2011 produced its standing record of 225 pounds of honey.

Bee hives came to the White House in 2009 and in 2011 produced its standing record of 225 pounds of honey.

That she is publicly energetic about the work, through engagement, through a blog that also delves into a vast array of other issues relevant to science and students –from analyzing the differences between NIH and NSF grant review processes and offering tips for doctoral students seeking dissertation grants, to her music picks for decompressing and discussions about wage discrepancies for women in science – and through her collaborative nature, Newton also provides IU with another opportunity for hosting an investigator working on the cusp of an issue that is vital to the U.S. economy and to the general health and well-being of our environment.

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Women of science, of technology, prepare to be empowered! Tue, 25 Mar 2014 13:54:12 +0000 I want to be a woman….studying science….at Indiana University….over the next week. If you already meet those prerequisites then prepare to be empowered.techie women muscles

IU Bloomington’s Center of Excellence for Women in Information Technology gets things started with this weekend’s Techie Women Have More conference. Poster battle royale gets underway first, beginning at 2 p.m. Friday at Union Street Center Auditorium and ending at 4:30 p.m. after all votes in the People’s Choice Award contest are counted. It’s the only event of the day open to non-registered folks and casting a ballot gets you a chance at the schwag: an iPad Mini!

The highlight of the evening for registrants is expected to be the dinner keynote from Melissa Gregg, director of Intel’s Science & Technology Center for Social Computing (ISTC-Social). More on this in just a bit as Indiana University has a pretty impressive presence on the ISTC-Social personnel roster, while also serving as a “spoke,” or partner, with the center’s hub at University of California, Irvine.

The Techie Women event runs through Saturday at Union Street Center, offering breakout sessions and flash talks until the event wraps-up for a closing session and presentation of prizes at 4:10 p.m. The cost for student attendees is $20, and online pre-registration will continue through Wednesday. On-site registration will be available, space permitting, at the Indiana Memorial Union Tudor Room from 4:30 to 6 p.m. Friday and from 9:30 to 10 a.m. Saturday at Union Street Center, 445 N. Union St.

Sunday is a day off from intellectual inspiration – refuel – but on Monday award-winning Harvard microbiologist Rachel J. Dutton ties together her passion for microbial ecosystems, most especially the foul-smelling cheesy ones, with some motivational speaking for women in science via IU Biology’s Joan Wood Lecture Series. Think science that ferments and foments, and it happens at 4 p.m. Monday in Myers Hall 130. She’ll speak again to undergraduate science majors attending a microbiology seminar Tuesday afternoon, and the word is she’ll don a fromager’s apron and dole out more than a few metabolically manipulated taste treats.

Harvard postdoctoral fellow Benjamin Wolfe and his mentor, microbiologist Rachel J. Dutton. (Boston Globe)

Harvard postdoctoral fellow Benjamin Wolfe and his mentor, microbiologist Rachel J. Dutton. (Boston Globe)

Gregg’s appearance Friday night is an opportunity to highlight the strong relationship that Intel and IU have had. In 2005 Intel bestowed upon IU its honorary title of “Most Unwired Campus” in the country based on wireless computing access on the Bloomington campus, a fine and deserving gesture. But the “money-where-your-mouth-is” event came in 2012 when three School of Informatics and Computing professors – Jeffrey Bardzell, Shaowen Bardzell and Erik A. Stoltermanreceived $1.85 million from Intel to establish IU’s own ISTC-Social in coordination with the UC Irvine center where Gregg is based.

Since that time IU has continued to add personnel to the roster of ISTC-Social, which now numbers seven: the Bardzells, Stolterman, Gabriele Ferri, Shad Gross, Shannon Schenck Grimme and Austin Toombs, and last fall Intel Perceptual Computing Lab director Rajiv Mongia and UX Studio designer-developer Robert Cooksey led a workshop for Shaowen Bardzell’s Advanced Prototyping class, where they discussed, among other things, natural user interaction projects – like embedding 3D cameras in tech devices that, for example, would allow your PC, your smart phone, etc., to monitor your heart rate and other personal biometrics ala wireless transmission.

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La traviata vs. Grand Theft Auto: How will scientists referee the cultural cage match? Thu, 06 Feb 2014 15:22:01 +0000 Last week Clifford Lynch, executive director of the Coalition for Networked Information, kicked off an impressive run of technology-oriented speakers here at IU Bloomington that continues next week with Google’s Blaise Agüera y Arcas on Monday and Research Data Alliance chair Fran Berman on Tuesday.

It goes to show you timing is everything … like the merger between the School of Informatics and Computing and the School of Library and Information Science, followed by IU President Michael A. McRobbie’s unveiling of a  $15 million Media Digitization and Preservation Initiative to preserve collections of video, music and other irreplaceable material assembled by IU over its nearly 200-year history.

book cover

Katy Börner’s book, Visual Insights: A Practical Guide to Making Sense of Data,” is an Amazon best seller.

It was at the merger’s inauguration ceremony that IU information scientist Katy Börner, posing a question to the audience, reminded us about timing: “How do we promote open education, open data, open code for 7 billion people in a sustainable manner?”

It’s a question Lynch, Berman and Agüera y Arcas are working to answer — in their own contexts — and it’s one becoming more relevant for scientists, corporate CEOs and, to be fair, future generations.

Digital conservation, sustainability and archaeology, e-preservation and data stewardship, data sharing and interoperability — these are components of the new data ecosystem these scientists want to foster for future generations. These strategies will create what Börner calls “intelligence amplifiers,” or macroscopes, for academia, governments and NGOs, but especially for use at the population level.

From bio-samples stuffed away in lab freezers to boxes of decades-old data sheets piled in a prof’s home garage, to the software, algorithms and data plots used as recently as at the Large Hadron Collider, where researchers are asking what can and should be saved, what should be publicly available, how will it be saved and who will pay for it?

Last week Lynch professed hope: E-preservation service Portico, longterm journal content steward Keepers Registry and financial backers like Web-archiving hero Brewster Kahle are setting foundations. Even Twitter has agreed to have its 170 billion-and-running tweets archived with the Library of Congress.

It’s an age where, Lynch notes, Grand Theft Auto is as culturally relevant as La traviata, forcing us to recognize the intellectual gaps that remain when navigating through the technical, cultural and legal requisites for archiving what somebody, someday, may consider really important stuff. News reports (TV, radio, print?), 2-D artwork (now available as exact copies) and websites like that uniquely personalize visits based on each visitor, are all examples.

A recent study published in Current Biology found that nearly 80 percent of current scientific research could be lost in 20 years. The threat that data accrued during the Higgs boson search could be lost was no joke, according to Cristinel Diaconu, a particle physicist and chair of the data preservation group at CERN. “When the LHC programme comes to an end, it will probably be the last data at this frontier for many years. We can’t afford to lose it,” Diaconu said.

Companies like Twitter, a growing number of academic publishers and other information clearinghouses are in the game, but detractors remain. “Facebook, for example, is noticeably disinterested, even hostile,” Lynch noted.

berman image

Fran Berman will speak Tuesday in State Room East of Indiana Memorial Union.

Answers may come Feb. 11 when Berman speaks to the public at 3 p.m. in State Room East of Indiana Memorial Union about creating sustainable ecosystems for data — our Information Age’s most valuable resource. Lynch called for a roadmap, and Berman is a leader in designing it to include the necessary components: technical infrastructure, social policy and practice, sustainable stewardship. These are the facilitators for Börner’s vision of population-wide “intelligence amplifiers.”

Berman is chair of the still-young international Research Data Alliance, founded just last year and already strong with representation from 53 countries and a 1,300-member participant mix of 66 percent academic, 17 percent public and 10 percent private. When Berman asks herself what path data will take, “Birth to death or birth to immortality?”, she knows the answer.

“Having a sophisticated citizenry that can understand what data means is tremendously important,” she said recently. “We are on the cusp of a tremendous wave of innovation, productivity and growth — all driven by big data. Strategic use of this data infrastructure can create $300 billion (in economic output) in the health care sector annually in the US. Data is needed for both big ideas and business.”

If anyone is living proof of how big ideas, empowered by technology, can drive innovation, that would be Agüera y Arcas, who will speak twice Monday, the day before Berman, first beginning at 2 p.m. in IMU’s Whittenberger Auditorium. Think designer of Bing Maps, Bing Mobile, Photosynth software suite, now doing machine learning at Google after leaving Microsoft as a distinguished engineer in December.

But all that will be off-topic when Agüera y Arcas instead provides us examples of data that empowers how we think about the future and the past, first by showing us his projections for how women will become economically dominant on the planet within “the next few years.”

gutenberg image

The historical legacy of Gutenberg will be one topic addressed by Google’s Blaise Agüera y Arcas on Monday.

