In 2017, Georgia Tech researchers were still celebrating the discovery of gravitational waves rippling through space-time when another celestial phenomenon captured their attention. College of Sciences Dean Paul Goldbart, who leaves us this summer to join the University of Texas at Austin, recalls the excitement over kilonovas and how they may be responsible for the gold in your wedding ring.
In this second part of our conversation with Goldbart, he charts the rapid growth of the new neuroscience degree program, tells us where he sees future opportunities for the College of Sciences, and explains why science matters — not just on campus, but in many aspects of daily life.
This audio news story also serves as a preview of ScienceMatters, the College of Sciences podcast coming in the summer. If you want to learn more about ScienceMatters, click here.
Click at the image on the right to listen or read the full transcript below.
Renay San Miguel: Hello. I’m Renay San Miguel with the Georgia Tech College of Sciences. We continue our conversation with Paul Goldbart, outgoing dean of the Georgia Tech College of Sciences, also the college’s Betsy Middleton and John Clark Southerland Chair. We taped this interview in February. With Paul’s appointment as the next dean of the College of Natural Sciences in the University of Texas at Austin, we’ve recast the interview as a two-part audio story serving as a valedictory for Paul, as well as a preview of our podcast “ScienceMatters,” coming in summer 2018.
A different kind of cosmic collision
We left off with a discussion of how College of Sciences’ researchers were part of a Nobel Prize-winning effort to confirm the existence of gravitational waves, something Einstein predicted 100 years ago. The first gravitational waves detected were the result of black holes colliding. It was a different kind of collision in summer 2017 that Georgia Tech’s researchers heard and saw while working with LIGO, or the Laser Interferometer Gravitational-Waves Observatories in Washington State and Louisiana. Here is School of Physics professor and LIGO deputy spokesperson Laura Cadonati, speaking in a 2017 Georgia Tech video.
Laura Cadonati: On August 17, something special happened. For the first time, we detected a gravitational wave that was coming not from the collision of black holes, but from the collision of two neutron stars. A neutron star is what’s left after a star burns some of its fuel and implodes under its own weight. And this is going to give us important clues in where heavy elements are formed, how matter as we know it is formed, and which processes.
This has been exciting because we are really making use of both gravitational wave and the electromagnetic wave information to learn new things. We have really— [audio fades]
Renay San Miguel: Again, here is College of Sciences Dean Paul Goldbart.
Paul Goldbart: So if you take a cubic kilometer of Earth, it weighs about as much as a thimble full of neutron star matter, so incredibly dense. I believe if you were to take the sun and have it become a neutron star it would be about the size of the Georgia Tech campus. So incredibly dense matter and remarkable astrophysical objects.
And every now and again, these are present in pairs out there in the cosmos orbiting around one another. And in this event, two neutron stars rotated around one another, radiated out energy, and merged. And as they did, in this cataclysmic eruption of merger, which is called a “kilonova,” that was where nature manufactures roughly half of the heavy elements.
So if I look now as I am at my wedding ring, it has gold in it, I believe. And that gold was almost certainly cooked, manufactured, through the collision of two neutron stars out there in the cosmos.
[Music]
A fast start for neuroscience at Georgia Tech
Renay San Miguel: Tell me about some of the disciplines that are offering some exciting potential for scientists and researchers here at Georgia Tech. You talked about astrobiology. What other research are you wanting to keep an eye on here in the future?
Paul Goldbart: Yes, let me tell you a little bit about neuroscience. Neural engineering at Georgia Tech has been a growth field for a number of years and is doing very well. It has an international reputation, very strong. We have also begun to grow in neuroscience—neuroscience as opposed to neural engineering, although as with many science and engineering disciplines, there’s a great deal of overlap; a very soft zone separating them. So we’re delighted, in fact, that we have a tremendously strong community of neural engineers here at Georgia Tech.
I’ll tell you a short story: About four years ago or so, my colleagues in the College of Engineering dropped by the College of Sciences to say, “Hello.” I’d been dean for a few months. And we sat down, and they chatted, and they said we should have a neuroscience degree. And I thought about it for a little while, and I thought, they’re absolutely right.
And I went to see Associate Dean David Collard, and we discussed the idea and both of us agreed that this would be a marvelous step forward. Tremendous campus support, tremendous campus enthusiasm, we’ve been hiring neuroscience faculty to complement the neural engineers and build a really thriving and broad community of neural researchers here at Georgia Tech.
Let me emphasize: That was not my idea. That was already running, well before I became dean. And it’s really been doing very well with great campus support.And the centerpiece of this step forward is the creation of a neuroscience bachelor’s degree at Georgia Tech. And so until the summer of 2017, if one wanted to study neurosciences in undergraduate, much as we would love to have you, Georgia Tech was not the place for you.
It is now! And I have to say I’m tremendously excited, and we are finding that students are wildly enthusiastic about this new major. And it’s actually quite a delight to construct a major after they have been constructed at other places, as you can look around and you can think and you can really focus on the future. So I think we’ve caught it just right: great neuroscience but also neural technology options built in so that you really can train yourself as an undergraduate to be a neuroscientist of the future right here at Georgia Tech.
Renay San Miguel: And it’s my understanding you expected a certain amount of interest in the first year of the program, but you exceeded that.
Paul Goldbart: We certainly did. We certainly did. So the numbers are somewhere like 150 students in the first cohort, and that is marvelous, and the more the merrier. Of course, growth like that brings the occasional strain, but those are the strains that every dean loves to have. No complaints from me.
Renay San Miguel: This is a problem you want! [Chuckles]
[Music]
Making the case for science: Why science matters
Renay San Miguel: The name of the [forthcoming College of Sciences] podcast is “ScienceMatters.” Tell me why all of the science and research that we’ve talked about here so far, why that matters. What’s in it for all of us?
Paul Goldbart: Yeah, so there’s a tremendous amount in it for all of us. Let me start with the obvious. So the obvious is that science brings new understanding, and new understanding brings new capabilities and new power for humankind to control, and work with, and adapt and manipulate, ideally for sound, solid, good purposes, the world around us. And so science has given us tremendous opportunities to do that.
