Santa Fe Institute Collaboration Platform


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Contact: Chris Kempes, Project Principal Investigator,


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<span>Research Interests: In the broadest terms, Chris aims to find theories and principles that apply to a wide range of biological scales and hierarchies. Chris generally focuses his work on biological architecture—which may include phenomena ranging from explicit biological morphology to metabolic and genetic network structure—as an intermediate between organism physiology and environmental conditions. Mathematical and physical theories lie at the heart of his methodologies to predict how evolution has shaped architecture and how this, in turn, forms a foundation for reliable predictions of environmental response and interaction. His work spans the scales of genetic information architecture to the morphology of microbial individuals and communities to the regional variation of plant traits and their feedback with climate and available resources. In so doing, he aims to connect these first-order trends to the limitations imposed by environments in order to predict specific evolutionary events and consequences. Several collaborations with experimentalists and theorists have led to models that inform experiments and assimilate empirical data in fields including single-cell experimental biology and forest dynamics.</span><span><span></span></span>  +
A computer scientist by training, an evolutionist by historical accident, an academic against better judgement, and a professional wanderer by choice. As a graduate student I spent several years at the Santa Fe Institute (SFI), which largely shaped my scientific outlook. After obtaining a Ph.D. in computer science, I worked on many short-term research, computing, and teaching projects all over the world. Currently I am just traveling around a bit, and will be looking for a new adventure sometime soon. Next to my scientific articles, I also regularly publish popular science pieces and travel stories, and post pictures from my hikes.  +
Biography  +
D. Eric Smith received the Bachelor of Science in Physics and Mathematics from the California Institute of Technology in 1987, and a Ph.D. in Physics from The University of Texas at Austin in 1993, with a dissertation on problems in string theory and high-temperature superconductivity. From 1993 to 2000 he worked in physical, nonlinear, and statistical acoustics at the Applied Research Labs: U. T. Austin, and at the Los Alamos National Laboratory. From 2000 he has worked at the Santa Fe Institute on problems of self-organization in thermal, chemical, and biological systems. A focus of his current work is the statistical mechanics of the transition from the geochemistry of the early earth to the first levels of biological organization, with some emphasis on the emergence of the metabolic network.  +
David’s research focuses on the evolutionary history of information processing mechanisms in biology and culture. This includes genetic, neural, linguistic and cultural mechanisms. The research spans multiple levels of organization, seeking analogous patterns and principles in genetics, cell biology, microbiology and in organismal behavior and society. At the cellular level David has been interested in molecular processes, which rely on volatile, error-prone, asynchronous, mechanisms, which can be used as a basis for decision making and patterning. David also investigates how signaling interactions at higher levels, including microbial and organismal, are used to coordinate complex life cycles and social systems, and under what conditions we observe the emergence of proto-grammars. Much of this work is motivated by the search for 'noisy-design' principles in biology and culture emerging through evolutionary dynamics that span hierarchical structures. Research projects includes work on the molecular logic of signaling pathways, the evolution of genome organization (redundancy, multiple encoding, quantization and compression), robust communication over networks, the evolution of distributed forms of biological information processing, dynamical memory systems, the logic of transmissible regulatory networks (such as virus life cycles) and the many ways in which organisms construct their environments (niche construction). Thinking about niche constructing niches provides us with a new perspective on the major evolutionary transitions. Many of these areas are characterized by the need to encode heritable information (genetic, epigenetic, auto-catalytic or linguistic) at distinct levels of biological organization, where selection pressures are often independent or in conflict. Furthermore, components are noisy and degrade and interactions are typically diffusively coupled. At each level David asks how information is acquired, stored, transmitted, replicated, transformed and robustly encoded. The big question that many are asking is what will evolutionary theory look like once it has become integrated with the sciences of adaptive information (information theory and computation), and of course, what will these sciences then look like? Krakauer was previously chair of the faculty and a resident professor and external professor at the Santa Fe Institute. A graduate of the University of London, where he went on to earn degrees in biology, and computer science. Dr. Krakauer received his D.Phil. in evolutionary theory from Oxford University in 1995. He remained at Oxford as a postdoctoral research fellow, and two years later was named a Wellcome Research Fellow in mathematical biology and lecturer at Pembroke College. In 1999, he accepted an appointment to the Institute for Advanced Study in Princeton and served as visiting professor of evolution at Princeton University. He moved on to the Santa Fe Institute as a professor three years later and was made faculty chair in 2009. Dr. Krakauer has been a visiting fellow at the Genomics Frontiers Institute at the University of Pennsylvania and a Sage Fellow at the Sage Center for the Study of the Mind at the University of Santa Barbara. In 2012 Dr. Krakauer was included in the Wired Magazine Smart List as one of 50 people "who will change the World." David Krakauer also served as the Director of the Wisconsin Institute for Discovery, the Co-Director of the Center for Complexity and Collective Computation, and was a Professor of Genetics at the University of Wisconsin, Madison.  
