Inquiry Fall 2015

News from the University of Chicago Physical Sciences Division INQUIRY FALL 2015 Tech speculation Forecasting the future of technology INQUIRY FALL 2015 Epigenetics 1 Blueprints 3 Software bugs 7 Future tech 9 Juggling math 10 Nambu Divisional 125 years of remembered 11 news 12 science 13 Note from the dean Gained in translation he University of Chicago has always been an institution to their projects. The network also helps identify outside built on fundamental research. For over a century, funding sources. TDivision of the Physical Sciences researchers have made Now in its fifth year, the Innovation Network’s outreach field-forming, groundbreaking discoveries (page 13), from efforts have already benefited computer science and measuring the charge of an electron in 1909 to helping to mathematics professor Ridgway Scott’s FEniCS Project discover the Higgs boson in 2012. (automated scientific computing software), chemistry Gaining foundational knowledge will always be a priority, professor Dmitri Talapin’s novel semiconductor soldering but it’s also crucial that such research gets translated into technique, and physics professor Heinrich Jaeger’s jamming practical solutions—sent out into the world to address our most materials-based robotic gripper. pressing needs. The PSD has opportunities to advance medicine (“Making Tech speculation Collaboration between academic and industrial settings a Mark,” page 1), IT (“Reliable Source,” page 7), and countless provides an optimal conduit for basic science to reach the other fields. With the support of the Innovation Network, masses. The PSD not only recognizes the value of application advocacy of the division, and inventive inclinations of PSD but actively encourages it. scientists, we have the power to improve the human experience, Forecasting the future of technology We foster entrepreneurial spirit by providing science by creating creature comforts, lifesaving procedures, and world- translation assistance. The Innovation Network—a changing technologies. subcommittee of the PSD Visiting Committee that includes alumni, friends of the University, and campus partners—was With all best wishes, created to help UChicago innovators navigate the path toward commercialization. In addition to offering their own expertise, members of the network help connect researchers with other alumni who have knowledge and resources relevant Edward W. “Rocky” Kolb, Dean Photography by Peter Barreras, Howard Hughes Medical Institute Chemistry discrepancy can be explained in part by For almost half a century, geneticists epigenetics: changes to gene expression have studied DNA methylation. For about that don’t change the underlying three decades, they have been studying Making a DNA sequence. the same type of modifications on Epigenetics “is basically a coding histones—the proteins around which DNA mark process,” says Chuan He, the John T. coils. But until recently, partly for practical Wilson Distinguished Service Professor and partly for conceptual reasons, no Chuan He breaks new in Chemistry. The DNA sequence is one considered the role RNA might play ground in RNA and DNA a predetermined template, but one in epigenetics. epigenetics. with hundreds of millions of spots that “In the beginning, it was easier to study can accept chemical flags that alter DNA and histones,” says He. “They’re much gene expression. One such template more stable. You can isolate them and hree billion—the number of base pairs modification is methylation. perform various analyses.” And because Tin the human genome—sounds like Three classes of proteins carry out RNA has a shorter half-life inside cells, a huge number. But of those billions of epigenetic coding: “writer” enzymes that scientists thought it might merely be a bases, humans appear to have only about apply tags or marks, “eraser” enzymes that template that transfers genetic information 19,000 protein-coding genes. And while remove the marks, and “reader” proteins from DNA to protein. Yet in the past that may sound like a large number as that recognize and bind to the marks. This few decades, as more capable analytic well, those genes alone can’t account for tagging provides an additional genetic sequencing technology has been invented, the vast complexity of a human being with coding process, expanding complexity researchers have discovered that RNA plays trillions of cells, all with their own identities. exponentially, and explains, for instance, major functional roles in many processes. The standard flow of information how cells with identical genome sequences He, who joined UChicago in 2002 and coded into DNA, transcribed into RNA, can develop into different cell types. A now directs the Institute for Biophysical and translated into protein provides too deeper understanding