I like to look—to take the long sweep. I was at the dentist yesterday, and I was very fondly thinking of the folks who came up with anesthetics —
[Laughter]
— and it’s not very long ago. And so the same with vaccinations — vaccinations are tremendously important. Let me take the example of weather forecasting. A hundred years ago or so, catastrophic weather events in the city of Galveston, but all around the world and throughout history, we’re now in a situation where we may not be able to forecast weather with the kind of precision that any naysayer might choose to impose.
But the fact is we are saving human lives; we are saving property by the millions of people per year and improving the human condition through that.
Now how does it come about? It doesn’t come about just by focusing on weather. It comes about by handshaking between all sorts of disciplines.
So without the understanding that silicon, in fact, is a semiconductor, we wouldn’t be in the situation of having solid-state circuitry and high-speed computers. And without beautiful ideas in applied mathematics, we wouldn’t be in a position to take accurate solutions of the complex nonlinear equations that describe the patterns of weather. Without electromagnetics, we wouldn’t have ultra-fast communications.
And so this handshaking of the web of understanding of the way the world works comes together and helps move forward to really change the human condition. Of course, that happens perhaps nowhere more importantly than in the fields of medicine where, across the board, one is confronted by examples in which it’s scientific understanding that has provided one, not all, but one of the keys to forward progress.
The example that I often like to cite is the laser. Lasers have had an amazing impact in eye surgery. I have friends who are ophthalmic surgeons, and they’re brilliant and I really appreciate them, but I don’t think any of them would have come up with the laser.
And so it’s this handshaking, this relationship, between the international web of science, international in space, but also going back in time, that has given human kind a sense of understanding, an ability to control, an ability to manipulate the world around us in terms of matter and energy; that is incredibly empowering.
A model for taking on complex problems
But I want to take it one step further if you don’t mind, Renay. I would like to argue, and I believe this quite deeply, that although science is not in a position to solve all our problems by any means — there are complex cultural and social and political problems that are challenging and hard to address, and I wouldn’t want to argue that all you need is a scientist to address them by any means — but I do think that we provide a model for how to think about and make progress with complex problems.
And I think the reason is that the scientific approach to problem solving has found a rather elegant and powerful balance between, on the one hand, reason, on the other hand, data, and on the other hand, third hand, creativity. And it’s this kind of intersection between all three together with the ability to let go of ideas that no longer seem to work and happily move on, that I think gives science not only its power in its own domain, but also serves as a great exemplar to the way that we, human beings, can address some of the deepest and most challenging issues that we face in economics and in politics and public health, so forth.
And I’ll also say that you may think of us, we scientists, as people who sit and solve complex equations. And we do do that from time to time.
But actually, what we really do is construct cartoon pictures of the way the world works in our heads or in our notebooks or on the chalkboard. And then what we do is make what we call back-of-the-envelope estimates: We sit down and we just ponder and reflect and put together the different pieces of scientific understanding and we make simple estimates — “Do I need a field that has the strength of one gauss to do this experiment, or do I need a field a million times bigger?” I need to know that before I consider the experiment or propose it to a funding agency.
So what we do all the time is make these estimates, and we get a feel for things. And that way of thinking, I think, is enormously empowering. I’ll call it semi-quantitative reasoning, and it’s something that I think we really need to advertise and propagate out into the world.
Just as an example: if I’m thinking about, let’s say, a topic like employment, I need to have some feeling for the numbers: What fraction of people are out of work? What fraction of people are looking for work? How many new jobs were created over the past eight years for example? So one has to have a kind of framework, a kind of feeling for numbers and relationships between them before one really seriously enters into arguments. And that way, one’s steered away from dogma and towards the light and that, I think, is what science can help us do.
[Music]
Planning for College of Sciences" growth
Renay San Miguel: Given what you’ve just talked about here since you’ve been here at the College of Sciences, what about your vision for the future here? How do you want to grow this college over the next, let’s say, five years?
Paul Goldbart: Yeah. So in my first five years or so as dean, we focused on many things including strengthening the infrastructure under which people can undertake research, building up tremendous capabilities in nuclear magnetic resonance and mass spectrometry and other areas, too, and I think that’s been great. We’ve also built facilities that people share and that creates community and promotes interaction. So I think we’ve supported the research endeavor with partnership with the campus well and I’m pleased with that.
We’ve also, I would say, we’re beginning to figure out how to create the best platforms for early-career scientists to learn how to navigate the complex web that is an academic life rather than leaving them to their own devices, but also without a heavy hand so we don’t too strongly influence the research that they choose to do. We are trying to find the middle ground to lift people up and really elevate the prospects for really great success.
I think we’ve also had an impact on the scale and energy in the undergraduate programs. We’re really in a marvelous partnership with the campus to increase the fraction of science majors and math majors at Georgia Tech from about 10 percent aiming for something like 20 percent just to give a kind of balance to the Georgia Tech community, and that’s coming along, I think, really well.
Looking forward to the next five years, I think for the college, one of the key objectives is to grow and strengthen the graduate programs. One of the reasons for this is that the reputation that we have worldwide and the impact, more importantly, that we have worldwide comes to a considerable degree from the quality and quantity of the research that we produce, and that signal is quite strongly carried by the people who we’re fortunate to train, and so by having an even stronger and even larger graduate program, we will be sending out into the world these marvelously trained, exciting, and thoughtful people who are carrying with them the Georgia Tech seal out into the scientific and mathematical worlds and carrying our story with them.
And so from my perspective, I think growing the graduate — growing and strengthening the graduate program is a key to our future success.
[Music]
Renay San Miguel: That was Paul Goldbart, dean of the Georgia Tech College of Sciences until the end of July. In August, Paul will take the position of dean of the College of Natural Sciences in the University of Texas at Austin. We wish him the best, and we thank him for his extraordinary work here in midtown Atlanta. I’m Renay San Miguel with the Georgia Tech College of Sciences.