Later in the day, at 5 p.m. at IU’s Lilly Library, he’ll veer to the topic of reinventing what we know about Johann Gutenberg by using modern analytic methods such as high-resolution imaging and shape clustering.

A software engineer and mathematician professing on gender economics and printing history? Sounds like proof that not only will the future continue to reshape our understanding of the past, but that these enlightening endeavors will only be made with the help of a healthy data ecosystem. This is exciting stuff.


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For IU’s job-seeking CS women, a chance to stick your boot in the door Mon, 27 Jan 2014 21:26:04 +0000 So it’s going to be a skin-sizzling 35 degrees Fahrenheit or so this Thursday – the highest climb the thermometer will make during this winter work week – but if you’re looking for someplace hot, really hot, ground zero will be the Bloomington Convention Center where IU students can immerse in a job market hotter than an atom-smashing supercollider: The IU School of Informatics and Computing’s annual spring career fair.

It’s a record year for the career fair: At least 60 companies are pre-registered and sending recruiters, from big-number employers like Amazon, JPMorgan, the U.S. Air Force and the “generals” — General Motors and General Electric, to a slew of health care folks (Cerner, Eli Lilly, Epic, Humana are a few) and financial service providers like Fifth Third Bank, CNO Financial, Discover and Liberty fair

There’s also a huge contingent of Indiana-based employers, from international industrial behemoths like ArcelorMittal, to smaller, fast-growing companies like Blue Horseshoe and Bloomington’s own netirrigate, health care systems specialists like, and IT solution experts Allegient and Apparatus.

Others that sound intriguing are Fluid, a San Francisco-based shop pushing e-commerce platforms, and Tk20, an Austin-based company that provides planning, assessment and reporting solutions for universities.

There’s also Wolfram Research, a company founded by scientist Stephen Wolfram – think the computational, symbolic math-based software Mathematica – who has a unique tie to IU: one of Wolfram’s thesis research supervisors was none other than the School of Informatics and Computing’s own associate dean for research and distinguished professor Geoffrey Fox. A complete list is here.

So yes, the tech job market is hot, as the “numbers” do reflect. U.S. Labor says there will be 1.4 million job openings for computer-related occupations this decade. A 15,000 percent increase was seen in data science job postings between 2011 and 2012, and billings by companies doing statistical analysis for others have shot up five-fold.

The career fair runs from 11 a.m. to 4 p.m. at the convention center, 302 S College Ave., and companies will be looking for interns, part-time employees and full-time employees. Positions are open across the nation, and many companies are in a position to sponsor non-resident workers through the U.S. H-1B visa program.

Prior to the 11 a.m. start, the folks at Informatics and Computing will be hosting a Women in IT Reception at the convention, and at least 22 of the employers attending the career fair will be arriving early to rub shoulders with female informatics and computing students who stop by the 9:30-11 a.m. reception.

To gear up appropriately for the day, female students can also visit Room 122 at Informatics East on 10th Street, Bloomington, any time after 8:15 a.m. for a continental breakfast and a ride over to the convention center. One thing: You need to sign-up here for the Women in IT Reception by tomorrow.

The Women in IT Reception marks a commitment from not only the School of Informatics and Computing, but also from the companies shopping for the tech workforce needs. Both school officials and the human resources folks at these companies have heard the dismal data of late regarding women in the IT workforce.

While tech jobs are expanding and starting pay for a new hire with a computer science bachelor’s degree are above average, the number of women receiving undergraduate degrees in the field continues to shrink. In 1985, 37 percent of undergrad CS degrees went to women; in 2010 that number was 18 percent, and 14 percent at R1 universities. Forecasting more woes, a 2010 estimate by the U. S. Department of Education found that only 0.4 percent of female college freshmen said they intended to major in computer science. Wow!the tech woman

In may be that high schools, and even grade schools, aren’t inserting CS into their programs. It doesn’t help that successful women in media products like television shows and movies are rarely portrayed working in CS (14 men to 1 women in those roles in family films; 5.4 to 1 in films). There may also be an issue with the U. S. H-1B visa program’s gender bias (85 to 1, men to women, for high tech jobs).

That said, the Women in IT Reception is an attempt to stick a boot in the door for women trying to squeeze into a tech world dominated by men. It’s an appropriate move for a program here at IU Bloomington that has been cognizant of the issue and trying to swing the gender numbers into balance for years now.

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IU’s data science certificate to keep workforce on pace with computing power Fri, 15 Nov 2013 15:27:46 +0000 The folks over at Indiana University’s School of Informatics and Computing kept seeing the data on data science piling up and the opportunities growing, both for the school and most importantly for a workforce in need of a bigger and better payday.

One analysis showed a 15,000 percent increase in data science job postings from 2011 to 2012; another predicted a shortage in five years of some 1.5 million managers with an ability to use the analysis of big data as an effective decision-making tool; and yet another found that hours billed for statistical analysis in the U.S. grew by 522 percent this year when compared to the same first quarter in 2011.

Amazing what you can learn about the past and the future with a little data analysis.

Hence the announcement Nov. 13 that the school would begin offering a certificate in data science next year makes complete sense. Designed to entice underemployed hackers, data-crunchers and freelance game designers, along with anyone else with a B.S. or M.S. in computer science, any of the math fields or information science or systems, the program looks to be a quick and quality fix (really quick if you’ve got the initiative) to a serious and growing economic quandary for the U.S.

Employment-related metasearch engine displays skyrocketing jobs in data science.

Employment-related metasearch engine displays skyrocketing jobs in data science.

The big sell is simple: Led by some of the school’s greatest talent, a coordinated path is being offered to a position where the average starting pay is around $80,000. And en route, those considering enrolling will see a three-fold draw: It’s affordable, at around $4,500; it’s completely online, so you can be anywhere; and it’s a finish-as-soon-as-you-can course, free of an inflexible completion deadline.

Since 2000, the computing power of the average desktop computer has multiplied by 75 times, and with that comes the ability for companies to serve their consumers better by using more captured and stored data to make improvements and predictions through sharing and analyzing data. So now CEOs, corporate boards, headhunters and stockholders alike can’t see growth and profit without the needed big data analyst, data solutions architect or information visualization expert that this program will create.

That means the demand for statisticians, information technology managers, business analysts, software developers and business intelligence professionals with some mix of math, hacker or machine learning skills will exceed supply for the foreseeable future, possibly decades. A student in the new certificate program, by design, could complete the required 12 credit hours and be on the market by this spring, or in less than six months.

That represents an incredible and unique opportunity for qualified candidates looking to grow their employment opportunities quickly and cost-effectively, and for the School of Informatics and Computing to become a bigger and better provider to a burgeoning sector of the U.S. economy.

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Research with wacky titles still yields miracles, like former IU biologist Brock’s PCR enzyme Fri, 13 Sep 2013 17:45:59 +0000 The technology known as polymerase chain reaction, or PCR, has been described as one of most pivotal discoveries in the life sciences in human history. The tool – the ability to generate unlimited copies of a fragment of DNA – has led to the creation of successful drugs and vaccines, accurate genetic tests for diseases, the tools forensic scientists use for maternity tests and crime scene analysis, and it’s made sequencing of the human genome possible.

A biochemist named Kary Mullis won the Nobel Prize in 1983 for creating the technology, but Mullis’ work would not have been possible if not for an Indiana University biology professor who in the summer of 1966 visited Yellowstone National Park along with an IU undergraduate biology student in an attempt to understand how organisms survived in the extreme conditions of the park’s geysers and hot springs.

A year later – Nov. 24, 1967, to be exact – IU professor Thomas D. Brock published “Life at High Temperatures: Evolutionary, ecological, and biochemical significance of organisms living in hot springs is discussed,” in the leading scientific journal Science. Little did Brock know that the bacterial sample he and then-undergraduate student Hudson Freeze gathered a year earlier at Mushroom Spring in Yellowstone – the sample that would yield the microbe they would call YT-1 – would allow Mullis to develop PCR. YT-1 would turn out to be a goose that laid a golden egg for mankind.

image of thermus aquaticus

Thomas D. Brock discovered the PCR-enabling Thermus aquaticus 47 years ago while a biology professor at IU.

To study DNA, scientists needed a lot of it, yet cells contain very small amounts. Attempts to copy DNA by unraveling it in the lab involved very high temperatures and the enzymes that occurred in DNA would either quit functioning or disassemble. Then came Thermus aquaticus, the Mushroom Springs microbe brought to IU by Brock and Freeze, that would soon be shown to stay alive in boiling water and to be widely distributed around the world, even in the water pipes of buildings at the IU Bloomington campus.

Since the microbe, which they nicknamed Taq, contained DNA, it also had the right enzymes to conduct replication. And eventually, the best enzyme for use in PCR was taken from that YT-1 strain that Brock and Freeze brought to IU for study.

