Santa Fe Institute Collaboration Platform


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Contact: Chris Kempes, Project Principal Investigator,


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My long-term research goals are in understanding the causes of biological diversity and complexity. While natural selection is the ultimate cause for both, that level of explanation is not sufficient to understand how the myriad forms of life have come to exist. My research program is essentially a series of studies of increasingly more complicated biological systems. By understanding more simple systems, we then work toward understanding more complicated, and realistic, biological systems. My first projects were with a single species of free-living bacteria, one of the simplest living systems that have biological complexity. Since those first experiments, my work has branched out to include simple eukaryotes, predator-prey interactions, and microbial communities, all of which was possible because of the earlier work.  +
My research group develops theoretical approaches and computational models for the study of complex biological networks. We are especially interested in the dynamics and evolution of metabolism, whose complex web of small-molecule transformations underlies fundamental aspects of biological organization, from energy transduction to cell-cell communication. In addition to helping understand how biological systems function and evolve, we seek to apply our methods to the design and optimization of engineered networks for bioenergy and biomedicine applications.  +
My research interest has been centered on the evolution of Earth as a platform for the emergence of life and its subsequent evolution in the solar system. I place a particular emphasis on the dynamics of Earth s mantle, because of its parental nature to the continental and oceanic crust, its thermal and chemical interaction with the core, and its potential role in the evolution of the atmosphere and oceans. I enjoy cracking long-standing problems by combining physics, chemistry, applied math, and statistics. My research adopts a holistic, multidisciplinary approach, often involving the development of new observational and theoretical methods along the way. I m a freestyle geophysicist, and my group has worked on a variety of problems, including the evolution of plate tectonics, the dynamics of lithosphere and mantle plumes, chemical geodynamics, the origins of large igneous provinces, global water cycle and the history of ocean volume, and the thermal evolution of Mars, Venus, and exoplanets. The currently ongoing projects span the synergy of experimental rock mechanics and geodynamical modeling, the physics and chemistry of protoplanetary disks, early Earth geodynamics and environments, and the seismic imaging of the deep Earth using USArray.  +
Nicolle Zellner's research involves understanding the impact history of the Earth-Moon system. Professor Zellner studies the geochemical and chronological information obtained from lunar impact glasses in order to understand how many impact events the lunar surface has suffered. This information can then be applied to understanding the conditions required for life on Earth and how impact events may have affected its origin and evolution. She is also interested in understanding how biomolecules are transferred among planetary bodies, such as via comet or asteroid impacts, and how their chemistry may change in an impact event. Professor Zellner has been affiliated with the New York Center for Astrobiology, a NASA Astrobiology Institute, with research funding from the American Astronomical Society and the NASA Astrobiology Institute. Her lunar research is currently supported by NASA and the NSF, and her impact research is supported by NASA. Both projects have additionally been supported by Albion College faculty development funds.  +
Origin-of-Life/Prebiotic Chemistry, Organic Chemistry, Inorganic Chemistry  +
Oscillatory chemical reactions, spatial pattern formation, dynamical systems and neurobiology. Many phenomena in living systems involve periodic changes. In recent years, oscillating chemical reactions have blossomed from a curiosity studied by an obscure group of Russians to a major area of scientific research. We study these systems both experimentally and theoretically, from several points of view. We have achieved the first successful design of a new chemical oscillator. We have used our systematic design algorithm to expand the family of chemical oscillators from two accidentally discovered reactions to dozens of deliberately constructed systems. We continue to search for new types of oscillators while probing, both experimentally and computationally, the mechanisms of those that have already been discovered. Chemical oscillators can be "tweaked" to give a variety of related phenomena, many with suggestive connections to biological systems. We study spatial pattern formation, in which an initially homogeneous medium spontaneously gives rise to concentric rings, or spiral patterns resembling those seen in embryonic development or the aggregation of slime molds, and chemical chaos, in which concentrations oscillate deterministically, but in an aperiodic and apparently irreproducible fashion that depends sensitively on the initial conditions. We investigate Turing structures, patterns that arise from the interaction of reaction and diffusion, which have been suggested as a mechanism of spatial pattern formation in phenomena ranging from biological morphogenesis to geological stratification. We are interested in the phenomena that can occur when two or more oscillators are coupled together, either physically, i.e., by diffusion or an electrical connection, or chemically, by having two oscillators share a common chemical species. Such systems can give rise to surprising phenomena, such as "oscillator death," the cessation of oscillation in two coupled oscillating systems, or the converse, "rhythmogenesis," in which coupling two systems at steady state causes them to start oscillating. Coupled chemical oscillators provide simple models for networks of oscillatory neurons. We have begun to apply some of the insights gained in our studies of coupled chemical oscillators to the modeling of small neural networks. More recently, we have begun to study chemomechanical transduction, a phenomenon in which changes in chemical composition are converted into motion, e.g., in the periodic shrinking and swelling of a gel composed of a polymer that contains the catalyst for an oscillatory reaction immersed in a solution containing the reactants of the chemical oscillator.  
