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Visualizing the Infinitesimal

September 29, 2022

Visualizing the Infinitesimal

Even before Andreas Vesalius (1514-1564) first put pen to paper to draw the human form in anatomical detail, scientists have illustrated their findings, not only to share information but to find greater footing on the terrain we call biology: the science of life.

These models have taken on new urgency with the advent of cell biology, where subjects are even smaller than cells. “This is an invisible space,” Janet Iwasa, molecular visualization expert and Assistant Professor of Biochemistry at the U, reminds us. “Most molecules are smaller than the wavelength of light. These things are moving at a time scale that is not intuitive. When the study objects are so foreign, you have to rely on creative approaches to describe them.”

For Iwasa, those approaches involve scientifically accurate digital animations which have cracked open an entirely new way of viewing diverse molecular and cellular processes. Information-rich and visually compelling visualizations that capture current understanding is what this classically-trained biologist has made a name for herself with.

Vol 324, Issue 5935

The need for reconsideration of the visual language that renders the invisible became urgent after a 2009 publication in Science of a much-cited article. The seminal paper posited that cellular structures called P granules are liquid droplets, and that they specify the future germline in a developing embryo through controlled dissolution and condensation.  This paper ignited one of the hottest ‘trends’ in cell biology – the study of biological liquid condensates – and earned the lead authors numerous prizes, including, most recently, the prestigious Breakthrough Prize.

For Ofer Rog, Assistant Professor and Mario Capecchi Chair in the School of Biological Sciences, this revelation completely revised the interpretation of his experiments, but also brought with it “whole sets of biological issues.” The existence of crowding in the cell was one of them. No longer could he try to reduce the behavior of the chromosomes he was studying to properties of single molecules that make them up. “Rather,” says Rog, “we had to understand them as collective or ‘emergent’ behavior.”

With this new understanding, Rog felt “stuck” in his teaching and research with an old graphical language which “was really great for depicting things that are best understood as single objects, but not so great to describe how big clusters work together, to describe how molecules interact with each other much more loosely and much more dynamically.” The recognition of the flexibility and dynamics of cellular components led to the impulse to better honor that complexity graphically.

“I started looking at papers, and how uniform they were,” Rog says. “Papers that were clearly written with a lot of careful attention to details, with exquisite experiments and data, were using graphical models that were very simplistic, inadequate to really capture . . . our new understandings about biology. I started wondering, ‘How did people solve this in the past? Who should we talk to?’ It wasn’t super clear. So I went and talked to Janet.”

Powerful Renderings
They say the most dangerous thing one can do is to introduce one person to another. It’s a tongue-in-cheek caution, reminding us how conversations, then collaborations, then innovations start. So it was with Iwasa’s animation expertise which, as part of her Animation Lab at the University of Utah, has already animated many subjects, including the life-cycles of HIV and SARS-CoV-2. Now the lab is pairing its expertise with Rog’s condensate research.

“We have a lot of people, like Ofer,” says Iwasa, “who are educators and who have been using our animations for their courses. Condensate research is so new, compared to other big concepts in biology, that a lot of textbooks don’t even cover it. So, having some visual materials for educators who need an intuitive way to introduce these ideas to students was something we were thinking about.” Iwasa’s team had already interviewed undergraduate instructors to find out how they were teaching about condensates and what kinds of challenges they were facing.

And how were professors like Rog teaching about this new paradigm? Not easily, it turns out. The terrain was daunting. Intrigued, the Animation Lab began collaborating with Rog and other cell biologists to better illustrate condensates. “This new paradigm,” writes Rog and Iwasa of their collaboration, challenges “the 20th century textbook view of cellular compartmentalization.” Condensates, she says, seem to play important roles in cells’ normal functioning and in disease, and, naturally, these concepts are now making their way into undergraduate classrooms.”

Metaphors can be dangerous
Introducing two people is not the only dangerous thing to happen out there. There are implications of and uses for blending digital animation with biology and other sciences: representations–visual or verbal–are essential tools but at the same time impose biases. Because of simplification, “metaphors can be dangerous,” Iwasa concedes. “[P]eople don’t know how far they can carry them on a molecular level.”

The “language” of graphic representations, according to Rog, have tended to focus on single atomized cell components, and also incorporated implicit assumptions taken from our daily lives.

Iwasa agrees. Imagining the molecular space is “unintuitive, since it is unlike the air- and gravity-filled world we live in. What does a molecule experience being inside the cell? It’s just very different and hard to conceive. Some metaphors can be misleading. For example, there are proteins in the cell that move using a walking-like motion. Says Rog, “We walk in air, but when a molecule “walks,’ it’s the equivalent of us walking through Jell-O . . .”

“. . . Or walking in one of those children’s ball pits,” interjects Iwasa. “Except the balls are as big as you are, and you’re constantly bumping into everything, having to push things around.” The constant collisions, the extreme crowding: biologists know about these qualities, but because they don’t often depict that space, “it’s easy to forget and not to consider that, and that influences the types of experiments and the types of models we create.”

Illustrations did occasionally remind biologists of the crowded environment that occupies their objects of study. David Goodsell, a structural biologist and watercolor artist at the Scripps Research Institute in San Diego, is famous for his colorful illustrations of the interior of cells. These paintings are based on state-of-the-art knowledge of what is in the cell–what molecules exist in different sub-cellular compartments and what structures each of them adopts–but also capture the incredible complexity of the cell and, crucially, its crowdedness.

The new science of condensates relies on crowding for the ability of cellular structures to come together and fall apart. Rog, excitedly, returns to the human model and talks about “a thousand objects, like humans, in a crowded subway station, loosely associated” which, nevertheless, remain discrete individuals. How do those individuals behave separately? And how does that behavior change when they function as a collective?

New visual language and recent technological development promise to do a better job of depicting such complexity. Such representations continue to inform scientific discourse, as startling and revealing as 16th Century drawings brought to life through Vesalius’s magisterial bodies-in-motion.

The Workshop
Which leads us to the Re-Imagining a Cellular Space Occupied by Condensates symposium and workshop, borne out of the ready collaboration between Rog and Iwasa. While the Animation Lab’s initial foray into condensates was, in the beginning, educationally focused, that somewhat limited approach may now be at an inflection point.