Next week Brock, now retired and living in Wisconsin, and Freeze, a professor and director of the genetic disease program at Sanford Children’s Health Research Center in La Jolla, Calif., will receive the Golden Goose Award in a ceremony on Capitol Hill in Washington, D.C. The award, created in 2012 by a coalition of organizations after being proposed by U.S. Congressman Jim Cooper of Tennessee, is designed to recognize the scientists and engineers whose federally funded research has had significant human and economic benefits.

Cooper is the kind of congressman scientists should love: “We’ve all read stories about the study with the wacky title, the research project from left field,” he has said. “But off-the-wall science yields medical miracles. We can’t abandon research funding only because we can’t predict how the next miracle will happen.”

Nothing could be more true, and Brock and Freeze remain living proof that those quests, like theirs 47 years ago, toward unveiling and solving new mysteries do indeed yield miracles … like PCR.

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IU in the catbird seat: SDN to benefit higher ed, U.S. economy … and who better to lead Thu, 27 Jun 2013 15:28:15 +0000 The U.S. Department of Defense grant of $900,000 to IU for working on challenges to secure SDN — software-defined networking — isn’t a huge amount of money in itself for a technology that is projected to grow in market value from $252 million in 2012 to as much as $35 billion by 2017.

More importantly, it’s another positive sign that IU made a good bet several years ago to invest its intellectual capital in a technology that promises to create more programmable networks, reduce costs of data centers and provide greater virtualization and automation. And scientists doing long-duration, high-throughput work flows that ideally offer both speed and affordability, though they may not care how their “bits” flow, are already benefiting from IU’s unique position in this market.

OpenFlow map

From students making credit card purchases to internationally recognized scientists analyzing genomic data, SDN is becoming ubiquitous at Indiana University.

IU was first funded in 2009 to explore OpenFlow and software-defined networks with $300,000 from the National Science Foundation. By 2011, through its Indiana Center for Network Translational Research and Education, or InCNTRE, IU was the only academic center on the block teaching OpenFlow, the open standard for running experimental protocols on software-defined networks. Later that year, NSF sent another $2.3 million to IU for further developing this new technology that moves the configuration and management of network routers into software and out of hardware.

As the U.S. government begins its huge consolidation of data centers — it’s closing 40 percent of them, still leaving just under 2,000 in operation — and as big privates like FedEx move to private (and soon, public) cloud architecture, it’s easy to see why the folks at DARPA are taking a proactive stance toward security of software-defined networks.

Sure SDN allows network virtualization and the ability to assemble and disassemble IT infrastructure as needed. But also well-known is the need to develop network-based solutions that acknowledge bad nodes — sketchy and compromised communication redistribution points and end points — that need to be operated around. IU’s Camp and Co. have therefore been charged, in part, with helping realize and then develop new protocols for assessing the health of those nodes.

When DARPA — the Department of Defense unit that originated the Internet — put out the call for proposals in 2012 for this project, the broad task put forth was to “help make wireless networks more resilient to unforeseen scenarios and malicious compromise.” Economically, software-defined networks are going to big business, putting security at the forefront for both private and public users. A Cisco Systems poll recently found that 71 percent of responding IT professionals said they would be implementing some form of SDN technology in the next year. Lending proof, FedEx was recently able to build a data center just one-fifth the size it had originally planned because it implemented a private cloud architecture with SDN components.

Steve Wallace

InCNTRE executive director Steven Wallace leads Indiana University’s software-defined network education and international collaboration initiatives.

These signs bode well for IU and especially the folks at InCNTRE, who are recognized by both private industry and public academia as the top neutral testing facility for SDN products like OpenFlow. In fact, InCNTRE is the first test lab in the world designated by the Open Networking Foundation to certify products that meet OpenFlow standards. Last fall 20 companies came together at IU to test OpenFlow products for certification, and it’s another good bet that IU will see this annual “plugfest” grow and grow.

For Indiana businesses desiring to learn more about SDN and OpenFlow, InCNTRE and IU’s Global Network Operations Center will host an IU Net Talk event July 30 at the Informatics and Communications Complex on the IUPUI campus. It will also be streamed and available for participation through videoconferencing. The presentation, “Addressing the challenges of massive, high-speed data transfers over the Internet,” will provide much greater detail on the future of OpenFlow, SDN and how Hoosiers will benefit from this still unrealized asset.

Writing earlier this month to Information Week’s 2.3 million unique monthly visitors, editor-at-large David F. Carr says as much while relying heavily on … you guessed it … IU’s own Steven Wallace, executive director of InCNTRE. Wallace lays out a clear picture for Carr on how small colleges and businesses, along with top tier research universities and giant corporations, will all evolve with SDN.



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Scientists confirm beautiful nano-butterflies, predicted decades ago by Hofstadter Tue, 21 May 2013 16:51:41 +0000 doug hof

IU’s Douglas Hofstadter

Butterflies were in the news last week. Hofstadter butterflies that is – the self-similar patterns of electrons in a magnetic field that Indiana University distinguished professor Douglas Hofstadter predicted to exist in 1976, shortly after Hofstadter had received his Ph.D. in physics from the University of Oregon.

Hofstadter’s nearly 40-year-old prediction of one of the first fractal phenomena in nature – he envisioned an endlessly repeating energy spectrum of electrons in crystal lattices forming butterfly patterns – was confirmed experimentally for the first time by a team of physicists from the U.S. and Japan. At the time he graphed the energy levels, he dubbed the phenomenon as Gplot, and it was a theory he referenced again in his Pulitzer Prize-winning nonfiction work “Gödel, Escher, Bach: an Eternal Golden Braid.”

The confirmation of the Hofstadter Butterfly has implications in any field where nanoscale materials are used and where lighter and faster is the order of the day – think drug delivery, communications, security, optics. Hofstadter at the time didn’t have the benefit of two-dimensional electron systems – the transistor-like structures made from semiconductors – to engineer a test for his theory. But after decades of lab experiments, scientists last week showed how they manufactured nanoscale ripples on two two-dimensional lattices of graphene coupled to hexagonal boron nitride. In case you’re wondering, the ripples were twenty-trillionths of a meter high (0.2 angstroms).


Columbia University engineers created this image illustration of a butterfly departing from a graphene pattern formed on the top of an atomically thin boron nitride substrate. Electron energy in the structure exhibits the butterfly like a self-recursive fractal quantum spectrum.

So now physicists and engineers have the best ever access to experimenting within the fractal spectrum, and the ability to tune in or tune out varying degrees of freedom within this self-repeating spectrum, all in order to better understand the behavior of electrons in a magnetic field. The work also confirms, if not once again, that Hofstadter is one of Indiana University’s greatest intellectual treasures.

An undergraduate mathematician who grew up around Stanford where his father was a Nobel Prize-winning physicist, Hofstadter is a distinguished professor in cognitive science and comparative literature in IU’s College of Arts and Sciences. He is director of the Center for Research on Concepts and Cognition. He and his students work within the Fluid Analogies Research Group, which is referred as FARG and the students as FARGonauts, and, as he’s stated before, their work is “perpetually in search of beauty.”

It’s been during that search that Hofstadter has helped generate a cadre of thinkers who’ve gone out into the world and proven over and over again how proud Indiana University Bloomington should be to have such a unique polymath, a true Renaissance man, at its campus. These FARGonauts and other students of Hofstadter, conducting research, inventing, writing and teaching around the globe, are IU’s reward.

One of them, who remains here at IU, is Donald Byrd, a senior scientist and adjunct professor in the School of Informatics and Computing at the forefront of computational music study. He’s designed music programs like SMUT and Nightingale; was a designer and software developer for the Kurzweil 250, which is recognized as one of the first synthesizers to convincingly reproduce the sounds of acoustic instruments; and his work on online music information retrieval is cutting edge.

classic hofstadter butterfly

The classic Hofstadter Butterfly from Hofstadter’s 1975 PhD dissertation.

Another is David Chalmers, a Distinguished Professor of Philosophy at Australian National University, where he founded the Centre for Consciousness, and a professor of philosophy at New York University. And Robert French is a cognitive scientist who is now research Director at the French National Center for Scientific Research, the largest fundamental science agency in Europe.

Computer scientist Melanie Mitchell, a professor at Portland State University, in 2009 published the high-successful book “Complexity: A Guided Tour.” called it one of the 10 best science books of that year, and Phi Beta Kappa honor society agreed, recognizing Mitchell with it 2010 best book award.

Scott A. Jones received his Bachelor of Science in computer science while working with Hofstadter and then went on in the 1980s to invent one of the first types of voicemail while co-founding Boston Technology. Still an Indiana resident and a global entrepreneur, Jones has been featured in various media, from MTV to USA Today.