of epigenetics Dynamics and is a Howard Hughes Medical small a genetic template to accommodate provides insight into essentially all life Institute Investigator, came to study RNA the diversity of living systems. This on earth. via the scenic route. A synthetic chemist 1 FALL 2015 • INQ UIRY Epigenetics provides an additional genetic coding process, expanding complexity exponentially. The methylation on messenger RNA that He’s team discovered is reversible, which could affect a range of properties and functions that play essential roles in medical and biological research. Image courtesy Chuan He. who had worked in organic synthesis, he with “the implication that this is going to With associate professor Laurens Mets also studied biochemistry; investigated impact most biological processes.” He in molecular genetics and cell biology, He pathogenic bacteria with Olaf Schneewind, suspects his lab will have a complete set off to find methylated DNA adenine the Louis Block Professor in Microbiology; characterization of the reader functions in in eukaryotes, and they did—in algae, and later collaborated with Tao Pan, a couple of years. worms, and fruit flies. The discovery led professor in biochemistry and molecular The next questions to address are to three Cell papers published in April biology, on RNA biology. how and why the erasers regulate by He’s group, a team at Harvard, and Researchers have long known about demethylation and the writers selectively a team in China. The DNA mark is also RNA methylation, but they believed it restore the mark. And in the longer term, found in mammals, according to as-yet was a static state, playing a minor role. In how these proteins and pathways affect or unpublished data. 2010 He—who had been working on DNA control cell differentiation, development, “This is a completely new mark,” says epigenetics—discovered the first RNA and human diseases. He. “This is new biology emerging.” These demethylase, called FTO, an eraser that While He is making waves in RNA, he epigenetic pathways, involving adenine removes a methyl group from RNA. His hasn’t given up his DNA work. A recent methylation in RNA and DNA in eukaryotes discovery proved that RNA methylation revelation, in fact, links back to his field- and mammals, play a critical role in is reversible and thus a dynamic making RNA discovery. Scientists know that innumerable biological processes, and He modification. Publishing the research in the DNA base cytosine gets methylated in is providing vital groundwork for advances 2011, He’s lab founded the research field of both multicellular and single-cell organisms in medical and life sciences. “We’re doing RNA epigenetics. alike. (Cytosine methylation is the most the fundamental research, mapping up the He’s team went on to discover and thoroughly researched and best understood players, the building blocks,” says He, “and describe the writer, eraser, and reader epigenetic DNA mark.) The DNA base then others can study immunology, proteins involved in RNA methylation. adenine was thought to be methylated only infection, cancer therapy, diabetes, Focusing particularly on the readers, in bacterial cells. However, homologues of metabolism, neurogenesis, plant biology, which ultimately affect the cell’s biological the RNA demethylase protein that He’s lab developmental biology. You name it, these functions, He is gaining a mechanistic discovered remove a methyl group from pathways are involved.” understanding of the methylation pathway, adenine in multicellular organisms. —M.S. INQ UIRY • FALL 2015 2 Physical Sciences Groundwork PSD facilities keep up with an ever- progressing scientific landscape. This September the William Eckhardt n 1961 faculty members conducting space exploration Iresearch, in both the Department of Physics and the Enrico Fermi Institute, were spread across and off campus; physicist Research Center John A. Simpson proposed a building to unite them. Completed in 1965, the Laboratory for Astrophysics and Space Research (LASR) boasted a foundation and roof designed with future opened, designed expansion in mind. Simpson knew that research would advance, and such progress requires leading-edge facilities. for precision science Half a century later, Simpson’s preparation is paying off. Just as science is built on previously laid groundwork, the University plans to build upon the original design, adding two floors and and collaboration making extensive internal renovations to LASR over the next two years. The modernization of LASR comes amid tremendous growth between the the Division of the Physical Sciences has ushered in over the past decade, notes Dean Rocky Kolb. In 2006 the Ellen physical sciences and Melvin Gordon Center for Integrative Science brought

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