“When Ofer and I talked,” says Iwasa, “we agreed that the research community had not yet reached any sort of consensus on how best to represent condensates. So our attempts to capture condensates by animation didn’t have a visual language to fall back on.”

Greater consensus may emerge at the symposium & workshop on October 11-13. Unlike the many traditional meetings dedicated to condensates, where scientists present and debate the minute details of their experiments, here scientists will interact with illustrators and other “tool builders,” to discuss the visual language of condensates.

While there is always a risk in illustration (including digital animation) of simplifying things too much and thus restricting future perceptions and scientific understanding, the symposium also pre-supposes that the conversation is essential. In short, the gathering promises to “daylight” how biologists represent a subcellular world in enabling as well as disabling ways, seeking “to build a community that will construct a visual language and new tools that will accurately capture the complexity of molecular condensates.” These representations will help generate experimentally-testable hypotheses, and will lead to the development of new techniques for scientific communication and teaching.

“One of the things that we realized,” says Rog, “is that challenges similar to the one we are facing now, in the condensate field, must have been figured out by other fields in the past, in biology and outside biology.” Symposium participants will include experts from diverse disciplines: about one-third of the participants are biologists, actively engaged in condensate research; one-third will be visualization and computation specialists—like watercolorist David Goodsell mentioned above—but also modeling experts, data visualization specialists, and molecular animators.

The final one-third will come from fields that are not commonly engaged with molecular biology but that have long been thinking about space and ways to represent it. This last group includes software and virtual reality developers and academics in architecture and history.

The symposium will take place at the Crocker Science Center at the University of Utah, on October 11, 2022, 9 AM to 5 PM, and is open to the public. It will be followed by a two-day workshop (by invitation only).

 

By David Pace. First published @ biology.utah.edu

 

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McMinn Chair

September 26, 2022

Trevor James McMinn Chair

Christopher Hacon

Christopher Hacon appointed to McMinn Chair in Mathematics

On July 1, 2022, University of Utah President Taylor Randall appointed Distinguished Professor Christopher Hacon as the Trevor James McMinn Professor in the Department of Mathematics. Hacon held the inaugural McMinn Chair for five years—that term ended last June.

According to the terms of the appointment, this is a five-year appointment. Only one faculty member in the department may hold the appointment of the McMinn Chair at a time—in exceptional cases, the current Professorship holder may be considered for reappointment after a review has been conducted pursuant to the university’s policies and procedures for professorship holders.

Davar Khoshnevisan Chair of the Dept of Mathematics

“Distinguished Professor Hacon's work has been groundbreaking, and he is recognized internationally as a mathematical scientist of the highest caliber, whose work has motivated and impacted the next generation of brilliant algebraic geometers.”

 

Born in England and raised in Italy, Hacon arrived at the U as a postdoctoral scholar in 1998 and came back as a professor in 2002. He is particularly interested in objects that exist in more than three dimensions. He and his colleagues have applied studies of these objects to extend the “minimal model program”—a foundational principle of algebraic geometry—into higher dimensions. The American Mathematical Society has lauded their work as “a watershed in algebraic geometry.”

He has been honored with prestigious awards such as his 2019 Election to The Royal Society of London, the 2018 Breakthrough Prize in Mathematics, the 2016 EH Moore Research Article Prize, the 2015 Distinguished Scholarly and Creative Research Award from the University of Utah, the 2011 Antonio Feltrinelli Prize in Mathematics Mechanics and Applications, the 2009 Frank Nelson Cole Prize in Algebra and the 2007 Clay Research Award. He is a member of the American Academy of Arts and Sciences, a fellow of the American Mathematical Society, and a member of the National Academy of Sciences.

 

first published @ math.utah.edu

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Related Posts

NDSEG Fellowship

September 21, 2022

NDSEG Fellowship

Aria Ballance

 

National Defense Science and Engineering Graduate Fellowship.

Aria Ballance is a third-year graduate student who was selected for the 2022 National Defense Science and Engineering Graduate Fellowship. Sponsored by the Air Force Office of Scientific Research, the Army Reserve Office, and the Office of Naval Research, it is a highly competitive fellowship with over 3,000 applicants and only 50 awardees.

Aria’s research is focused on evaluating crescent shaped nanostructures as a tunable platform for vibrational circular dichroism (VCD). The proposal she wrote for NDSEG involved using the nanocrescents she fabricates to optimize the detection of chiral molecules. “Ultimately, the chiral detection will be used to identify the presence of life outside of our solar system.”

In fact, Aria credits Star Trek with her love of science and her decision to become a chemist. She credits her PI Dr. Jennifer Shumaker-Parry with supporting and guiding her through her graduate career. When not in the lab she loves to backpack, she paints in watercolors, she loves rock climbing, goes white water kayaking, and enjoys skiing and swing dancing.

 

first published @ chem.utah.edu

 

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Armentrout Interview

September 21, 2022

Peter B. Armentrout

Journal of the American Society for Mass Spectrometry

An Appreciation for, and an Interview with, Professor Peter B. Armentrout.

Peter B. Armentrout the Henry Eyring Presidential Endowed Chair of Chemistry at the University of Utah is the 2021 recipient of the John B. Fenn Award for Distinguished Contribution in Mass Spectrometry.

List of contributions from the following research groups: Ryan Julian, Scott McLuckey, Kit Bowen, R. Graham Cooks, Dave Clemmer, Air Force Research Laboratory, Mathias Schaefer, Joost Bakker, Diethard Bohme, Peter Armentrout, Konrad Koszinowski, Jana Roithová, Mary Rodgers, and Richard O’Hair.

It is a pleasure to introduce a special focus of the Journal of the American Society for Mass Spectrometry to celebrate the accomplishments of Prof. Peter B. Armentrout, Henry Eyring Presidential Endowed Chair of Chemistry, University of Utah, on the occasion of his receiving the 2021 ASMS John B. Fenn Award for a Distinguished Contribution in Mass Spectrometry. The award recognizes Peter’s development of (1) robust experimental and statistical techniques for the determination of accurate thermochemistry via the guided ion beam method, which has provided insights into the thermochemistry, kinetics, and dynamics of simple and complex chemical reactions, and (2) a suite of software programs for statistically modeling the energy dependence of product formation. As a consequence of these developments, nearly 2500 distinct bond energies have been measured during his career. These fundamental measurements have impact in many fields, including catalysis, biochemistry, surface chemistry, organometallic chemistry, and plasma chemistry.