The list could go on, and will go on, and many of the freshest faces leaving FARG are being grabbed up by Google – like Eric Nichols and Abhijit Mahabal – and other tech research companies. Together, as a collective, they give Indiana University a unique presence in the domain where technology and the human mind intersect, and that’s all because Hofstadter calls IU and Bloomington home.

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Science mentoring at IU Bloomington: An ever-appreciating, unquantifiable investment Mon, 18 Mar 2013 15:16:12 +0000 Some of you may have missed the news in January about Indiana University Bloomington physicist John Beggs and his long-distance cyber-mentoring of Horace Greely (N.Y.) High School senior Jiayi Peng to a second-place and $50,000 finish in the prestigious Siemens Competition in Math, Science and Technology. The story of Beggs’ mentoring, above and beyond the call of duty, appeared in one of our new internal newsletters, Inside IU Bloomington, so it may not have been as widely distributed as much of IU’s news traditionally is.

child with test tube

Mentoring is an exciting direction for maintaining strong investments in the future of our nation’s youth.

With last week’s announcement of the top 40 finalists in what is considered THE top high-school-age science and technology competition, the Intel Science Talent Search and its $1.25 million in prize money, there is more than an opportunity to recall Beggs’ mentoring. It’s also the perfect time to better expose the width and breadth of the work that IU’s scientists do, of their own accord and on their own dime, empowering pre-college-age youths to become inspired about science and technology.

Peng, by the way, did finish as a Top 40 finalist from an original group of 1,712 entries and so shared in the Intel prize money and prestige. While she didn’t finish in the Top 10, where awards ranged from $100,000 for the winner to $20,000 for 10th, Peng is on her way to a top-flight, world-class education in part due to Beggs’ influence and assistance.

Peng won $50,000 from Siemens, and Beggs’ work was recognized because of that. But it’s impossible to equate in U.S. dollars the enhanced value – both personally and financially – that scores of young students have obtained thanks to the entrenched dedication so many IU scientists have for sharing the love of their vocation. Service is a component of university life, and it most often translates to action on campus. And quite often scientists personally benefit by outreach in meeting a stipulation in federal grant requirements that calls for an awardee to have a “broader impacts” component in their work.

But broader impacts and university service don’t necessarily need to entail weekends at the local discovery museum scaling down the tenets of evolutionary biology for 6-year-olds, like IU Bloomington biologist Armin Moczek can often be found doing. Nor would it seem to require gathering pre-teens at your home after work hours to organize and operate the Bloomington Math Circle, which IU Distinguished Professor of Mathematics Michael Larsen so loves to do.

Beggs, Moczek and Larsen aren’t even the tip of the iceberg when it comes to IU scientists expressing the dedication and love of their work through mentoring; it seems to be a genetic predisposition for these explorers, and they are passing that code on to their university students. Benjamin Franklin nailed the educative process when he said, “Tell me and I forget; teach me and I may remember; involve me and I learn.”

kids looking at bugs

“Tell me and I forget, teach me and I may remember, involve me and I learn.” – Benjamin Franklin

And that’s just what IU mentors like chemists Erin Carlson (Brilliant Minds) and Jill Robinson (Molecules Matter), astronomer Caty Pilachowski (Public Outreach) and information scientist Katy Bӧrner (Science Maps for Kids) do with their after-hours work: They involve fresh young minds in learning experiences that most of these students (and maybe even their parents) could never have imagined. Some of us are lucky enough to grow up in the house of a scientist where strewn-about fossils, the smell of sulfur and stacks of motherboards are commonplace points of childhood inquiry  … but most of us aren’t.

Carlson, Robinson, Pilachowski and Bӧrner – like Larsen and Beggs and Moczek – are the scientist “parents” most kids will never have, and they are training others, in their classrooms and their laboratories here in Bloomington, to one day do the same in their stead.

It’s impossible to quantify the value and the spin-off benefits realized through mentoring by these IU scientists, and scores more, that go on beyond the university confines. The benefits can’t be listed on a grant form, nor in a fiscal budget, nor in an annual review examining costs vs. benefits. But science mentoring needs to be recognized as often as possible for what it is: an unquantifiable, inestimable service of good directed solely at bettering society.

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The disruptive environment at IU Informatics that could improve U.S. health care Tue, 26 Feb 2013 15:21:10 +0000 Things are starting to get a little disruptive over at IU Bloomington’s School of Informatics and Computing, particularly at the west building. That is where Kris Hauser, an assistant professor of computer science now in his fourth year at IU, and Ph.D. student Casey Bennett have been absorbing the feedback from their paper, “Artificial Intelligence Framework for Simulating Clinical Decision-Making: A Markov Decision Process Approach,” published last month.

One of the hottest topics in the U.S. right now - as evidenced by March cover story in The Atlantic - is the discussion centering on technology and how it might change health care. New research from IU's Kris Hauser and Casey Bennett is at the cusp of that discussion.

One of the hottest topics in the U.S. right now – as evidenced by March cover story in The Atlantic – is the discussion centering on technology and how it might change health care. New research from IU’s Kris Hauser and Casey Bennett is at the cusp of that discussion.

And we mean disruptive in a good way, the Clayton M. Christensen “Innovator’s Dilemma” kind of way, where traditional systems get pushed aside by technological innovation, whether practitioners like it or not. Manufacturing and retail have seen it happen, and in 2008 Christensen laid out the same scenario for education in his book “Disrupting Class.”

Now it’s health care’s turn, according to the work by Hauser, who came here with a postdoc record at UC Berkeley and a Ph.D. from Stanford, and Bennett, who besides being a student at IU is also a research fellow for Centerstone, the largest ongoing clinical mental health data repository in the U.S.

Their recent work laid bare both some startling facts that if we didn’t already know, we should have, and some fresh numbers produced from their research in dynamical, machine-learning systems that provide a ray of hope. They reiterated that as health care spending in the U.S. last year rang in at $2.7 trillion, that bill is expected to balloon to 30 percent of our country’s gross domestic product by 2050. It also noted other soft spots in our health care system: that patients receive a correct diagnosis less than half the time on a first visit, and that successful research in the lab takes years — 13 to 17 — to become practice at the hospital.

The good news from Hauser and Bennett is that this scenario is ripe for technological disruption to the tune of reducing costs by 50 percent while improving patient outcomes by an equivalent degree, all by taking advantage of advances in machine-learning tools coupled with the greater availability of shared health care information. By pouring more and more personalized health data into the system and then feeding that through specialized algorithms designed to generate varied-scenario outcomes, they see both patients and physicians being offered a high-powered technical tool that benefits all.

The media jumped all over IU’s press release about the work, and the research resounded with their peers. The two have been invited to present to one of the largest private health care managers in the world later this year; researchers from other universities and private institutions have connected with them; and IU has benefited by having its voice heard in one of the hottest discussions on the planet: Health Care 2.0.

It’s here, it’s coming, and IU looks to be positioned strongly — both the Bloomington and Indianapolis campuses, no less — for a job market where health IT job advertisements tripled from 2009 to 2010; for a development market where consumers already have smartphone apps for monitoring blood pressure, glucose levels, sexually transmitted diseases and electrocardiograms; and for expanding academic inquiry.

You can only manage what you can measure, and there are over 400 vendors offering different electronic medical records products in the U.S. today. So one of the big challenges is developing standardized, shareable medical data formats — especially ones that doctors have been consulted on and have invested in.

That was highlighted in another piece of fresh research from IU, this from the IU School of Medicine’s Regenstrief Institute and lead investigator Brian Dixon, who looked at how well hospital infection specialists were utilizing electronic health records. The gist of the research, according to Dixon: The doctors “say they want electronic alerts and reminders when the system detects something of potential importance. There needs to be concerted research and development to meet this gap in decision support.”

One complaint of physicians is that they have not been involved in the design of electronic medical records systems, and IU research supports that: "While 70 percent of infection preventionists surveyed reported access to an electronic medical record system, less than 20 percent were involved in the design, selection or implementation of the system."

One complaint of physicians is that they have not been involved in the design of electronic medical records systems, and IU research supports that: “While 70 percent of infection preventionists surveyed reported access to an electronic medical record system, less than 20 percent were involved in the design, selection or implementation of the system.”

And businessmen and investors in health care artificial intelligence agree. Tom Coss, CEO of HeartCloud, a California company that captures remote clinical data from the monitoring devices of at-home patients, was one of the folks who contacted Hauser and Bennett. His company sees opportunities to do what the IU researchers are suggesting — to save money and lives — but HeartCloud needs that right mix of technology and medical information.

“The challenge we have is determining meaningful changes in patient weight over short periods of time which may indicate fluid retention and impending congestive heart failure, which if left untreated will place the patient back in the hospital,” he said.

