UC SANTA CRUZ inquiry RESEARCH MAGAZINE 2018–19

Beyond the middle passage

GEOENGINEERING | DEADLY BIOFILMS | LOST LANDSCAPES UC SANTA CRUZ RESEARCH MAGAZINE inquiry2018–19

The spirit of inquiry@UC Santa Cruz BRIEF inquiries page 4 inquiries&INNOVATIONS page 11

The Offices of Research and University Relations on marine mammals, and social sciences FEATURES are proud to present the 4th edition of inquiry@UC tackling complex issues in geoengineering and Santa Cruz! This issue of our campus environmental politics. Beyond the Middle Passage Detecting human diversity Variation graphs facilitate genomic discovery page 29 research magazine—written and edited This issue also incorporates several new Intra-American trafficking magnified slavery’s impact page 12 by graduates of UCSC’s internationally features. We have a new department, Viewing lost landscapes renowned Science Communication inquiries&INNOVATIONS, which highlights our Save the data! Home movies capture history through a personal Program—continues to highlight the campus’s intellectual property and industry Scholar activism seeks social and environmental lens page 33 superb research being conducted partnerships. And readers will now find a robust justice page 18 across all disciplines on the campus. e-magazine at inquiry.ucsc.edu, with hyperlinks Guided by the light This year’s reporting covers work in and references for those who want to conduct A three-minute challenge Stars bring biology into focus page 37 the humanities aimed at generating a Competition showcases graduate student research “further inquiry” into the topics presented. page 21 deeper understanding of the African Crossed currents Welcome to the 2018–19 issue of inquiry. We slave experience in the Americas, Conflicting stress responses may beach marine hope that you enjoy its samplings of the breadth, Canvassing bacterial mammals page 38 Credit: Steve Kurtz art exploring lost urban landscapes, depth, and creativity of the UCSC research communities engineering providing innovations in microscopy* enterprise! Targeting biofilms to bust cholera Geoengineering’s dilemma page 22 and telescopy, physical and biological sciences What comes first, research or governance? page 40 probing of bacterial biofilms and stressors A window to the early universe Witnessing the birth of galaxies page 28 Scott A. Brandt Vice Chancellor for Research and Professor of Computer Science PEN&INQ page 46

*Shortly before publication we received the sad INQUIRINGminds page 47 news that Joel Kubby, professor of electrical engineering, had passed away. We are glad to be About the cover: The schooner Amistad is one of thousands of slave ships included in the new Intra- able to honor him in these pages for a life well lived American Slave Trade Database. Its African captives revolted in 1839 while the Amistad was transporting advancing inquiry across many scientific fields, them from one end of Cuba to the other, as chronicled in the 1997 Steven Spielberg blockbuster movie. including, most recently, microscopy (see page 37). CREDIT: WIKIPEDIA COMMONS.

2 inquiry@UC Santa Cruz For further inquiry, go to inquiry.ucsc.edu 3 BRIEF inquiries UNIVERSITY OF CALIFORNIA SOCIOLOGY ultimately for the kids would likely have led impact future hydrology. to accurately predict how SANTA CRUZ ECONOMICS and families of Silicon to more intense storms In California, for example, that will impact things Valley, particularly those Chancellor Big data for kids at higher latitudes and Zachos’s work supports like precipitation, so George Blumenthal Preparing for recession at risk for poor outcomes. poleward shifts in dry models that predict more communities can plan.” “Imagine you’re a school That’s what’s driving us.” and wet regions. severe droughts and —Ula Chrobak Campus Provost and principal with a struggling —Sascha Zubryd Although the heating storms. Executive Vice Chancellor student and you have no during the PETM didn’t “We’re basically doing Marlene Tromp information about what’s LINGUISTICS occur nearly as fast as forensics,” said Zachos, going on,” said Rebecca EARTH AND Vice Chancellor, Research today’s human-caused who has been studying London, assistant PLANETARY SCIENCES Scott Brandt climate change, such ancient ocean sediments Lost languages professor of sociology case studies can be used for 30 years. “CO2 levels Vice Chancellor, University Relations and research liaison to the The task of saving Sedimentary to inform theories about are going to go up, and Keith Brant Silicon Valley Regional indigenous languages how global warming will climate specialists want inquiry@UC Santa Cruz Data Trust (SVRDT). climate clues has acquired increased 2018–19 Substantial information To what extent has human Editor about health, living activity contributed to MOLECULAR, CELL AND DEVELOPMENTAL BIOLOGY David Egerter (SciCom ’88) situation, and other social today’s powerful storms factors—which contribute and heat waves? To help Creative Director in major ways to school answer this key climate Stiffing cancer Lisa Nielsen performance—resides in change question, James Within the body’s Art Director Zachos, professor Distinguished professor of economics Carl Walsh speaks public agency databases, tissues, a framework Linda Knudson (Cowell ’76) said Rodney Ogawa, and chair of Earth and of molecules called the on monetary policy at Norges Bank, the central bank of planetary sciences, looks Norway. Credit: Courtesy of Carl Walsh. research professor of extracellular matrix Designer to the past. Janice Lasnier (Cowell ’99) education and a SVRDT (ECM) holds cells During the 2008 Other safeguards may director. However, Fifty-six million years ago, together. As tumors Associate Editors financial crisis, the be needed. Walsh and because each agency’s during the Paleocene- develop in many Quentin Williams, principal Federal Reserve other economists are data are isolated, they’re Eocene Thermal types of cancer, this Jeanne Lance reinvigorated the evaluating whether unavailable to outside Maximum (PETM), the framework stiffens. educators and health Contributors economy by slashing central banks should Earth heated up 6° C “A lump felt during a and human service Sukee Bennett (SciCom ’17) its benchmark interest move away from current and stayed warm for monthly breast exam Ula Chrobak (SciCom ’17) workers trying to help rate to zero. Today, as policies that work to 150 thousand years. In a does not necessarily Emma Hiolski (SciCom ’17) children. The SVRDT aims the economy continues maintain a certain recently published study, reflect the number Adam Mann (SciCom ’10) to change that, Ogawa to rebound, interest inflation rate. They senior author Zachos and of cancer cells,” said Sarah McQuate (SciCom ’17) said, while safeguarding rates are climbing. could instead aim to collaborators analyzed Lindsay Hinck, Katharine Miller (SciCom ’01) keep general prices at a students’ privacy. ancient plankton shells Chris Palmer (SciCom ’13) But due to shifts in professor of molecular, certain level or promise from this period to Robert Pollie (SciCom ’82) the global economy— Working with San cell and developmental to keep future interest reveal increasing ocean Barbra A. Rodriquez (SciCom ’97) in particular, the Mateo, Santa Clara, and biology. “It reflects both rates low. Such forward salinity and temperature. Patricia Waldron (SciCom ’14) emergence of China— Santa Cruz county child the cancer cells and the Activation of ROBO1 by its signaling partner SLIT2 guidance policies are By producing greater Cameron Walker (SciCom ’02) economists expect welfare services, Offices stiffened extracellular induces breast epithelial cells to produce cell-matrix discussed in a new evaporation near the Amy West (SciCom ’12) slower growth and of Education, juvenile matrix.” adhesion molecules (red, arrows), helping the cells to chapter in the recently probation, and behavioral equator, these changes Sarah C. P. Williams (SciCom ’07) interest rates to remain ECM stiffening maintain their position within the extracellular matrix. Marcus Woo (SciCom ’07) published fourth edition health staff, the SVRDT low overall. If there’s appears to block The cytoskeleton and DNA are labeled green and blue, Sascha Zubryd (SciCom ’11) of Walsh’s textbook, has nearly completed a respectively. Credit: Reprinted from Le, et al., Journal of another financial crisis, cancer progression by Monetary Theory and prototype Internet “portal” Cell Biology 2016:212(6):707-19. © 2016, with permission inflation will again maintaining a balanced Produced by UC Santa Cruz Policy. that will allow authorized from The Rockefeller University Press. plummet, taking interest state, or homeostasis, Communications & Marketing individuals—including rates down with it. If and when another of intracellular tension. 1156 High Street teachers, social workers, epithelial cells sense and changes that help cells recession hits, investors Conversely, loss of Santa Cruz, CA 95064-1077 With rates already low, policymakers, and UC respond to increased retain their shape and would expect these this homeostasis Email: [email protected] the Fed won’t be able Santa Cruz researchers— ECM stiffness by position within the price-level targeting can contribute to Web: inquiry.ucsc.edu to cut them further to to access certain student reducing levels of the stiffened ECM. The policies to bump cancer progression spur spending. “When information. Made microRNA miR-203, a investigators also found 5/18 (1718-245/2.5M) IM6 prices—and inflation— by promoting tissue interest rates hit an possible by recent short, noncoding RNA that breast cancer back up, Walsh said. disorganization and effective lower bound, California legislation, fragment that normally patients with low- The anticipation of metastasis. monetary policy is the “big data” sharing Professor of Earth and suppresses the Robo1 miR-203/high-ROBO1– higher inflation coupled planetary sciences constrained in its ability collaboration so far Hinck’s research focuses gene. This raises levels expressing tumors had with rock-bottom James Zachos analyzes to help stabilize the includes information about on understanding this of the protein ROBO1, improved survival, interest rates would the chemistry of ancient economy,” said Carl complex biology. Senior which, in turn, alters the identifying this pathway incentivize people to some 265,000 students. plankton shells like this one Walsh, distinguished author Hinck and cell’s cytoskeleton and as a potential borrow and spend, thus “We expected some (~200 microns in diameter) professor of economics. collaborators now report boosts production of therapeutic target. stabilizing the economy. hesitation, but everyone to infer what the climate was adhesion molecules, like when the plankton were that normal breast —Chris Palmer —Marcus Woo said ‘yes, we need this,’” Ogawa said, “This is alive. Credit: James Zachos.

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urgency as more and language from Oaxaca, an open access database aspect of what it means ECOLOGY AND more are threatened by Mexico. Of the 100,000 integrated with a to be human. If we’re LITERATURE EVOLUTIONARY BIOLOGY emigration, rapid cultural Oaxacan immigrants dictionary. interested in saving the changes, and the failure who live in communities world’s diversity, we Toosarvandani and his A traveling memory space Resilience to teach native tongues across California, should be interested in colleague, associate to children. including Santa Cruz, saving these languages.” under redwoods professor of linguistics How did history’s first nearly all speak Spanish. Associate professor Pranav Anand, have —Sukee Bennett ghetto affect Western There’s more to redwood Fortunately, some also of linguistics Maziar also partnered with the culture and Jewish forests than iconic trees. speak Zapotec. Toosarvandani stands organization Senderos ASTRONOMY identity? That’s what On the drought-prone on the forefront of this In their research, to establish Nido de AND ASTROPHYSICS Murray Baumgarten, Central Coast, the forest effort. To preserve their Toosarvandani and his Lenguas, a nonprofit distinguished professor understory includes emeritus of English and a typically tropical rapidly disappearing team collect stories, oral that sponsors monthly Flash in the sky language, Toosarvandani narratives, and historical language classes and comparative literature, resident—ferns. seeks to understand. partnered with Northern texts from which they summer camps where Assistant professor Jarmila Pittermann, Paiute speaking elders infer the structure of native speakers teach of astronomy Ryan Created to impose associate professor of near Mono Lake—of the language. Then, by their ancestral language Foley was enjoying surveillance and control ecology and evolutionary whom only a handful speaking Zapotec with to other Oaxacan an afternoon off in while also allowing a biology, and Emily Burns remain. He’s now taken native speakers, they immigrants. This work Copenhagen when a measure of autonomy, of Save the Redwoods on the Santiago Laxopa test their hypotheses is vital, Toosarvandani student texted him. the Venice Ghetto is a League, noticed that variety of Zapotec, an about its structure and said. “When we lose a LIGO, the Laser- walled-off section of during persistent endangered native collate their findings in language, we lose an Interferometer the city in which Jews drought, ferns’ fronds dry were forced to live from From 1516 to 1870, Jews were forced to live in the out and often become 1516 until 1870. Venice Ghetto (view of present-day outer wall). Credit: infested with tiny insects COMPUTATIONAL MEDIA “The Venice Ghetto Getty Images. called thrips. To unveil drought’s physiological shaped how many Baumgarten brings this science and art are effects and how the ferns Connecting the dots Jews and Jewish insight to his current subtly intertwined recover during rainy communities think study of the writing of and reciprocally spells, Pittermann’s team Widely used by clinicians of themselves in Primo Levi, an Italian illuminating.” studied the region’s two for decades, noninvasive relation to their outside chemist and Holocaust “You have to look most abundant species neuroimaging techniques social situation,” said survivor. Describing in many places, of fern, Polystichum such as CT, MRI, and Baumgarten, whose Levi’s book The Periodic because this space has munitum and Dryopteris PET have also enabled research has focused Table (1975) in a recent traveled, and it is also arguta, comparing ferns neuroscientists to on how its impacts essay, Baumgarten a memory space,” said growing in the forests explore structural are described in both writes, “…Primo Levi, Baumgarten. “It’s also a surrounding UCSC to and functional networks, fiction and nonfiction writer, is inseparable space of trauma that has potted, greenhouse or “connectomes,” in writing, such as Coryat’s from Primo Levi, changed many things.” specimens that they the brain. Critical to this Crudities, a travelogue Holocaust witness, periodically dried out and research are tools for published in 1611. and the discourses of —Ula Chrobak effectively visualizing rehydrated. and interpreting the As reported in New great mass of data Gravitational Wave flash of light. Just 17 that also produced Phytologist, the ferns generated by these Observatory—which minutes into their search gravitational waves. The were surprisingly imaging modalities. NeuroCave representation of human subject functional MRI data broken into 2514 had previously detected using the Swope observations revealed resilient, but didn’t A common task in regions. The map on the right shows the anatomical clustering of the regions, while ripples in the fabric of Telescope at the Carnegie that these mergers produce many fronds studying neurological the map on the left arranges them according to specific functional characteristics. space-time for the first Institution’s Las could have produced disorders such as Credit: Keiriz, et al., Network Neuroscience. ©2018 Massachusetts Institute of time, garnering fanfare Campanas Observatory most of the elements Alzheimer’s disease Technology, Creative Commons 4.0. and a Nobel Prize— in Chile, Foley and his heavier than iron in involves comparing had found another team found it: a bright the universe. This kind researchers, working via a standard desktop connectome with the the connectomes of gravitational-wave signal. dot in a galaxy 130 of measurement also with collaborators environment or, for average connectome healthy and diseased million light-years away. provides a new way to at the University of a more immersive for any number This time, the signal groups to identify brain Their and others’ probe the expansion rate Illinois, Chicago, built experience, portable VR of diseases,” said likely came from merging changes due to illness. observations were of the cosmos—crucial the first system for 3D headsets. Angus Forbes, neutron stars—exotic, However, no application quickly published in for understanding deep visualization of multiple assistant professor of city-sized objects with Polystichum munitum, existed that allowed “The ultimate goal multiple papers in questions like the nature connectome datasets computational media the mass of one or two commonly called sword fern, robust comparisons in is for a psychiatrist Science, Nature, and of dark energy, Foley via a synchronized and senior author on suns. And unlike previous is one of the most robust real-time of two or more or neurologist to do Astrophysical Journal said. “It’s really just side-by-side layout. the paper describing the detections, this cosmic species of fern on California’s connectome datasets. precision medicine by Letters. the beginning of a new Central Coast. Its leaves, Brain researchers and tool. crash was expected to using NeuroCave to scientific field.” called fronds, are much To address this need, clinicians can access light up. It was the first time compare a patient’s —Chris Palmer thicker and more resilient UC Santa Cruz anyone measured the —Marcus Woo the system, NeuroCave, Astronomers around the than those of tropical ferns. world raced to find that light from an event Credit: Jarmila Pittermann.