This issue contains a total of 14 papers around the theme of “Thermodynamics, Kinetics and Mechanisms in Gas-Phase Ion Chemistry”. We thank all of the authors and reviewers for helping this issue come to fruition.

Although Peter’s achievements have been documented in other editorials (1−4) and he has written a short autobiography, (5) here we asked Peter some questions on issues that have intrigued us (note: this interview is a COVID19 “timecapsule” as it was carried out in mid-2021 during the height of lockdowns and travel bans):

Question 1: Many of us were inspired to pursue science by our high school teachers. In your autobiography, (5) you mentioned that you had excellent chemistry and physics teachers at Oakwood High School, Dayton, OH. Did they help ignite a spark, or were you already doing experiments at home before then?

PBA answer: You know I was never one to really do experiments at home. I had a home chemistry set (with lots of dangerous chemicals that people would be horrified to give to kids these days), but I mainly mixed them up to generate goo and never followed the recipes given. However, I was always interested in how things worked and knew I would be a scientist shortly after I gave up the prospect of being a professional pony express rider (in the fifth grade or so).

Question 2: I enjoyed reading about your early research with the late Rob Dunbar (Case Western Reserve University) and with Jack Beauchamp (Caltech). (5) Since then, you have had a wonderfully productive career. What is your favorite piece of work that you have been involved in?

PBA answer: It is not often you get a call out of nowhere asking if you can do an experiment, but Al Viggiano did just that several years back. Turns out the Metal Oxide Space Cloud (MOSC) group at the Air Force Research Laboratory was interested in samarium chemistry. They needed to know the bond energy of SmO+ with more precision and accuracy than was available in the literature. I told him we would try to measure this if they bought us the samarium sample, which turned out to cost $200. Apparently, Al went to the MOSC group and said I would do the research but it would cost 200. They hesitated until they learned he did not mean $200K. We successfully measured the SmO+ bond energy, (6) which enabled them to understand an ongoing atmospheric test. Subsequently, this has led to grants that enable us to continue studying the oxidation of lanthanides, including revisiting the Sm system. I’m not sure that many scientists would have thought that understanding simple gas-phase diatomic molecules better is still an important avenue for research.

Armentrout in the lab.

Question 3: What is the role of a mentor in science? Who mentored you and what has been your style of mentoring?

PBA answer: The enterprise of chemistry is a complex and detailed world, with lots of places where you can go astray. The role of a mentor is to alert a student of chemistry about some of the realities of getting things done and provide guidance. My mentors were Jack Beauchamp, Rob Dunbar, and John Fackler (inorganic chemist at Case and then Texas A&M). Like them, I tell my students that they work with me, not for me. I’m largely a hands-off mentor who provides advice and direction but willingly become hands-on when the situation needs it. I try to make sure my students not only learn to take good data and analyze it but also to present it clearly in both written and oral venues. My door (these days, my email box) is always open.

Question 4: What are the challenges for young scientists?

PBA answer: There are so many. I’m not sure the challenges have changed over the years, but I do think they have intensified. Funding, life–work balance, just dealing with students and people, they all need work to make happen. One could imagine that finding a new scientific niche that you can be the expert in has become harder because all the “easy” targets have already been taken. This belief neglects the fact that new techniques and new technologies provide new opportunities, but that does not make them any easier to identify. When I started out, I realized that if only I could understand and control things better, then I really ought to be able to measure thresholds of reactions and learn not only some thermochemistry but also something about the dynamics and mechanisms of reactions. I identified radio frequency (rf) manipulations as a means to improve the technology considerably and that led to the very first guided ion beam tandem mass spectrometer that my group built at UC Berkeley. In subsequent years, we have also thought hard about how to interpret the kinetic energy dependence of reactions that has enabled us to make a lot of progress along those lines over the years, but there is a lot we still do not know or understand as well as we might.

Question 5: What is the future of peer-review publishing? How are you personally coping with the ever-increasing number of scientific articles?

PBA answer: Honestly, I’m not sure I am successfully coping at all. The only saving grace is that you can almost instantaneously search the literature for relevant articles through the Internet. I still remember having to go to the library and search Chemical Abstracts in order to search the literature. An Internet search does not always find every relevant article, but it always finds more than you really want.

Question 6: 2020 was a rather strange and challenging year. This is reflected in the fact that the Oxford English Dictionary was not able to decide on a single “word of the year”. What is your “word of the year” to describe 2020 and why?

PBA answer: Interesting question. My short answer also involves multiple words: pandemic, virtual, remote. If I had to pick one, it would be remote. The last year has kept us apart in ways we never conceived of and yet brought us together (often using technology) in ways that have expanded the way we will go forward. It is been an interesting process but one that will hopefully provide benefits in the future.

Question 7: Mary Rodgers’ recounting anticipating brutal questions from the holy trinity of gas-phase ion chemists (Jack Beauchamp, Mike Bowers, and Peter Armentrout) at the 1993 Lake Arrowhead Conference resonated with me. (2) I too was warned that you guys had exquisite “BS” detectors. Thus, it was with trepidation that when John Bowie fell ill I presented his talk at the eighth Asilomar Conference on Mass Spectrometry in 1990. (7) That was the first time that I met you, Jack, and Mike and other leading gas-phase ion chemists. I learned a lot but was also impressed by the spirit of the questions, which were aimed at getting the most out of the science. I also felt that this community was welcoming and that there was a sense of fun. Given that COVID19 has curtailed travel and many conferences have been canceled or rescheduled, what are your thoughts about the future of conferences? Are face-to-face conferences still important?