Coss wonders “who” is going to sift through the data to pick out what is important and what is not, what should become a red flag to a physician and what should be disregarded, but what he really meant was “what” is going to sift through that data? That would be the exact artificial intelligence framework Hauser and Bennett are developing, a system coupled with a physician — and maybe not even a physician one day — intended to identify optimal decisions in the most complex and uncertain environments.

If there is another area of scientific endeavor that is closer to the cusp of meeting a point of disruptive innovation that would also have a direct impact on the lives of as many Americans as advances in artificial intelligence in health care would, I certainly can’t think of what that would be.


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For IU scientists, banner accomplishments; for U.S. science, a dismal season Wed, 26 Sep 2012 19:18:13 +0000

Former Carl Sagan student Bill Nye, “the science guy,” left, and astrophysicist Neil deGrasse Tyson have both been busy defending and promoting investment in science. See a You Tube video of Tyson explaining global competition with U.S. science.

It’s been a super couple of weeks with respect to science news at Indiana University, as numerous announcements have highlighted achievements that are going to directly affect humanity. Most specifically, young chemist Silas Cook’s achievement synthesizing the world’s most successful anti-malarial drug, artemisinin, which is too expensive to produce naturally at the scale needed to be successful. If able to be scaled up, the new formula could be a game-changer against a disease that kills 2,000 children a day in Africa.

Then there was Patricia Foster and her team’s work at IU Biology broadening our understanding of spontaneous DNA mutations via the study of 200,000 generations of E. coli in conditions remiss of any natural selective pressures. The U.S. Army Research Office funded the work, in part because a better understanding of how DNA mismatch repair works – either in or out of the presence of environmental pressures – could help lead to new sleuthing tools for tracking where bacterial strains originate.

Another announcement – this one in the “work still to be done” category – highlighted the important path low-vision optometrist Dr. Shirin E. Hassan finds herself on to ensure elderly, blind and vision-impaired pedestrians have the best possible tools to improve their quality of life. In this case it’s either validating or offering improvements to an existing street-crossing training program used nationwide to benefit low-vision citizens. The program has never been “tested” and the National Institutes of Health has provided Hassan with $1.9 million to do just that.

In laboratories across the IU network, where thousands of faculty, grad students, postdocs and research scientists work, these are but three quantifiable, recognizable successes through science. As clear and objective as these examples are, it remains the case today that science has never been more in the arena of the politically contentious, and even more so in this year of a presidential election.

Even Bill Nye, the Science Guy, jumped into the polarization pool with a stinging critique of creationist-based child-rearing on the heels of a June Gallup poll that found 46 percent of Americans believing humans were created by God in one day. There are beliefs – we all have them – and there are facts, and they are unavoidable. That’s why you can’t open windows on airplanes.

Other facts of late are more life-threatening, especially for those of us recognizing the benefits folks like Cook, Foster and Hassan can and will afford us. The National Science Board on Sept. 25 said state support for public universities had fallen, on average, 20 percent. Earlier this month the Council of the Great City Schools released a benchmark report on college readiness that found only 31 percent of students taking the ACT “college ready” in science. A similar report last year found 43 percent of SAT takers ready for college, but sadly, the SAT doesn’t even test for science skills.

It was but a few months ago that the U.S. House of Representatives adopted an amendment to end funding political science through the National Science Foundation. That’s political science as in IU Nobel Prize-winning Elinor Ostrom political science, the kind that links human decision-making techniques to “more sciencey” things like dwindling fish species and water quality degradation. Common sense, apparently, is not always politically expedient sense, it would seem.

So now we have scientists like NASA’s Alan Stern and UC Berkeley astronomer Geoffrey Marcy announcing their own version of KickStarter for scientists, Uwingu (Swahili for “sky”), to engage the public in an effort to better fund space science. This in an age where we’re spending $11 billion on a single new aircraft carrier, that as Harold Levy of Kaplan University and New York Public Schools fame noted, is twice what it could cost to give four-year scholarships (in-state tuition) to State University of New York to enough would-be teachers to fill every science teaching position in this country’s middle schools and high schools.

Levy wasn’t saying we should replace the existing ones, he’s just pointing out the magnitude of where our money isn’t going and where he thinks investments should be made. Nobel laureate and physicist Steven Weinberg recently echoed some of Levy’s concerns, pointing out that if America wants to play on the global scale of excellence, it will eventually have to pay – and not by shuffling money from Wall Street oversight, or health care, or police and fire, or other areas already in funding danger. He directly suggests more progressive tax structures, specifically on investment income.

It’s not been a good week or two for IU scientists, it’s been a great week or two, but beyond the confines of the labs and the classrooms, on the not-so-grand scale of U.S. politics, science has been taking an underserved beating in the brawl going on over government spending in general.

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Science at Work: It’s all about you, the citizen scientist Thu, 09 Aug 2012 16:56:45 +0000 “Life on Earth: Preserving, Utilizing, and Sustaining our Ecosystems” is the theme of the Ecological Society of America’s annual meeting under way in Portland, Ore., and one thing many of the world’s leading ecologists are making clear here is that the theme may never come to fruition without a little help from their friends. That would be you, the citizen scientist.

Photo of woman at computer screen

As part of a broader movement to empower citizen scientists, NSF is asking citizens to pick which types of scientific information they would like to see made available through a new application programming interface.

Scientists have always used the public to forward their work. The great botanist Carl Linnaeus asked citizens to assist with collecting plant specimens from around the world during the late 18th century. And before science was institutionalized, citizens were the scientists: The Chinese have recorded locust outbreaks for more than 3,500 years; the Japanese, cherry blossom festivals for over 1,200 years; French vintners, grape harvest statistics for nearly 650 years.

So it should come as no surprise that the organizers of Portland ESA 2012 saw an opportunity to facilitate a unique exploration of this historical relationship not only with a timely special edition of ESA’s flagship journal, Frontiers in Ecology and the Environment, devoted to the topic, but also with a conference-opening two days of workshops titled Pubic Participation in Scientific Research. Couple those initiatives with a variety of presentations on the topic over the course of the weeklong annual meeting, and it becomes clear that thanks to advances in communications technology and a new willingness to engage the public as collaborators, scientists are ready to take on non-specialists as partners.

Even the National Science Foundation made this known Aug. 8 when it began accepting public input in helping it prioritize which data sets, or digital collections of information, to open more broadly to the public through interactive search and display functionality. The new NSF website allows anyone to vote for collections of information that are under consideration for expanded access.

And here at ESA, Indiana University’s stake in this new integration of non-scientists into science research is not only evident, but outstanding. Citizen science components were evident in work presented by faculty and graduate students from IU Bloomington’s School of Public and Environmental Affairs and the Office of the Vice Provost for Research’s Center for the Study of Institutions, Population, and Environmental Change, where projects based in Bloomington and Indianapolis were squarely focused on public participation.

In Bloomington, 14 neighborhood and homeowner associations participated in a study about individual tree management and the impact of city and association rules and norms upon it, and the owners of another 106 residential parcels took part in questionnaires about private and public right-of-way trees. One of the initial findings: Neighborhoods that agreed to water trees as a group had higher tree survival rates than neighborhoods that chose to water trees individually.

Using Indianapolis neighborhoods and trees planted there between 2006 and 2009 as the laboratory, SPEA researchers worked with the nonprofit Keep Indianapolis Beautiful and a group of dedicated high school students during the summers of 2011 and 2012 to assess the social-ecological variables that affect tree mortality and growth rates. Using ethnographic semi-structured interviews and participatory action research methods, the team also looked at how involvement in neighborhood-initiated tree planting programs — as a form of collective action — might have social impacts at both the neighborhood and individual level.

And IU wasn’t alone with respect to scientists empowering Indiana citizens. A team led by Butler University that included representatives from the Indianapolis Art Museum reported on the use of a mobile device application, called “Raindrop,” that used geographic information systems and mobile device satellite technology to map a raindrop’s path from a user’s home to the White River. It was fun, it was a successful environmental outreach tool, and it used a combination of science, art and technology to educate.

As citizens become closer partners with scientists by contributing, collaborating and co-creating on research, new answers to old questions like worries about the quality of data and validating are being found. In one case, new automated smart filters cull out quirky data points at Web-based citizen data collection sites. But as public university scientists increasingly engage citizens in their science, they will also engage a public in learning, expand the diversity of stakeholders interested in the work at hand, and most importantly for IU, offer an effective way to engage their students.

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Science at Work: A rare science story with “legs,” and IU’s Ogren carrying the baton Tue, 31 Jul 2012 19:44:54 +0000 The news media love stories with “legs,” those gifts that just keep on giving, keep on going, and in science news – short of the natural disaster – they come few and far between. Take the sports cliché, “You’re only as good as your last game,” and replace “game” with “research paper” and you get the idea. Then recall last year’s UNESCO report on science that cited the latest figure (2007) of more than 1.58 million research papers published worldwide in that year alone.