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when it was particularly PSYCHOLOGY when racial differences between racial groups, making semiconductor dry. Doing so would are simply ignored, said whether students felt they MUSIC chips, ALD creates a cause them to “consume Race in schools Christy Byrd, assistant were treated fairly, and if dense, even film by their supply of water and professor of psychology. there were opportunities Gender equality via music coating surfaces one carbohydrates too fast,” Students who feel they Byrd studies how to learn about other atomic layer at a time. Pittermann said. The ferns belong perform better. cultures, prejudice, and students perceive their Women stand at the Because ALD systems can also rehydrate quickly, And when students racial inequality. school environment in forefront of music are designed for small, taking up water—including feel stereotyped in relation to their racial Her work also shows that in Uzbekistan, a thin silicon wafers, the from fog—directly from school, their academic and cultural identities. students with a strong stature rooted in the researchers had to build their fronds, as previously performance suffers. Her survey of adolescent sense of belonging in hujum, a Soviet-era a much larger one to shown by Burns. Years of sociological students led to a new their school’s racial women’s emancipation accommodate telescope research bear this out. “People think of ferns as framework that combines climate felt more movement. Women mirrors. While the But there are other, inferior to angiosperms a wide variety of factors motivated compared to went free of culturally prototype is still being subtler elements that can and conifers, and that’s impacting students’ students who believed sanctioned, modest tested, proof-of-principle contribute to a school’s untrue,” Pittermann sense of belonging. their racial identities were attire, and, through experiments have shown racial climate and impact said. “Ferns are holding represented negatively or music, found “a natural promising results, student outcomes. “It’s about how they all fit themselves up. They space at the table together,” said Byrd, who not at all. And crucially, Kobayashi said. have had to be resistant “The biggest surprise strong intrinsic motivation in the state music hopes her framework will —Marcus Woo to make it through 350 was how understudied conservatory and inform future research. correlated closely with million years of our some of these factors other institutions,” The most influential academic engagement changing planet.” are,” especially the said Tanya Merchant, Associate professor of music Tanya Merchant (left) plays COMPUTER SCIENCE factors included the and success. negative outcomes associate professor the dutor, a two-stringed lute from Central Asia, with her —Sukee Bennett quality of interactions —Sascha Zubryd of music. primary Uzbek musical mentor, Malika Ziyaeva. Ziyaeva visited UC Santa Cruz in 2014 to teach and also perform Bringing storage Merchant’s 2015 book, with the Eurasian Ensemble. Credit: Courtesy of Tanya up to speed CHEMISTRY AND BIOCHEMISTRY Women Musicians Merchant. of Uzbekistan: Storage systems—the From Courtyard to software that connects traditionally played it difficult for Merchant Beneficial binding Conservatory, draws on an electronic device’s her almost 20 years of by women. Because to bring dutor teachers applications to its disk Prion diseases, including studying Uzbek music. of this, after the fall from Uzbekistan to or solid-state drives— mad cow and, in humans, Her research focuses of the Soviet Union, help “immerse” her have lagged behind Creutzfeldt-Jakob, are fatal on the female artists women continued students in Uzbek other improvements in neurodegenerative diseases. who have contributed their prominence with musical practices. computer systems. New They arise, usually late in life, to modern Uzbek the instrument, rising “Ethnomusicology isn’t applications normally from massive aggregations of music, many of whom to positions of power about sitting down, add layers of software to endogenous prion proteins. play the Uzbek dutor rare in any patriarchal listening to sounds, and get what they want from society. making assertions,” storage systems, leading Compared to the hallmark (also spelled dutar). A Merchant said. “It’s to bloated software and aggregating proteins of two-stringed lute, the Unfortunately, the dutor is the only non- current political climate best to be embedded in inefficiency. Alzheimer’s and Parkinson’s, the culture.” “the prion protein is quite percussive instrument and travel bans make “Storage systems are complex,” said Glenn —Sukee Bennett complicated and they Millhauser, distinguished slow things down,” professor of chemistry. “Its said Carlos Maltzahn, multiple domains with all sorts ELECTRICAL ENGINEERING To combat this the pinholes to reach professor of computer of chemical modifications point degradation, telescope the silver,” said Nobby science and director of When the prion protein (orange, gray and pink) binds copper (blue sphere), it toward an important function in New coats makers coat the silver Kobayashi, professor of the Center for Research the central nervous system.” neutralizes the toxicity of the unbound metal ion. This binding also prevents with a protective layer electrical engineering. in Open Source Software the flexible, extended end of the protein (gray and pink) from unfurling and for telescopes using physical vapor (CROSS). The bulky end of the prion protein With collaborators triggering the toxicity associated with prion-induced neuronal death and its fatal deposition, spraying, binds to the surface of neurons Silver makes better UC Observatories To address this problem, consequences. Credit: Reprinted from Evans, et al., Structure 2016:24:1057-67, for instance, aluminum where it modulates the flow of telescope mirrors. It astronomers Andrew the CROSS team © 2016, with permission from Elsevier. oxide vapor onto the chemical messengers. Research reflects more visible Phillips and Michael created a uniquely silver. Even so, the has also shown that the extended, and infrared light than Bolte, UCSC postdoc programmable storage copper ions. Scientists believe the that copper, in turn, also regulates mirrors still corrode after flexible end, in an unfolded aluminum, the metal David Fryauf, and system based on protein binds copper to regulate the prion protein by forcing its a couple years. configuration, drives prion the metal ion, which is essential extended end to fold inward, most telescope mirrors Structured Materials Ceph, a widely used, toxicity and neuronal death. for cellular function but extremely thereby keeping its disease- are made from. But The problem is that this Industries (SMI), open source storage while aluminum forms a coating method leaves Kobayashi designed a system also created at Millhauser has been studying the toxic if left unbound. Based on related activity in check. natural protective layer pinhole-like gaps. “All new instrument that UC Santa Cruz. Called prion protein structure for two nuclear magnetic resonance —Chris Palmer when exposed to air, kinds of stuff—oxygen, employs atomic layer Malacology (after the decades. Of particular interest spectroscopy, Millhauser and silver doesn’t—that’s water, sulfur—those deposition (ALD) to coat science of molluscs: to him is how the protein binds collaborators have now reported why it tarnishes. elements go through the silver. Widely used in cephalopod molluscs,

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like octopi, are agile to flow much more and have many arms freely and appear Diagnosis on a chip new silicon detector that does both. No other technology can examine moving in parallel), the much more quickly To diagnose diseases like Ebola, Researchers will use the improved a cell in this way without killing new storage system lets on the market than clinicians seek viral or bacterial detectors to start building a new it, said UCSC professor of programmers tap into proprietary solutions,” instrument for the LHC as early as biomolecular engineering Nader existing storage system said Maltzahn. He DNA or RNA in patient samples. Traditionally, tests used for this 2021, Seiden said. Pourmand. The nanopipette software and adapt it thinks Malacology will provides a powerful tool to study for new purposes, while help enable innovation employ PCR (polymerase chain The technology could also be how a living cell changes and retaining code that took and entrepreneurship, reaction), a method that induces used to improve medical imaging years to optimize. The ultimately leading to those molecules to replicate, systems that doctors use to target behaves. group published their improved computers, making them easier to detect. and destroy cancerous tumors with His lab uses the nanopipette to work at the EuroSys 2017 smartphones, and other Computer scientists at the UCSC Center for Research in Open By eliminating the PCR step, UC proton beams. study how a variety of dynamic conference. digital technology. Source Software (CROSS) created the new storage system processes within single cells Malacology, which allows programmers to efficiently adapt Santa Cruz professor of electrical Sadrozinski H, Seiden A, Cartiglia N. “Open source software —Ula Chrobak Segmented AC-coupled readout from contribute to degenerative brain existing software to suit their needs. (l to r: graduate students engineering Holger Schmidt community efforts are continuous collection electrodes in Ivo Jimenez, Jianshen Liu, and Yiming Zhang). Credit: Carolyn and collaborator Brigham Young diseases and drug resistance in allowing innovation semiconductor sensors. U.S. Patent Lagattuta. University professor Aaron 9,613,993, filed June 30, 2016, issued cancer, Pourmand said. Hawkins invented a potentially March 9, 2017. Karhanek M, Webb CD, Umehara S, simpler, quicker, and cheaper Pourmand N. Functionalized nanopipette Dimmable LEDs biosensor. U.S. Patent 9,766,204, filed ENVIRONMENTAL STUDIES way to diagnose diseases. January 22, 2015, issued September In 2013, as part of a senior design 19, 2017. The lab-on-a-chip device engineering class, UCSC students channels a liquid like blood or A dwindling wellspring built an LED (light-emitting diode) saliva containing fluorescently Superior sequencing light bulb that would cost only $5 to During Peru’s long labeled, infectious DNA across Technology developed at UCSC make—substantially less than what dry season, seasonal an optical waveguide, a tiny underlies the MinION, a handheld they sold for at the time. glacier melt releases tunnel that steers light. When gene sequencer manufactured by sorely needed water light hits tagged DNA, the dye The experience taught them real- Oxford Nanopore Technologies from frozen storage. The glows, revealing the presence of world skills, said Julian Dahan, (Oxford, U.K.). The MinION warming climate initially the pathogen. student lead on the project. “It put us reads sequences via nucleotide- increased the flow, ahead of the curve in job interviews.” specific changes in ion current “This could hopefully be a new boosting agriculture and as DNA strands pass through a hydroelectric power. But way to do medical testing,” They also discovered a new circuitry nanopore, a tiny hole in a polymer Andean glaciers have Schmidt said, providing a practical design that allowed the brightness membrane. The nanopore continued to shrink, and point-of-care tool to use in clinics of the LED to be controlled with a approach has led to smaller, so has the water supply. and the field. switch, knob, or even via Wi-Fi. In faster, and cheaper devices, contrast to most adjustable LEDs “It’s much farther along Schmidt H, Hawkins AR. Method expanding access to sequencing than we thought,” said for amplification-free nucleic acid now on the market, this adjustability and invigorating genome research. Jeffrey Bury, professor detection on optofluidic chips. U.S. is built right into the LED itself. of environmental studies Patent 9,551,667, filed November 18, UCSC professor of biomolecular 2011, issued January 24, 2017. “That was the novelty that no one and faculty director of engineering Mark Akeson and had ever done before,” said David the Center for Integrated collaborators have now devised a Time and place Munday, the lecturer who teaches Spatial Research. Bury’s novel method that applies voltage the class. “Just plug it in and go.” research focuses on how The Large Hadron Collider (LHC) to move a DNA strand back and glacier loss and social in Switzerland slams trillions of Munday D, Baker R, Dahan J, Peterson R, forth through a nanopore at a factors impact access protons together, each collision Sloan C. Switchable luminance LED light bulb. U.S. Patent 9,730,282, filed August controlled rate. to water in Peru, from producing hundreds of particles its high mountains to its 5, 2015, issued August 8, 2017. The invention could be useful The Cuchillacocha—shown here during the dry season—and other glaciers in the Andes spraying in all directions. Particle coastal cities. for new sequencing technologies, are receding, significantly reducing access to water in Peru, from its high mountains all detectors must then track their In a living cell Bury and collaborators the way to its coastal cities. Credit: Bryan G. Mark, courtesy of Jeffrey Bury. trajectories. Akeson said. “It’s a terrific way now report that the Its tip is so small you can’t see it to couple electronics to biology Cuchillacocha glacier In addition, heavy metals “The scale of these and expanding cities But a typical silicon detector with an optical microscope. Like a directly at the single-molecule can only accurately measure a is shrinking 37% from bedrock exposed changes is astounding,” consuming more clean tiny needle, the nanopipette pierces level.” faster than previously by the receding glacier Bury said. Demand is water and power. “There particle’s position—not how long a living cell and extracts contents predicted. Streams and it’s been traveling. So UCSC Olasagasti FA, Lieberman KR, Benner and the area’s long growing, with cultivation will be a point when from its organelle structures—all S, Akeson MA. Compositions, devices, wells have dried up, history of mining have of profitable, water- supply won’t meet professor of physics Abraham without harming the cell. The device systems, and methods for using a forcing people to travel, contaminated mountain intensive crops for demand,” he said. “It’s Seiden and research physicist can also inject biologically relevant nanopore. U.S. Patent 9,481,908, filed build new infrastructure, streams. export on the rise, just a matter of time.” and adjunct professor Hartmut chemicals, to test single-cell effects February 27, 2014, issued November 1, or relocate to find water. 2016. —Sascha Zubryd Sadrozinski helped design a of potential drugs, for example.

10 inquiry@UC Santa Cruz For further inquiry, go to inquiry.ucsc.edu 11 By Robert Pollie

an essential tool for researchers. One prominent historian likened its impact on the study of slavery to that of the Hubble Space Telescope on astronomy. But like the Hubble—before it was repaired by the Beyond the crew of the space shuttle Endeavour—the TSTD suffers from a kind of myopia. True to its name, it only includes voyages that made the transatlantic crossing from Africa, the infamous “Middle Passage.” But slave shipping didn’t stop there. It continued full throttle on this side of the Atlantic, with Middle Passage thousands of vessels and voyages ferrying enslaved people to and from points within the Americas. Intra-American trafficking magnified The TSTD isn’t alone in overlooking that second stage of slave shipping. “For a long time, most slavery’s impact research on the American slave trade focused on the shipments coming into major slaveholding colonies, and those were almost all arriving directly from Africa,” said UC Santa Cruz associate professor of history Greg O’Malley. “It missed a big piece of the overall picture.” The missing piece—the bustling intra-American slave trade—played a critical role in spreading slavery across the Western Hemisphere and embedding it deep in the economic and social foundations of the New World. To grasp the full scope of that commerce is to gain a broader understanding of the way slavery shaped life in the Americas, with repercussions that are still playing out today. O’Malley has spent much of his career as a historian advancing that broader understanding. The work began in graduate school, when he built his own database of thousands of slave shipments in British Enslaved as a sailor on intercolonial vessels, Olaudah Colonial America (the 13 North American colonies Equiano witnessed the brutality of the intra-American slave trade firsthand. His best-selling 1789 memoir was one of the and British Caribbean islands) as part of his Ph.D. slave narratives associate professor of history Greg O’Malley thesis. He expanded on that research in his 2014 drew on when writing his own book. Credit: ©John Carter book, Final Passages: The Intercolonial Slave Trade Brown Library, Brown University, Providence, RI. of British America, 1619–1807, a wide-ranging look at intra-American slave trading and its economic, An unexpected detour political, and cultural consequences. O’Malley had a very different project in mind when, as a Ph.D. candidate in history at Johns Hopkins Now he’s taking another step, pooling his data with University specializing in British Colonial America, that of fellow historians to compile an even larger he began scouting for a dissertation topic in 2003. database, to be added to the slavevoyages.org “I was thinking about the complex mix of people in Slaves cutting sugar cane on the island of Antigua. The sugar industry’s relentless demand for labor turned the Caribbean into site later in 2018. With information on more than the colonies,” he said, “with a particular interest in a hub of intra-American slave trading. Credit: ©John Carter Brown Library, Brown University, Providence, RI. 11,000 voyages, the new Intra-American Slave Trade the cultures that enslaved Africans were bringing to Database will fill a crucial gap in the historical record America.” and provide an essential complement to the TSTD. To understand those cultural currents, he had to get R Between the early 1500s and the mid-1860s, apt. Nothing conveys the scale of it better than the “The Intra-American Slave Trade Database will give a handle on the demographics—who the enslaved millions of Africans were captured, sold into slavery, Trans-Atlantic Slave Trade Database (TSTD). Hosted us a far richer picture of the slave experience,” said people were, where they came from, and in what and transported to the New World to live out their at slavevoyages.org, the TSTD provides details of David Eltis, professor emeritus of history at Emory numbers. And the numbers weren’t adding up. days in bondage. The African diaspora is believed almost 36,000 slave-trading shipments that took University and one of the creators of the TSTD. to have been the largest forced migration in human place over three centuries. It’s the most complete “I think it will inform a wide range of historical “I’d be reading a book, for example, that said there history, though “mass abduction” might be more record we have of transoceanic slave routes and scholarship.” were 90,000 people of African descent in North

12 inquiry@UC Santa Cruz For further inquiry, go to inquiry.ucsc.edu 13 Beyond the Middle Passage