PBA answer: The triumvirate did indeed have a well-deserved reputation, but you are spot on with regard to the intent of those questions. I’ve been to a few virtual conferences in the past year. They accomplish a fair bit of what is needed to communicate science to your peers. They reduce our carbon footprint and can enable many more people to attend than might otherwise be able to afford it. However, the personal interactions, the bump-into-you-in-the-hall moments, the scribbles on a napkin, are missing from virtual conferences. The ability to share a drink and dine with friends and speculate together provides real opportunities to advance science. The time away from your routine at home can be mind expanding. Face-to-face conferences remain relevant and needed.

Question 8: If you had a time machine, which scientist(s) from history would you like to meet? What would you ask them?

PBA answer: Leonardo da Vinci. I’ve always thought he was the epitome of the Renaissance man, doing both art and science that was well ahead of its time. In that regard, I think most people do not appreciate how much art and inspiration there is in doing good science. I would ask him where he derived his inspiration and why he ever thought man could fly.

Question 9: Much of your work focuses on thermodynamics, with the 2013 tribute (4) mentioning over 2000 distinct bond energies measured. What is the motivation for your intense interest, perhaps even obsession, with this aspect of chemistry?

PBA answer: I have always valued the quantitative aspects of chemistry. I can recall early in my graduate career an interaction with the late Ben Freiser, then also a graduate student with Jack Beauchamp, where he took one of the pieces of thermochemistry I had recently measured and proceeded to break it down a number of different ways. Thermodynamics has an eternal quality to it: a good measurement will be valuable to many future generations. Thermodynamics is predictive; it can definitively tell you whether a reaction is possible or not. A recent example is a study that generated a fair bit of interest because it claimed to observe catalytic conversion of methane to ethene on gold dimer cations at temperatures as low as 200 K. The problem is that this reaction is endothermic by over 200 kJ/mol, which means it is impossible to catalyze at thermal energies. Collaborators and I investigated a number of alternative explanations for the observations. (8)

 

First published at ASMS.org

 

This article references 8 other publications.

  1. 1

    Bierbaum, V. M. Focus on ion thermochemistry in honor of Peter B. Armentrout, recipient of the 2001 Biemann Medal. J. Am. Soc. Mass Spectrom. 2002, 13 (5), 417– 418,  DOI: 10.1016/S1044-0305(02)00377-X

    [ACS Full Text ACS Full Text], [CAS], Google Scholaropen URL
  2. 2

    Rodgers, M. T.; Clemmer, D. E. An appreciation. Int. J. Mass Spectrom. 2012, 330–332, 2– 3,  DOI: 10.1016/j.ijms.2012.11.003

    [Crossref], [CAS], Google Scholaropen URL
  3. 3

    Rodgers, M. T.; Clemmer, D. E. A Celebration of the Scientific and Personal Contributions of Peter B. Armentrout, Int. J. Mass Spectrom. 2012, 330–332, 4– 5,  DOI: 10.1016/j.ijms.2012.11.004

    [Crossref], Google Scholaropen URL
  4. 4

    Ervin, K. M.; Rodgers, M. T. 2140 Bond Energies and Counting: A Tribute to Peter B. Armentrout. J. Phys. Chem. A 2013, 117 (6), 967– 969,  DOI: 10.1021/jp401080r

    [ACS Full Text ACS Full Text], [CAS], Google Scholaropen URL
  5. 5

    Armentrout, P. B. The Ties That Bind: An Autobiographical Sketch of Peter B. Armentrout. J. Phys. Chem. A 2013, 117 (6), 970– 973,  DOI: 10.1021/jp400039t

    [ACS Full Text ACS Full Text], [CAS], Google Scholaropen URL
  6. 6

    Cox, R. M.; Kim, J.; Armentrout, P. B.; Bartlett, J.; VanGundy, R. A.; Heaven, M. C.; Ard, S. G.; Melko, J. J.; Shuman, N. S.; Viggiano, A. A. Evaluation of the exothermicity of the chemi-ionization reaction Sm + O– → SmO+ + e–. J. Chem. Phys. 2015, 142, 134307,  DOI: 10.1063/1.4916396

    [Crossref], [PubMed], [CAS], Google Scholaropen URL
  7. 7

    Bierbaum, V. M. 8th Asilomar Conference on Mass Spectrometry. Rapid Commun. Mass Spectrom. 1991, 5, 144– 144,  DOI: 10.1002/rcm.1290050313

    [Crossref], Google Scholaropen URL
  8. 8

    Shuman, N. S.; Ard, S. G.; Sweeny, B. C.; Pan, H.; Viggiano, A. A.; Keyes, N. R.; Guo, H.; Owen, C. J.; Armentrout, P. B. Au2+ cannot catalyze conversion of methane to ethene at low temperature. Catal. Sci. Technol. 2019, 9, 2767– 2780,  DOI: 10.1039/C9CY00523D

    [Crossref], [CAS], Google Scholaropen URL

 

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STAR-X Proposal

September 20, 2022

STAR-X Proposal

Daniel Wik

Astrophysicist Dan Wik proposal selected by NASA

NASA has selected four mission proposals submitted to the agency’s Explorers Program for further study. U astrophysicist Dan Wik is a member of the STAR-X Proposal Team, one of the two Astrophysics Medium Explorer missions selected by NASA for further study. The proposals include missions that would study exploding stars, distant clusters of galaxies, and nearby galaxies and stars.

Adapted from a news release by NASA

Two Astrophysics Medium Explorer missions and two Explorer Missions of Opportunity have been selected to conduct mission concept studies. After detailed evaluation of those studies, NASA plans to select one Mission of Opportunity and one Medium Explorer in 2024 to proceed with implementation. The selected missions will be targeted for launch in 2027 and 2028, respectively.

Daniel Wik, assistant professor in the Department of Physics & Astronomy at the University of Utah, is a member of the STAR-X Proposal Team, one of the two Astrophysics Medium Explorer missions selected by NASA for further study. For more information about Wik and the STAR-X team, visit: http://star-x.xraydeep.org/.

“The fact that STAR-X has passed this competitive milestone is a testament to the hard work and vision of both the hardware and science teams, and it has been enormous fun for me to contribute to this effort and collaborate with such a talented and convivial group of scientists. I hope this collaboration will continue for years,” said Wik.

