“An unexpectedly useful transformation – the Burrows-Wheeler Transform”
Data often needs to be processed in some way to make it more efficient to store and access, or to extract relevant information from it. One particular method of processing data that’s in the form of text is called the Burrows-Wheeler Transform (BWT). This transform shuffles text by rotating the order of the letters, sorting the rotations alphabetically, and then taking the last character of each sorted rotation.
At first glance, the transformation seems ridiculous and unlikely to be useful. However, the shuffle is clever, as it produces a unique result for each input and has the property of clustering repeated characters together. What’s more, the BWT is reversible, so you can get back the original text from its transform. In my talk, I’ll walk through the BWT and share how it is used in different scientific fields – from computer science (data compression) to genomics (sequence alignment).
Aalok is a biologist and avid science communicator. Formally trained in neuroscience, he obtained a PhD from the National Centre for Biological Sciences (NCBS) in Bangalore, India. He is currently a postdoctoral fellow in Dr. Loren Looger’s lab at UC San Diego, where he works on understanding how ancient viruses shaped evolution, using cephalopods (squids, octopuses, and cuttlefish) as models. Sometimes he’s interesting (reading books, blogging and writing fiction, tidepooling, playing tennis, swimming, giving science talks), and sometimes he’s into resting (watching TV in bed). His blood is almost always caffeinated, yet sleep is his superpower. Learn more about Aalok at varmaalok22.github.io.
Laura Gonzalez
“Why Mars Needs Anthropologists”
Human space exploration and anthropology may not seem to have anything in common. However, when the focus on space travel and settlement is stuck on the question “how can we science it?” it’s important to also ask “how the heck is it all going to work once we get there?” Our carbon flesh units are much less equipped for space settlement than the STEM folks give us credit for. This talk will address some human aspects of space exploration that we don’t talk about, but probably should.
Laura Tubelle de González (she/her) couldn’t believe it when she learned in college that you could be nosy for a living as a cultural anthropologist. She combines her love for ethnographic research and teaching as a professor of anthropology at San Diego Miramar College. She is the author/co-author of two anthropology textbooks and a 2021 ACLS/Mellon Fellow for research on the anthropology of human space exploration. If Laura could live in a sci-fi universe, it would be as a crew member on the original 1966 Star Trek, mostly just to walk through the doors as they go whoosh. She would prefer not to be wearing a red shirt, however.
This event is sold out, keep an eye out for details of our next Nerd Nite!
Jay Vu, MD
“A brief history of medicine: from mystery to mechanism”
This is a journey exploring the evolution of medicine, from the ancient era to modern times. It is more than just a list of medical achievements. Tectonic shifts in how we thought about the human body and disease mirrored changes to the cultural zeitgeist of the times – from affliction as a consequence of moral failure to disease as a disturbance in the internal homeostasis of the human body.
Jay is a father of two, a husband to one, and an emergency physician to any. When he’s not in the ER pulling bags of Meth out of a patient’s butt, you can find him in a coffee shop. His drug is caffeine and a well crafted story. He mainly writes for his daughters, but sadly, they are the least interested. He hopes that one day they will be, but until then his wife suffers his stories gladly.
Learn about new technologies impacting people with disabilities, both good and bad, including innovations on the horizon and around the corner presenting promise and risk. We’ll explore how bias in AI can discriminate against marginalized groups and why. AI is trained on history and the internet – both terrible sources of equality and truth; so if we don’t fix this now, the future will be written by racists.
Christopher Land is a UX designer, accessibility consultant (note: not an AI engineer) and co-organizer of the San Diego Accessibility & Inclusive Design group [ a11ySD ]. Chris has experience in training, coding, design, UX and enterprise systems. He sees digital accessibility as crucial in providing people with disabilities an unprecedented level of independence. Chris is simultaneously fascinated and terrified by the speed and power of today’s new technologies. https://a11ysd.com/ https://www.meetup.com/a11ysd/events/306271144/
Madeline Meade
“APEocalypse Now?”
We all know and love Planet of the Apes, but how scared should we really be of a chimpanzee-initiated apocalypse? Together, we’ll take a whirlwind tour of the Rise of the Planet of the Apes movie from the perspective of a cognitive scientist.
We’ll examine what the movie got right and what it got wrong about how great apes think & act, draw parallels with the real history of the field of comparative cognition, and ponder the cognitive changes that the movie’s miracle drug might need to induce in a chimpanzee’s mind to make a real-life Caesar.
Madeline is a second year PhD student in the Cognitive Science Department at UC San Diego, where she is a member of the Comparative Cognition Lab. Madeline studies nonhuman primate cognition, ranging from social intelligence to logical reasoning, as an approach to understanding the evolution of human intelligence. She received her B.S. in Ecology & Evolutionary Biology from Yale University, and managed Yale’s Comparative Cognition Lab after graduating. If she’s not hiking around an island full of free-ranging monkeys, she’s probably hiking around San Diego with her friends.
Tickets are available for our next Nerd Nite on Thursday, February 26! Get them here
Catherine Schrankel
“The Real Superpowers of Weird Invertebrates in the Ocean”
Ever wondered why the Octopus is SO good at disguising itself? Do you think there are other animals that have unique superpowers compared to us humble humans? And who the heck studies this, and why should we in the first place?? Come join me under the sea to explore the answer to these questions and more!