[Music]
For the foreseeable future, the only real tool to find life on potentially habitable planets that are light years away from Earth is to probe their atmospheres for biological fingerprints of life, called biosignatures.
This approach has two drawbacks, according to School of Earth and Atmospheric Sciences Assistant Professor Christopher Reinhard. “Some biosignatures can be made by abiotic processes, leading to false positives. Others can be masked by processes that consume biosignatures, leading to false negatives.”
To overcome these problems, Reinhard and colleagues in the NASA Astrobiology Institute Alternative Earths and Virtual Planetary Laboratory Teams are proposing use of dynamic biosignatures based on seasonal changes in Earth’s atmosphere. The approach – described recently in Astrophysical Journal Letters – uses the seasonal variation of biologically important gases as a way to deal with false positives and false negatives, Reinhard says.
Seasonality of Atmospheric Gases
As Earth orbits the sun, its tilted axis means different regions receive more rays at different times of the year. The most visible signs of this phenomenon are changes in the weather and length of the days, but atmospheric composition is also affected. For example, in the Northern Hemisphere, which contains most the world’s vegetation, plant growth in summer results in noticeably lower levels of carbon dioxide in the atmosphere. The reverse is true for oxygen.
“Atmospheric seasonality is a promising biosignature because it is biologically modulated on Earth and is likely to occur on other inhabited worlds,” says lead author Stephanie Olson, a graduate student in the Department of Earth Sciences of the University of California, Riverside (UCR). “Inferring life based on seasonality wouldn’t require a detailed understanding of alien biochemistry because it arises as a biological response to seasonal changes in the environment, rather than as a consequence of a specific biological activity that might be unique to Earth.”
In the study – funded by the NASA Astrobiology Institute and the National Science Foundation Frontiers in Earth System Dynamics – the researchers identify the opportunities and pitfalls in monitoring the seasonal ebbs and flows of oxygen, carbon dioxide, methane, and ozone. They also modeled fluctuations of atmospheric oxygen on a life-bearing planet with low oxygen content, just as Earth was billions of years ago. “Based on these evaluations,” Reinhard says, “seasonal variations in ozone could be a sensitive biosignature on planets with undetectable levels of oxygen in their atmospheres.”
Ozone as Indicator of Life
At Georgia Tech, the Reinhard research group develops comprehensive models for the production and maintenance of robust atmospheric biosignatures on habitable planets, and it played a key role in developing the concept of ozone seasonality as a fingerprint for life on low-oxygen planets. The idea emerged in part as an answer to the “biosignature blind spot” problem Reinhard and colleagues posed in the 2017 Astrobiology paper “False Negatives for Remote Life Detection on Ocean-Bearing Planets: Lessons from Early Earth.”
“We are particularly excited about the prospect of characterizing oxygen fluctuations at the low levels we would expect to find on an early version of Earth,” says Timothy Lyons, a professor of biogeochemistry in UCR’s Department of Earth Science and director of the Alternative Earths Astrobiology Center. “Seasonal variations as revealed by ozone would be most readily detectable on a planet like Earth was billions of years ago, when most life was still microscopic and ocean dwelling.”
“Although we think the conceptual framework for this approach is robust,” Reinhard says, “observing and quantifying seasonality represents a daunting challenge. Research will need to take into account modulation of seasonal signals by the angle at which we observe a planet and the shape of its orbit, among other factors. Nevertheless, seasonality represents a potentially powerful approach toward finding life beyond our solar system.”
Most of what we know today about deadly bacteria such as Pseudomonas aeruginosa was obtained from studies done in laboratory settings. Research reported May 14 in the journal Proceedings of the National Academy of Sciences shows that this laboratory-based information may have important limits for predicting how these bugs behave once they’ve invaded humans.
Among the differences are increased expression of genes responsible for antibiotic resistance, the bane of drugs currently used to treat a wide range of infections. The new research could help scientists understand how to draw more accurate conclusions from their laboratory work – and provide doctors with better information on treating bacterial infections.
“Bacteria in human infections are often tolerant of antibiotics, but when we culture them outside the human they are highly susceptible,” said Marvin Whiteley, a professor in the School of Biological Sciences at the Georgia Institute of Technology and co-director of the Emory-Children’s Cystic Fibrosis Center. “In this paper, we show that several genes important for antibiotic tolerance are highly induced in humans compared to our laboratory and mouse modeling systems. There appears to be something unique in the human that is promoting resistance.”
What might be causing that difference remains a mystery, though bacteria are known to be affected by their environment. Understanding how bacterial genes and their expression levels differ in humans could allow researchers to search for laboratory conditions that better mimic the human conditions – and provide better guidance for the use of antibiotics.
“Understanding which antibiotic resistance genes are highly expressed in humans may inform our therapeutic decisions on antibiotic usage,” said Whiteley, who holds the Bennie H. & Nelson D. Abell Chair in Molecular and Cellular Biology at Georgia Tech and is a Georgia Research Alliance Eminent Scholar. “For instance, one might predict antibiotic resistance of an infecting community from gene expression data without the need for culturing microbes in the clinical lab.”
The study was supported by the National Institutes of Health, the Cystic Fibrosis Foundation, and the Lundbeck Foundation. In addition to the Georgia Tech researchers, the research team included scientists at the Texas Tech University Health Sciences Center, the University of Mississippi Medical Center, the University of California, and several clinical and research organizations in Denmark.
Pseudomonas aeruginosa is an important pathogen that threatens immunocompromised people, including those with cystic fibrosis, diabetes and obesity. It is a major hospital-acquired infection, and the Centers for Disease Control and Prevention characterizes multi-drug resistant strains of the bacteria as a serious threat.
In their research, the scientists analyzed RNA sequencing data from both human clinical infections and laboratory experiments. The human samples were obtained from collaborating clinicians, who took the samples directly from patients and put them into a chemical that preserved their RNA for later processing. The laboratory experiments studied different strains of the bacterium under a variety of growth conditions, from antibiotic treatment to competition with other bacteria.