Daniel Wik

Wik is an X-ray astronomer, who primarily works with observations conducted by the NuSTAR mission, along with data from other X-ray observatories, such as XMM-Newton, Chandra, and the soon-to-launch XRISM, studying galaxies and galaxy clusters. Before joining the U in 2017, he was a research scientist at the NASA Goddard Space Flight Center outside of Washington, D.C.

“NASA’s Explorers Program has a proud tradition of supporting innovative approaches to exceptional science, and these selections hold that same promise,” said Thomas Zurbuchen, associate administrator for NASA’s Science Mission Directorate at NASA Headquarters in Washington. “From studying the evolution of galaxies to explosive, high-energy events, these proposals are inspiring in their scope and creativity to explore the unknown in our universe.”

NASA Explorer missions conduct focused scientific investigations and develop instruments that fill scientific gaps between the agency’s larger space science missions. The proposals were competitively selected based on potential science value and feasibility of development plans.

The two Medium Explorer teams selected at this stage will each receive $3 million to conduct a nine-month mission concept study. Astrophysics Medium Explorer mission costs are capped at $300 million each, excluding the launch vehicle. The selected proposals are:

UltraViolet EXplorer (UVEX)

  • UVEX would conduct a deep survey of the whole sky in two bands of ultraviolet light, to provide new insights into galaxy evolution and the lifecycle of stars. The spacecraft would have the ability to repoint rapidly to capture ultraviolet light from the explosion that follows a burst of gravitational waves caused by merging neutron stars. UVEX would carry an ultraviolet spectrograph for detailed study of massive stars and stellar explosions.
  • Principal investigator: Fiona Harrison at Caltech in Pasadena, California

Survey and Time-domain Astrophysical Research Explorer (STAR-X)

  • The STAR-X spacecraft would be able to turn rapidly to point a sensitive wide-field X-ray telescope and an ultraviolet telescope at transient cosmic sources, such as supernova explosions and active galaxies. Deep X-ray surveys would map hot gas trapped in distant clusters of galaxies; combined with infrared observations from NASA’s upcoming Roman Space Telescope, these observations would trace how massive clusters of galaxies built up over cosmic history.
  • Principal investigator: William Zhang at NASA’s Goddard Space Flight Center in Greenbelt, Maryland

The two Mission of Opportunity teams selected at this stage will each receive $750,000 to conduct a nine-month implementation concept study. NASA Mission of Opportunity costs are capped at $80 million each. The selected proposals are:

Moon Burst Energetics All-sky Monitor (MoonBEAM)

  • In its orbit between Earth and the Moon, MoonBEAM would see almost the whole sky at any time, watching for bursts of gamma rays from distant cosmic explosions and rapidly alerting other telescopes to study the source. MoonBEAM would see gamma rays earlier or later than telescopes on Earth or in low orbit, and astronomers could use that time difference to pinpoint the gamma-ray source in the sky.
  • Principal investigator: Chiumun Michelle Hui at NASA’s Marshall Space Flight Center in Huntsville, Alabama

A LargE Area burst Polarimeter (LEAP)

  • Mounted on the International Space Station, LEAP would study gamma-ray bursts from the energetic jets launched during the formation of a black hole after the explosive death of a massive star, or in the merger of compact objects. The high-energy gamma-ray radiation can be polarized, or vibrate in a particular direction, which can distinguish between competing theories for the nature of the jets.
  • Principal investigator: Mark McConnell at the University of New Hampshire in Durham

The Explorers Program is the oldest continuous NASA program. The program is designed to provide frequent, low-cost access to space using principal investigator-led space science investigations relevant to the Science Mission Directorate’s astrophysics and heliophysics programs.

Since the launch of Explorer 1 in 1958, which discovered the Earth’s radiation belts, the Explorers Program has launched more than 90 missions, including the Uhuru and Cosmic Background Explorer (COBE) missions that led to Nobel prizes for their investigators.

The program is managed by NASA Goddard for NASA’s Science Mission Directorate in Washington, which conducts a wide variety of research and scientific exploration programs for Earth studies, space weather, the solar system, and the universe.

For more information about the Explorers Program, visit: https://explorers.gsfc.nasa.gov.

first published @ physics.utah.edu

 

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Golden Goose 2022

September 20, 2022

Golden Goose Award

Baldomero "Toto" Olivera

A side hustle that transformed neuroscience.

As scientists working in the Philippines in the 1970s, biochemists Baldomero Olivera and Lourdes Cruz, professor emeritus of the University of the Philippines Diliman, found it tough to get hold of the right supplies for DNA research.

“We had to find something to do that didn’t require fancy equipment because we had none,” said Olivera, a distinguished professor at The University of Utah’s School of Biological Sciences, in a video produced for the Golden Goose awards.

Olivera and Cruz came up with what they hoped would be a fruitful side project. Cone snails are commonplace in the Philippines, and they had always fascinated Olivera, who had collected shells as a child. The pair decided to research the nature of the venom that the snails used to paralyze their tiny fish prey.

Cone Snail Shells

The team discovered the bioactive compounds in the venom were tiny proteins known as peptides. After moving to the US and teaming up with University of Utah grad students Dr. Michael McIntosh and the late Craig T. Clark, Olivera and Cruz learned that some of the venom peptides reacted differently in mice than in fish and frogs. It turned out in mammals the compounds were involved in the sensation of pain, rather than muscle paralysis.

“There was this incredible gold mine of compounds,” said McIntosh in the video. He is now a professor and director of research of psychiatry in the School of Biological Sciences at The University of Utah.

On September 14, 2022, the American Association for the Advancement of Science (AAAS), the world’s largest multidisciplinary scientific society, hosted the 11th annual Golden Goose Award ceremony, a celebration of federally funded research that unexpectedly benefits society. AAAS awarded University of Utah research of a non-opioid pain reliever, hidden in the venom of tiny cone snails, which greatly decreases pain for patients with chronic illnesses while helping scientists develop new ways to map the body’s nervous system. As undergraduate researchers, Craig Clark (in memoriam) and J. Michael McIntosh, now a professor of psychiatry at the U, isolated a compound that eventually led to an approved non-opioid pain killer. Baldomero M. Olivera, Distinguished Professor in the School of Biological Sciences, and Lourdes J. Cruz, then faculty of biology at the U and now Professor Emeritus at the University of the Philippines, supervised the research. The award recognizes all four individuals.