Carolina on the eve of the American Revolution,” “Although some of the enslaved were purchased added to the ordeal. The port records O’Malley O’Malley said. “And yet the book cited only one slave by plantation owners and put to work near where examined showed many intra-American slave- ship carrying at most a few hundred people that had they made landfall, many were bought by merchant trading ships arriving at their destinations with come to the colony from Africa. So where did those speculators who then transported them for resale fewer captives than they set out with, owing to other 89,000-plus people come from?” elsewhere in the colonial world,” O’Malley said. In deaths en route. Comparing the numbers, he was It was a glaring discrepancy, one that O’Malley ran other words, the major ports served as hubs in a vast able to calculate an average mortality rate of 5% into again and again as he surveyed the literature. distribution network. for enslaved people on intra-American voyages. “There was a lot of scholarship on the transatlantic The busiest hubs in the British Americas were in That’s lower than the estimated 20% who perished portion of the slave trade, describing where people the Caribbean, principally Kingston, Jamaica, and during the Middle Passage. “But given that the intra- landed in the Americas from Africa,” he said, “but Bridgetown, Barbados. From there, large numbers American voyages were much shorter, it tells us that that data didn’t line up with where we knew enslaved of slaves were shipped to North American colonies people were actually dying at faster rate,” he said. people actually lived in the New World.” or shuttled between various British Caribbean Those who survived found themselves increasingly He did have a hunch. There had to be an extensive territories. Even more were exported to other colonial isolated with each step of the journey, as friends, shipping system that was moving people from a empires, going mostly to the French Antilles and family members, and people with common ethnic small number of arrival points—like Charleston, Spanish settlements in South and Central America. backgrounds who’d managed to stick together or South Carolina, the Chesapeake Bay in Virginia, and The colonies of Barbados and Jamaica were the major “If you look at the transatlantic data alone, you see form bonds during the trip from Africa were split up Kingston, Jamaica—to the many places they lived centers of the British American trade, where slaves from a few key hot spots,” said O’Malley. “But with this and sent their separate ways according to the needs Africa were reshipped to many locations in North, South, and labored throughout the Americas. broader data set you get a more powerful sense of of merchants. and Central America. Credit: Greg O’Malley. the real pervasiveness of slave trading.” To confirm that hypothesis, O’Malley went to the As for the merchants themselves, many were only detailed records that still survive—British Naval middlemen who purchased enslaved people at their database, which he modeled on the TSTD. “I had the Longer journeys, greater hardships Office shipping lists, where colonial officials dutifully initial port of arrival, then resold them wherever they notion even then that the editors of the TSTD might logged the contents of arriving and departing ships For people who’d already endured the deprivations could fetch a higher price; in effect, buying wholesale someday incorporate my data,” he said. at ports throughout British America. The innocuous- of the oceanic crossing, the further passages only and selling retail. “Most of the previous work looking ledgers contained a grim accounting. By the time he was done, he’d documented intra- assessing the economics of slave trading considered American slave trading on a previously unknown only the transatlantic trade. They looked at the price scale—over 7,000 voyages from the 17th through By sea and by land paid on the coast of Africa, the transportation costs, Finding the Amistad 19th centuries. “The magnitude of it surprised even and the price received in America,” O’Malley said. me,” he said. The first iteration of theIntra-American Slave “But this complicates that picture, adding a whole Tens of thousands of visitors explore the Trans-Atlantic Slave Trade Database consists almost exclusively other round of buying, selling, and profits.” Trade Database (TSTD) at slavevoyages.org each year. Many of Behind the numbers of maritime voyages. In part that’s because them search for one ship in particular: the schooner Amistad, most colonial settlements were on coasts and A hidden logic depicted on the cover and famed for a slave revolt in 1839 and It was depressing work at times, and not only waterways, and ships were the most efficient a Steven Spielberg blockbuster more than 150 years later. because of the sheer monotony of combing through means of transport. Many ships’ cargoes While the transatlantic trade was run largely by shipping lists day in and day out. “There was a were also carefully logged, helping historians slave specialists, the players in this second layer of But those queries come up empty. The TSTD lists only terrible tension between the boredom on the one construct a detailed picture of seaborne trafficking were often ordinary merchants happy transoceanic voyages, whereas the Amistad was engaged hand and the realization that all those numbers trafficking. to sell whatever the market wanted, be it raw in more local business. When its African captives rebelled, flashing past on microfilm were human beings,” materials, products, or people. Slaves were treated Overland transport of slaves tended to they were being transported from one end of Cuba to the O’Malley said. “I really wanted to present a human like livestock and frequently combined with other involve spottier record keeping, making other. That’s one of many gaps the Intra-American Slave Trade story of what the captives suffered in this horrific cargoes such as rum, timber, and cloth. The mix such movements harder to track. One major Database will fill. When it’s published on theslavevoyages. business, but these documents are the opposite of sought to maximize the returns on each leg of a exception was in Brazil, where large convoys org site this year, the new database will provide searchable humanizing.” ship’s travels. records of thousands of slave-carrying ships that sailed of captives were marched to mines deep in American waters—including the Amistad. Eventually, by analyzing the numbers along with the country’s interior and official records were This financial logic became clear when O’Malley other sources such as merchant correspondence preserved. That’s enabled Daniel Domingues, studied the letters that merchants wrote each and slave narratives, he was able to flesh out a assistant professor of African history at Rice other as they negotiated deals and planned their fuller story. In his Ph.D. dissertation and later book, University, to collect data on thousands of shipments, and it helped explain trade patterns that at first glance seemed nonsensical. Alongside entries for goods like sugar, rum, salt he showed how, for many enslaved Africans, the overland journeys, which will be added to the pork, and naval supplies, many had a column for transatlantic passage was just a segment of a longer Intra-American Slave Trade Database by 2019, He discovered, for example, that many of the slaves “Negroes.” journey. He estimates that more than 400,000 of the pushing the total number of records to more in North Carolina were being brought from Kingston, Africans brought to British American ports between than 15,000. Efforts by other researchers Jamaica. That helped to solve the original puzzle O’Malley spent a year systematically cross-checking the mid-17th and early 19th centuries were promptly are also underway to document overland that started him investigating slave routes in the thousands of such records (most were available on packed aboard other ships and dispatched to distant slave trafficking in North America, further first place, but it begged another question. Why microfilm at Johns Hopkins’s Eisenhower Library), parts of the Americas. expanding the database. would anyone ship slaves all the way from Jamaica tallying the shipments and creating his own growing when there were plenty available in the neighboring

14 inquiry@UC Santa Cruz For further inquiry, go to inquiry.ucsc.edu 15 Beyond the Middle Passage

The British exploited this loophole, gaining entry to Funded by a National Endowment for the Humanities Spanish American ports by bringing slaves for sale grant administered by the UCSC Humanities while simultaneously smuggling in mass-produced Institute, Borucki and O’Malley have been combining goods such as textiles. Selling those products was the their data with that of other researchers tracing real endgame. It gave a timely lift to British factories slave routes in the Dutch and Spanish Caribbean to at the dawn of the industrial revolution and helped create the new Intra-American Slave Trade Database. fuel a boom in manufacturing. (Many of the same When the database goes live at slavevoyages.com manufacturers depended on raw materials supplied by later this year, scholars, students, and the general slave labor in the Americas, especially cotton.) public will be able to search its 11,000-plus voyages using criteria such as the name of the ship, the date Slavery at the center of the voyage, the itinerary, and even the outcome (for example, if slaves were successfully delivered The overview that emerges is of a slave trade or rebelled). “It’s really an astonishing expansion of thoroughly entwined with, and instrumental to, the the raw data we have,” said Linford Fisher, associate economic growth of the colonized Western World. professor of history at Brown University. “It’s giving O’Malley’s research makes the case for what the us a much deeper understanding of the mechanics of writer Ta-Nehisi Coates calls “the centrality of the slave trade in the Americas.” slavery in American history.” In this view, slavery wasn’t an ugly footnote in the story of American Slave trafficking dates back to antiquity, but the prosperity and economic opportunity—it was a mechanics that Fisher refers to reflected modern driving force. economic developments. As the intra-American slave trade grew, an entire ecosystem of merchant And it wasn’t just slave traders and slaveholders speculators took shape and inserted itself between who benefited. It was everyone who shared in slave suppliers and slaveholders. This middle layer the wealth of the New World. The slave business of resellers valued slaves not as laborers, but as went far beyond plantations, and touched all commodities, fungible assets used to exploit price sorts of people. There were the sailors and differentials in markets (buy low, sell high). That dockworkers who transported slaves, the brokers cold-blooded calculus is manifest in the port records and auctioneers who sold them, the bankers who O’Malley examined. Their rows and columns offer handled the transactions, the farmers who sold no information on who the slaves were—not even provisions to arriving slave ships, and the ordinary their ages, genders, or origins—just quantities: the consumers buying goods whose availability number of units shipped. Auction of estates, pictures, and slaves in a hotel rotunda in New Orleans. Slaves were bought and sold like any other depended on slave trafficking. The reduction of persons to financial abstractions merchandise, reflecting what O’Malley calls “human commodification.” Credit: Wikipedia Commons. This ubiquitous commerce had a normalizing effect, pushed the dehumanization of enslaved people to O’Malley believes. Many European Americans new depths. Plantation owners and overseers at came to accept slavery as a necessary part of doing colonies of Virginia and South Carolina? “It only that was needed to reap the spoils was cheap least had to live beside and interact directly with business and getting ahead, while turning a blind makes sense if you look closely at the commerce,” labor. Slaves became a widely accepted medium of slaves over extended periods. But for many of the eye to the human toll. That indifference is painfully O’Malley said. “Traders in North Carolina were exchange, a bargaining chip that merchants could merchants and others in the trafficking business— clear in the merchant letters. Amid pleasantries exporting food and materials to the sugar plantations trade for almost anything else. aside from the relatively small number of sailors and and small talk, the businessmen casually mention in the Caribbean, and they needed something to take handlers who did the actual dirty work—the enslaved “I found examples of merchants writing to each shipments of slaves, with no sign of empathy or back in return. North Carolina could only handle so other, saying, ‘If you want to get into this business were mere line items on balance sheets. much sugar and rum, but there was always a market recognition that these were actual people. or that business, get some slaves, because there This industrial-scale “human commodification,” for slaves.” are always planters in need of labor who will deal Illuminating past and present O’Malley contends, was part of a “systematic It was the imperatives of the marketplace, O’Malley with a slave trader,’” O’Malley said. “So if you devaluation of black lives that’s still with us.” He argues, that spread slavery far beyond the plantation wanted to get into the rice export business in South The British American trafficking O’Malley studied believes a reckoning is long overdue, and that zones to many corners of the Americas, including Carolina, the advice was, ‘Pick up some slaves in the was just a slice of the overall intra-American slave historical research has a vital role to play. “My areas we don’t typically associate with slavery today, Caribbean. There will almost always be a plantation trade. Other colonial powers—Portugal, Holland, hope is that the work that I and other historians like New York, Massachusetts, and Pennsylvania. owner who will sell his rice to you for slaves.’” Spain, France—were doing their own trading, and are doing helps American society finally come to a number of historians have been collecting data on Slave trading greased the wheels of commerce, British manufacturers went a step further, using the grips with the legacy of enslavement and how it those networks. For example, Alex Borucki, UC Irvine and helped entrepreneurs get a toehold in new cover of slave trading to break into lucrative Spanish shaped the inequalities we see today,” he said. associate professor of history, has amassed details of markets. While demand for other goods ebbed and American markets in the late 17th and early 18th “If the information in this database can move us roughly 1,000 slave voyages in the Portuguese colony flowed with supply, the need for workers was nearly centuries. At the time, Spain barred foreign imports toward a more honest appraisal of our past— of Brazil and in Spanish South America (areas that unquenchable. The Americas offered up a seemingly to its American colonies, but made an exception for and our present—that would be the ultimate became Venezuela, Uruguay, and Argentina). endless bounty of land and natural resources. All slave traders because of the pressing need for labor. accomplishment.”

16 inquiry@UC Santa Cruz For further inquiry, go to inquiry.ucsc.edu 17 By Amy West

Copy that unnecessarily. “There was so much going on, it’s easy to think website changes were a conspiracy. Unlike history preserved through physical media like We didn’t want to play into that,” Dillon said. newspapers and books, virtual history is intrinsically ephemeral, potentially vanishing with the tap of a EDGI continuously monitors tens of thousands of delete key. To preserve this rich digital history, the web pages, but thus far has only identified “socially Internet Archive, headquartered in San Francisco, meaningful” changes, leaving deeper contextual has archived billions of web pages since 1996. analysis and probing to journalists. Their third report, Their digital library collection occupies more than Changing the Digital Climate, details how words like 30 petabytes (1 PB=1 million GB) of server space, “climate change” and “greenhouse gases” have with multiple copies saved in other cities around been replaced with less clear language. Links to raw the globe. Their web crawler tool, the Wayback Machine, captures snapshots of websites, allowing anyone to view a website’s history. Although federal websites often change when a new president takes office, this time the very real threat of rapidly losing access to valuable environmental data inspired activists to first gather in Toronto, then throughout the U.S. Coders at these “archive-a-thons” first designated important URLs (web addresses) for the Internet Archive to capture, such as the EPA climate change pages, to guide web crawlers beyond the first few links of a web page. Anyone can nominate web pages for archiving, but EDGI developed a web tool to make that easier, as well as a toolkit for anyone wanting Save the data! to host a DataRescue event. They also worked to archive uncrawlable pages containing complicated Scholar activism seeks social or dynamic data, like maps of greenhouse gases or marine protected areas. In total, the organized and environmental justice data rallies nominated more than 100,000 new web pages or datasets—a major contribution to a pre- A newly constructed condominium looks out over the Hunters Point Naval existing project that had aimed to archive all federal Shipyard, where workers decontaminated ships from nuclear weapons R Following the 2016 presidential election, what archiving event in the San Francisco Bay Area with testing and disposed of radioactive waste on site. This industrial area of started as a flurry of emails between academic 170 volunteers. She also became deeply involved websites by the time President Obama left office. southeastern San Francisco, the focus of Dillon’s primary research, has also colleagues launched a new watchdog for science in EDGI collaborative research that has generated housed a power plant, sewage treatment plant, and waste transfer station, and the environment: an online activist network three comprehensive reports to date. For the first, Out in the open and is now vulnerable to storm surge and sea-level rise. called the Environmental Data and Governance the group interviewed more than 60 former and Federal records law prohibits unannounced Initiative (EDGI, pronounced “edgy”). Troubled by current OSHA and EPA employees, some of whom destruction of government information. Once data have also been removed, essentially limiting the incoming administration’s anti–climate change had worked at these agencies since the 1970s. removed from public access or taken offline, this access, but the group found no evidence that any of stance, the group of scholar activists, including The resulting The EPA Under Siege compares the information must remain stored and available this valuable resource has been deleted. “I’d love to UC Santa Cruz sociologist Lindsey Dillon, threat in the current situation to that in the Reagan through public requests via the Freedom of attribute that to the work we are doing, the spotlight coordinated teams of volunteers to pre-emptively years. The second report, Pursuing a Toxic Agenda, Information Act. But you have to know what we put on,” said Dillon. copy government websites. Anticipating the reveals how the new administration’s environmental information you are looking for to know if it potential loss of years of environmental research, policy changes disproportionately affect vulnerable It’s important to recognize that some website vanished, said Dillon, and the process to track down this systematic rescue of federal data occurred at communities that are already marginalized. The manipulations can have greater negative impacts that information can be convoluted. 49 events in 2017 and helped build a comprehensive topic dovetails with Dillon’s own primary research than others. There’s a difference between simply archive of federal websites and data. It also sparked into the environmental politics of San Francisco’s Take, for instance, one case involving major website changing words and removing access altogether, hundreds of media mentions of the work, including Bayview–Hunters Point neighborhood. facelifts to the EPA’s climate action plans for cities. Dillon said, like when the EPA eliminated links a bit on The Daily Show. Although the EPA relocated the original pages to an to web pages listing educational climate change Above: UCSC assistant professor of sociology Lindsey accessible online archive, the archive is incomplete, resources for students. Limiting access to such Dillon, who had just begun her first year as a UCSC Dillon addresses the room of volunteers during a daylong ending in broken links. Changes like this are not public information is a form of social injustice, assistant professor, took on the role of co-chairing DataRescue event held at the Berkeley Institute for Data necessarily deliberate. In some cases, agencies Dillon believes, because not everyone has the EDGI’s 11-member steering committee. Following Science at UC Berkeley. The event focused on archiving pages from the websites of the DOE National Laboratories have rewritten climate science pages to escape time, awareness the information ever existed, or the inauguration—in between the Women’s March and NASA Earth Science. Credit, all photographs: ©Jamie defunding, so EDGI did not want to alarm people the know-how to find it once it’s gone. “Changes and airport protests—she helped coordinate a data Lyons, with permission.