The researchers also included previously published in vitro and mouse experiment data from the Whiteley laboratory and other research teams. Data analysis techniques included a machine learning approach known as Support Vector Machines, which was used to distinguish between gene expression profiles of samples taken from human and in vitro sources.
“We saw high expression in several genes notorious for antibiotic resistance, including genes that encode efflux pumps that extrude antibiotics from the cell as well as an enzyme that degrades certain antibiotics, such as ampicillin,” said Daniel Cornforth, a research scientist in Whiteley’s laboratory and the paper’s first author. “There were also less studied antibiotic resistance genes, including three related to zinc transport that our previous work has identified as critical antibiotic resistance determinants that were also highly expressed in the human patients.”
Though the research focused only on a single troublesome pathogen, Whiteley believes the results could have broader implications. “We actually know very little about bacteria behaviors during human infection and most model systems cannot replicate most aspects of human infection. I expect that this work would be generalizable to other bacteria.”
By identifying how bacteria behave differently in humans compared to standard laboratory settings, the work could provide a foundation for additional study with more samples and different types of infection.
“The key takeaway from this work is that now microbiologists can perform transcriptomics on bacterial populations in a range of human infections, so we can better understand what bacteria are actually doing in these clinical infections,” said Cornforth. “We can also determine where our laboratory models succeed and where they fail in mimicking these infection environments.”
This study was funded by National Institutes of Health Grant R01GM116547-01A1, a Human Frontiers Science grant, Cystic Fibrosis Foundation Grant WHITEL16G0, Lundbeck Foundation Grant R204-2015-4205 and Lundbeck Foundation Grant R105-A9791, and by Cystic Fibrosis postdoctoral Fellowships CORNFO15F0 and IBBERS16F0.
CITATION: Daniel Cornforth, et al., “Pseudomonas aeruginosa transcriptome during human infection,” (Proceedings of the National Academy of Sciences, 2018). https://doi.org/10.1073/pnas.1717525115
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A new national project, which includes the Georgia Institute of Technology, aims to convey the benefits of physics’ age-old intertwining with math upon biology, a science historically less connected with it. The National Science Foundation and the Simons Foundation have launched four centers to do this, funded with $40 million, one of which is headquartered at Georgia Tech and will receive a fourth of the funding.
For centuries, together mathematics and physics have shifted paradigms in science and rattled human perception by predicting planetary orbits, theorizing relativity or explaining how one particle can be in two places at the same time. Can theoretical math and biosystems team up to similarly shake the foundations of knowledge?
“We certainly think it’s possible,” said Christine Heitsch, a professor in Georgia Tech’s School of Mathematics who leads the new regional center. “But our immediate goals are more realistic,” she said. “Our first step is getting more mathematicians and bioscience researchers working together in research collaborations."
Bio-math synergy
On an everyday basis, that means the Southeast Center for Mathematics and Biology (SCMB) headquartered at Georgia Tech will tackle open questions in biology using novel math.
“Math can potentially change the way we do our experiments,” said Hang Lu, a professor in Georgia Tech’s School of Chemical and Biomolecular Engineering who co-leads of the center. “If you model your data with topology (a field of mathematics) you see that your data can have a shape,” Lu said. “And that can make you go look for different kinds of data.”
“It will be a two-way street,” Heitsch said. “Math always benefits when it’s challenged by reality.”
Over time, the math-bio spiral could lead to eureka moments.
“Biological systems can look overwhelmingly complex, and that just means we haven’t found the right way of looking at them yet,” Heitsch said.
NSF vision
The SCMB is one of three NSF-Simons Research Centers for Mathematics of Complex Biological Systems. The other two are based at Harvard University and at the University of California, Irvine. Together, they will not only advance the math-biosciences synergy but also spread their knowledge to hundreds of undergraduate and K-12 students throughout the region through educational outreaches.
The SCMB comprises 14 researchers, including collaborators throughout the Southeastern United States. Tulane University, the University of Florida, the University of South Florida, Clemson University, and the Oak Ridge National Laboratory are each contributing a mathematician, and one bioscientist is based at Duke University.
“This project has visionary potential to shake up the way we view biological systems, and also expand mathematics,” said Julia Kubanek, Associate Dean of Research in Georgia Tech’s College of Sciences. “The National Science Foundation and the Simons Foundation have shown tremendous foresight in creating these three centers, and I think headquartering one at Georgia Tech is a great fit because cross-connecting research disciplines is already one of our core missions.”
Biosciences enigmas
To understand the particular value of combining math with biosciences, it’s important to not conflate the latter with physics.
A graphic depiction of canalization. The path of the ball represents the development toward a phenotype, which may start with varying genetic foundations but roll out to secure phenotypical outcomes. But canalization can also lead to more than one possible phenotypical outcome from one set of genes.
For example, in relativity, near-light speeds change an object’s mass, its length, and its passage through time. Those warped phenomena and their equations aren’t so applicable in the world of experimental biosciences, which live in a more Newtonian reality, but one with intricate enigmas for math to demystify.
Take the phenomenon called canalization, which saves living things from the little genetic snafus inside of us all by making sure that proper physical traits usually get produced in spite of mutations.
Clone contradictions
Canalization shatters a stubborn popular notion that genes determine how an organism is built.
“Genes are not deterministic,” said Lu, who is Love Family Professor. She studies the intricate pathways that lead from genetic foundations to measurable physical or behavioral traits, or phenotypes, in C. elegans roundworms. “You often have two individuals with identical genotypes (specific sets of genes) that have different sets of phenotypes.”
That means that canalization may not offer just one but two options -- or more -- to form a trait based on a single set of genes. “What fascinates me is that you can have (C. elegans) clones that are genetically identical but exhibit different behavior,” Heitsch said.
Canalization is not new; it dates to 1942. But its labyrinthine mechanisms and how they “chose” one phenotypical pathway over the other still contain many mysteries. “Maybe math can help us find answers,” Lu said.