Dr. Karyn Rogers joined the faculty at Rensselaer Polytechnic Institute in 2013 after serving as a Research Scientist at the Carnegie Institution of Washington, Assistant Professor at the University of Missouri, and a Deep Ocean Exploration Institute Postdoctoral Scholar at Woods Hole Oceanographic Institution. Dr. Rogers completed her PhD in Earth and Planetary Sciences at Washington University in St. Louis, with previous degrees awarded from Stanford University (M.S. 2001) and Harvard University (A.B. 1996). Dr. Rogers is a member of the New York Center for Astrobiology (NYCA) and the Institute for Data Exploration and Applications (IDEA). Dr. Rogersâ research focuses on the relationships between microbial communities and environmental conditions in extreme ecosystems, and is broadly applied to understanding the nature of the origin of life on Earth, the potential for life throughout the solar system, and the extent of life in modern extreme environments. To advance our understanding of environmental microbiomes in these systems, Dr. Rogers research program includes field research in early Earth and Mars analog environments as well as laboratory experimental studies of microbial behavior under extreme conditions. Additionally, the group is exploring the viability of abiotic synthesis of biomolecules over a range of early Earth conditions. The driving question in this research is how realistic environmental conditions combine to form habitable niches that can both support the early emergence of life as well as the long-term survival of life in these environments. Dr. Rogersâ fieldwork includes several terrestrial hydrothermal systems including Cerro Negro Volcano, Nicaragua, the Vulcano shallow marine hydrothermal system in Italy, and several modern deep-sea mid-ocean ridge environments. These field endeavors are combined with extensive laboratory analytical and experimental techniques to develop a holistic picture of functional microbial ecosystems. More specifically, laboratory techniques include cultivation of extremophiles under high pressure, high temperature, acidic, and anaerobic conditions; a next-generation genomics approach to determine the functional environmental microbiome in extreme systems; geochemical analyses and modeling of environmental and bioenergetics parameters; and the synthesis of these datasets using novel data analytics.  
Dr. Laurie Barge is a research scientist in Astrobiology at the NASA Jet Propulsion Laboratory in Pasadena, CA, and is also affiliated with the Blue Marble Space Institute of Science in Seattle, WA and the Oak Crest Institute of Science in Monrovia, CA. Laurie received her B.S. in Astronomy and Astrophysics from Villanova University and her Ph.D. in Geological Sciences from the University of Southern California. Laurie studies the emergence of life on Earth and ways to search for life elsewhere. Her focus is on how minerals affect chemistry for the emergence of life and habitability on wet rocky planets, including early Earth, Mars, and "ocean worlds" such as Jupiter's moon Europa and Saturn's moon Enceladus. Dr. Barge's research group seeks to understand mineral-driven organic reactions and geochemistry relevant to biological and prebiotic systems. This work includes planetary environment simulations in the lab including making mini vent chimneys, making early Earth and Mars minerals, and simulating the energy in ocean systems using fuel cells. At JPL Laurie is also the Investigation Scientist for the HiRISE instrument on the Mars Reconnaissance Orbiter.  +
Dr. Mary A. Voytek took charge of NASA s Astrobiology Program on September 15, 2008, as Senior Scientist for Astrobiology in the Science Mission Directorate at NASA HQ. In addition to managing the Core and Strategic Astrobiology Programs, in 2015, Dr. Voytek formed Nexus for Exoplanet System Science (NExSS), a systems science initiative by NASA, to search for life on exoplanets. Prior to NASA, Dr. Voytek headed the USGS Microbiology and Molecular Ecology Laboratory in the U.S. Geological Survey in Reston, VA. Dr. Voytek s primary research interest is aquatic microbial ecology and biogeochemistry. She has studied environmental controls on microbial transformations of nutrients, xenobiotics, and metals in freshwater and marine systems. She has worked in several extreme environments including Antarctica, the arctic, hypersaline lakes, deep-sea hydrothermal vents, and terrestrial deep- subsurface sites. She has served on several advisory groups to Department of the Interior, Department of Energy, the National Science Foundation and NASA, including the Planetary Protection Subcommittee. She has also supported NASA s Astrobiology Program serving as a NASA representative to a number of COSPAR convened studies exploring the potential for life in the universe. She has held positions in several science societies and is currently a board member of the American Geophysical Union.  +