18 inquiry@UC Santa Cruz For further inquiry, go to inquiry.ucsc.edu 19 IS IT POSSIBLE TO GET HIGHER RES COPIES By Marcus Woo OF EACH IMAGE IN Save the data! THIS STORY?

in accessibility are important,” concurred Nicholas voiced their concerns about living in San Francisco’s Shapiro, Dillon’s co-chair on the EDGI steering most polluted area. “There’s a connection between committee and research fellow at the Science race and urban inequality in the U.S.,” said Dillon. History Institute in Philadelphia, “They really affect “The place where you live really does influence your public knowledge and discourse.” health.” Hunters Point drew African Americans with its Urban assault shipyard jobs during World War II. But racist real A three-minute Dillon knows her way around government records. estate practices and urban planning also limited Such information provides the foundation for where new migrants could live, relegating them her primary research on the history, social, to less desirable—and frequently polluted—parts and economic dynamics of San Francisco’s of the city. Dillon’s research explores the ways challenge Bayview–Hunters Point. Historically, this industrial humans experience racism through the lens of neighborhood had the highest concentrations of environmental pollution. “It’s not discrete from pollutants in the city, coupled with abnormally class, or gender, or environment, or pollution,” said Competition showcases graduate student research high rates of diseases, like asthma and heart Dillon. “Racism is entangled in all of those.” Credit: Judy Glass failure, compared to the rest of California. In Developers have now begun to breathe new life addition, radioactive and other hazardous waste into Hunters Point, but not without protest and R As a graduate student, you spend years on your economics, has found that scheduled payment plans contaminating the soil and water qualified the controversy over the cleanup. With Bay Area thesis or dissertation, mastering every detail of your can help people in the developing world—who often World War II Hunters Point Naval Shipyard as an real estate at a premium, the area has started experiments, calculations, interpretations, and analysis. don’t have bank accounts—save money. Sharmistha EPA superfund site. The area has been a hotbed of to gentrify, increasing housing costs and further Now try distilling all that expertise into a talk just three Guha, a Ph.D. student in statistics and applied environmental justice activism; residents have long disenfranchising long-time residents. Dillon minutes long. And do it in an engaging and entertaining mathematics, uses statistics to analyze brain networks, advocates that such way with no jargon, so any intelligent person can hoping to unlock the secrets of creativity. And Tiffany “urban greening” understand it. Thang, an M.S. student in computational media, is projects should This year, more than two dozen UC Santa Cruz developing virtual-reality games to help people with incorporate policies for graduate students took on that challenge, competing developmental disabilities learn to recognize emotions. equitable housing and against one another as part of the fourth annual UCSC Taking home the runner-up prize (and $1,500) was environmental planning. Grad Slam. “Experiencing the diversity of the work Nickolas Knightly, a Ph.D. student in philosophy. He’s Her book-in-progress our grad students are doing in all kinds of areas and in tackling one of the deepest questions around: how uses Hunters Point as all disciplines—that’s very exciting,” said Vice Provost we know what we know. Events like the Grad Slam a model to examine the and Dean of Graduate Studies Tyrus Miller, who underscore the importance of being able to clearly political ecologies of emceed the final round of competition, held at the communicate your research, he said. “If people can’t toxic cleanup and urban Music Center Recital Hall in late February. understand what we are working on, they cannot redevelopment. A systemwide, UC-only, annual contest with its possibly open up to what it might mean and how it Scholar activism comes own rules, Grad Slam is similar to the popular Three might help us all to grow.” with the territory, said Minute Thesis (3MT®) competition that originated at In the end, Ph.D. student Kimberley Kanani Julie Sze, UC Davis the University of Queensland in Australia. Each UC Bitterwolf emerged victorious as both the UCSC professor of American campus holds its own competition to choose one Grad Slam champion and the people’s choice studies. “Not everyone champion to compete in the final systemwide event (audience vote) winner, receiving $3,000 and $750 for does it, but there are (runner-ups are also invited to attend). For the first each prize, respectively. Glory by association goes to people who work on race round of the UCSC competition, students submitted her fellow finalist and husband, Stephan Bitterwolf, and social movements videos of their three-minute talks—some honed with a Ph.D. student whose research aims to identify for whom there is no the help of a series of workshops on presentation molecular signatures of environmental stress on coral separation between skills. Twelve finalists—chosen by a group of UCSC reefs. Her own research analyzes the geochemistry their research and their administrator and staff screening judges—presented of river systems to calibrate measurements of activism,” she said. live onstage in front of an audience and a final judging ancient climate. “I didn’t think that paleoclimate was “Many of the leading panel that included Santa Cruz mayor David Terrazas, something that people would get excited about,” activist scholars are in the city council members, and other community leaders. she said. “I’m really surprised and happy.” In May, UC system, and Lindsey For the first time, all five academic divisions were Bitterwolf represented UCSC at the UC-systemwide is part of that tradition.” represented in the competition. Finalists included Tony Grad Slam at the offices of LinkedIn in San Francisco, Assi, an M.F.A. student in digital arts and new media, where she competed against the champions from In July 2017, a protest against pollution and gentrification took place in front of the housing who uses eye-tracking technology to understand the other UC campuses. To learn the final results office for the San Francisco Shipyard, an upscale housing development being built on the perception of visual art, such as Leonardo da Vinci’s and watch the presentations, point your browser to former site of the Hunters Point Naval Shipyard. . The Last Supper. Eilin Francis, a Ph.D. student in gradslam.universityofcalifornia.edu

20 inquiry@UC Santa Cruz For further inquiry, go to inquiry.ucsc.edu 21 By Sarah C. P. Williams

seeking to better understand biofilms. The goal? To The first step in making a biofilm is when individual develop new strategies to prevent biofilm formation bacteria attach to a surface—whether on the shell and potentially discover new drugs urgently needed of a plankton, the lining of your gut, or the interior to combat the often antibiotic-resistant diseases of a sewage pipe. For V. cholerae and many other caused by these bacterial communities. pathogens, clutching onto a surface involves pili— “Scientists used to believe that most bacteria were hair-like appendages that extend from the bacteria. free-living,” said Yildiz. “Now we know that the Some types of bacteria also use pili to move, majority of bacteria live on surfaces in biofilms, extending and retracting them like grappling hooks. and yet we understand very little of biofilm biology. V. cholerae, though, mostly rely on their single long There’s a lot to be discovered.” flagellum—like the tail of a sperm—to swim in a fashion characteristic of the genus. When they first Bacterial biofilms of one sort or another are reach a surface, weak interactions between pili and everywhere: coating your teeth before you brush the surface may cause them to move in small tight them and making your dirty dinner dishes slimy when circles. they’ve sat in the sink overnight. They can grow so large they clog sewage pipes and cover the bottoms Without pili, bacteria like V. cholerae can’t attach to of ships. And they cause infections when they grow a surface and can’t form biofilms. So understanding on the lining of a person’s lungs, gut, or urinary tract, how cells produce and control pili is critical to or on contact lenses, pacemakers, artificial heart understanding biofilms. But there are more questions valves, or replacement joints. Yet the vast majority than answers about these miniscule limbs. of all research on bacteria—including antibiotic “Right now, we don’t know a lot about how the development—is performed using bacterial cultures bacteria regulate the production of pili,” said Kyle Scanning electron micrographs of an entire V. cholerae biofilm colony (left) and a small section of a biofilm (right). The colony contains cells producing ample matrix (wrinkled part) and cells producing less matrix (smooth part). Credit, all images: Fitnat Yildiz. containing bacteria in their single, or planktonic, form. Floyd, a postdoctoral fellow in the Yildiz lab. “We By focusing on V. cholerae in biofilms, Yildiz’s lab also don’t know exactly how they sense a surface.” has already revealed many of the major components What is known is that a signaling molecule found of biofilms, including the molecules that make up only in bacteria, called cyclic dimeric guanosine the matrix—or glue—between the bacteria. The monophosphate or c-di-GMP, is required for the researchers have now turned their focus to how these components Canvassing interact and how microbes know when to form a biofilm. “If you know what’s in the matrix and how all these steps are regulated, you can use it to your bacterial advantage,” said Yildiz. Gripping and grabbing In nature, cholera bacteria live in rivers and estuaries, alternating between a solo, free-floating “planktonic” state communities and biofilms depending on all sorts of poorly understood environmental Targeting biofilms to bust cholera factors including salinity, temperature, and nutrient availability. In general, though, it seems that harsher From above, the cholera colony looks like a piece protect themselves from environmental stressors R conditions promote biofilm formation, of brain or a work of modern art. Deep grooves and optimize resources, groups of bacteria often with the gatherings acting as a kind of wind between wrinkly mountains of Vibrio cholerae interact, building communities held together safety net for bacterial survival. bacteria. It’s tempting to reach out and touch this with a kind of molecular glue. By virtue of their living landscape, but one swipe could kill. This is the teamwork, their sheer number, and their structural Like all biofilms,V. cholerae biofilms same bacteria that sickens millions of people around properties, bacteria in these biofilms are more of form on surfaces. They often coat the the world each year, killing many of them, and it’s an environmental nuisance and health hazard than exoskeletons of tiny plankton, which especially dangerous in its current form: a biofilm. populations of solo bacteria. That’s why researchers explains why large plankton blooms like Fitnat Yildiz, UC Santa Cruz professor of often go hand-in-hand with cholera Confocal microscopy shows growing (left) and mature (right) V. cholerae biofilms. Bacteria are single-celled organisms; by definition Bottom panels show side views. The intensity (black to red and white) correlates microbiology and environmental toxicology, are outbreaks. they exist and function as lone entities. But to with bacterial density.

22 inquiry@UC Santa Cruz For further inquiry, go to inquiry.ucsc.edu 23 Canvassing bacterial communities

cells to latch onto surfaces. In 2015, the Yildiz is required to switch between closed and open group discovered that c-di-GMP binds directly to conformations to bind VPS and coax the sugar a molecular motor that helps assemble MshA, molecules into the right architecture for a strong A killer with history the main protein component of pili. C-di-GMP, as biofilm. Later, when the biofilm is more structured, reported in PLOS Pathogens, promotes the assembly this relationship isn’t needed, and VPS takes on its Anywhere from a few hours to of MshA, leading to new pili. The higher the levels of shorter form. In this short form, the protein may a few days after being exposed c-di-GMP, the more MshA is made and the more pili have other functions, potentially including recruiting to cholera, the vomiting and that can form. bacteria that aren’t yet producing VPS to join the uncontrollable, watery diarrhea starts. As your body loses water, To uncover more about this interaction, as well community. your muscles cramp, and your eyes as what other molecules help V. cholerae sense Another biofilm question the lab is focusing on is and mouth feel as dry as cotton. surfaces and produce pili, Floyd is now labeling pili how VPS is produced in the first place. To address When people die of this disease— proteins with fluorescent tags, so he can see and this, postdoctoral fellow Carmen Schwechheimer sometimes within mere hours after study them in real-time. “Hopefully we’ll be able to has homed in on two proteins with seemingly symptoms appear—it’s because of watch them extend and retract,” he said. “And once opposing functions—VpsO and VpsU. While the dehydration. When they survive, we can do that, we can start manipulating other work is still ongoing, Yildiz’s group has shown it’s because they stayed hydrated molecules and observe the effect on pili.” Learning that VpsO is a tyrosine kinase, an enzyme which through this seemingly endless how to stop bacteria from producing pili, he added, adds a phosphate chemical group to tyrosine—a diarrhea and vomiting. could lead to ways to completely block their ability to nucleic acid building block of proteins. VpsU, on the form biofilms. other hand, is a tyrosine phosphatase, which does In the 16th century, people living the exact opposite—removing phosphates from in the Ganges River delta—near The matrix revealed tyrosine. In addition, VpsO itself switches between the border of modern-day India a phosphorylated and nonphosphorylated form. And and Bangladesh—called cholera A biofilm isn’t just composed of bacteria that when it does this, it appears to interact with VPS. “moryxy” and one historian wrote gather on a surface, pili tightly gripping each other. of how it killed so many that “It seems like you need that cycle of phosphorylation To form a biofilm, the bacteria must produce the communities struggled to bury all for the matrix to form,” said Schwechheimer. sticky molecular matrix that holds them together. their dead. Biofilm matrices are mostly composed of large “If you delete VpsO, the bacteria don’t make sugar molecules called exopolysaccharides, but also exopolysaccharides and don’t form biofilms, so it’s In 1817, contaminated rice from the Ganges delta began cholera’s A cholera treatment facility operated by Partners in Health in Mirebalais, Haiti, in 2011. include proteins, fats, and even bits of DNA. clearly critical.” Credit: © Kendra Helmer/USAID, Wikimedia Commons. spread around the globe. Within Schwechheimer is working with professor of In V. cholerae biofilms, Yildiz and her colleagues had six years it had killed hundreds of chemistry and biochemistry Seth Rubin and his previously shown that the major components are thousands of people in Thailand, lab members to create tyrosine-mutated VpsO Vibrio exopolysaccharide (VPS)—about half the mass Indonesia, the Philippines, China, Japan, the In recent years, the vast majority of cholera cases variants. These should enable the researchers to of the matrix—and the proteins RbmA, RbmC, and Persian Gulf, Turkey, and Syria. have occurred in Africa, with occasional small Bap1. In a recent collaboration with Carrie Partch, determine which tyrosines in the VpsO protein are outbreaks in Iraq and India. In 2010, after a massive associate professor of chemistry and biochemistry, phosphorylated, and how the changes contribute In 1829, another cholera pandemic emerged, again earthquake weakened Haiti’s already poor public the researchers created mutant versions of RbmA to VPS production. The kinase, Schwechheimer following trade and military routes from India—this health and sanitation infrastructure, cholera began that let them probe exactly how the protein said, is particularly attractive to study because it’s time heading to Russia, where it killed hundreds to spread throughout the country. Hurricanes and contributes to biofilm formation. As recently reported different from any of the native tyrosine kinases of thousands, then spreading throughout Europe, slow rebuilding efforts led to a ripe ground for in eLife, RbmA binds directly to VPS, helping to found in mammals, including humans. That thanks to Russian soldiers, and finally reaching further spread over the coming years, and, as of organize the exopolysaccharide structure. means that drugs blocking VpsO—and biofilm North America by the 1840s, where it claimed the 2017, over 800,000 Haitians were sickened, and production—would likely not impact the many life of former U.S. president James Polk, as well as “This was really exciting work,” said Yildiz. “It is the nearly ten thousand died of the infection. tyrosine kinases that are endogenously expressed hundreds of thousands of others. first direct interaction we’ve shown between matrix In Yemen, a cholera epidemic that began in in the human body. “It definitely has potential as an components.” Throughout the 19th century, cholera epidemics 2016—tied to the ongoing war and collapsing antibiotic target,” she said. and pandemics continued around the globe, But that wasn’t all the RbmA mutants revealed. infrastructure—has sickened more than a spreading with the global movements of immigrants million people and killed thousands. Based on The team also showed that the protein has multiple Sending signals and travelers. During a large 1854 outbreak in possible forms—an open conformation and a the suspected number of cases, it’s considered Underlying all these molecular mechanisms is the London, physician John Snow discovered that a the worst cholera epidemic in history and is not more closed conformation, as well as a processed, contaminated pump was responsible for spreading shorter version. When the researchers mutated central question of how bacteria first sense changes currently under control. in their environment that trigger them to start the disease—a finding credited with making Snow RbmA, locking it in the closed formation, the the father of modern epidemiology and eventually normally mountainous V. cholerae biofilm instead building biofilms. “In bacteria, everything is about sensing and responding,” said Yildiz. “Cholera has leading to hygienic changes in the water and waste appeared smooth and shiny, suggesting a role in systems of major cities. biofilm conformation. In the initial stages of biofilm to respond to all sorts of changes in its environment, formation, Yildiz hypothesizes, full-length, RbmA from changing salinity in the water to a whole new set of factors when it’s ingested by humans.”