Labyrinthine intricacies
Algebra has already taken up canalization but at the SCMB, more maths will join in. Topology, computation, stochastics (principles of randomness), and geometry may enlighten canalization’s myriad interworkings of DNA, RNA, enzymes, protein folding, and just plain randomness.
Other questions SCMB bioscientists and mathematicians are pursuing:
How do stem cells know whether to become a neuron or a skin cell?
How does one cell transport molecules to others?
What exactly does RNA do to help repair DNA damage?
Heitsch, for example, specializes in a field of mathematics called combinatorics, and she applies it to the way molecules of RNA fold.
Historical divergence
Biology is no stranger to stochastics or computation in the analysis of its data, but it has been much less connected than other sciences to the aerial acrobatics of theoretical mathematics.
“There is enormous unrealized potential in applying more theoretical areas of math like algebra, topology, and geometry,” Heitsch said. “That’s new territory, which also means new risks. But we’ve hedged our bets with mathematics already more used in biology to get guaranteed returns.”
Biology and theoretical math have not interfaced much in the past for a couple of reasons.
The endless intricacies of biology, from hundreds of thousands of species to countless biomolecular structures, has made it a gathering and cataloging science for centuries with data that is tough to unify. Also, much data has had to wait for technology to be invented to collect it.
“Biology hasn’t had the measurement tools until just recently, like mass spectrometry and high-end microscopy, to get the hard data needed for math to work with,” Lu said. “Now is a great time for biology and math to come together,” she said.
Cultural exchange
Also, history has separated the disciplines. For centuries, physicists were also mathematicians and vice versa. “And they were engineers,” Lu said. But biologists?
“Darwin was assuredly not a mathematician,” Heitsch said. “He said he didn’t understand as much math as he would have liked to.”
Not many mathematicians have been biologists either.
The NSF-Simons Foundation centers are building the bridge to join them, and the SCMB at Georgia Tech makes for a good pillar. Most of its bioscience researchers already know engineering or physics math, and its mathematicians are already delving into life sciences.
Editor's Note: This article is a slightly modified clone of the feature story by Ben Brumfield published on May 24, 2018 in Research Horizons online.
This article was corrected on May 30, 2018, to reflect corrections in the original story about the number of centers (four), total funding ($40 M), and the Georgia Tech's share (one-fourth).
School of Chemistry and Biochemistry Assistant Professor Henry La Pierre has received a Beckman Young Investigator Award. He will use the award, from the Arnold and Mabel Beckman Foundation, to pursue research that would establish the foundation for innovations in magnetic materials based on f-block elements.
The f-block elements are the lanthanides and actinides. They are characterized by partially filled f-orbitals. The property imparts unique magnetic properties, making the naturally occurring members commercially important.
According to La Pierre, f-block elements are in materials for energy production, conversion, and use. They are also driving advances in lighting, hard magnets, and electronics.
Because of strong demand, geopolitical factors, and limited availability, the U.S. Department of Energy has deemed five lanthanide elements to be in critical supply: praseodymium (Pr), neodymium (Nd), europium (Eu), terbium (Tb), and dysprosium (Dy).
La Pierre will use X-ray absorption spectroscopy to determine the fundamental basis of the magnetic exchange properties of f-block materials. “A primary goal of my group is to establish chemistry-based rules that will provide a new basis for innovation in controlling magnetic properties of f-block element materials,” La Pierre says.
The new understanding, he adds, “will be applied to the synthesis and characterization of materials that potentially can be exploited for a variety of applications, including high-temperature superconductivity and quantum information technologies.”
La Pierre received a Bachelor of Arts degree from Harvard University and a Ph.D. from the University of California, Berkeley. After postdoctoral appointments in Friederich Alexander University, in Erlangen, Germany, and Los Alamos National Laboratory, he joined Georgia Tech in 2016.
La Pierre’s research program develops the molecular and solid-state coordination chemistry of the f-block elements for unique and scalable solutions to contemporary problems in energy use. He uses a broad range of physical methods – including single-crystal and powder X-ray diffraction, magnetometry, multinuclear magnetic resonance spectrometry, and X-ray absorption spectroscopy – to characterize new materials.
Mark Wheeler has been named interim chair of the School of Psychology, effective on July 1, 2018. Wheeler is currently the school’s associate chair with oversight of operations and graduate studies.
Wheeler joined Georgia Tech in 2014. His lab investigates how cognitive abilities are affected by lifestyle factors such as sleep quality and physical activity, as well as how these abilities may change in healthy aging.
Wheeler specialized in functional brain imaging of human memory for his Ph.D. from Washington University in St. Louis.
After a postdoctoral stint at Washington University School of Medicine, he joined the University of Pittsburgh. There, he developed functional imaging techniques to study neural dynamics of the accumulation and representation of evidence during decision-making.
Wheeler takes over from Frank Durso, who has served as interim chair since July 1, 2017.
“It is a pleasure for me to thank Professor Frank Durso for his exemplary contributions during his service as interim chair of the school,” says College of Sciences Dean and Sutherland Chair Paul Goldbart. “Under Frank’s leadership, the school has developed relationships that will be of enduring value to the school, both across the campus and beyond.”
“A large part of my research is thinking about how bacteria communicate,” says Sophie Darch. The postdoctoral researcher works with School of Biological Sciences Professor Marvin Whiteley, studying the social lives of bacteria.
Darch observes the conversations of bacteria, which take place via molecules they release into the environment and are sensed by other bacteria. In Darch’s experiments, completed messages are marked by the red-to-green change in the color of the bacterium sensing the molecule.
By sending and receiving extracellular signals, bacteria sense their neighbors. When enough bacteria are in the conversation, things happen. Sometimes it leads to changes in virulence or ability to establish an infection. The phenomenon is called quorum sensing.
Yet little is known about how quorum sensing proceeds during infection “Much of what is known about quorum sensing,” Darch says, “comes from studies of large populations of bacteria in an environment that does not compare with the natural infection site.” In infections, for example, bacteria are often found in small, dense clusters, called aggregates. “It’s really important for us as scientists to think about what bacterial growth looks like in an infection,” Darch says.