Dr. Maurer is interested in the abiogenesis from both the origins-of-life and artificial life perspectives. She builds model cells from amphiphiles, and examines possible life-like properties, such as metabolism or growth and division. Her current projects include: - Changes in populations of model cells when put under environmental pressure. The goal of this work is to examine the ability of cells to survive in the absence of reproduction (prebiotic conditions). This project seeks to model the evolution of cellular containers available on early Earth. - Damage to model cells from ultraviolet light. This seeks to address the ability of cells to survive in the absence of an atmosphere. Comets, meteors, and asteroids are exposed to greater UV radiation. Also certain stars, the distance a planet is from its star, and the atmosphere of the planet can all lead to higher degrees of UV radiation in locations where life may now be forming. - Artificial photosynthesis under prebiotic conditions generating reduced carbon and a proton gradient using transmembrane electron transport.  +
Dr. Templeton is a Geomicrobiologist with a special focus on microbe-mineral interactions. At the University of Colorado, Alexis Templeton has established field and laboratory based studies of biomineralization processes in subsurface terrestrial systems in Colorado, the High Arctic and Oman. These projects include mechanistic studies of water/rock interactions, such as the hydration of mafic and ultramafic rocks, and the isolation and characterization of Fe, Mn, S and hydrogen cycling bacteria dependent upon geological energy sources. Prof. Templeton trains students and postdoctoral scholars in the realms of geochemistry, geomicrobiology and astrobiology and supervises the Raman Chemical Imaging laboratory. Prof. Templeton is also the Principal Investigator of the 'Rock-Powered Life' NASA Astrobiology Institute.  +
I am interested in molecular evolution and the biochemistry of catalytic RNAs (ribozymes). Research in my lab utilizes powerful in vitro evolution techniques to discover RNA sequences with new or improved functions, for example, in regard to RNA-metal ion interactions. We are particularly keen to use these techniques to test fundamental evolutionary hypotheses, such as the antiquity of recombination.  +
In thinking about Geobiology, two facts offer a clear guide. The first is that microbes dominate elemental cycling on modern Earth. The second is the age of Earth. Together, they imply a long co-evolutionary relationship between the geochemistry of earth surface environments and the activity of their microbial inhabitants. Our research in Geobiology is aimed at understanding this relationship over the long arc of Earth's history, and at making that understanding as quantitative as possible. By studying modern microbes in culture or in the natural environment, we can learn in great detail about their metabolisms. In particular, modern microbial metabolisms can produce characteristic chemical or isotopic signatures, sometimes in their biosynthetic products, sometimes in their waste products. This knowledge is then put to task, with the presence of these signatures in geological materials used to infer the appearance and activity of microbes in the deep past. Interpretations of these microbial bio-signatures in the ancient rock record are based on a critical peculiar assumption: their metabolic origin has not changed in a long, long time. This is a funny assumption for a couple of reasons. Microbial metabolisms can evolve on human timescales, as recognized by anyone who has hesitated going to the hospital for fear of a super bug . In deep time, the paradox becomes even more dramatic. There are 5x1030 bacteria and archaea on Earth today. Mean turnover times of natural microbial populations are days to millenia (10-2 to 103 years). Assuming that a similar-sized microbial biosphere has been maintained since 3.5 billion years ago, the number of microbes that have ever lived on Earth is awesome: >1037 to 1042. In broad brush, though not in detail, these numbers can be thought of as the number of individual microbial evolution experiments run by Nature. Even if only a small percentage of these impacted the microbial traits that produce geologically significant bio-signatures, it seems incredible that the characteristic chemical or isotopic products of the relevant metabolisms have remained immune to evolutionary modification. We investigate this paradox in a couple of ways. First, we go out in the field and collect large suites of samples from well-characterized modern and paleo environments, and see if the isotopic and geochemical patterns that we observe are consistent with bio-signatures from microbial cultures in the laboratory. Second, we take modern microbial populations and subject them to experimental evolution in the lab, and see if their adaptive changes have isotopic or geochemical consequences that can inform our interpretations of bio-signatures from the ancient rock record. This work cuts across many disciplines, from molecular biology to geochronology, and is rooted in real-time hypothesis testing, from one outcrop (and one generation) to the next. As a result, it is totally collaborative, highly uncertain, and wicked fun. Although our culturing work currently focuses on cyanobacteria and sulfate-reducing bacteria and archea (the alpha and omega of the global carbon cycle) and recent field studies have focused on bizarre biogeochemical changes at the beginning and end of the Proterozoic Eon, our research is, at its root, hypothesis-based. Once a stimulating geobiological question is identified (no hard task given the critical mass of geobio types here at CU Boulder!), we design new field studies, analytical techniques, and laboratory experiments to test it.  