24 inquiry@UC Santa Cruz For further inquiry, go to inquiry.ucsc.edu 25 Canvassing bacterial communities

Researchers know that c-di-GMP is one of the changes, triggering, in turn, the increase in c-di-GMP With Linington, who specializes in screening natural As always, there’s a lot more research to be done. important intermediaries in this sensory cycle, helping that promotes biofilm formation. products for their therapeutic potential, Yildiz has Not many biofilms in the natural world are composed to communicate messages within bacterial cells. helped identify other molecules that break up V. of a single species of bacteria, Yildiz said. An Its role isn’t just limited to producing pili, as Floyd Biofilm busters cholerae biofilms. She hopes this combination of additional important question for biofilm researchers is studying, but also appears to include biofilm and natural chemical screening for existing anti-biofilm moving forward is how different species of bacteria In the U.S. alone, it’s estimated that every year matrix formation more broadly. Studies by Yildiz and molecules plus working out biofilm biology to interact. Just as biofilm research has uncovered a nearly 2 million hospital-acquired infections involve her colleagues over the past two decades have shown rationally design drugs will eventually lead to new more complicated biology than that associated with bacteria in their biofilm state, costing health-care that high levels of c-di-GMP mean production of antibiotics to treat biofilm-associated infections. isolated bacteria, investigating how biofilms relate systems more than $10 billion. These infections higher levels of a variety of proteins needed to produce Such drugs could stop pili from extending, keep to the larger picture of microbiomes will likely add are often resistant to antibiotics—in some cases, biofilms. Currently, postdoctoral it’s hard for the drugs to penetrate fellow Jin Hwan Park is leading the dense biofilms; in others, a project to study how c-di-GMP antibiotics simply don’t work against inhibits V. cholerae motility and the altered molecular state of the controls biofilm matrix production. biofilm-associated bacteria. When a “C-di-GMP is a key, bacterial- replacement knee or hip becomes specific signal for biofilm formation coated with a biofilm infection, a and maturation. Because it is not complication affecting as many found in the host, it could make Overlay of fluorescence and as 2% of patients, the standard an outstanding drug target,” said phase contrast images shows pili treatment recourse is repeat surgery George O’Toole, professor of (pink) on the surface of several V. cholerae cells. to replace the prosthesis. In general, microbiology and immunology at antibiotic resistance remains a critical the Dartmouth Geisel School of and persistent public health concern, Medicine and another biofilm expert. Work by the for which new drug strategies are urgently needed. Yildiz lab on c-di-GMP has inspired studies in his own As with other bacterial pathogens, it’s clear that V. lab, he added. cholerae in biofilms are more infectious than bacteria But exactly how c-di-GMP receives an initial signal in their planktonic form. A study in Bangladesh to trigger biofilm formation remains unclear. Yildiz showed that using even a crude filter—such as one and former graduate student Andrew Cheng (now made from sari cloth—to filter drinking water can a senior scientist at Whole Biome, Inc., in San reduce the incidence of cholera by nearly half. That’s Francisco) wondered whether a two-component in part because such a filter removes the microscopic system might play a role. Common in bacteria, plankton that are coated with the most dangerous, these systems are made up of two proteins—one biofilm-associated bacteria, Yildiz said. that senses conditions outside the organism, and When biofilm-associatedV. cholerae are ingested, a “response regulator” that reacts, carrying out though, what happens to them in the human gut changes inside the cell. “Two-component systems Scanning electron (left) and fluorescence (right) micrographs ofin vivo intestinal V. cholerae biofilms. In the image on the right, epithelial remains unclear. In a collaboration with Roger are capable of sensing environmental conditions and cells—those that line the gut—are blue and the bacteria are green. Linington, a former UCSC associate professor of telling bacteria how to adjust their physiology, so it chemistry and biochemistry now at Simon Fraser certainly makes sense that these could be involved University, Yildiz discovered that bile acids, which exopolysaccharides from assembling to form a even more complexity. “Nothing lives in isolation, in biofilm formation,” said current graduate student break down fats in the gut, can disperse biofilms. But matrix, or block signaling by c-di-GMP, among other and—as with so much of biology—the challenge Jennifer Teschler. studies of cholera patients have found evidence of mechanisms. is going to be seeing what happens when we start Teschler, Cheng, and Yildiz deleted all 52 known intact biofilms in their stool samples. This suggests And while Yildiz’s research focuses on V. cholerae, increasing the complexity of biofilms,” said Yildiz. response regulators in V. cholerae, one at a time, that bacterial biofilms may be broken up during other researchers are focusing on the biofilms of “Will everything we’ve found so far still hold true?” and studied the effect of each deletion on the early digestion, but form again during later stages other bacteria. At Dartmouth, for instance, O’Toole bacteria’s ability to form a biofilm. Seven of the of infection. In the human disease setting, “There’s mainly studies Pseudomonas aeruginosa, which response regulators, they found, impacted biofilm this interesting dispersal and reformation cycle going forms biofilms in the lungs of cystic fibrosis patients. formation, with the biofilms developing abnormally on,” said Yildiz. “And there are certain situations in He said, however, that V. cholerae is a good choice in their absence. One, called vxrB, had never been which bacteria really need to form biofilms to be for this work. “V. cholerae is a terrific model. The characterized before so the researchers looked at better protected, and other times it’s perhaps not as factors that drive maturation of the biofilm forV. it in more detail. Levels of vxrB, they discovered, advantageous.” Studies focused on this important cholerae are conserved across a number of other impacted levels of c-di-GMP. Their findings, area, the molecular biology underlying V. cholerae microbes.” published in the Journal of Bacteriology, suggest biofilmsin vivo, are being led by postdoctoral fellow that a two-component system involving vxrB could Ana Gallego. be one way that V. cholerae senses environmental

26 inquiry@UC Santa Cruz For further inquiry, go to inquiry.ucsc.edu 27 By Adam Mann By Katharine Miller A window to the early universe

Astronomers are using the Atacama Large Witnessing the birth of galaxies Millimeter Array (ALMA)—a radio telescope with 66 massive antennas (“dishes”) in the Chilean desert—to observe celestial R The present day is relatively dull, cosmologically “It’s sort of a phenomena that occurred near the dawn of time. Credit: ESO/C. Malin, public use. speaking. Most of the action happened in the first few new window, and billion years after the Big Bang, when enormous swirls when you open a of gas and dust collapsed down to produce the earliest new window you see different physical phenomena,” stars and galaxies, filling the universe with their light. Half said Christopher Carilli, who also studies the earliest of today’s stars arose during this peak era of formation. galaxies at the National Radio Astronomy Observatory, Teasing out the details of this active early epoch has a major radio telescope facility in the U.S. that hosts the proven difficult. It’s only recently that astronomers have North American ALMA Science Center. Whereas most switched on facilities like the Atacama Large Millimeter astronomical observations have been of stars, “the Detecting Array (ALMA), one of the world’s most powerful radio focus is now shifting to the source of those stars, and telescopes, allowing them to draw back the curtain to completing the picture of the conversion of gas to stars very nearly the dawn of time. as a function of cosmic time.” “With these new tools we will be able to really map out Some limited physical clues were already available. the distribution of star formation in individual galaxies 12 Strange cosmic beats called quasars formed during an human diversity billion years ago,” said J. Xavier Prochaska, UC Santa even earlier period, sending out powerful light beams that Cruz professor of astronomy and astrophysics and ALMA intersected the later gas and dust, imparting characteristic researcher. signatures onto it. Astronomers have used these indirect observations to locate and study a few early galaxies. Astronomers have used sophisticated computer models Variation graphs facilitate genomic discovery to develop ideas about this period. Simulations of the As reported by Prochaska and colleagues in a 2017 paper effects of dark matter and dark energy, plus in Science, the more direct ALMA observations have After the first human genome was successfully inversions, and translocations. When these the matter content of planets and stars, produced surprises. For instance, quasar light R sequenced in 2003, researchers established interesting and potentially important variants exist show virtual galaxies coalescing out of an had pegged one of the team’s galactic targets it as the reference genome. It became the in a new sample that is being mapped against unstructured fog. The results suggest that to a specific location. But ALMA placed singular, highest-quality, most well-understood, the reference, they might not be seen at all. As a uneven distributions of massive dark matter the object about 100,000 light-years away, standardized genome against which all other human consequence, the new sample is deemed more drew gas and dust into galactic knots, where suggesting that the quasar light had passed genomes would be mapped and compared for the similar to the reference than it actually is. The failure the material cooled and fragmented into stars. through a much-larger-than-expected halo of foreseeable future. to find important variants can have consequential Astronomers have long awaited physical data gas and dust. The galaxy also glowed much downstream implications for patients if a missed to corroborate or challenge these views, and brighter than predicted, indicating prodigious It turns out this commitment to a single reference variant is the cause of a genetic disorder or plays ALMA—which became fully operational in star formation of roughly 100 suns per year, genome has a big downside. Called reference bias a key role in a patient’s cancer. And as the pace 2013—has begun to deliver. A quasar was originally 100 times greater than the modern rate. or mapping bias, it can cause potentially important of sequencing-based genomic research continues used to indirectly find And this is just one galaxy. These first observations to be misinterpreted or rejected when Observatories like ALMA work in radio this distant galaxy (*) to increase, so too have the potential impacts of observations mainly show that ALMA, built in they don’t fit the expected pattern. “With the bands, searching for light coming from the in the early universe. existing reference genome,” said Benedict Paten, reference bias. glowing gas and dust present in the first When researchers part for this purpose, is capable of performing used ALMA to directly UC Santa Cruz assistant professor of biomolecular galaxies. Only slightly warmed by young as planned. Prochaska and collaborators intend Above: UCSC assistant professor of biomolecular image the object, it engineering, “it’s easier to find variants that are in massive stars, this material is much fainter to follow this promising early work with close engineering Benedict Paten (left) with the genome graphs was 100,000 light- looks at the births of many more galaxies. “It’s the reference genome than ones that aren’t.” team: (left to right) graduate students Charles Markello and and further away than recently formed years off from where inspired us to start a large survey of these Yohei Rosen, and senior software engineer Adam Novak. objects. ALMA, located in the Chilean high they thought it would The problem is particularly acute for structural phenomena,” he said. “That’s really how The genome graph visualization on the computer screen was desert, can capture these light signatures be. Credit: Neeleman variations in the genome—long stretches of DNA created by Wolfgang Beyer. Credit: Tina Bernard. with its large array of 66 massive antennas & Prochaska (UCSC), you learn and rigorously test these models of that differ from the reference in various ways, courtesy of Xavier galaxy formation.” (“dishes”). Prochaska. including changes known as insertions, deletions,

28 inquiry@UC Santa Cruz For further inquiry, go to inquiry.ucsc.edu 29 Detecting human diversity

To address this critical and growing concern, Paten Tina Graves-Lindsay, leader of the reference result, reads that diverge from the reference may called “SNPs” (pronounced “snips”) or single- and colleagues at UCSC and the Sanger Institute genomes group at Washington University’s map incorrectly or fail to map altogether. nucleotide polymorphisms. In addition, each human set out to build a set of technologies for replacing McDonnell Genome Institute in St. Louis, agreed, For example, if a researcher tries to map 100–600 genome contains about 2500 structural variations the existing reference genome with a more “When we get to the point where they’re ready base-pair short reads from an individual who has that aren’t included in the reference—variations comprehensive foundational structure. “The natural to be used, genome graphs are the future a 10,000 base-pair insertion that isn’t represented that affect about 8.9 million bases per person. The thing is to have a graph that includes all the known representation.” in the reference, this structural variant gets a poor human genome variation graphs developed by Paten gene variants,” Paten said. And though the idea of matching score. Essentially, there is no place to and collaborators capture and display all this diversity replacing the linear reference genome with a graph Genomic fake news map those reads against the reference, and the in one visualization. might sound simple, he said, “we’ve had to solve Understanding the source of reference bias requires insertion is ignored. some pretty tricky computer science problems to at least a passing understanding of how sequencing Graphing genomes make this work.” It’s also true that no single reference can truly technology works. The most common approach represent the genetic diversity present in a To imagine a genome variation graph, picture the Having a great solution doesn’t mean it will be to genome sequencing today relies on repeated worldwide population full of varied and interesting 3-billion base-pair linear reference genome itself used, especially given the deep entrenchment sequencing of short stretches of DNA—typically ethnic groups. Curiously, the human reference as a single path through a graph with an incredibly of the single reference genome in the field. 100–600 base pairs (the A, C, T, and G nucleotides genome used today does not even represent long horizontal axis. Next, imagine many other Nevertheless, even members of the Genome that make up DNA). Researchers generally try to get the set of genes from a specific human being. paths converging with the reference for stretches Reference Consortium who’ve spent their careers 10x to 30x coverage of every portion of a genome This mosaic model of a single set of unpaired where their sequences are identical, but diverging maintaining and improving upon the linear reference using these short “reads.” They must then piece chromosomes gets 70% of its 3-billion base-pair at other points before converging again. One agree that genome variation graphs make sense. these together to create a contiguous model of a DNA sequence from a single male of mixed African divergence might be a bubble that represents a “The representation of variation in the human person’s genome, a task accomplished by mapping and European ancestry, and the remaining 30% single nucleotide change; another might be an population is a type of data that fits very neatly the short reads against the latest generation from an assortment of more than 50 individuals. inserted sequence or even an inverted stretch of into and is well-represented by a graph model,” of the very first genome ever sequenced—the “The idea at the time was that a linear reference DNA that can be conceptualized as a loop-de-loop said Valerie Schneider, program head for sequence human reference genome, now in its 20th iteration derived from many individuals would be a good that leaves the path and rejoins it. There can also be displays and tools at the NIH’s National Center for (GRCh38). During this genome assembly task, the way to capture diversity,” said NCBI’s Schneider. bubbles within bubbles or loops that have additional Biotechnology Information (NCBI) and team lead for reads are scored relative to how well they match divergences internally. Any observed variant can the NCBI’s involvement in the Genome Reference the reference. “The more similar a read is to the We now know that humans are more genetically be accounted for in the graph representation. “The Consortium. “Benedict is at the leading edge of reference genome, the higher probability that the diverse than expected. Today, geneticists estimate graph captures information about what we’d expect where this is going.” mapping will be deemed correct,” Paten said. As a that the average person’s genome differs from the a human to look like in a computationally practical reference by about 3.6 million base-pair changes,

Genomic graph visualizations C. D. A. B.

In these visualizations of Paten’s human genome variation reads are blue, and the letters on top are the sequences graph (created with ivg, the visualization portion of the vg node. The segmented lines below the haplotypes (in A, of the graph’s nodes. Letters, asterisks, and grey toolkit), the continuous lines toward the top of the graphs B, and C) are sequence reads aligned to the haplotypes. rectangles shown on the reads are, respectively, represent haplotypes (known genomic sequences from Like the haplotype paths, these sometimes bypass a longer than the longest ones in A but are compressed substitutions, insertions, and deletions. When viewed one of a given person’s two chromosomes) in a node, signifying a deletion of the sequence at that node. horizontally (leaving insufficient room to label them with on a computer, one can hover the cursor over an asterisk 2500-person population cohort. The shaded rectangles A. In this zoomed-in visualization of the human their nucleotide sequences). Here, 13 haplotypes are to see the inserted sequence. D. The visualization tool represent nodes (shared DNA sequences) with the node’s genome variation graph for a short sequence from shown in gray with unvarying widths. Forward sequence can also provide an intuitive graphical view of inversions, nucleotide sequence (A, C, T, or G) shown at top. The human chromosome 22, the red lines represent seven reads are shown in shades of red, while backward reads as shown by the green and red loops in this simulated colored ribbons between the nodes are paths/edges haplotypes and their widths encode their prevalence in (from the opposite strand of the DNA) are shown in blue. example. (not sequences). When a haplotype’s path bypasses a the population. B. In this zoomed-out visualization of a C. Here we see a sample with higher read coverage. Credit: Courtesy of Benedict Paten and Wolfgang Beyer, software node, this signifies a deletion of the sequence at that different piece of chromosome 22, the nodes are actually Haplotypes are grey, forward reads are red, backward developer for the Computational Genomics Laboratory at UCSC.