In a paper in the Proceedings of the National Academy of Sciences USA, Darch, Whiteley, and colleagues describe for the first time how close bacteria need to be to “talk” with each other in an environment similar to an infection. Their findings could reveal new ways to disrupt bacterial signaling and provide other targets to treat infections.
The work was supported by the National Institutes of Health, the Cystic Fibrosis Foundation, Human Frontiers Science, and the Welch Foundation.
Cystic Fibrosis Model
The study uses an environment similar to the chronic infection of the cystic fibrosis (CF) lung.
CF is a genetic disease that causes buildup of sticky mucus in the lung. The viscous setting CF creates makes the organ prime real estate for disease-causing bacteria. Among the most prevalent of these in the CF lung is Pseudomonas aeruginosa.
P. aeruginosa infections pose a huge problem because they are resistant to many antibiotics and are difficult to treat. Often P. aeruginosa infection is what causes death among patients with CF.
The team used a synthetic CF sputum media (SCFM2), based on the makeup of lung secretions from patients. In nutritional content and physical form, the medium is similar to sputum from the lung. Importantly, P. aeruginosa forms aggregates in SCFM2 that are similar in size to those observed in CF lung tissue.
3-D Printed Bacteria
To begin to answer the question “How close do you have to be to talk to your neighbor?” the team collaborated with Jason Shear at the University of Texas, Austin. The Shear Lab had developed a micro-3D-printing platform that could be used to engineer the growth of bacteria to mimic infections.
Bacteria are not uniformly distributed in infections. “Instead we see bacterial aggregates that vary in size and can be separated by large distances,” Whiteley says. “We needed an experimental method to engineer these types of infection landscapes in the lab.”
Using Shear’s micro-3D-printing platform, the team printed bacterial aggregates of exact positions and sizes.
A typical experiment starts by enclosing one producer cell in a picoliter-sized trap, using micro-3D-printing. After multiple cell divisions, the population fills the volume of the trap. Then SCFM2-containing aggregates of responder cells are overlaid the porous trap.
They observe the one-way flow of signals from aggregates in a trap (producers) to aggregates outside receiving signals (responders). They could see the response of completed conversations by responders changing color from red to green.
Implications for Cystic Fibrosis
“We found that bacterial aggregates slightly larger than those in CF lung – containing about 2,000 cells – were not large enough to signal to other aggregates,” Darch says.
Prior to this study, it was thought that bacterial signaling could occur over extended distances. However, in the CF lung, small populations of bacteria are scattered across a large volume and separated by large distances. Aggregates are unlikely to “talk” to each other.
It took aggregates containing at least 5,000 cells to successfully send signals to neighbors as far away as 176 micrometers. “These aggregates are around five times the size of the average aggregate observed in CF lung tissue” Darch says “From these data, communication is likely confined within an individual aggregate rather than being a population-wide phenomenon”.
Among CF patients who are at least 20 years old, 80% are infected with P. aeruginosa. “Infection with P. aeruginosa remains a significant clinical problem in immunocompromised patients, particularly those with CF,” Darch says. “Understanding better how bacteria communicate has the potential to find ways of disrupting the communication and potentially diminishing bacterial virulence.”
“The study provides benchmark data for how quorum sensing might proceed in an environment similar to the CF lung,” says Whiteley, who is a member of the Parker H. Petit Institute for Bioengineering and Bioscience. “In different settings, where P. aeruginosa and other bacteria exist as aggregates of different sizes, communication may look different. Future studies will involve experimental and modeling work to further examine the spatial parameters of quorum sensing in CF and other infections, such as a chronic wound.”
Figure Caption
(Left) Rendered confocal laser-scanning micrograph of a micro-3D-printed trap (red) surrounded by P. aeruginosa aggregates responding to quorum-sensing signals (green) in a synthetic CF sputum media (SCFM2).
(Right) Rendered confocal laser-scanning micrograph of responding (green) and non-responding (red) P. aeruginosa aggregates formed in a synthetic CF sputum media (SCFM2).
Curvy baseball pitches have surprising things in common with quantum particles described in a new physics study, though the latter fly much more weirdly.
In fact, ultracold paired particles called fermions must behave even weirder than physicists previously thought, according to theoretical physicists from the Georgia Institute of Technology, who mathematically studied their flight patterns. The researchers even predicted that the particles can act like different quantum balls called bosons to mimic the manner that photons, or particles of light, fly.
Already, flying quantum particles were renowned for their weirdness. To understand why, start with similarities to a baseball then add significant differences.
A pitcher imparts spin, momentum, and energy to a baseball when throwing a curveball, a change-up, or a slider. Fermions’ funny flights are likewise carved by spins, momenta, and energies, but also by powerful quantum eccentricities like entanglement, which Albert Einstein once called “spooky action at a distance” between quantum particles.
A simplified explanation of these ultracold paired particles and their odd flights is below.
Light-matter modeling
Those influences all combine to give fermions a trajectory repertoire much odder than that of any master baseball pitcher, and the new study maps it out and opens new ways to observe it experimentally. The Georgia Tech team took the offbeat approach of adding quantum optical -- or light-like – ideas to their predictive calculations of these specks of matter and arrived at eyebrow-raising, insightful results.
“The particle behavior we predicted is just schizophrenic,” said Uzi Landman, Regents’ and Institute Professor and F.E. Callaway Endowed Chair in Georgia Tech’s School of Physics.
Mathematical and theoretical details can be found in the study in the journal Physical Review A, which Landman, first author Benedikt Brandt, who is a graduate research assistant, and senior scientist Constantine Yannouleas published on May 4, 2018. Their research was funded by the Air Force Office of Scientific Research.
Flying fermions explained
Tracing quantum curveballs is counterintuitive by nature with concepts like fermions, bosons, spins, spooky entanglement, and particle-wave duality. So, let’s go step-by-step to understand them and the study’s insights.