Kate received a MSc in chemistry from the University of Warsaw, Poland, studying synthetic organic chemistry. In grad school, she worked with professor Pier Luigi Luisi from University Roma Tre and Jack Szostak from Harvard University. She studied RNA biophysics, small peptide catalysis and liposome dynamics, in an effort to build a chemical system capable of Darwinian evolution. Kate's postdoctoral work in Ed Boyden's Synthetic Neurobiology group at MIT focused on developing novel methods for multiplex control and readout of mammalian cells. Her full first name spells Katarzyna; she goes by Kate for the benefit of friends speaking less consonant-enriched languages.  +
Linden is a farmer and scientist, with a passion for soils, chemistry, plants, food, languages, and water. She recently earned her Masters degree from the University of California, Berkeley in Biogeochemistry. She is currently cultivating relationships with communities in northern New Mexico through science and math education, as well as, farming. As a member of the Complexity Explorer Team, she is excited to help share complexity science with the non-traditional students that SFI's online education platform serves!  +
Loren Williams was born in Seattle, Washington. He received his B.Sc. in Chemistry from the University of Washington where he worked in the laboratory of Martin Gouterman. He received his Ph.D. in Physical Chemistry from Duke University, where he worked the laboratory of Barbara Shaw. He was an American Cancer Society Postdoctoral Fellow first at Duke then at Harvard. From 1988 to 1992 he was an NIH Postdoctoral Fellow with Alexander Rich in the Department of Biology at MIT. He joined the School of Chemistry and Biochemistry at Georgia Tech in 1992 where is he currently a professor. Loren received an NSF CAREER Award in 1995, and a Sigma Xi Award for best paper from Georgia Tech in 1996. He received SAIC Student Advisement Award in 2012, the Petit Institute "Above and Beyond" Award in 2012, Georgia Tech's Faculty Award for Academic Outreach in 2013, and the Georgia Tech College of Science Faculty Mentor Award in 2013. He was director of the NASA Astrobiology Institute funded Ribo Evo Center from 2008 to 2015 and is currently Directer of the NASA-funded Center for the Origin of Life.  +
Lynn Rothschild is passionate about the origin and evolution of life on Earth or elsewhere, while at the same time pioneering the use of synthetic biology to enable space exploration. Just as travel abroad permits new insights into home, so too the search for life elsewhere allows a more mature scientific, philosophical and ethical perception of life on Earth. She wears several hats as a senior scientist NASA s Ames Research Center and Bio and Bio-Inspired Technologies, Research and Technology Lead for NASA Headquarters Space Technology Mission Directorate, as well as Adjunct Professor at Brown University, and the University of California Santa Cruz. Her research has focused on how life, particularly microbes, has evolved in the context of the physical environment, both here and potentially elsewhere. She founded and ran the first three Astrobiology Science Conferences (AbSciCon), was the founding co-editor of the International Journal of Astrobiology, and is the former director of the Astrobiology Strategic Analysis and Support Office for NASA. Astrobiology research includes examining a protein-based scenario for the origin of life, hunting for the most radiation-resistant organisms, and determining signatures for life on extrasolar planets. More recently Rothschild has brought her creativity to the burgeoning field of synthetic biology, articulating a vision for the future of synthetic biology as an enabling technology for NASA s missions, including human space exploration and astrobiology. Since 2011 she has been the faculty advisor of the award-winning Stanford-Brown iGEM team, which has pioneered the use of synthetic biology to accomplish NASA s missions, particularly focusing on the human settlement of Mars, astrobiology and such innovative technologies as BioWires and making a biodegradable UAS (drone) and a bioballoon. Her lab will be move these plans into space in the form of the PowerCell synthetic biology secondary payload on a DLR satellite, EuCROPIS, scheduled to launch in July 2017. She is a fellow of the Linnean Society of London, The California Academy of Sciences and the Explorer s Club. In 2015, she was awarded the Isaac Asimov Award from the American Humanist Association, and was the recipient of the Horace Mann Award from Brown University, and has been a NASA Innovative Advanced Concepts (NIAC) fellow three times, most recently in 2018. She frequently appears on documentaries, tv and radio, and lectures worldwide, including Windsor Castle, Comi Con and the Vatican.  