So it’s thrilling to see news still trickling out after the July 4 announcement by CERN, the European Organization for Nuclear Research, of the identification of a subatomic particle that appears to confirm the existence of the Higgs field.

Harold Ogren smiling alongside the Transition Radiation Tracker that helped confirm the existence of the Higgs field.

From The Huffington Post to Al Jazeera to Britain’s leading tech pub, The Register, you could still find columnists, science writers and even philosophers using the Higgs particle as a jumping off point for exposes on future physics experiments, juxtapositions with the Affordable Care Act and, as might be expected, queries about the dangers of “Western materialist rationality.” Even the Times of Malta, three weeks after its July 5 announcement on the Higgs boson, retracted the paper’s use of “the God particle” term for being misleading.

But the real muscle behind the legs to the Higgs story isn’t the “What will future experiments bring?” angle, or the attempts at stirring up a brouhaha between theology and contemporary rationalism. The story with legs is the look along the long road that thousands of scientists  – if not tens of thousands – took to obtain the result from the Large Hadron Collider, or what theoretical physicist Lawrence M. Krauss described in the New York Times as “the most complex machine humans have ever built.”

At Indiana University that road inevitably turns back to one Harold O. Ogren, professor emeritus in the Bloomington College of Arts and Sciences’ Department of Physics, a CERN Fellow, and a leader of the IU group that built the $11 million Transition Radiation Tracker, a system designed in the basement of Swain Hall to measure the momentum of particles emitted from proton-proton collisions.

ATLAS, one of the seven experiments at the LHC that took data from colliding beams, depended on the TRT to accurately identify the paths of charged particles, and the work went off without a hitch, thanks to Ogren and his team. He called it “the high point in my physics career.”

But before there ever was an LHC there was Ogren, in the early 1990s, working on and laboring for construction of the Superconducting Super Collider in Texas before Congress voted to de-fund the project in 1993.

“Harold certainly saved my career after SSC was canceled,” said IU senior scientist Fred Luehring, a specialist in grid computing and high energy physics software, of Ogren’s successful plan to design (about 10 years) and build (about five years) the TRT for ATLAS in the basement of Swain. “It was really a big deal and damn hard. Harold was always calm, fatherly, and helpful in guiding the project through the day to day crises in designing and building a one-of-a-kind particle detector.”

Craig Stewart, executive director of IU’s Pervasive Technology Institute, is quick to pin credit on Ogren for bringing an international air about the IU campus, thanks to the ATLAS experiment and the TRT.

“When Harold was involved in building the equipment for ATLAS he was the highest ranking person within the ATLAS management structure working in the U.S.,” Stewart recalled. “The top leader in the country on the ATLAS project detector construction lives in Bloomington and worked on Third Street in Swain Hall. How cool is that?”

Ogren teaching at Swain Hall.

With Ogren and team building pieces of an experimental detector that was going to collect data, and IU physicists also involved in figuring out the mathematics and physics of how to analyze the data, it also served as a gateway for what is now IU’s internationally recognized status as a leader in computing and networking to analyze data.

And while Stewart was in awe of Ogren’s level of involvement, another senior scientist at IU who played a key role in constructing the TRT, Pauline Gagnon, identified him as the source of a contagion called enthusiasm: “He was almost like a kid in a candy shop, every new problem stimulating him. He was creative, fun and tireless.”

Associate professor Hal Evans missed the TRT construction phase but participated in the ATLAS experiment, including data analysis. He agreed with Physics Department chair Rick Van Kooten’s assessment that Ogren has been an ultimate mentor who can teach physics through a conversational style that strikes of “youthful joy.”

“He is a role model for me,” said Evans. “His wide-ranging enthusiasm and his ability to retain calm and good humor during the deepest crises are things that I strive to emulate, but don’t always succeed at!”

Luehring agreed by recalling the time Ogren and group of physicists were ordering dinner in Texas while working on the old SSC project. “He told us he’d put his name on the waiting list and that we’d recognize it when called. Sure enough, the server called out, ‘The Higgs party!’ That’s typical of his sense of humor.”


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Science at Work: IU’s IT plan is working … again and again Tue, 26 Jun 2012 20:18:19 +0000 It wasn’t exactly a shocker when the National Science Foundation and the U.S. Department of Energy announced last week that IU would receive $3.82 million as the university’s share in a $27 million second round of funding for the Open Science Grid, initiated in 2008 with $30 million from NSF and DOE to advance state-of-the-art computing resources in support of education and research in science domains.

NSF and DOE were already invested, as were the nine institutions including IU that shared in the second round of funding. By the time 2017 rolls around, signaling the end of the second phase, IU will have received over $6.6 million, primarily for operating OSG’s Grid Operations Center in Indianapolis – the single point of operations support for a computing grid that has 65 sites worldwide and that last year provided 280 million hours of reliable, secure computing time for some of the most complex science analysis in the world.

What is shocking is to take a step back and look at how IU and its supporting communities have successfully broadened the university’s investment in information technology assets. It’s gone beyond receipt of some of the most lucrative funding awards to where IT has become integrated into the very fabric of academia. Making supercomputing assets ubiquitous tosses roadblocks to collaboration to the side and empowers individual investigators working on narrow projects with the same assets – they are called virtual data toolkits – that the thousands of scientists, including those from IU, working with Europe’s Large Hadron Collider have available.

Photo of IU vice president for information technology brad wheeler

Indiana University’s Vice President for Information Technology and Chief Information Office Brad Wheeler spearheaded development and release in 2009 of “Empowering People: Indiana University’s Strategic Plan for Information Technology.” That plan is working, over and over again.

In 2009, a year after the Open Science Grid was funded to support data analysis from the Large Hadron Collider, and just on the heels of IU being selected as the lead on another international supercomputing project, FutureGrid, IU Vice President for Information Technology Brad Wheeler proclaimed, “The strategy is working.” IU had, he said, “gone from the bench to the big leagues.”

It’s going on three years now, and Wheeler now has the capital – financial, intellectual, experiential and cultural – to remind, “The strategy is working … again, and again, and again.” From social sciences to law, physics to health care, sustainability to business, it’s hard to find a niche of academia where IU’s information technology assets are not a necessary collaborator.

You can take a look at a timeline of notable IT events and awards for IU from 1998 to early 2009, and then amend from later in 2009 to include IU as one of 10 partners sharing $10.1 million for NSF’s FutureGrid, and another $1.5 million from the National Institutes of Health for IU-specific work tied to FutureGrid. Last year IU was awarded $2.3 from NSF for Global Environment for Network Innovations to build, test and support innovative computer networks; another $1.5 million for the new National Center for Genome Analysis Support, and then a share among 17 institutions of $121 million for the new TeraGrid, called XSEDE.

But it hasn’t been just the feds who’ve saddled up to Wheeler and Co.’s vision. IBM, the Indiana Economic Development Corp., the Indiana General Assembly and of course Lilly Endowment Inc., IU IT’s most stalwart supporter providing over $208 million to IU for tech-related projects since 1999, have all been on board.

It’s behind these financial assets that IU’s other riches are stored, riches like distinguished professor Geoffrey Fox, whose work on scalable scientific computing influenced the design of nearly every supercomputer out there. There is Craig Stewart, director of the Lilly-funded Pervasive Technology Institute, which last year reported that since its inception in 1999, it had solely or collaboratively with other IU units, pulled in over $173 million in external funding (that’s not including Lilly’s cumulative $208 million) to benefit, most broadly, the Indiana economy through jobs, discoveries, new products and new collaborative opportunities.

Stewart’s influence seeps beyond the state borders, exemplified last year through his chairmanship of NSF’s Advisory Committee for Cyberinfrastructure Task Force on Campus Bridging. Not only was IU represented with the lead seat in an effort to integrate seamless cyberinfrastructure use from campus to campus to state, regional, national and international networks, but it stood apart with three other IU faculty members – D. Scott McCaulay, David Jent and Von Welch – on the team. Only one other institute – the RENCI collaboration between Duke, University of North Carolina at Chapel Hill and North Carolina State – had more than one rep, and RENCI had two.

iu president michael a. mcrobbie

In 1998, under the charge of then-vice president for information technology and current university president Michael A. McRobbie, IU’s first ambitious Information Technology Strategic Plan was developed. It went on to serve as a model for institutions across the nation.

Welch is another treasure like Stewart whose work exemplifies the breadth of IU’s commitment to cyberinfrastructure, technology and collaborative research. Beyond grid and network building is security and policy, and Welch, as deputy director of IU’s Center for Applied Cybersecurity Research, is one of IU’s new stars in that domain. Proof? His “Security for Grid Services” research paper was named one of the top 20 papers in the past 20 years of publications from the International ACM Symposium on High-Performance Parallel and Distributed Computing.