30 inquiry@UC Santa Cruz For further inquiry, go to inquiry.ucsc.edu 31 By Cameron Walker Detecting human diversity

manner,” Paten said, “so that when we get a new can already do almost as good a job as the linear sample we can infer things that are correct.” reference genome at finding small genome variants (e.g., SNPs) in a new sample, and a far better job Viewing lost Ultimately, the linear reference genome will be just one path through a graph that contains many of finding structural variations, particularly if these possible paths. Any other haplotype (the set of involve long stretches of DNA, Paten said. alleles—gene variants—a person inherits from each parent) could be represented as a path as Transition tools well. While that might sound like a simple concept, landscapes As previously mentioned, in the field of genomics it presented a challenge for Paten’s team: how where large data sets that rely on the linear to encode a population’s haplotypes through a reference already exist, changing the foundational graph in a way that would be small, compact, and structure for genome mapping won’t happen searchable on a computer? “We found a really overnight. Even uptake of formal updates to the beautiful solution to that,” Paten said, which linear reference is slow. GRCh38, the current involves weighting different paths according to iteration of the standardized reference genome, their prevalence in the population. “If I trace a was released more than four years ago, yet many path through a graph that might correspond to a projects are still using GRCh37, Paten said. “It takes haplotype, it’s actually very useful, from a genetics that long to accomplish all the things you have to do point of view, to be able to ask, ‘What’s the to switch from one to another—it’s an enormous probability of that path given what we know about headache.” the population?’” Paten said. Paten predicts the shift to the genome graph will The team also had to establish a novel coordinate be even slower and may also proceed in an uneven system for the human genome variation graph. way. During the transition, it’s likely that researchers “When you live in the topsy-turvy world of graphs, will use the graph and then project their findings it isn’t initially that clear how you represent alleles back onto the reference genome, he said. “This and sites,” Paten said. The coordinate system for should provide a compatibility layer for a good Home movies capture history the linear reference genome is straightforward. while.” Indeed, he said, the graph may never fully Each chromosome begins at a point A and ends at replace the reference genome, “but that’s just fine through a personal lens a point B with defined locations all along the way. because it’s just a set of paths in our graph.” To define the unambiguous position of an allele in The shift to genome graphs also faces major a genome graph (as well as what its alternatives technical hurdles. All of the tools for genome are) and do it in a way that works for all forms of mapping and variant analysis are built around variation, “took some really hard thinking,” Paten alignments to one linear reference. “When you During the late 1930s, Ivan Besse, a theater again on the Strand’s movie screen. During most said. But it is a problem his team has now solved by R introduce these new models, such as graphs, you manager in Britton, South Dakota, filmed home films, the audience sits silently while the movie plays. developing a mathematical model that represents need a robust tool suite that can take advantage of movies of his town and its inhabitants and showed But this time, when Prelinger turned on the projector, an allele’s coordinates relative to its neighbors. the additional information,” Schneider said. them as shorts before the features he screened at people started talking. They pointed at the screen, “The graph is a way to organize a population’s calling out the names of people, of places, of relatives To that end, Paten’s team has created a software the local Strand Theater. In these films, men husk genomic information together so that we can and friends—some long gone, others, like Besse, toolkit called “vg” (short for variation graph). Publicly corn, snowstorms blow in, kids pour out of the answer questions in an efficient manner,” Paten sitting in the theater with them. “I’d never seen available on GitHub, vg is already the most popular schoolhouse at the end of the day—each scene said. Given a new sample, it should be easier to find people talk back to the screen like that,” said Prelinger. software of its kind, Paten said. “Several hundred recording a moment of daily life during the waning the variants it shares with the population because people have started trying to use it. That’s not big, years of the Great Depression. Prelinger, a film archivist, had been amassing a they are already contained in the graph. And finding but it’s promising.” Paten also plans to release When UC Santa Cruz collection of “forgotten” 20th-century films, from new variants should also be easier because the probability-weighted paths for the current map’s professor of film and advertising to educational and industrial films, to graph allows researchers to make better inferences 2500 human genomes in the next year. digital media Rick government-sponsored shorts. Home movies like about what’s possible or probable. the ones he showed in South Dakota turned him Eventually, Paten hopes there will be consensus Prelinger found these Paten’s human genome variation map currently into a filmmaker. In theLost Landscapes series, his around the human genome variation graph just as films 50 years later, he contains data from a 2500-person cohort. To these compiled and edited films provide portraits of a city there is now consensus around the linear reference was enchanted, and he plans to add additional variant information from and its people through this most personal of lenses. genome. The graph model offers an intuitive way brought them back to 150,000 individuals. But the 2500-person graph So far, he’s presented films about San Francisco, for computers to infer the next genome, he said. Britton to show them “It’s a much better basis for making inferences in Left: UC Santa Cruz professor of film and digital media Rick Prelinger sorts through his human genomics.” And that could ultimately power extensive collection of ephemeral film and home movies, part of the Prelinger Archives. much more precise precision medicine. Credit: Megan Prelinger. Top: Still image from Prelinger’s 2013 filmNo More Road Trips?, an automobile-based adventure across the country as told through home movies. Credit: The Prelinger Archives.

32 inquiry@UC Santa Cruz For further inquiry, go to inquiry.ucsc.edu 33 Viewing lost landscapes

contemplative,” he said. Viewers pick out buildings place and people and experiences of the past.” the 1990s, he realized that, rather than just sitting in lost to modernization, recognize changing styles in While most people think of the 1950s as a single a New York warehouse, these films would be best clothing and social interactions, and become cultural decade where everyone had the same traditional preserved as part of a public resource. In 2002, the ethnographers and geographers in their own right. experience, these small, filmed moments show the Library of Congress acquired most of the films as the “Home movies,” said Prelinger, “turn ordinary heterogeneity of the past. For example, films made Prelinger Collection. A number of the films can also be viewers into sophisticated visual analysts.” by the head teacher of a northern English nursery accessed online as a companion piece to Prelinger’s While usually intended to document personal school during this period document many men 2006 book, The Field Guide to Sponsored Films. moments, home movies also preserve the landscape dropping off and picking up their children. This could Making both these ephemeral films and home movie that surrounds them. Scenes of children riding bicycles counter the notion that men were not as involved footage available for a wider audience is an essential down the street can include backdrops of buildings with child care during that time. But it could also part of Prelinger’s work. Currently, the Prelinger now lost to new developments; footage of rural areas reflect male unemployment in the area, or parents Archives has approximately 7,000 films digitized and Still images from Prelinger’s 2017 filmLost Landscapes of New York may document the arrival of telephone lines, roads, needing to balance shiftwork at the local mill. “There capture the prewar atmosphere at a 1936 May Day parade (right) available online for people to view, download, and and, in postwar 1948, an informal gathering on an East Harlem street tracts of homes in place of fields. In Prelinger’s films is always so much that remains unknown and create their own projects. Prelinger estimates that corner. Credit: The Prelinger Archives. of San Francisco, footage from a glider club in the unknowable with amateur film, whether visual details hundreds of thousands of projects have been created 1920s reveals a Sunset District covered with dunes, or a filmmaker’s intentions, or what was just out of from the archives since 2001. Detroit, Oakland, Los Angeles, and, in 2017, New not houses. “These films create a visual history of view,” she said. “This is why it challenges our ways York City. He has also created several thematic the 20th century, captured by people who didn’t of thinking about the past.” Such open, reusable film archives are unusual, with films, includingNo More Road Trips?, an automobile- have public agendas, who weren’t working to an many closed to all but select researchers pursuing based adventure across the country, told through official brief,” said Heather Norris Nicholson, visiting Forgotten films scholarly projects. While this is changing, very few home movies. For researchers, home movies can researcher at the University of Huddersfield, United archives allow visitors to watch short segments of Prelinger’s initial entry into film collection was broaden their understanding of issues such as Kingdom. film online and to download and use them in their gender dynamics and reveal history not caught through what he calls “ephemeral film.” From own work. “The old archive is a place things go to on mainstream film. The films also offer a path to Hidden history government films showing what to do in the event of die. They’re like mortuaries—you can go in and look the future, Prelinger said, one in which people can a nuclear bomb, to business films training workers on at the dead bodies,” Besser said. Instead, he said, Home movies, and the films that Prelinger has collectively experience these images of the past a new project, to educational material for high school film archives should be “lively places” that facilitate made from them, reveal lost cultural as well as and use them to help shape what they want their students, these films were made for a purpose—and interactions with a wide community. physical landscapes. Once 8 mm cameras and film communities to become. were usually discarded once their useful life seemed were introduced in 1933, home movies became over. In 1982, Prelinger began collecting these Community building more affordable and accessible to a wider segment films, some straight from the dumpster, others from Personal to public of America, enabling families of color and those production companies that were closing their doors That lively place is in evidence at Lost Landscapes Home movies are typically considered second- in working-class and rural communities to start or transferring their film collections to videotape. At screenings, annually in San Francisco and at frequent class citizens of the film world. “Home movies shooting their own films. some point, he realized this footage provided visual special showings and film festivals around the have been treated by professionals and cinema In editing footage for his San Francisco films—he has evidence of a hidden American history. The films experts—scholars, critics, and serious filmmakers— been showing a new one each year since 2006 to show everyday life, the environment, and visual as something that hobbyists and amateurs did that sold-out crowds—Prelinger uncovered movies from records of culture, including dress and hairstyles. But was of, at best, documentary value,” said Prelinger’s a 1950s Latino family that showed them celebrating they also contain subtle, pervasive fingerprints of the UCSC colleague Jonathan Kahana, professor of birthdays, confirmations, and family holidays. “The past, revealing, for example, how the government film and digital media. People began using handheld family is so charismatic. Their body language is a joy aimed to create and encourage patriotism and how movie cameras in the 1920s, and their use expanded to observe,” he said. Their home movies counter society defined and reinforced gender roles. in the following decades. These cameras allowed the notion that working-class San Francisco at the “These are some of the richest artifacts telling people to record their personal lives—from family time was all white and Catholic; other segments stories about the time period in which they were birthdays to summer vacations—and to preserve and show street scenes with diverse pedestrians, the made,” said Howard Besser, professor of cinema share these memories on a small scale. Capturing homeless population in the 1950s before the South studies and associate director of the Moving Image time, places, and people through a small lens, of Market area was developed, African Americans in Archiving and Preservation Program at New York the resulting movies were “treated as unskilled, the crowd at the 1956 Republican Party Convention. University. “In fact, if you’re trying to understand unpolished, unreliable, and, to anyone but their “There’s a sense of justice in filling gaps in the gender dynamics in the ’50s and ’60s, one of the subjects, nearly unwatchable,” Kahana said. record,” said Prelinger, who joined the UC Santa Cruz best places to look is the instructional films kids were But as Prelinger observed in the South Dakota faculty in 2013. being shown in school.” Ephemeral films, including theater, these movies are transformed when they This information can help shift preconceived advertising and other promotional material, provide emerge from the family room, and so are the perceptions about the past. Nicholson, coauthor “amazing insights into the mindsets and ideologies of people watching them. “Something very interesting of the forthcoming book British Women Amateur a particular time,” Besser said. happens when movies made for showing on a small Filmmakers: National Memories and Global Identities, Prelinger’s interest in these films grew into the Still image from one of Prelinger’s Lost Landscapes in San Francisco films scale get blown up to the size of a theater screen. said one of the things she loves about amateur film expansive Prelinger Archives, a San Francisco–based shows women from a Latino family dancing on San Francisco’s Ocean Details jump out. Audiences become much more is its ability to “open up alternative ways of seeing collection of more than 60,000 films. By the end of Beach, circa 1951. Credit: The Prelinger Archives.

34 inquiry@UC Santa Cruz For further inquiry, go to inquiry.ucsc.edu 35 By Sarah McQuate Viewing lost landscapes

country. “In a way, the actual screening of the edited attended of Lost Landscapes of Detroit, he said the works is an extension of the idea of opening up the conversation started less than two minutes into the archives,” Besser said. “People are contributing film, and continued throughout. “As someone who cataloging to the work as they’re watching. What never lived in Detroit, I merely listened, feeling like used to take place in a darkened back room is now I was at a combination of a family gathering and a happening in the public space of a theater.” graduate seminar in cultural geography,” he said. Tom Rankin, a professor in the Art, Art History & Prelinger is trying to further expand this community Visual Studies Department at Duke University in participation by giving the films he’s made back to North Carolina, concurs. Recalling a screening he the public. In some cases, he has transferred Lost Landscape films to local residents, allowing them to use the films to build and create community From 8 mm to 5G to ? ties in whatever form they envision. In Oakland, filmmaker, writer, and artist alex cruse has screened We’ve come a long way since 1893 when Lost Landscapes of Oakland both with Prelinger, the first film production studio in the world, and, more recently, on her own. This year she plans Guided by the light Thomas Edison’s “Black Maria” in West to incorporate additional footage into the film. She Orange, New Jersey, began shooting magic uses the film to work with local historians and people Stars bring biology into focus shows and vaudeville performances, lit via who’ve lived in the Bay Area for generations. Each a retractable roof. Today, most of us have time she shows the film to someone, she said, she UC Santa Cruz professors Joel Kubby (far right) and William Sullivan (far left) work with (at the time) graduate students Oscar Azucena high-definition video cameras in our pockets, learns more. and Justin Crest and postdoctoral fellow Shaila Kotadia on a fluorescence microscope equipped with the “guide star” adaptive optics smartphones that give us the ability to system. Credit: Courtesy of Joel Kubby. Elsewhere, scholars have been using this emerging chronicle every last second of our lives. appreciation of forgotten films to shape their own thought it’d be interesting to take a that was developed for astronomy in The rapid evolution of technology has led work. In Montreal, Concordia University professor R When we look at the stars, we look at why,” he said. microscopy.” to substantial changes in the way we relate of film studies Catherine Russell tasked her often marvel at the vast universe to video. We make movies whenever we undergraduates with finding footage of their city for a surrounding us. Joel Kubby, UC The astronomy method first In his system, Kubby uses want with the virtual push of a button, class project inspired by Lost Landscapes, and one of Santa Cruz professor of electrical measures how the light from fluorescent regions in tissues as capturing realities that used to be subject her graduate students included a chapter discussing engineering, saw a tool that could galaxies and planets gets distorted. guide stars. He first illuminates a to “he said, she said” and trumpeting our Prelinger’s films in her dissertation. Russell’s own help scientists understand cell It does this by focusing on a “guide tiny point in a fluorescently labeled accomplishments and adventures to the new book, Archiveology, explores how archives biology. star,” either a nearby star or a sample so that it glows, and then entire world in real-time. Kids growing up can go beyond film preservation to become rich Neuroscientists use microscopes to spot generated by a yellow laser corrects it into a perfect circle today live with technology that wasn’t even resources for artists and the public to learn about and study cells in living tissues. However, pointed into the sky. Then the with adaptive optics to clarify the imagined in Star Trek. No one bothers to create new understandings of history and memory. simple light microscopes—like those adaptive optics system bounces image of the target tissue. Faster think of how amazing it is to so easily record This process is made possible with collections like found in high school classrooms— the reference starlight off small than the radio-dial system, Kubby’s baby’s first steps or school plays, to capture the Prelinger Archives, she said, although “their don’t provide enough contrast mirrors that rapidly deform to erase system is now being used by many lip-synching in the car or suspected police actual uses and the knowledge we can gain are still to see cellular details. This task its distortions. When the guide star researchers, including Ji, particularly brutality. Software automatically stabilizes very much untapped.” requires fluorescence microscopes, comes into crisp focus, it brings with live samples that are rapidly images and enhances them to illuminate a clearer image of its celestial changing. It may also open new areas Along with future Lost Landscapes films, Prelinger instruments that capture light from and define details. Artificial intelligence now neighbors with it. of research by unveiling previously plans to create a more ambitious film of 20th-century molecular probes that glow when powers wearable cameras that capture hidden cellular physiology. At UCSC, America, to help this century’s viewers connect with they’re added to cells. But even with In cells, however, there are no “interesting” moments throughout the day, all Kubby and team are planning to their recent past. Prelinger hopes his films will inspire these beacons, overlying tissues can stars. Adaptive optics systems for without a person ever having to touch record. explore what happens when neurons more of these connections. Seeing Lost Landscapes obscure the cells deep within, for microscopy estimated the biological in the brain misfire, like during On top of it all, we can almost with a community of others—like the South Dakota example, the brain of a fruit fly. light distortion, allowing viewers epilepsy or Parkinson’s disease. instantaneously watch a virtually limitless audience in the Strand Theater absorbing Ivan In the early 2000s, engineers started to adjust the light until the image smorgasbord of video. By 2021, video is Besse’s view of their world 50 years earlier—can using adaptive optics, a technique became clear, like finding the best Although his system is still limited projected to account for more than 80% of give viewers a better understanding of where developed for astronomy, to improve sound with a radio dial. Knowing how to use by engineers who are all consumer Internet traffic; every second, they are and a deeper commitment to further that fluorescence microscopy. The well the guide-star method worked microscopy experts, Kubby hopes a million minutes of video will cross the understanding. “I invite viewers of my films to look swirling gases in our atmosphere for astronomy, Kubby decided to it will become ubiquitous as more network. This video tsunami begs the into the future and extrapolate to how environments blur the light coming from celestial adapt it for microscopy. biologists see how it can improve question: What will future archivists, the Rick to come will evolve from those that exist today,” objects, just like biological tissues “Joel is one of the early pioneers,” their imaging studies. He sees a Prelingers of 50 years from now, be looking Prelinger said. blur fluorescence coming from said Na Ji, UC Berkeley associate future where adaptive optics is a at, preserving, and researching? cells. Kubby noticed these efforts professor of physics and standard feature on fluorescence – David Egerter employed a different method than neuroscience. “He is the first microscopes. “You just press your the one used in astronomy. “I person to use the measurement ‘AO button’ and there it is,” he said.

