FAQ: The NASA Astrobiology Institute for Universal Biology at UIUC
PI: N. Goldenfeld. Co-I: E. Branscomb, I. Cann, S. Dawson (UC Davis), L. Deville, B. Fouke, P. Hastings (Baylor), Z. Luthey-Schulten, R. Mackie, G. Olsen, S. Rosenberg (Baylor), C. Werth (U. Texas), R. Whitaker, C.R. Woese (deceased)
What are the big questions addressed at the IUB?
- Why does the phenomenon of life occur at all?
- What general principles govern how it arises in different environments and planets?
- How did life evolve before there were genes, species, individual organisms and cells?
- What was the nature of evolution at this early time?
How are these questions being addressed at the IUB?
- Develop a mathematical understanding of the general physical principles underlying the emergence of life and the open-ended growth of complexity. Life to us means evolvable systems that spontaneously create ever-increasing levels of hierarchical organization with multiple levels of feedback. We wish to understand whether the phenomenon of life is a generic one, inexorably the outcome of the laws of physics, and what governs its complexity and diversity.
- Constrain the nature of life before the Last Universal Common Ancestor (LUCA). The term “Last Universal Common Ancestor” implies that there were earlier organisms and modern life by chance descended from one of them. However, our prior work and the preliminary results in this proposal suggest that on generic and universal grounds, the modern era of vertical descent was preceded by a communal state for which there was no notion of “tree of life”. We wish to explore the properties of this state -- the progenote -- using detailed and sophisticated analyses of core translational machinery, building in some sense the genomic analogue of the Hubble telescope to see further back in time than has been possible by simple comparative genomics.
- Explore how life made the transition from a communal progenote state to the present era of vertically-dominated evolution. To do this, we propose an unprecedentedly detailed study of the Archaeal domain and its transition to the Eukaryote lineage. The significance of this research is that we will obtain an understanding of why there are only three Domains of life, and not many more. We expect that our conclusions will be of general applicability to all life that balances the requirements of energy utilization, information processing, replication and evolvability.
- Determine what factors govern the rate of evolution, and how organisms interact with their environment. How do cells observe their environment and regulate their response to stress? How do cells regulate their ability to evolve? We will answer these questions through detailed experimentation with microbial systems in culture and in microfluidic devices.
What are the hypotheses being explored?
(1) Early life was a collective. In 2006, Nigel Goldenfeld and Carl Woese developed a mathematical theory for the dynamics of a genetic code, co-evolving with the proteins as organisms became more complex over evolutionary time. Early life would have used much less finely-tuned cellular machinery, and would therefore not have required precision in the amino acids building proteins. Early translation would have been predominantly statistical, producing equivalence classes of amino acids to build proteins, and over evolutionary time refining these equivalence classes into the genetic code we have today. These dynamics were explored in numerical experiments using digital life --- artificial organisms built from computer code that compete for environmental resources, possess primitive cellular translational machinery, and are able to evolve through plasticity of their genomes. Goldenfeld and Woese discovered that the genetic code’s statistical properties could only be explained if early evolution was dominated by strong horizontal gene transfer, distinct from today’s era where well-defined lineages evolve. This research led to the idea of a collective state of life with no notion of species, a weak genotype/phenotype distinction, and perhaps not even a well-defined notion of organismal individuality. The genomic signatures of this state, the “progenote”, are the main target of our NAI’s activity.
(2) Early life on Earth arose in a geochemical environment with serpentinization. Team member Elbert Branscomb and Michael Russell (JPL-NASA) are advocating the notion that the proton gradient found across the membrane of modern cells is a vestige of the conditions from which early life emerged. For this to be true, early life would have had to evolve in an alkaline hydrothermal event such as Lost City. The thermodynamics and geochemistry of this scenario are an active part of our research.
What is Universal Biology?
The analysis leading up to the idea of the progenote state of life was rather general: it required of life that it be capable of information processing, able to sense its environment, and endowed with primitive genome dynamics that includes gene transfer as well as vertical evolution. Because this analysis focuses on the dynamical processes of evolution, rather than the specific molecules that instantiate these processes, it is an example of “universal biology”.
How are these questions being explored?
Theme 1: General physical principles underlying the emergence of life: The target is to obtain an understanding of the physical laws that drive or constrain the open-ended growth of complexity, in the same way that weak gradients in nature drive currents that are constrained by linear irreversible thermodynamics. The focus is mathematical basis for the emergence of evolvable dynamical processes, capable of instantiation in molecular biochemistry, not necessarily restricted to that particular realization, and fundamentally reliant on collective effects.
Theme 2: Windows on the progenote: We are identifying constraints on the nature of this universal, collective phase of life, through detailed analysis of evolutionary relationships between components of modern translation machinery.
Theme 3: Emergence of cellular machinery from the breakdown of the progenote state: We are exploring the emergence of three Domains of life from the progenote. The transition from a horizontal-dominated to a vertical-dominated mode of evolution would have left signatures, in particular the freezing in of particular cellular functions. With the large number of genomes from different lineages that have been sequenced, we have for the first time an opportunity to explore this in some detail. Through extensive mining of the available genomes, we will determine the diversity of mechanisms (emphasis on components) of “early life processes” such as translation, transcription and replication, and design experiments to determine which of the extant processes have crossed Woese’s proposed “Darwinian threshold”.
Theme 4: How cells respond to their environments: What is the response of microbes to variations in environmental conditions and the speed with which evolutionary adaptation takes place? Microbial response with respect to information exchange, metabolism and biochemistry are being tracked using next generation genomic and transcriptomic techniques in the context of simultaneously parameterized micro-environmental physical and chemical conditions. This is a critically important question for astrobiology, because it dictates the nature of, and speed of evolution, and this may be a factor in assessing the forms of life that may exist elsewhere in the universe.
Impact: The study of the emergence of life requires full consideration of collective biological interactions, but the study of these mechanisms in present day biology is still in its infancy. Our work will transform our understanding of collective mechanisms in biology and the origin of cellular organization through three focus areas: (1) Field observation and characterization of the mechanisms by which individuals contribute to the collective evolution of a community through horizontal gene transfer, eg. as mediated by viruses, thus engendering system-scale stability and diversity; (2) Laboratory studies of rapid evolution and collective community dynamics under extreme conditions, (e.g.) using synthetic biology techniques to engineer biofilms and manipulate their emergent properties including antibiotic resistance, cellular communication and immunity; (3) Theoretical and computational studies of co-evolutionary dynamics in natural and digital life systems, using cooperative game theory and novel mathematical methods to explore the open-ended growth of complexity, the pervasiveness of modularity at all levels of biological organization, and the emergence of well-defined lineages from early life.
Our NASA Astrobiology Institute coordinates the efforts of a diverse and interdisciplinary team of microbiologists, virologists, chemists, geologists, systems and synthetic biologists, computational biologists and physicists. The scope of the project includes not only systems evolutionary biology, but also observational work in a variety of environments with distinctive gradients or extreme aspects, including Yellowstone National Park. Ultimately, our project will provide a sound conceptual and quantitative framework for estimating the timescales and the nature of chemical self-organization leading to life on other planets.