Professor Sara Walker is an astrobiologist and theoretical physicist interested in the origin of life and how to find life on other worlds. While there are many things to be solved, she is most interested in whether or not there are laws of life - related to how information structures the physical world - that could universally describe life here on Earth and on other planets. Sara's research team aims to develop new theory for living systems, to explain their origins, and to identify them on other worlds. The team studies living processes across many scales: from the microscale interactions of the chemistry happening within cells to the macroscale interactions of societies and planets. At Arizona State University she is Deputy Director of the Beyond Center for Fundamental Concepts in Science, Associate Director of the ASU-Santa Fe Institute Center for Biosocial Complex Systems and Assistant Professor in the School of Earth and Space Exploration. She is also Co-founder of the astrobiology-themed social website, and is a member of the Board of Directors of Blue Marble Space. She is active in public engagement in science, with appearances at the World Science Festival and on "Through the Wormhole" and NPR's Science Friday.  +
Research Interests: Before there was life on earth, molecules already displayed behaviour that resembles life, such as reproduction and evolution. My research focuses on complexity, in prebiotic evolution (origin of life) and in man-made synthetic, biological and chemical systems. I’m mainly working on building and refining computer models that mimic chemical systems. I’m fortunate to collaborate with Sijbren Otto’s research group here in Groningen, so I can use real data from their experiments in my work. Those researchers have created a system of chemical replicators that spontaneously form larger rings. The rings then accumulate into something like small fibres that, in turn, exhibit interesting behaviour. That system is the starting point for my models. I then combine it with insights from evolutionary biology to discover the circumstances that are necessary to initiate chemical evolution.  +
Research Interests: Biological homochirality, chiral symmetry breaking, molecular fitness landscapes, prebiotic evolution, and the RNA world as a model system.  +
Research Interests: Dr. Carja works to quantitatively understand the evolutionary architecture of intelligent, collective systems, using the tools of dynamical systems, network theory, population genetics, machine learning and statistical inference, and widely available, yet underused, datasets.  +
Research Interests: I am an evolutionary biologist broadly interested in the evolution of complex life. My Ph.D. training focused on the evolutionary stability of cooperation in the legume-rhizorium symbiosis. A similar evolutionary tension lies at the heart of all key events in the origin of complex life, termed the ‘Major Transitions in Evolution’: namely, how do new organisms arise and evolve to be more complex without succumbing to within-organism conflict? Studying the early evolution of multicellular organisms has been particularly difficult because these transitions occurred deep in the past, and transitional forms have largely lost to extinction. As a postdoc, I circumvented this constraint by creating a new approach to study the evolution of multicellularity: we evolved it de novo. Since founding my own research group at Georgia Tech in 2014, I have combined this approach with mathematical modeling and synthetic biology to examine how simple clumps of cells evolve to be more complex. Our research has shown how classical constraints in the origin of multicellularity –e.g., the origin of life cycles, multicellular development, cellular differentiation, and cellular interdependence– can be solved by Darwinian evolution.  +
Research Interests: I develop mathematical, computational, and conceptual models to study natural selection and the evolution of organismal design. My work makes testable predictions on topics ranging from microbial life history to sociality to cancer. My study of particular topics leads to syntheses of natural selection, robustness in relation to biological design, and the commonly observed patterns that emerge from information flow and scale.  +
Research Interests: Inclusive fitness, social coevolution, enzymatic cooperation, and RNA world evolution and kin selection.  +
Research Interests: My overarching research goal is to understand how evolution works to generate the remarkable diversity of living organisms around us today. In addition to various theoretical and conceptual interests, I have focused on evolutionary-developmental and molecular phylogenetic research on flowering plants. Additionally, we have begun a new empirical research program on the origins of life-like chemical systems.  +