This ballgame revolves around fermion pairs. Fermions can be subatomic particles or whole atoms. In this case, the physicists modeled using atoms.
The term fermion refers to quantum-statistical properties that the particle has as opposed the properties of its counterpart particle called a boson, in particular, the particle’s spin, which is called half-integer for fermions and full-integer for bosons. (These spins aren’t exactly like those on a ball. For more, see: Fermions and Bosons for Dummies.)
"Photons and Higgs bosons are examples of bosons," Landman said. "Bosons are gregarious: Two or more bosons can share the exact same space. This allows many of them to be superimposed onto each other on the same tiny spot."
"Fermions, on the other hand, are standoffish. They lay claim to their own space, and don't share it with other particles. Fermions can be stacked upon each other but do not occupy the same space."
Electrons, protons, neutrons, and many atoms are common examples of fermions.
Laser-tweezing baseballs
The theoretical study envisions two fermionic atoms starting out carefully held next to each other by two pairs of “tweezers” made of intersecting laser beams, as is actually done in applicable physics experiments. In the study's theoretical setup, lasers and special magnetic fields would also be used to slow the fermions to a near halt, making them “ultracold” at 0.000000001 degrees Kelvin, or -273.15 degrees Celsius (-459.67 degrees Fahrenheit).
That’s a sliver above absolute zero, the lowest possible temperature in the universe, and particles that cold do strange things.
“A particle’s motion is usually frantic, but the cooling slows it down almost to a stand-still,” said Landman, who is also director of the Georgia Tech Center for Computational Materials Science. “And these particles also have wave properties, and at that temperature, the wavelength grows enormously long.”
“The waves become microns in size. That would be like a pebble growing to be a third of the size of this country. When that happens, the atom actually becomes visible under an optical microscope.”
The inflated size makes it easier for researchers to know the two particles’ starting locations. When they turn the laser tweezers off, the fermions fly away. The particles’ wave properties also have a lot to do with their weird flights.
“A particle in motion will act as a projectile under certain circumstances. But in others, it will behave like a wave,” Landman said. “We call it the quantum world duality.”
Together or apart
“If you set up two detectors at different positions but the same distance from the particle pair, how often the two fly into the same detector or how often they fly into separate ones says a lot about those particles,” Landman said. “And that’s where our weird findings come in.”
Fermions are expected to fly differently from bosons, but the theoretical physicists’ study on fermions revises this idea. Depending on the degree of quantum entanglement between the two fermions before they’re released and depending on their energy level, they can act like fermions or act like bosons.
“This adds new weirdness to the already established schizophrenic particle-wave duality,” Landman said.
“A pair of photons (which are bosons) fly to the same place. They stay as a pair,” Landman said. “They’re social animals, and you find them either both in the one detector or both in the other. We call this phenomenon ‘bunching.’”
Weirdo flight paths
Fermions are often expected to do the opposite, referred to as anti-bunching, but according to the study, how they fly depends on whether or not they have spooky interaction and, if so, whether the interaction is attractive or repulsive.
“If they’re interacting, and depending on the starting energy level, we predict that they may do strange things when they fly,” Landman said. “That’s new.”
“At the base energy level, called ground state, our two fermions that interact with ultra-strong repulsion behave fermionically, meaning they avoid each other. Now, if they interact with strong attraction, they aggregate the way bosons do,” Landman said. “So far, all as expected.”
But bumping up the trapped particles’ level of energy, or excitation, via an additional laser or a magnetic field, would appear to heighten the particles’ weirdness. The excitation levels can twist the rules of what interactions do to a fermion’s flight, according to the theoretical study.
For example, the above mentioned fermionic behavior usually connected with strong repulsive interaction could turn bosonic, according to the physicists’ calculations. In other words, the two particles would fly to the same detector the way bosons do.
Orderly quantum schizophrenia
“As crazy as all this looks, there appears to be strong reliability in these behaviors that could even be predictably and practically manipulated,” Landman said.
As with a pitcher who finesses a screwball’s path, physicists could determine a fermion’s weird flight using quantum mechanical formulation, advanced computational simulation, and experimentation, the study said.
“It looks like you may even be able to engineer what this quantum weirdness does,” Landman said. "If you know particle states reliably, you may be able to use them as a resource for quantum computations and information storage and retrieval."
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The research was funded by the Air Force Office of Scientific Research (award # FA9550-418 15-1-0519). Findings and opinions are those of the authors and not necessarily of the sponsoring agency. Georgia Tech's Brice Zimmerman contributed baseball background to this report.
Writer & Contact: Ben Brumfield (404-660-1408)
David M. Collard, professor and associate dean, will serve as interim dean of the College of Sciences. Collard will officially assume the role Aug. 1, following the departure of the current dean, Paul Goldbart.
“Dr. Collard is a valued member of the faculty and administration in the College of Sciences,” said Rafael L. Bras, provost and executive vice president for Academic Affairs and K. Harrison Brown Family Chair. “We are grateful for his continued leadership and trust the College is in great hands during this transition.”
Collard joined the Georgia Tech faculty in the School of Chemistry and Biochemistry in 1991. He served as the director of Graduate Studies from 1997 to 2005, and then as associate chair from 2005 to 2010.
Academic Leadership
Collard has served as the associate dean for Academic Programs in the College of Sciences since 2010. In this role he coordinates activities related to recruitment, retention, curricula, instructional facilities, scholarships, and awards.
He also directs initiatives to broaden participation in STEM, build capacity for undergraduate research, and foster partnerships with neighboring, predominantly undergraduate institutions.
Research and Instruction
His teaching interests are in the field of organic chemistry, and he maintains a research program in polymer chemistry.
Along with his teaching and research interests, Collard has served in leadership roles of on-campus experiential learning programs including National Science Foundation (NSF) Research Experiences for Undergraduate programs (REU), a 3M Undergraduate Summer Research Program, an NSF Scholarships in STEM & Living-Learning Community, and a number of U.S. Department of Education Graduate Assistantships in Areas of National Need programs (GAANN).