From policy to practice, collaboration to individual excellence, at a time when higher education’s public presence is unduly weighted by politics (Virginia and Louisiana), questions of value (student debt) and distractions created by the criminal-minded (Sandusky), it’s hard to imagine a more exciting time to be exercising intellect at Indiana University. And it’s important we recognize a primary and vital energy source fueling those workouts.

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New partnership with Crane strengthens IU’s mission, benefits state’s taxpayers Mon, 18 Jun 2012 16:59:51 +0000 It’s been shown time and time again that stronger higher education has a direct correlation to a state’s economic, social and cultural health, and at a time when growing attention is being paid to global competition challenging America for science and technology prominence, one would think policymakers would be leaning to invest more heavily in higher education.

In fact, the proportion of revenues public colleges and universities received from state appropriations dropped from 38.3 percent in 1991-1992 to 24.4 percent in 2008-2009. And even though total state appropriations rose nationally from $65.1 billion to $75.6 billion during that period, state funding actually declined in relative terms: If states had provided the same level of funding per public, full-time equivalent student as in 1990-1991, total appropriations in 2009-2010 would have equaled approximately $102 billion, an amount 35.3 percent higher than the actual appropriation.

Hand holding example of smart skin mesh

Crane is developing a smart skin that detects impacts, tampering or other events that affect the integrity of an object, and then processes information about the event, including severity and how to correct damages.

So over the last week or so, while faculty at another of the nation’s top business schools – UCLA’s Anderson School of Management – voted to adapt to ongoing state disinvestment in public higher education by going private at the same time the flagship school in neighboring Kentucky addressed disinvestment by announcing it would sell land and take hundreds of staff positions off the payroll by either firing people or not filling vacancies, it was good news to learn of the new partnership between IU and the Naval Surface Warfare Center, Crane Division, that will allow IU campuses to work more closely with Crane and with private-sector partners to transfer technology to the private sector.

These types of ambitious partnerships are examples of a more diverse higher education market that is emerging in response to government changes to the higher education sector, including funding cuts and an increasing commitment to keeping a college education affordable for students and their families.

Crane, having survived five Base Realignment and Closure Commission rounds (there’s another in 2015), is the number two employer next to IU located south of Indianapolis, and it’s not just hiring, it’s hiring IU’s kind of people: Five years ago Crane may have had 20 employees with PhDs; today there are 62 PhDs working there, with another 16 in process to be hired. These are folks with degrees in information technology security, chemistry, engineering, materials science, physics, and nuclear energy.

At a time when America’s global ranking in the number of college degrees earned by young adults has dropped from first to 16th, for IU to have a working partnership with Crane designed to enhance opportunities for third party, non-profit and for-profit businesses that will undoubtedly be connected to similar skill sets, it bodes well for how prominent science and technology will play in the landscape for the IU network.

It will remain a challenging landscape as online learning continues to provide inroads for for-profit companies to move into higher education in a country where one in four higher education institutions are already outside state control, and since those universities under state control have no guarantees that state support levels will return, let alone increase. But partnerships between highly skilled entities like IU and Crane specifically designed to enhance third party opportunities are a needed hybridization that should not infringe on the important public mission IU remains charged with. In fact, it well could become a template for a public-private mix, or in this case a public-public-private design, which enhances that important mission.

Photo of two-band imager device

A two-band imager being developed by Crane examines both the radiance level and the temperature of two objects while viewing simultaneous images in real time. Current technology limits the spectral bandwidth of a single focal plane sensor.

We’ve already seen how start-ups based out of the IU system and faciliated by IU’s Research and Technology Corp. not only are successfully spun-out, but also provide important mentoring. The big ones are most memorable – Marcadia sold to Roche for $287 million plus another $250 million as drugs are developed, $100 million from Blackboard for Ali Jafari’s Angel Learning, and Derwent Funds $40 million for Johan Bollen’s Guidewave Consulting.

Then there is CS-Keys, FAST Diagnostics, ImmuneWorks, Therametric Technologies, Information in Place and WisdomTools, and Predictive Physiology and Medicine, all spinouts that not only created Indiana jobs, but also fomented mentoring opportunities for advancing IU students and researchers. This new IU-Crane collaboration presents itself as another example of IU excellence facilitating success through working with others outside the confines of the Sample Gates, and it’s also proof positive of IU’s commitment to excel in the face of ongoing challenges to higher education.


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Science at Work: Losing a great like Gest illuminates the gifts received of academia Thu, 31 May 2012 19:05:28 +0000 One of Indiana University’s and this nation’s great scientists will be celebrated tomorrow (June 1) in Bloomington when friends, family and peers gather to honor the life of Howard Gest at Unitarian Universalist Church.

Gest had retired from full-time teaching here in 1987 after originally coming to Indiana University as chair of its Department of Bacteriology in 1966, but he remained active until just shortly before his April 24 death here in Bloomington from complications associated with a stroke.

Gest was a great scientist who learned from and with other greats. He did his undergraduate work at UCLA in the early 1940s under the tutelage of Salvador E. Luria and Max Delbruck, who in 1969 both won the Nobel for their work on the genetic structure of viruses. In total, he would end up working with nine Nobel laureates.

Howard Gest, Distinguished Professor Emeritus of Biology

But before he could pursue graduate work World War II had erupted and by the fall of 1942 Gest was working with another UCLA professor, the chemist Charles Coryell, on the Manhattan project when Coryell discovered the element promethium.

While working on the project Gest joined a group of scientists signing a petition drafted by physicist Leo Szilard – the Szilard Petition – that called on President Harry Truman to not use the new weapon yet because “its powers should be adequately described and demonstrated, and the Japanese nation should be given the opportunity to consider the consequences of further refusal to surrender.”

It was later learned that military sources prevented Truman’s receipt of the letter, which was dated July 17, 1945, one day after the first atomic bomb explosion at Alamogordo, N.M., and less than three weeks before it fell on Hiroshima.

Gest had told reporters as recently as in 1995 that he still had mixed feelings about the use of the bomb, and most especially about the need for a second one to be dropped two days later on Nagasaki. “More than 95 percent of the roughly 225,000 people killed in Hiroshima and Nagasaki were civilians, and most were women and children,” he told the Bloomington Herald-Times in a 2005 interview. He also wrote about the personal experience here.

When the war had ended, and on Coryell’s recommendation, Gest went for graduate study under another Manhattan project scientist, Martin Kamen, who had co-discovered the isotope carbon-14 and was a researcher in photosynthesis, an area of research that would set a course for Gest to become one of the great bacterial photosynthesis investigators.

That successful path was evidenced, in part, by his 1980 discovery of the new organism Heliobacterium Chlorum and the accolades he received for editing in 2006 the 1,300-page “Discoveries in Photosynthesis,” which Current Science called “easily among the most outstanding and valuable books published in the biological sciences in the last 100 years.”

But standing on higher ground than his 300 published research papers or his membership in esteemed organizations like the American Academy of Arts and Sciences, the American Association for the Advancement of Science, the American Society of Microbiology, and the American Academy of Microbiology, Gest was a teacher and a mentor – to his undergraduate students who may never have taken another microbiology course again, to his graduate students and to the young faculty members he would draw to IU and mentor.

IU Professor Emeritus of Biology Milton Taylor will speak about his relationship with Gest during the celebration tomorrow, and Taylor stands as proof of Gest’s deep commitment to nurturing and passing on the torch of knowledge to those of a younger generation. Gest talked Taylor into IU after the young scientist had finished a PhD at Stanford in 1966, and a year later Taylor was here.

“I still remember this visit which was in the spring, and Howard and Jan (Gest’s late wife) showed me around and had arranged for us to go together to a musical in the auditorium. After the weekend and the hospitality of the Gests, I had no doubts of my future. In the early years here in Bloomington, Howard and Jan were like our parents, looking after us, and we interacted with the family a great deal.”

A photocopy of the Szilard petition, signed by Gest while a scientist on the Manhattan project.

Just as Gest never shied away from his responsibilities, and his love for, being a mentor, his zeal for scientific endeavor never waned, not even in the months prior to his death. As recently as January he’d updated thoughts on some of his scientific pet peeves, taking to task the new media for skewing scientific findings and taking a dig at the speculations of some scientists in other fields.

“Clearly, the Internet and the blogosphere have created new problems in communication of scientific advances to the public,” he said of the recent fixation by writers and some scientists connecting microbial extremophiles on Earth as a positive correlation to extraterrestrial life.

“Why is it that biologists never advance hypotheses on problems of physics relating to quarks, gluons, black holes, etc., whereas many physical scientists (physicists, astronomers, geologists, etc.) have attempted to explain major complex unsolved problems of biology?” Gest asked, tongue firmly planted in cheek, wondering aloud how huge questions in biology can be solved by the input of a little physics-derived “common sense.”