Catherine (or “Dr.Cat” to her students), opened her cell biology lab at San Diego State University in Fall 2022. Her research is focused on the tools used by different cell types in animals (specifically Urchins–both the human and marine animal kind!). Anchored by her background in toxicology in mammalian cells (PostDoc at UC San Diego), Evolution of Immune Systems (PhD at University of Toronto), and developmental biology (honestly, since 5th grade?), DrCat’s lab seeks to understand how cells and tissue protect themselves from non-self in their environment. We are also committed to training students and improving the workforce development of the next generations in STEM research and education. Outside of the lab, DrCat enjoys cooking, exploring East County with her partner and their ridiculous fluffy dog, and doing arts and crafts in her spare time
Gillian Belk
“Life Under the Cheese”
Let’s take a walk through a cheese rind. Filamentous fungi stretch up high over our heads. Floating around us are tiny, comma-shaped bacteria and large, round yeast bumping into one another. As we float up closer to the surface, the ecosystem around us shifts. The species of yeast and bacteria begin to change, until we burst through the tangle of fungi filaments to the surface. Standing on top of the cheese rind, we marvel at many microbes working together to make the cheese smell taste delicious!
The world is full of microbes and the microscopic communities they create. Microbiomes exist in and on our bodies and inhabit nearly every niche on Earth. But the question is, how do these microbes actually interact with one another? At the microscopic level, do these tiny organisms work together or compete for resources? Or will they break our understanding of how living things can interact with one another? And… what does cheese have to do with this?
Gillian Belk is a San Diego native with a Bachelors and Masters degrees from UC San Diego. She is a scientist, educator, friend, sister, daughter, a book lover, and occasional mediocre comedian. She is fascinated by the infinite variety of microbes and their norm-breaking social interactions as well as potential to create a better world. You can find her crouching over tidepools, marveling at the world around her, and hanging out with our local sea lions. Oh, and she also loves dinosaurs.
Ian Coley
“An introduction to algebraic K-theory via cardboard paper and safety scissors”
Tackling 21st century mathematics in a 20-minute talk is a little tough, so I’ll be taking us back a century to the origins of my doctoral thesis topic, algebraic K-theory. The goal of my talk is to convince you that we can understand* both polygons and polyhedra with less information than you’d expect*. I’ll also give a robust description of what happens when we start to add holes to things (which gets considerably more complicated).
* For certain levels of understanding and expectation
Ian Coley received his PhD in Mathematics from UCLA in 2019, focusing on algebraic K-theory and higher homotopy theory. From there, he moved to Rutgers University in New Jersey and served as a Hill Assistant Professor (postdoc) from 2019-22. Following that role, with a little motivation from a global pandemic, he transitioned from academia to management consulting, joining the Boston Consulting Group’s new San Diego office in January 2023. Since joining BCG, Ian has tried to avoid being pigeonholed as a quant before coming back to that stereotype of his own accord, working primarily in the Health Care and Tech/Fintech. Having achieved employement at BCG more less by accident rather than through careful planning, he now makes a strong effort to help PhDs (and other non-MBAs) figure out how to properly network and break into management consulting as a side project.
How do we know how far objects in space are from Earth? Find out how astronomers measure distances in our Universe. Hint: You’ll need a ladder.
Jae Calanog is a Physicsand Astronomy Professorat San Diego Miramar College, and the chair of Physical Sciences. Jae earned his B.A. from UC Berkeley and his PhD from UC Irvine, where he specialized in using gravity as a telescope toexplore distant galaxies. As one of the first Filipino-American astrophysicists, he is driven to help underrepresented students succeed in STEM by creating connections and experiential learning opportunities. In his spare time, you can find him breaking(breakdancing), behind a camera, or exploring the world through travel.
Robert Quimby
“SuperAwesome SuperLuminous SuperNovae”
At the end of their lives, most stars fade quietly into the night, but a few go out with a bang. When stars explode as supernovae they can shine almost as bright as their whole galaxy of stars for a few weeks or, in the case of superluminous supernovae, even brighter for longer. What makes these supernovae so much more powerful than the rest? Ok, we’re still working on that–but we have some great leads! Some superluminous supernovae could be explosions within explosions. Others may get a power boost from super-dense, super-magnetized neutron stars at their cores. These giant explosions help shape galaxies and help seed the cosmos with the elements necessary to make people and beer, so let’s drink in this tale.
Robert Quimby is a Professor of Astronomy at San Diego State University and Director of the Mount Laguna Observatory. As an undergraduate at UC Berkeley, he contributed to the discovery of the accelerating expansion of the Universe. As a graduate student in Texas, he played a key role in identifying the first superluminous supernovae. He went on to postdoctoral positions at Caltech and the Kavli IPMU in Japan, where he discovered the first Type Ia supernova magnified by a gravitational lens. Back in high school, he joined the marching band so he wouldn’t have to take P.E.–a decision that somehow led to a brief stint playing trombone in a ska band. More recently, he ran a marathon, so he never has to do that again.
Aravind Valluvan
“The Cosmic Origins of the Periodic Table”
Tonight on Cosmic Secrets Live… How did Earth get all its gold? Can you whip up gold by mixing water and lead, or is there a hidden treasure factory bubbling deep underground? Spoiler alert: Earth hasn’t created any gold since it formed 4.5 billion years ago – then where did they really come from? In a quickfire 25 minutes, I’ll take you on a tour of the Universe’s ultimate fireworks show – where gold, oxygen, and every other element on the periodic table were created in the most energetic explosions ever. Think cosmic alchemy, supernova drama, and neutron star smash-ups. It’s the story of how the stuff in your jewelry, the oxygen in the air, and the calcium in your bones were born from stars going boom.
My journey into physics started when the only thing I could do at the cinema was whine about reversed time and quantum flying buses. I am now a Ph.D. student in astrophysics at UC San Diego working on a gamma-ray space telescope called COSI – which might, just maybe, find the gold I am looking for. I got my bachelor’s degree in physics from the Indian Institute of Technology Bombay and I have since traded-in the tropical rains for eternal sunshine. When I am not in my lab, I’m probably testing gravity on my mountain bike or working on my next kitchen disaster.