36 inquiry@UC Santa Cruz For further inquiry, go to inquiry.ucsc.edu 37 By Barbra A. Rodriguez

the first monitor for wild cetaceans that records detailed information about their heart rates. Initial studies with the device, which also tracks fin speed Crossed currents and depth, were performed with bottlenose dolphins at UCSC’s Long Marine Laboratory and Weddell Conflicting stress responses may beach seals in the Antarctic. The results, reported in 2015 in Nature marine mammals Communications, disproved the prevailing dogma. During normal hunting dives, the hearts of these deep-ocean dwellers rapidly switched between slowing down and speeding up. The greater the depth, the greater the heartbeat irregularities. In effect, the involuntary dive response that slowed down the heart appeared to oppose the exercise- related messages the brain sent to accelerate it while chasing prey. And blood flow stalled by the erratic heart rate would be expected to decrease the oxygen and nutrients reaching vital organs. “The more we looked at the heart and exercise responses of these animals, the more we wondered how they were getting enough oxygen to the brain,” Williams said. Testing her monitors on narwhals in Greenland provided additional key insights—reported in While retrieving a monitoring device, Williams holds a A narwhal pod near Scoresby Sound in Greenland. As part of receiver at the bow of an Inuit fishing skiff, searching among their physiological research, UC Santa Cruz professor Terrie Science in December—about how the stress of icebergs for the signal from the device’s radio satellite tag. Williams and her team visually monitor the movements human interaction impacts this physiology. Working of these whales that reside among icebergs. Credit, all with Inuit that hunt narwhals in Scoresby Sound, photographs: Mads Peter Heide-Jørgensen, courtesy of Terrie Williams. Williams, former postdoctoral researcher Susanna their initial dive plunged to as low as three or four Blackwell, and lead collaborator Mads Peter Heide- beats a minute and stayed there much longer than Jørgensen have now tagged and studied nine of normal. “I realized we had recorded a type of stress these elusive tusked whales. response,” Williams said. The longer the net-entangled narwhals were Stress-triggered, whole-body freezes in which heart R For millennia, ocean mammals have beached whales and dolphins. The resulting disjointed stress handled, the further their heart rates dropped once rates dropped by half had been reported in marine themselves along coastlines, and people have response could indirectly damage their brains—and released. Moreover, the animals’ heart rates during mammals. But not the extreme cardiac freeze (heart wondered why. But while theories abound, the cause clear-thinking skills—leaving them prone to stranding. rates more than 90% below normal) observed in the of mass strandings in particular has remained elusive. Rescuers often describe disorientation in stranded released narwhals, which could last ten minutes. New clues are now emerging thanks to submersible cetaceans that fits with brain damage, said Williams, Importantly, during this period of likely reduced technology that allows near real-time observations of who has studied the physiology of large mammals blood flow, the fleeing narwhals also often doubled marine mammal physiology and behavior. for three decades. All kinds of things, from sunspots their normal swimming speed. That is, the heart Because they share the same basic anatomy of all to geomagnetic anomalies, have been proposed to freeze and flight response occurred simultaneously, mammals, whales and dolphins (cetaceans) hold explain this confused behavior, she said. “Maybe it’s requiring the animals to pump their muscles into on to a single breath of air while diving so deep simpler—something happened before they got to the overdrive on an emptying “tank.” Fear exacerbating that their lungs may temporarily collapse. This beach that disrupted their normal brain function.” these opposing freeze and flight responses appeared to create a “trifecta” effect with the hypothetical reliance on the “plumbing” of land dwellers could All mammals react similarly to cold water exposure potential to instigate brain damage, Williams said. play a heretofore unrecognized role in stranding, of their faces. To conserve oxygen and warm blood said Terrie Williams, UC Santa Cruz professor of for vital organs like the brain, the involuntary part Ultimately, Williams’s research aims to make a ecology and evolutionary biology. of the nervous system slows the heart rate and difference in the survival of the animals she studies. Using sophisticated monitoring technology to study constricts blood vessels in the extremities. In some “Every day we’re getting reports of species either becoming endangered or becoming extinct,” deep dives, Williams and her team have found humans, this “dive response” also produces irregular Williams touches a narwhal to which she has attached suggestive evidence that being startled—by human- heartbeats. monitoring equipment. The heart-rate monitor is along the Williams said. “We’ve got to try to get ahead of that extinction curve and figure out the information that’s produced sounds like marine sonar, for example— Given their underwater skills, marine mammals were curved line at upper right on the animal’s back, while fin- during a demanding dive that already taxes their speed and dive-depth monitors sit below the yellow float necessary to prevent these rapid declines.” expected to keep a steady heart rate during deep that enables the team to retrieve the device when it releases physiological limits could overstress deep-ocean dives. To test this assumption, Williams developed from the animal.

38 inquiry@UC Santa Cruz For further inquiry, go to inquiry.ucsc.edu 39 By Patricia Waldron

interested in the emerging field of geoengineering governance as an assistant professor of international A geoengineering glossary relations at American University in Washington, D.C. She quickly established her standing in the field and Bioenergy with carbon capture and was invited by her American University colleague storage (BECCS) A proposed technology Simon Nicholson, assistant professor and director of to achieve negative carbon emissions by the Global Environmental Politics Program, to join the generating energy using biomass and storing academic working group for his research and public the resulting carbon dioxide underground in policy initiative, the Forum for Climate Engineering geological formations. Assessment. The working group attempts to Carbon dioxide removal (CDR) A diverse bridge academic and policy conversations on group of technologies designed to remove geoengineering governance and will publish their carbon dioxide gas from the atmosphere. first comprehensive policy recommendations later Geoengineering’s this year. Intergovernmental Panel on Climate Change (IPCC) A scientific advisory Geoengineering attracted Jinnah for both its council formed under the U.N. that makes enormous potential and incredible risks. “It’s the assessments and publishes reports on climate most alive space I’ve ever worked in,” she said. “It’s change research. not just a banal academic topic. People who are engaged in this have strong and deep feelings about Paris Agreement A climate agreement under dilemma the U.N. Framework Convention on Climate what they’re doing and what it means for present and future generations.” In 2017 she received an Change where each country sets its own Andrew Carnegie Fellowship to further her work on goals for greenhouse gas emissions mitigation geoengineering governance. and adaptation by 2020. The agreement was What comes first, research or governance? adopted in Paris on December 12, 2015, and Climate control went into effect November 4, 2016. Solar radiation management (SRM) A type Geoengineering is not a new idea, but it is receiving of geoengineering that reflects sunlight back increased attention as the debate over what to do R Geoengineering may be the most controversial research creates a chicken-or-egg conundrum. into space to reduce global temperatures, about climate change intensifies. Its roots lie in technology that doesn’t yet exist. Also called Scientists need better governance to support potentially by injecting aerosols into the cloud-seeding operations from the 1950s designed climate engineering, it’s a group of proposed responsible geoengineering research, but efforts atmosphere or making clouds more reflective. to bring more rain to farmlands and military strategies with the potential to counteract climate to develop an international governance system attempts to flood the Ho Chi Minh Trail in Vietnam U.N. Educational, Scientific and Cultural change by altering climate on a global scale. Critics are stalled by resistance to the poorly defined in the 1960s. Nobel Prize–winning atmospheric Organization (UNESCO) A U.N. agency assert that geoengineering could cause tremendous technology. chemist Paul Crutzen brought the idea to the that encourages international cooperation to environmental harm and distract from established To break this stalemate, Sikina Jinnah, UC forefront in 2006 when he proposed a form of promote quality education, scientific advances, efforts to reduce greenhouse gas emissions. Santa Cruz associate professor of politics, geoengineering as an antidote to global warming. and the preservation of cultural heritage. However, as nations have struggled to reduce their thinks that governance and research need to In 2009, The Royal Society amplified that message U.N. Environment A U.N. program that emissions, geoengineering may be the only way ensue simultaneously. “We shouldn’t hold off by releasing a report on geoengineering aimed at advises developing countries on sound to meet the internationally agreed upon target of on initiating governance mechanisms until we policymakers. environmental practices and policy. keeping the global temperature rise well below 2° C. know if these technologies are viable or not,” she Geoengineering technologies roughly fall into two Perhaps because geoengineering does not yet exist said. “Governance and research need to inform U.N. Framework Convention on Climate camps: solar radiation management (SRM) and on any significant scale, there are no national laws each other—neither should evolve in a vacuum.” Change (UNFCCC) An international carbon dioxide removal (CDR). SRM approaches or international treaties restricting or enabling its Jinnah and colleagues are proposing an initial path environmental treaty adopted on May 9, would attempt to reflect more sunlight back into use. Any country could attempt a geoengineering forward using a polycentric approach that taps into 1992. The treaty was created with the space, in effect dimming the sun. One strategy, scheme with Earth-changing effects within its existing international institutions at multiple levels. goal of stabilizing atmospheric greenhouse called stratospheric aerosol injection, would own borders or the global commons, and there is Her research suggests that public discussion and gas concentrations at a level that prevents mimic the effects of a volcanic eruption by using no oversight to guide the necessary research into decisions on geoengineering can be guided in the dangerous anthropogenic changes to the an airplane or balloon to spray particles into the how—and, more importantly, if—nations should near-term using governance systems that already climate. stratosphere to block sunlight. A second strategy, use this technology. This lack of governance and exist, not necessarily the ones that ultimately may called marine cloud brightening, would seed the World Meteorological Organization (WMO) Above: When ships traverse the ocean, their exhaust causes be needed if large-scale geoengineering becomes A U.N. specialized agency that provides a reality. formation of brighter, more reflective clouds. The water vapor to condense into thin bright clouds called ship effect would be the same as the long strings of leadership and expertise regarding weather, tracks. These clouds reflect solar radiation away from Earth, Jinnah has spent almost two decades researching climate, and hydrology issues. leading some scientists to propose that creating more clouds called “ship tracks” that form from boat marine clouds would cool the global temperature. Credit: how international institutions respond to exhaust, but on a far larger scale. NASA (public domain). environmental problems. In 2014, she became

40 inquiry@UC Santa Cruz For further inquiry, go to inquiry.ucsc.edu 41 Geoengineering’s dilemma