The Golden Goose Award spotlights scientific research that may have appeared obscure, sounded funny, or for which the results were unforeseen at the outset but ultimately, and often serendipitously, led to breakthroughs. This year, the award comes on the heels of the U.S. Congress passing and President Biden signing the bipartisan and historic CHIPS and Science Act. This new law reauthorizes key federal agencies whose projects will propel discovery, build on our strengths, and show what American investment, intellect, ingenuity and risk-taking can accomplish — precisely the type of innovation the Golden Goose Award honors.

U.S. Representative Jim Cooper (D-TN), often referred to as “Father Goose,” will retire from Congress at the end of this term. He conceived of the award as a strong counterpoint to criticisms of basic research as wasteful federal spending, such as the late Sen. William Proxmire’s (D-WI) Golden Fleece Award, leading to a coalition of business, university, and scientific organizations establishing the award in 2012. Thanks to his legacy, the award will continue to elevate the importance of recognizing basic science that ultimately improves people’s quality of life.

“The Golden Goose Award reminds us that potential discoveries could be hidden in every corner and illustrates the benefits of investing in basic research to propel innovation,” said Sudip S. Parikh, chief executive officer at AAAS and executive publisher of the Science family of journals. “AAAS is honored to elevate this important work since the award’s inception, and we thank Representative Cooper for his tireless leadership and dedicated support to this award and the scientific community.”

Tiny snail, big impact
In the 1970s, Olivera and collaborator Cruz were interested in the deadly venom used by cone snails, marine creatures native to the Philippines. When Olivera moved to the U, his focus shifted to other areas, but he kept the cone snail venom as a side project. In 1979 he assigned two undergraduate researchers the task of isolating the venom’s components and testing their impacts on mice. Craig Clark, a sophomore biology major, and McIntosh, a 19-year-old who just graduated high school, discovered something unexpected—a compound they named “shaker peptide” blocked calcium channels in the mice, which are the nerve’s ability to communicate with the rest of the body. Later, they found that the shaker peptide specifically targeted the channels related to pain in mammals and is 1,000 times as powerful as morphine. McIntosh is now a professor of psychiatry at the U with his own lab and thirty years later, continues to work with Olivera to explore the therapeutic potential of cone snail venom that has one of the most promising non-opioid alternatives to manage pain. One compound become an FDA-approved painkiller.

2022 Golden Goose Awards Ceremony

The student project of Clark and McIntosh is part of a long tradition of undergraduate research in the U’s College of Science. Fifty years ago, K. Gordon Lark, the first chair of the Department of Biology at the U, started an initiative to support undergrad research opportunities in faculty laboratories, an initiative that led to recruiting biology undergraduates such as Clark and McIntosh. The College of Science is expanding his legacy under a newly created Science Research Initiative, which provides most U science undergraduates with a unique opportunity to pursue their own independent research projects.

2022 Golden Goose Awardees:

Craig T. Clark (in memoriam), Lourdes J. Cruz (University of the Philippines), J. Michael McIntosh (University of Utah; George E. Wahlen VA Medical Center), and Baldomero Marquez Olivera (University of Utah)
Tiny Snail, Big Impact: Cone Snail Venom Eases Pain and Injects New Energy into Neuroscience
Impeded by supply chain issues while conducting DNA research in the Philippines, Lourdes Cruz and Baldomero Olivera began examining cone snails, a group of highly venomous sea mollusks which happened to be in abundant supply along the country’s coastal waters. Several decades and countless airline miles later, and with the help of then-undergraduate students Craig Clark and Michael McIntosh, the team discovered the raw material for a non-opioid pain reliever and a powerful new tool for studying the central nervous system, all hidden in the cone snail’s potent venom

Ron Kurtz (RxSight), Tibor Juhasz (ViaLase), Detao Du (Rayz Technologies), Gerard Mourou (Ecole Polytechnique), and Donna Strickland (University of Waterloo)
How a Lab Incident Led to Better Eye Surgery for Millions of People
Nearly 30 years ago, a graduate student at the University of Michigan’s Center for Ultrafast Optical Science (CUOS) experienced an accidental laser injury to his eye. Fortunately, his vision was not severely affected. However, the observation of the very precise and perfectly circular damage produced by the laser led to a collaboration. Eight years later, that group of researchers developed of a bladeless approach to corrective eye surgery. The new procedure, also known as bladeless LASIK, uses a femtosecond laser rather than a precision scalpel cut into the human cornea before it is reshaped to improve the patient’s vision.

Manu Prakash (Stanford University) and Jim Cybulski (Foldscope Instruments Inc.)
Foldscopes and Frugal Science: Paper Microscopes Make Science Accessible
While researching in remote areas of India and Thailand, a technical challenge piqued Manu Prakash’s curiosity. In certain areas of the world, transport, training, and maintenance barriers can make state-of-the-art microscopes inaccessible. Prakash found a potential solution in a decidedly un-technical material: paper. Using principles of origami applied to printer paper, matchboxes, and file folders, Prakash and graduate student Jim Cybulski designed a paper microscope known as the Foldscope that can achieve powerful magnification with materials that cost less than $1 to manufacture. Today, just over a decade later, two million Foldscopes have been distributed in over 160 countries and have been used to diagnose infectious diseases, diagnose new species, and identify fake drugs, among many other applications.

 

first published @ CNN and @theU

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Jack Simons Award

September 14, 2022

Jack Simons Award

Jack Simons Award in Theoretical Physical Chemistry.

Professor Jack Simons:
Professor Jack Simons received his Ph.D. training in theoretical chemistry from the University of Wisconsin, Madison in 1970. After spending time as an NSF postdoctoral fellow at the Massachusetts Institute of Technology, he joined the faculty of Chemistry at the University of Utah in 1971.