Marcelo I. Guzman is an Associate Professor of Chemistry in the University of Kentucky. In 2013, he received a NSF CAREER award. He holds a Licentiate in Chemistry degree from National University of Tucuman, Argentina (2000). He received undergraduate and graduate research fellowships from the Research Council of the National University of Tucuman (1999 to 2002), to perform research in various projects in the Organic Chemistry Department. In 2001, he was awarded The Argentine Chemical Society award and the National Research Council of Argentina (CONICET) offered him a fellowship as the top ranked Chemistry graduate. In 2002, he was an Andrew W. Mellon Fellow at the Metropolitan Museum of Art (New York) working on Paper and Photograph Conservation in the Sherman Fairchild Center. He earned his Ph.D. at the California Institute of Technology (Caltech, 2007) working on ice chemistry with Michael R. Hoffmann. For his postdoctoral experience he joined the Origins of Life Initiative at Harvard University as an Origins Fellow working with Scot T. Martin.  +
Michael Lachmann is a theoretical biologist whose primary interests lie in understanding evolutionary processes and their origins. He received his B.Sc. at the Tel Aviv university in the interdisciplinary program for fostering excellence founded by the late Yehuda Elkana. He received his Ph.D. in Biology at Stanford University, was a postdoctoral fellow at the Santa Fe Institute, and worked at the Max Planck institute for mathematics in the sciences. Between 2004 and 2014 he was a group leader at the Max Planck Institute for evolutionary anthropology in Leipzig working, among others, on the sequencing of the Neanderthal genome. Michael's work focused on the interface between evolution and information. He studied how an ant colony could make global decisions based on the information acquired by the single ants, on the connection between the fitness advantage a signal provides and the information it provides, on how costly signals in biology need to be to be believable, and on epigenetic information transfer. He is a Professor at the Santa Fe Institute.  +
Michael New was born and raised in New York City, specifically the Bronx and Queens. Tired of the fast-paced urban experience, he decamped to the wilds of New Haven, CT. After four years of experiments aimed at settling the age-old question of whether Pepe's or Sally's made the better pizza ended inconclusively, Yale University banished him from Elm City with a BS in chemistry. Undeterred, he returned home, where he earned a PhD in chemical physics at Columbia University in 1994. In search of the world's worst pastrami sandwich, he then relocated to the left coast, specifically to the People's Republic of Berkeley, where he held post-doctoral positions in the UC Berkeley chemistry department and the UC San Francisco department of pharmaceutical chemistry. He is quick to point out that, due to the presence of deer in his backyard, Berkeley is the most rural place he has ever lived. Following a long-time addiction to Star Trek, Michael joined the civil servant staff of the Exobiology Branch at NASA Ames Research Center in 1998. He was disappointed when he wasn't issued a phaser and a stretchy red shirt. In 2001, Michael agreed, despite the advice of friends and strangers alike, to become the Deputy Branch Chief where he dealt with several major safety and financial crises, in the process learning more than he never wanted to know about the Legionella bacterium and full-cost accounting. Shaken by this compound exposure to bacteria and accounting, and having discovered the worst pastrami sandwich in the world (in a deli in Berkeley who's name must not be spoken aloud) and an unexplainable interest in NASA management, Michael relocated back to the east and became the Astrobiology Discipline Scientist at NASA HQ.  +
My interests stem from my basic curiosity to understand matter and energy relationships in biological processes, especially those that may lead to insights into how life started. Current projects seek to investigate hydrogen oxidation and carbon reduction in hydrothermal vent simulation experiments, the sulfur isotope fractionation factors of the enzymes involved in microbial dissimilatory sulfate reduction, and direct interspecies electron transfer as a mechanism of syntrophic metabolic coupling. Other topics include the microbial ecology of hot springs in Japan with relevance to early ocean chemistry, and metal abundance distributions across microbial taxa.  +