Thus far, scientists have limited SRM research directly from the air and a system called bioenergy anything about geoengineering,” said Edward primarily to theoretical modeling. While most with carbon capture and storage (BECCS), where Parson, professor of environmental law at UC Los models predict that SRM could rapidly and cheaply power plants would burn biomass to generate Angeles. He noted that parties to the Convention on A geoengineering fish story lower global temperatures, some of those same energy and then pump the resulting carbon dioxide Biological Diversity have requested that participating Greater international governance of models predict that the technology would cause underground. These options are generally more countries not employ geoengineering until research geoengineering may help rein in rogue Carbon Dioxide Removal Carbonsignificant Dioxide changes Removal to global rainfall patterns that appealing to the public because they feel more has adequately considered its environmental, experiments, such as the ocean fertilization could affect agriculture. SRM could buy humanity contained than SRM. However, these strategies economic, and social impacts, but the decision scheme attempted by the Haida Salmon more time to reduce emissions, thus avoiding would have to be greatly scaled up and widely is nonbinding. And the IPCC is simply a scientific Restoration Corporation in 2012. The group the worst effects of climate change, but it does adopted to have a global impact, an effort likely to assessment body and the U.N. Framework dumped about 120 tons of iron dust into Socialnothing sciences to address and governance greenhouse gas emissionsnical feasibility. or An exceptioncarry is a ocean hefty iron price fertilisa tag.- Convention on Climate Change (UNFCCC), the the Pacific Ocean off the coast of British Socio-economic research has largely focused on two tion, which has received attention due to 13 scientific ocean acidification. Also, if SRM begins without international environmental treaty, whose 2015 Columbia in the hope that adding this nutrient approaches: bioenergy with carbon capture and stor- field experiments conductedThough in the most1990s and of 2000s,these technologies remain closer ageconcurrent and, to a more aggressive limited extent, reductions afforestation toand atmosphericas well as high-profile tocampaigning science andfiction attempted than applied science, CDR has annual meeting produced the Paris Agreement, to iron-deficient waters would trigger a reforestation.carbon dioxide, This has been any supplemented interruption by solicita could- causedemonstrations global in oceanrecently waters by private assumed companies a more prominent position in does not address geoengineering. If it did, it would phytoplankton bloom that would revive the tiontemperatures of views from public to jumpand expert up groups. to what they hopingwould to haveuse ocean iron fertilisation towards earning not have the administrative capacity to regulate local salmon population. To undertake the carbon credits. Besides this,the most climate other social change science governance discussion. In been without the intervention, which could have the U.N.’s Intergovernmental Panel on Climate it, said Parson. “What it would take to effectively project, American entrepreneur Russ George Researchersbrutal impacts. highlight the need for further investiga- research has been conducted in the form of case stud- govern geoengineering at the international level is partnered with the Haida tribe, a First Nations tions into land-use constraints and other repercus- ies that explore more generalChange issues (IPCC)in relation Fifth to the Assessment Report from sionsIn the for crop second production, camp food ofpricing, geoengineering, and land man- development CDR of controversial2014, technologiesa majority rather of presented scenarios depend very much an open question.” society on Canada’s Queen Charlotte Islands agementcomprises and ownership. a range Otherof technologies open questions that than remove contemplating and theon concrete BECCS application to reach of car -negative carbon emissions by One emerging international governance that historically has depended on salmon for concern the possibility that the promise of carbon bon dioxide removal technologies. mechanism is a code of conduct put forth by its livelihood. The tribe invested $2.5 million dioxidesequester removal couldcarbon delay dioxideor impede immediatefrom the and atmosphere. mid-century and to keep the global temperature CDR includes large-scale tree planting and increase below 2° C. The 2015 Paris Agreement, Anna-Maria Hubert, assistant professor of law dollars in the corporation, which in turn, had comprehensive mitigation efforts by reducing incen- Future research fields planned to sell carbon offset credits on the tivesbiochar—the to switch to renewable burial energy of charred sources. organic wasteFurther explorationfor of whichthe environmental provides and a ecoframework- for individual countries at the University of Calgary. The code provides long-term carbon storage—as well as thenomic more implications of deploymentto set their is likely own to draw goals on to reduce carbon emissions, guidance for responsible geoengineering research international market for the carbon dioxide that Researchextreme in the idea social ofsciences fertilizing on direct the air capture ocean or withearth iron systems so models, impactsdoes andnot integrated mention assess geoengineering- but also has with the objectives of minimizing environmental the phytoplankton consumed. The dumping marine-based approaches like enhanced weathering is ment models, and calculations of investment and that phytoplankton blooms soak up atmospheric called for a net negative carbon economy after harm, enhancing legitimacy, and creating a better ignored the 1972 London Convention and almost non-existent, with assessments generally lim- infrastructural needs. This will need to be comple- London Protocol on preventing marine pollution itedcarbon to calculations dioxide of costs, (see energy sidebar). demand, Companiesand tech- mented are byalso critical assessments2050, ofa goalthe assumptions that some argue may be impossible understanding of the technologies’ efficacy and developing machines that suck carbon dioxide to reach without CDR technologies. “Suddenly risks. Hubert’s code is an important contribution, and the Convention on Biological Diversity’s voluntary moratorium on ocean fertilization. somethingFigure 1: Climate that engin- wasn’t really but further governance mechanisms are also eering measures can The corporation released the data from the partbe divided of the into twointernational needed, Jinnah said. CLIMATE ENGINEERING MEASURES UNDER DISCUSSION climategroups: those change intended conversation experiment and claims that a subsequent to remove atmospheric In addition to the absence of governance, there phytoplankton bloom created bigger salmon iscarbon very dioxide much and a part of the is the problem of “moral hazard,” the concern mixthose becauseintended to alterthese models, hauls the following year. Independent 3 the Earth’s solar radia- that pursuing these technologies could divert scientists, however, say it is unclear what whichtion balance. the world depends institutional resources needed to reduce emissions. on© IASS for its policy decisions, impact the fertilization had on the salmon 5 “Even thinking about geoengineering, let alone population, and whether the bloom resulted in have started to incorporate deploying it, could have adverse effects on 4 them,” said Nicholson. In any long-term carbon storage. 2 mitigation efforts, because it creates this idea of a addition, if its withdrawal 6 technological fix that maybe provides a get-out-of- from the Paris Agreement jail free card for fossil fuel companies,” said Rob means that the U.S. fails to 7 Bellamy, a University of Oxford research fellow Outlook cloudy 8 deliver on its greenhouse gas 1 with a particular interest in how public participation reduction commitments, this affects issues related to climate change, including Two impending SRM field experiments highlight the could increase demand for need for greater governance. Neither experiment 9 geoengineering governance. geoengineering solutions. will have any impact on the climate, but some fear Several major environmental nongovernmental that outdoor experiments could initiate a slippery No rules organizations (NGOs) have taken a precautionary slope toward reliance on such technological fixes to 1 2 3 4 5 stance against geoengineering, due to the moral Marine cloud Cirrus cloud thinning Reflective aerosol Ocean fertilisation Enhanced weathering address climate change, said Jinnah. brightening particles Despite emerging awareness hazard and environmental concerns, said Jinnah. of geoengineering’s SCoPEx, which stands for Stratospheric Controlled 6 7 8 9 This view has kept NGOs from having a meaningful Large-scale Biochar Bioenergy with carbon capture Direct chemical capture potentially pivotal role, how voice in the geoengineering discussion. Through the Perturbation Experiment, involves sending a production and storage and storage of CO2 and if it should be applied are Forum for Climate Engineering Assessment, Jinnah, balloon more than 12 miles into the atmosphere questions that remain largely Nicholson, and others are trying to change that. to spray two pounds of ice or limestone dust. In Altering the Earth's radiation balance Removing carbon dioxide (CO2) from the atmosphere unaddressed. “There are no “We’re working to help NGOs and policymakers a later stage, a small amount of sulfur-containing existing laws or institutions understand the existing information so we can have aerosols may be released. Harvard University Researchers have proposed multiple geoengineering strategies to counteract rising researchers Frank Keutsch, professor of chemistry temperatures, which vary greatly in popularity, feasibility, and environmental risk. at the international level to a real and meaningful conversation,” said Nicholson. 3_Credit: IASS Fact © IASS,Sheet 1/2017Fact Sheet 1, 2017, reprinted with permission. regulate or control or do and chemical biology, and David Keith, professor of

42 inquiry@UC Santa Cruz For further inquiry, go to inquiry.ucsc.edu 43 Geoengineering’s dilemma

applied physics, lead the Harvard-funded project, at a scale that could impact global warming. This A key part of this which aims to show how the aerosols move and relatively low price tag means that a single country approach is to increase interact with gases in the atmosphere. The results or even a billionaire with a balloon could initiate the transparency of will inform future models of the potential risks and SRM with worldwide consequences. “SRM would SRM research. “I effectiveness of large-scale spraying. have trans-boundary impacts,” said Jinnah. “It has advocate strongly “In the grander scheme of things, this is a to involve cooperation between different countries for some sort relatively benign project in terms of environmental because it’s not going to be contained within the of transparency impact,” said Jinnah. “That said, a lot of people boundaries of a single country.” mechanism so that are up in arms about it because some think of it as In an ideal world, representatives from each country people who are opening the door to more invasive types of field would gather to negotiate a treaty regarding SRM interested in being experimentation.” and other geoengineering approaches. However, it’s engaged in these unrealistic to think that this will happen in the near- discussions have Equally benign is the Marine Cloud Brightening a pathway through Project, proposed by Thomas Ackerman, professor term, said Jinnah. “There’s no political appetite for it right now.” which to understand of atmospheric sciences at the University of what’s happening,” Washington in Seattle. Ackerman’s group wants to A last resort said Jinnah. Both spray saltwater droplets to seed cloud formation over Keith and Ackerman a small area of Monterey Bay, just down the road from In lieu of a new, international, top-down agreement, maintain highly UCSC at Moss Landing. The experiment would show Jinnah, Nicholson, and colleague Alexander Gillespie, informative websites the size and quantity of aerosols needed to form professor of international law at the University of on their proposed SRM brighter clouds, but has not yet received funding. Waikato in New Zealand, propose three concrete experiments, In the SCoPEx experiment, Harvard researchers propose to launch a balloon into the stratosphere. They plan Experts estimate that viable SRM technologies policy recommendations as part of a polycentric but an international approach to governing SRM, in which multiple to release environmentally insignificant amounts of aerosols to understand how these particles behave in could be ready in about 20 years at a cost of $1 clearinghouse might the atmosphere and to inform future solar geoengineering research. Credit: © Dykema, et al., Philosophical billion to $10 billion U.S. dollars annually to deploy existing institutions can take on different roles to better inform policy Transactions of the Royal Society A 2014;372:20140059. Creative Commons 4.0. govern geoengineering technologies. decisions, create funding opportunities, more comprehensive studies. Such engagement and help researchers coordinate their activities. efforts have been conducted by researchers in the Jinnah and her colleagues suggest that the United Kingdom, Germany, and the U.S., but it will World Meteorological Organization (WMO) could be important to engage stakeholders worldwide. develop such a clearinghouse, as it not only has Finally, Jinnah and colleagues recommend that SRM a mandate as an agency of the U.N., but already assessment be included in the next “global stocktake” facilitates worldwide weather monitoring and the under the Paris Agreement, due out in 2023. sharing of information, expertise, and resources Scheduled every five years (beginning with an initial for weather, climate, and hydrology research. exercise in 2018), the global stocktake reviews global Alternatively, the U.N. Educational, Scientific and progress toward climate change goals. As an existing Cultural Organization (UNESCO) could fill this niche. vehicle, it could lend transparency to country-level UNESCO helps researchers coordinate their efforts activities regarding geoengineering research. and advises countries on science policy, especially with regard to emerging technologies. Its Global While these recommendations do not constitute a Ethics Observatory, a database of researchers, comprehensive governance plan for geoengineering, institutions, codes of conduct, and resources related they represent a good start to cracking the chicken- to scientific ethics, could be expanded to include or-egg dilemma. With at least a rudimentary SRM research. governance framework in place, important research can be encouraged to help inform decisions about The second recommendation from Jinnah and her geoengineering’s possible role in managing climate colleagues would establish a global forum that change. Mid-century, when the IPCC estimates that unites policymakers, NGOs, and other stakeholders. humans must soak up as much carbon dioxide as This forum, which could be organized through U.N. they emit to stay below a 2° C increase, is just three Environment, would help advise governments and decades away. Stratospheric aerosol injection has a good chance of guide public engagement on SRM. The role of lowering global temperatures because it mimics a volcanic U.N. Environment is to coordinate environmental “The possibility of this being a last ditch resort for eruption. The 1991 eruption of Mt. Pinatubo launched about solving climate change if we find ourselves in a 15 million tons of sulfur dioxide into the stratosphere, which An artist’s conception of a ship designed by Stephen Salter, activities and sustainability efforts through the dropped the global temperatures by half a degree Celsius emeritus professor of engineering design at the University U.N. system. The program also has experience in terrible situation is a big part of why I’m engaged,” for 18 months. Credit: Richard P. Hoblitt, USGS (public of Edinburgh, to spray saltwater into the air for marine cloud advancing public engagement, which could help said Jinnah. “There’s so much at stake.” domain). brightening. Credit: © John MacNeill, with permission. legitimize research, leading to greater funding and

44 inquiry@UC Santa Cruz For further inquiry, go to inquiry.ucsc.edu 45 PEN&INQ By Emma Hiolski INQUIRINGMINDS

Sukee Bennett (’17)* Ula Chrobak (’17) David Egerter, Editor (’88) Emma Hiolski (’17)

Adam Mann (’10) Sarah McQuate (’17) Katharine Miller (’01) Emotional Hitting the Between Dream Plant Chris Palmer (’13)3 Gaming Beach World Wars Theory Sexuality

Although video Gary Griggs, UC Santa During the 1930s, “Our minds are Long after sexual Robert Pollie (’82) games have now Cruz distinguished globalization was restless,” said reproduction in beguiled players for professor of Earth on the decline: G. William Domhoff, animals became Barbra A. Rodriquez (’97) 40 years, we don’t sciences, has spent countries cut ties UC Santa Cruz scientific canon, Patricia Waldron (’14) have nuanced cultural a lifetime observing with one another, the distinguished plant reproduction conversations about coasts. That’s where it Great Depression professor emeritus remained a mystery. Cameron Walker (’02) them, said Katherine all comes together, he was devastating of sociology and It wasn’t until the end Isbister, UC Santa said. “Over the years, the United States, psychology. During of the 17th century Cruz professor I’ve worked on water and fascism was waking hours, this is that the idea of Amy West (’12) of computational pollution and dabbled on the rise around obvious: Our thoughts pollination and plant media. According to in desalination, sand, the world. At least flit between current sex arose. Sarah C. P. Williams (’07) Isbister, the language dams, offshore oil, that’s the perspective tasks to future errands This discovery was Marcus Woo (’07) to support rich and nuclear power.” that history books or past problems. “hotly debated” until discussions—like typically offer, said As it turns out, our Sascha Zubryd (’11) In his ninth book, the middle of the 19th those we have about Marc Matera, UC minds do something Coasts in Crisis: century, said Lincoln books or movies— Santa Cruz associate similar when we A Global Challenge, Taiz, UC Santa Cruz hardly exists. professor of history. sleep. *Names are listed left to right. Griggs explores professor emeritus In How Games Move growing human Matera and coauthor In The Emergence of molecular, cell, Us: Emotion by impacts on coastal Susan Kingsley Kent of Dreaming: Mind- and developmental Design, Isbister aims environments. Written shed a different light Wandering, Embodied biology. The primary With the expertise of scientists-turned-journalists, At a time when the credibility of science and the to give readers a clear to accompany his on the decade in The Simulation, and the objection, he said, understanding of undergraduate course Global 1930s: The Default Network, stemmed from the the 16 graduates of the UC Santa Cruz Science news media remains under scrutiny, the SciCom how design choices of the same name, the International Decade. Domhoff explores strong association Communication Program shown above created program and its mission to “strive to use accurate influence the way book also discusses They synthesize nearly 15 years of new between plants and these stories about research that span the and engaging science journalism to improve players feel—and the increasing interdisciplinary research on dreams the female gender. a way to talk about dangers coastal readings from global and dreaming. He Flowers and plants, university’s five divisions: Arts, Humanities, society,” is more important than ever, said Check what’s happening and hazards pose to scholars to share concludes that like women, were Physical & Biological Sciences, Social Sciences, and Hayden, an international investigative reporter why. swelling populations voices typically dreaming is an supposed to be chaste Engineering. As their reporting well documents, and social media expert. “Through our students, worldwide. Griggs excluded from history intensified version of and pure. Eschewing violent makes sure to include books—those of mind-wandering. while the academicians at UCSC may keep offices, alumni, and instructors, we have a huge role to play games, she instead Taiz and his spouse, a positive note—like women, minorities, laboratories, and studios on the redwood tree– in promoting well-informed dialogue on science.” analyzes video Dreaming and mind- Lee Taiz—a former the great strides made and colonized peoples. games designed to wandering activate UCSC research studded campus, the breadth and depth of their in wind and solar Despite concerns about the current media climate, build empathy. Such Through this new specific, closely biologist—spent energy technology— work—and its impact—reaches around the world. games can provide lens, they illustrate overlapping regions 20 years traveling with the sensationalism and click-ability of “fake at the end of every a space for people pervasive global of the brain. When we and unraveling this This sizable impact also applies to the “SciCom” news” threatening to overshadow real news, Check chapter. “We always to experience real connections between dream, brain regions story. The result is have to have hope,” graduate certificate program (scicom.ucsc.edu). Hayden is optimistic about the sway of UCSC’s emotional responses these marginalized linked to imagination Flora Unveiled: The he said. to both the choices groups during the are activated and Discovery and Denial Begun in 1981, the program has 300-plus graduates science-savvy SciCom media specialists: “Doing they make and Griggs is also co- 1930s. They also our sleeping minds of Sex in Plants. who work regionally, nationally, and internationally. our jobs as communicators means telling stories the subsequent author, with Kim demonstrate that “escape from time,” “It is a fascinating They communicate on science and related issues in that resonate with readers, listeners, and viewers in consequences. The Steinhardt, of The these connections Domhoff said. And, topic,” said Lee “emotional texture” Edge: The Pressured formed a foundation while some suggest newspapers, radio, television, online media, peer- ways that make true news far more compelling.” Taiz, “and it says so of these games can Past and Precarious for later global that dreaming is reviewed journals, magazines, and university public much about cultural We hope you find compelling reading in this closely match that of Future of California’s movements promoting an evolutionary development and the relations. Required to have scientific training and life, said Isbister. Coast, in which decolonization and adaptation, he argues edition of inquiry@UC Santa Cruz. way that culture either they share tales of— civil rights. “If we that imagination is the experience, SciCom students spend a year on “It’s worthwhile to enhances or stands in and their personal look at things from true adaptation. “We campus honing their storytelling skills in journalism develop literacy about the way of scientific connections to— a different angle,” just happen to dream games,” she said, fact.” training and internships now overseen by the California’s coastal said Matera, “we can as a byproduct of “because they really history. see that the global that,” he said. program’s third director, Erika Check Hayden. are the medium of the connections were as 21st century.” important as ever.” Learn more: news.ucsc.edu

46 inquiry@UC Santa Cruz For further inquiry, go to inquiry.ucsc.edu 47 where startup breakthroughs sandbox happen CREDIT: EUGENE ZELENKO EUGENE CREDIT:

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48 inquiry@UC Santa Cruz For further inquiry, go to inquiry.ucsc.edu PB