While his family still mourns the loss of their loved one, we here at IU need recognize gaining so much from Gest and the string of dedicated teachers and researchers and, as Milton Taylor noted, “parents,” he has left in his wake. Howard Gest has left IU so much more than he could ever take with him in passing.

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Science at Work: Cowboys, hot peppers and sea turtles….at Indiana University? Thu, 24 May 2012 19:27:19 +0000 It is an Indiana science blog so how often are cowboys, hot peppers and sea turtles going to pop up as topical in an east-of-the-Mississippi, oceanfront-devoid, tomato-over-capiscum lovin’ environment? More often than not, actually, thanks to the incredibly diverse family of researchers found within the Indiana University system, highlighted most recently by a series of unrelated research papers all with roots in Central and South America. IU research spans the globe and beyond, but today the focus is on cowboys, hot peppers and sea turtles and the connection each have to Indiana University.

First, to the turtles, and specifically the oldest and largest living reptile on the planet, the critically-endangered leatherback, and the work done by IU-Purdue University Fort Wayne distinguished biology professor Frank Paladino that made a splash at MSNBC and media partner TechMediaNetwork. Paladino and longtime mentor James R. Spotila (Drexel University) joined researchers from nine other universities, institutes and agencies to link variations in Pacific and Atlantic leatherback feeding patterns and the resultant success or lack thereof in their foraging to the unusual differences in population recovery being seen in the Atlantic and Pacific oceans.

Paladino and a Ph.D. student conducting an ovary ultrasound on a green sea turtle in Costa Rica.

Leatherback habitat spans the globe, but the vast majority of both Atlantic and Pacific leatherbacks nest along Central and South American coasts. What the team found was that Atlantic leatherbacks, which are making a comeback, traveled in two swimming gears, high for transit and low for feeding, while Pacific turtles were basically pedal-to-the-metal and always hunting for their primary prey, jellyfish.

The announcement of the discovery came at an opportune time – May 22 was International Day for Biological Diversity – that helped put Paladino’s enduring work on a proper stage and raised the profile of the plight of this amazing species and the challenges it still faces from shrimp trawling, habitat loss from oceanfront development, egg poaching and other threats.

On a far more palatable note, yet still in the Pan American biodiversity spotlight, one of IU Bloomington Department of Biology‘s fine postdoctoral catches, David C. Haak, had his “Why are not all chilies hot? A trade-off limits pungency” paper published in hard copy form after online publication a few months ago. So it may not be habanero-hot news to some, but for Indiana home pepper growers finally finding the proper soil temp and daylight hours for good growth, it remains an intriguing case study in adaptive trade-offs and why some peppers of the same species are hot, while others are not.

Red savina habaneros from New Mexico rank at 248,500 Scoville Heat Units, compared to the average orange habanero at around 200,000 units. Photo: National Science Foundation

Haak’s paper suggested a causal relationship between low-moisture environments and the production of less pungent chilies and fewer seeds, influenced by the plant’s relationship with fighting off the fungal pathogen Fusarium semitectum. The fungus doesn’t fare well in low water environs, but thrives in wet soils. When F. semitectum threatens pepper plants, Haak found the plants in turn produce more of the heat-giving capsaicinoid compounds to defend their fruit from the fungus. Remember that Haak’s work involved wild chilies from the center of diversity for the plant, southeastern Bolivia, but for experimental gardeners looking to achieve world-record Scoville units, it might be fun to turn up the water and see if a battle between fungus F. semitectum and compound capsaicinoid ensues. Later this summer, the proof may be in the pepper.

Finally, three IU professors address the legacy of the late Mexican-American scholar Americo Paredes, who died in 1999 after nearly a half-century of examining the traits of expressive culture through his critical dissection of the cowboy as an American folk hero. Paredes, through his seminal work “With His Pistol in His Hand: A Border Ballad and Its Hero,” told Americans the story of Mexican folk hero Gregorio Cortez’s conflict with the Texas Rangers that later became a major motion picture starring Edward James Olmos. In a special Winter 2012 issue of the Journal of American Folklore, professors John Holmes McDowell, Richard Bauman and Beverly J. Stoeltje show why the National Research Council recognizes the IU Department of Folklore and Ethnomusicology as one of the best non-performance music study programs in the U.S.

In the edition McDowell, the department chair, recognizes Paredes as a man conditioned by Mexican-American border conflict to “appreciate deeply the factors that draw peoples together and set them apart and the ways that expressive culture enters into and shapes this process.” Bauman, a distinguished professor emeritus in the department, educates us on and engages us with Paredes’ fascination with the decima, a poetry and song form that along the border dealt with social relationships and family identity in the ranching and farming communities. Then it’s anthropologist and folklorist Stoeltje who reminds us of the incontrovertible evidence offered by Paredes that the “figure of the cowboy was fabricated into that of a national folk here, embodied as a macho figure” while railroads, corporate ranches and Northern industrial influences pushed the culture into “Wild West shows, rodeos and movies.”

Book cover of Paredes' "With His Pistol in His Hand"

Stoeltje’s writing on Paredes’ ability to distinguish true heroes of the people like Gregorio Cortez from “the creation of a heroic figure by external forces to serve hegemonic purposes” is a worthy reminder that things are not always as they seem. So should it really be that surprising that one could come to the Midwest and Indiana University and find oneself working with world leaders in the study of cowboys, hot peppers and sea turtles? On the contrary, it really should be expected.

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Welcome! It’s Science at Work: The Blog! Mon, 07 May 2012 17:59:27 +0000 And as far as Indiana University’s physicists, anthropologists, informaticists, statisticians, biologists and others of the “hard” or “STEM” sciences go, this blog will presuppose to reflect on the science work that’s already completed, that is still under way, and that is still to be done – the stuff of NSF and NIH pre-proposals – with the hope being to add richness, depth and some intriguing nuggets of heretofore unpublicized information about IU’s scientists that the more than 156 million other bloggers on the planet may have missed.

There will be reflection.

When IU biologists announce they’ve hit an international milestone – as they did in a recent, warranted press release on IU Bloomington’s remarkable, quarter-century-old Drosophila Stock Center – this blog should create the space to delve deeper than a 600-word press release designed to tease media interest. Rather, Science at Work will hopefully offer the elbow room to recall connections like this university’s committed history in genetics research as underscored by someone like Hermann J. Muller, that IU faculty member who received the Nobel Prize in 1946 for his discovery of the production of mutations from X-ray irradiation, proved from his study of fruit flies. From there a family tree began to sprout that to this day continues to be fruitful.Microscopy photo of fly head.

We’ll also recall our Indiana University science heroes as they fall from the tree of life, like former dean for information technology and Thomas Hart Benton Mural Medallion honoree Christopher Peebles who passed April 16, and who was followed by Howard Gest, distinguished professor emeriti of microbiology and Manhattan Project scientist, on April 24. More than note will be made of these losses, as we offer a venue for their closest co-workers to reflect on the work and legacies they’ve left to us.

There will be timely topics.

As science calls on the past and projects into the future, Science at Work will also stay in stream with those “now” topics that professors and postdoctoral researchers are talking about, topics that if not now will invariably affect our daily lives, from how social media influences our everyday actions and reactions to issues like the high cost of both publishing and providing scientific research and the new trend toward open access publishing. We’ll rely on those in the midst of this discussion, like the many researchers who edit and review for journals, and from those who might question the mechanics of high-profile journals, like IU mathematician Russell Lyons. His work has not only pointed out serious statistical flaws in highly publicized research, but also asked broader questions about review and critique processes in many of these same types of journals.

And then there will be us!

“Us” being the new Indiana University Communications branding, marketing and media division of Public Affairs and Government Relations, where media relations specialists work to keep IU’s work deservedly in the spotlight. We’ll remind you here, in case you missed it, why heavy-hitters like The New York Times and NPR recently called on the Department of Anthropology’s still young Anthropology of Food program not once, but twice, for help with news stories over a period of just three weeks. Wind turbine with birds flying around it.

This is where we’ll hope to move beyond reflection, step forward from the immediate and attempt to lift the curtain on the fascinating new work being done in programs like Anthropology of Food, and by students like School of Informatics and Computing recent graduate Russell Conard, whose future bodes well as he leaves IU’s undergraduate ranks with a Provost’s Award for Undergraduate Research and Creative Activity and a significant cash prize from the Building Entrepreneurs in Software and Technology (BEST) competition held by SOIC and Kelley School of Business. Conard’s building a device to help companies installing wind turbines survey for birds that could become endangered, and it’s an idea and a growth industry that anyone interested in IU science will want to know more about … right here.

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