Professor Simons has made numerous contributions to the field of theoretical chemistry, especially methodologies relevant to the understanding of physical and chemical properties of negative molecular ions. He has published more than 340 papers and several monographs on various topics in theoretical chemistry, and he has been recognized by numerous awards for his contributions, including the International Academy of Quantum Molecular Science Medal, the Joseph O. Hirschfelder Prize in Theoretical Chemistry, fellowships from the Alfred P. Sloan Foundation, the Camille and Henry Dreyfus Foundation and the J. S. Guggenheim Foundation, and various named lectureships at institutions around the world.

Professor Simons has a passion for chemical education, having written several widely used textbooks on physical chemistry as well as web-based educational materials on theoretical chemistry and the principles of chemical reactivities. Professor Simons has also dedicated a tremendous amount of his time and resources to the physical chemistry community in the US, having helped establish the Telluride Summer School in Theoretical Chemistry and the ACS – PHYS divisional awards. In recognition of Professor Simons’ scientific accomplishments and service to the theoretical chemistry community, the Executive Committee of the Physical Chemistry Division of the American Chemical Society voted at the Fall 2022 to rename the Senior Theory Award to the Jack Simons Award in Theoretical Physical Chemistry.

Purpose: 
To recognize outstanding contributions in theoretical chemistry.

Nature:
At the fall ACS meeting that immediately follows the announcement of the award the recipient will present their research in one of the PHYS symposia, be honored at the annual PHYS reception, and receive a $5k honorarium. The recipient will also be invited to the next Telluride School on Theoretical Chemistry (TSTC), which are held every other summer, starting in 2009. At that meeting, he/she will present a plenary lecture.

Eligibility:
Eligibility is restricted to Physical Chemistry Division members who, at the time of the nomination, have not yet won a national award from a scientific society that is based on the nominee & scientific accomplishments. Members of the National Academy of Science are also ineligible, but fellowship in a professional society is not considered a national award in this context nor are awards that recognize service to the chemistry community. The intent of this award is to recognize a top-notch mid- or senior-career scientist who is a key player in the physical chemistry community with a long history of exemplary research contributions, but not a commensurate level of national or international recognitions. At the time of the nomination, currently serving members of the PHYS Division Executive Committee in any capacity, including subdivisions and councilors as well as individuals who are up for election to these positions, are ineligible for nomination for this award until after their term of service.

Nomination Procedures:
1. A nomination letter of not more than 2 pages.
2. At least two seconding letters with no page limit.
3. The applicant’s CV.
4. A list of the publications that the nominee is most proud.
5. A written assurance that, if selected, the nominee will attend the PHYS awards banquet
and give their seminar at the ACS meeting in person.

Application Deadline:
All materials should be sent electronically to acspchem@vt.edu. The deadline is November 1st each year. Please include the nominee’s name in the subject line of the e-mail.

Sponsor:
PHYS Division and the Telluride School on Theoretical Chemistry.

The award was established in 2008, updated in 2019, and named after Professor Jack Simons in 2022.

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U Presidential Scholar

August 29, 2022

2022 U Presidential Scholar

Luisa Whittaker-Brooks

Luisa Whittaker-Brooks named 2022 U presidential scholar.

As an associate professor in the Department of Chemistry who organized a research program with national prominence, Luisa Whittaker-Brooks has been called a “trailblazing role model.” Whittaker-Brooks’ program focuses on the synthesis of organic and inorganic materials for energy conversion and storage, among other things. Whittaker-Brooks’ research results have appeared in premier journals of chemistry and materials science, and she has received numerous awards for her work, including being selected as a Department of Energy Career awardee, a Cottrell Scholar and a Scialog Fellow.

Four new associate professors have been named as Presidential Scholars at the University of Utah. Each of the scholars will be recognized as a Presidential Scholar for three academic years, from 2022 to 2025.

The annual awards recognize excellence and achievement for faculty members at the assistant or associate professor level, and come with $10,000 in annual funding for three years to support their scholarship and enrich their research activities. The program is made possible by a donor who wishes to remain anonymous.

The 2022 recipients are Ashley Spear, associate professor in the Department of Mechanical Engineering; Lauri Linder, associate professor in the Acute and Chronic Care Division of the College of Nursing; Luisa Whittaker-Brooks, associate professor in the Department of Chemistry; and Marcel Paret, associate professor in the Department of Sociology.

“I am so proud of the work these scholars are doing in the classroom, and in their field of study,” said Interim Senior Vice President for Academic Affairs Martell Teasley. “As educators at the U, they are positioned to guide their students and impact our whole community. I’m excited to see what the future holds.”

 

by Amy Choate-Nielsen, first published @theU

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Crystal Su

August 24, 2022

Crystal Su

A new paper in Current Biology describes the development of a novel, synthetic insect-bacterial symbiosis.

The symbiotic bacteria express a red fluorescent protein that is visible through the insect cuticle, facilitating characterization of the mechanics of infection and transmission in insect tissues and cells. In addition, Su et al. engineered the bacteria to modify their ability to synthesize aromatic amino acids, which are used by the insect host to fuel cuticle strengthening. Correspondingly, insects maintaining bacteria that overproduce these nutrients exhibited stronger cuticles, signifying mutualistic function. The establishment of this synthetic symbiosis will facilitate detailed molecular genetic analysis of symbiotic interactions and presents a foundation for the use of genetically-modified symbionts in the engineering of insects that transmit diseases of medical and agricultural importance. The paper is titled “Rational engineering of a synthetic insect-bacterial mutualism.”

Red fluorescent proteins in a weevil.

Broader context
SBS Professor and Principal Investigator Colin Dale says, “the work described in the paper was catalyzed and conducted by Crystal Su, an extremely brave and dedicated graduate student in SBS, who took on this very high risk and transformative project and pushed through numerous roadblocks, doggedly refusing to take no for an answer.” Su engaged three additional labs–Golic, Rog and Gagnon–in SBS to assist with specialist techniques, highlighting the utility of interdisciplinary science and the breadth of talent and collaborative spirit that exists in SBS.

Dale views Su’s work as a “bucket list” accomplishment, “something I dreamed about while playing cricket games at Bristol University Vet School during my Ph.D. While Crystal dedicated six years of her life to bring this novel new biology to life, it’s also the product of foundational work by SBS graduate students in the decade prior, involving the identification, characterization, culture and development of genetic tools for proto-symbionts free-living bacteria that have the capability to establish stable, maternally-transmitted associations with insects.”