Collard also co-directs the Chemistry Collaborations, Workshops, and Communities of Scholars (cCWCS) faculty development initiative, which has engaged thousands of faculty members from institutions across the United States.
He has authored or co-authored more than 100 papers in refereed journals. Collard’s commitment to individual student research mentorship has included 24 Ph.D. graduates, 12 M.S. graduates, and 37 undergraduate researchers.
Honors and Awards
During his tenure, Collard has received all three of the Institute’s top teaching awards: the Class of 1940 W. Roane Beard Outstanding Teacher Award, the Class of 1940 Howard Ector Outstanding Teacher Award, and the Eichholz Award.
He is also the recipient of the Georgia Tech Class of 1934 Outstanding Use of Educational Technology Award and the Outstanding Ph.D. Advisor Award.
His work in undergraduate education has also garnered awards from the National Science Foundation, the Camille and Henry Dreyfus Foundation, and the Research Corporation for the Advancement of Science.
In 2017, he was the recipient of the University System of Georgia’s Felton Jenkins Jr. Hall of Fame Faculty Award in recognition of his commitment to teaching and student success.
Collard received his Ph.D. in Chemistry from the University of Massachusetts – Amherst in 1989 and a Bachelor of Science in Chemical Sciences from the University of East Anglia, U.K., in 1983.
Collard will serve until a new dean is named. A search chair and advisory committee will be selected in the next several weeks to conduct an international search for the College’s next leader. Jennifer Herazy, associate provost for Operations, will serve as search director.
EDITOR'S NOTE: This item is a slightly modified version of the original story by Susie Ivy published on June 1, 2018, in the Georgia Tech News Center.
There’s a long way to go before neuroscience can fathom the vastness of human consciousness, but researchers pushing that envelope have uncovered a mechanism that helps create a simple visual awareness. In a new study, they describe brain functions that give you confidence that you did see what you just saw.
Though that may be a very modest level of awareness that humans perhaps share with hamsters, psychologists at the Georgia Institute of Technology were fascinated to observe how two regions of the brain work together to produce this visual confidence.
“We had already thought of the prefrontal cortex (PFC) as producing that confidence, but we haven’t previously distinguished two regions of it as having distinct, separate roles,” said Dobromir Rahnev, an assistant professor in Georgia Tech’s School of Psychology.
Awareness of seeing
The observed phenomenon is a type of metacognition, which is broadly defined as when the brain registers, i.e. becomes aware of, something else that the brain is doing. Metacognition can be as complex as pondering your own thoughts or as simple as knowing you feel itchy, or that you just saw something.
The two regions of the PFC that the researchers studied were the dorsolateral prefrontal cortex (DLPFC) and the anterior prefrontal cortex (aPFC). The aPFC is about two inches above the eyebrow, near the top of the forehead and DLPFC is about a few inches directly behind aPFC.
The upper area collects visual sensory input, according to the study, and when it has strong inputs, it signals down to the aPFC, which usually correctly and confidently registers – yes, I’m aware I see that.
“The aPFC takes the evidence from the DLPFC and matches it to a level of confidence of what is being seen,” said graduate research assistant Medha Shekhar.
Rahnev and Shekhar published their study in May in the Journal of Neuroscience.
Two-stage signoff
Though they have separate roles, neither region appears to lay claim to being the chief confidence maker of having seen something.
“I would say that it’s both parts together,” Rahnev said. “The whole process of generating a confidence rating can be thought of as metacognition, so both the DLPFC and aPFC contribute to the process.”
The DLPFC collects all the inputs. Then it nudges the aPFC to put the stamp on the final confidence rating, according to the psychologists’ model.
To do that, the aPFC probably pulls in additional data from elsewhere in the brain.
“There is research that suggests that we take into account other, non-perceptual factors when making our confidence judgment,” Shekhar said. “Our previous confidence about past things we’ve seen influences current confidence about what we’re seeing now. We hypothesize that there are other things like attention and arousal that the aPFC is taking into account.”
Running brain interference
Researchers currently can’t directly see the processes that interested them, since neurological imaging technologies are not yet that far along, so the psychologists had to come up with creative ways of observing the mechanisms. They used transcranial magnetic stimulation (TMS), which some people know from its application to treat depression, to interfere with activity in one brain region then separately in the other.
“By dissociating the contributions made by the two regions, we could discern some mechanisms in these processes we were interested in,” Shekhar said.
To track the effects of the dissociation caused by the magnetism, the psychologists had volunteers look at two faint patterns on a drab, gray background that appeared in sequence, and then indicate what they saw. It was nothing fancy, just a series of lined patterns like this one \\\\ or this one ////.
“These are very standard visual inputs for an experiment like this,” Rahnev said. “They’re the most boring stimuli one can imagine. They’re called Gabor patches. We use them because we want to minimize interfering neurological activity by not encouraging the brain to do a lot of additional things.”
The volunteers pressed buttons to say that the respective line patterns that they saw pointed up to the left \\\\ or up to the right //// and how sure they were about what they saw.
Confidence up and down
While the volunteers did this, the researchers used TMS to run interference in the volunteers’ DLPFC and then their aPFC. The TMS affected whether subjects got the line direction right or wrong and how sure subjects felt about what they were seeing.
Applying TMS to the DLPFC caused the subjects’ confidence levels to sink, presumably because that interfered with it gathering or passing on enough data to trigger confidence. TMS to the aPFC, which had to be applied for a longer period to have relevant effect, actually increased visual metacognitive ability.
The two effects were strong evidence that the two brain regions were carrying out separate roles in visual metacognition. The researchers also computationally modeled the brain processes, and their simulation concurred with the experimental results.
Peeking at consciousness
Did the researchers observe a piece of what makes consciousness work?
“Consciousness is tricky because so many processes feed it and help generate it, so we stay agnostic about this and stick with the immediate phenomenon we observe,” Rahnev said.
But he did think it may be fair to say that this kind of metacognition stands in the threshold of what we humans like to think of as consciousness.
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