Research Interests: My research interests are focused on the intersection of computer science, ecology, and evolutionary biology. This involves doing ''in silico'' experiments to understand general properties of ecology and evolution, and using principles from biology to solve computational problems. Often these goals intersect. Many of my ''in silico'' experiments are carried out on the Avida Platform. The primary theme uniting my research is that I am fascinated by how evolution shapes and is shaped by ecological communities. This often leads me to ask questions about how evolutionary processes generate and maintain diversity, particularly in the presence of spatial structure.  +
Research Interests: The origin and early evolution of life with an emphasis on RNA world theories. Non-coding RNAs as tools in artificial gene regulation and synthetic biology.  +
Research Interests: Using a combination of analytical, simulation-based and lab-experimental techniques, we study different biological systems that possess strong niche construction elements, including fire-prone flora with plant traits that enhance flammability, learning organisms that alter the form and frequency of their stimuli, bacteria that produce anti-bacterial toxins, and hosts and pathogens that continually coevolve. Recently, we have focused on how the incorporation of spatial structure can drastically affect the eco-evolutionary dynamics of these and other niche construction systems. We have also started to explore (both theoretically and experimentally) how altruistic forms of niche construction evolve in relation to various forms of population structure.  +
Stephen Freeland is an evolutionary biologist whose research focuses upon how and why life on our planet evolved a system of genetic encoding. He received Bachelor s degree in zoology from Oxford University, a Master s degree in Computing and Mathematics from the University of York, UK, and a Ph.D from Cambridge University s Department of Genetics before crossing the Atlantic to pursue a scientific career in the USA. A Human Frontiers Science Program post-doctoral fellowship at Princeton University led to a faculty position in bioinformatics at UMBC, where Stephen was tenured in 2007. His subsequent marriage to a member of the US Navy led him to relocate to Hawaii in 2009 where he worked as the project manager for the University of Hawaii node of the NASA Astrobiology Institute the UHNAI supervising a highly interdisciplinary team of scientists who seek to understand how habitable environments are formed within the cosmos. Throughout this period, his research focus has been how and why life on our planet established a system of genetic coding ( the evolution of the genetic code ). In 2013, Stephen returned to UMBC as Director of the Interdisciplinary Studies Program (INDS) where he complements his research interests in astrobiology, with a focus upon the interface of science and religion and (more recently) using the full spectrum of creative arts to visualize and communicate social science, natural science and engineering.  +
The Goldman lab studies protein and proteome evolution with a special focus on early cellular life and the emergence of ancient metabolic systems. The evolutionary tree of life coalesces into a single root representing an ancestral population that lived about 3.5 billion years ago. Many features of these ancestors are still buried within the genomes of organisms alive today. Evolution over billions of years has obscured the ancient signature of most of these features, making them difficult to identify. Our lab takes advantage of the tremendous growth in genomic and proteomic data to find these ancient genes and reassemble them into metabolic and physiological systems. Much of this work begins with our database, which brings multiple independent lines of evidence together into a single framework. We develop complex algorithms and use a range of computational biology methods to identify ancient genes and test hypotheses about early evolutionary history.  +
The Kacar Lab investigates key questions regarding molecular mechanisms of evolution and the origins of life. We are interested in understanding how the ancestral behaviors of proteins and their host systems change through time. The overall goal of our work is to assess the possible environmental impacts of ancient enzymes on global-scale signatures that record biological activity. What do we aspire to know? -What can the phenotypes of inferred ancient proteins tell us about the origins of critical metabolic pathways? - How can we reconstruct ancient biological functions representing key evolutionary innovations of our planet s past? - Did life in the past function or evolve similarly to life today? How do we travel in time? To answer these questions, we attempt to combine evidence from the Earth's environmental and biological past. We use revenant genes as a proxy to understand critical elements of life s origins and early evolution. We use a new approach that reconstructs ancient DNA using phylogenetics, then we engineer this ancient DNA inside microbial genomes, and finally we reanimate these ancient sequences as revenant genes to produce ancient enzymes with phenotypes that can be studied. Our overarching goal is to use this paleophenotype reconstruction method to interpret ancient biosignatures.  +