Synthetic Biology
Synthetic Biology focuses on utilizing engineering approaches to design and fabricate organisms (including associations and communities) that do not exist in the natural world. It can yield practical solutions for a wide range of problems in medicine, agriculture, materials and environmental sciences. In addition, it can be used to investigate the functions of natural systems, via replication and manipulation, as highlighted in the Su et al. paper. To understand its potential, it is useful to think of the contribution of synthetic approaches to other disciplines in science, most notably in chemistry, says Dale who also serves in the School of Biological Sciences as Section Head, Genetics and Evolution.

 

Read the paper in Current Biology
Read the article on Undergraduate Research in the Dale Lab

 

by David Pace, first published @biology.utah.edu

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Ants of the World

August 15, 2022

Ants of the World

Seeing the world through ants.

Known affectionately as “Ant Man” in the School of Biological Sciences at the University of Utah and beyond, John “Jack” Longino is part of a globe-spanning initiative called the Ants of the World Project that aims to generate the most complete phylogenetic tree of the ant family (Formicidae) to date.

Part of that project is Ant Course, a regularly-occurring field course on ant biology and identification. After three years of accommodating the pandemic, this year the group, involving multiple research universities, is convening in Vietnam August 1-13. During the course, the world’s ant identification experts get together to teach 24 students all about ants. Beginning in 2001, the course has been staged in the United States, Costa Rica, Venezuela, French Guiana, Peru, Uganda, Mozambique, Borneo, and Australia.

“These courses have become famous,” says Longino, “with generations of students being shaped and connected by their Ant Course experience.” The Ants of the World project, he explains, integrates teaching and research. The initiative funds three new Ant Courses in locations that are poorly known, training new generations of ant biologists while they learn about the ants of these regions.

 

John “Jack” Longino

"These courses have become famous," says Longino, "with generations of students being shaped and connected by their Ant Course experience."

 

“After a long delay due to COVID, we are finally offering our first Ant Course, in Vietnam,” says Longino of their field site in Cúc Phương National Park, just south of Hanoi. “I’m really looking forward to meeting this new group of students, interacting with Asian colleagues, and experiencing first-hand the ant fauna of Southeast Asia.” Situated in the foothills of the northern Annamite Range, the national park consists of verdant karst mountains and lush valleys with an elevation that varies from 150 meters (500 feet) to 656 m (2,152 feet) at the summit of May Bac Mountain, or Silver Cloud Mountain.

It’s all part of Ants of the World Project’s attempt to survey nearly all ant genera and just under half the described species using advanced genome reduction techniques. The result will be a comprehensive evolutionary tree of ants, out to the smallest branch tips.

The resulting data set will help researchers answer questions: Are there predictable patterns of intercontinental dispersal and diversification? Following dispersal to a new region, is there accelerated filling of morphological and climate space? How have biotas responded to climate shifts in the past? Can we predict how ants will respond to current rapid climate change?

Eurhopalothrix semicapillum, named for the hairy patches on its face.

Longino and Elaine Tan, a graduate student in the Longino lab, will be meeting up with 34 other ant specialists and ant specialists-to-be. Along with “Ant Man,” course faculty include the other principal investigators of the Ants of the World Project: Michael Branstetter (USDA-ARS), Bonnie Blaimer (Museum für Naturkunde in Berlin, Germany), Brian Fisher (California Academy of Sciences) and Philip Ward (UC Davis).

Ants of the World is a collaboration of four different institutions, including the School of Biological Sciences. Ant Course is organized and run by the California Academy of Science and is designed for scholars to share information and discover together the ants of a particular region. It applies ant biology to established areas of inquiry but also encourages students to ask new questions.

Zahra Saifee is a University of Utah intern who will be accompanying the team as a scientific communications specialist. She says of Ant Course, “it really is about the ants, what new species there are in [a particular region and] where species overlap. The team discusses their observations of what they’re doing with others across the world. The core is bringing diverse people to ‘nerd out’ about it for two weeks.”

A lot of the time in Vietnam, says Saifee, is set up just to explore and see what people will find. “Curiosity is at a premium, bringing observations to the group as a sounding board. People can bring to the group ‘rough drafts’ of research and ideas.”

This open-door approach to discovery was transformative for Rodolfo Probst, PhD, a member of the Longino lab who successfully defended his dissertation just this month. His 2013 Ant Course experience in Borneo connected him to a year’s work back east following his graduation from college before he settled into graduate school as part of Longino’s lab.

Ants are the focus of that lab’s research but it’s not just about ants. The research goals of the Longino lab involve “reciprocal illumination,” in which the latest evolutionary concepts of species formation, combined with the latest genetic tools, allow the construction of a detailed “biodiversity map” of ants. The patterns revealed in the map then inform general concepts of biological diversification.

The research has the additional benefit of allowing other researchers, like those students participating in Ant Course, to more easily identify ants. To this end, Longino helps curate a large on-line specimen and image database (Antweb.org), a major resource for ant researchers worldwide.

To study the way ants network can potentially speak to the design and character of larger eco-systems, Saifee suggests, making the study of ants more than a niche science. It propels one to look at the larger picture of life—not just its wonders, but its changes and adaptations. In short, its ecology and evolution. “There are a lot of different species [of ants] and how we organize data is key to new scientific discoveries,” concludes Saifee.

Making new discoveries about ants is important because, as subject models, they are on par with vertebrates and vascular plants as key taxa for ecology, evolutionary biology, biogeography, conservation biology, and public interest. Having a solid phylogenetic history opens entire new worlds of biological exploration, and has been achieved for vertebrates and many plants. With a little more effort, much of which is being addressed by the NSF-funded Ants of the World project, the same can be true for ants.

Ant Course in Vietnam is currently at the center of that ambition. Follow the Ant Course blog and on Twitter @AntsProject. Read the profile of graduate student Elaine Tan, who is accompanying Jack Longino to Vietnam here.

 

First published at biology.utah.edu