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All sourcesNASA NTRSDOE OSTI
NASA NTRS2016

Synthetic Astrobiology

Synthetic biology - the design and construction of new biological parts and systems and the redesign of existing ones for useful purposes - has the potential to transform fields from pharmaceuticals to fuels. Our lab has focused on the potential of synthetic biology to revolutionize all three major parts of astrobiology: Where do we come from? Where are we going? and Are we alone? For the first and third, synthetic biology is allowing us to answer whether the evolutionary narrative that has played out on planet earth is likely to have been unique or universal. For example, in our lab we are re-evolving the biosynthetic pathways of amino acids in order to understand potential capabilities of an early organism with a limited repertoire of amino acids and developing techniques for the recovery of metals from spent electronics on other planetary bodies. And what about the limits for life? Can we create organisms that expand the envelope for life? In the future synthetic biology will play an increasing role in human activities both on earth, in fields as diverse as human health and the industrial production of novel bio-composites. Beyond earth, we will rely increasingly on biologically-provided life support, as we have throughout our evolutionary history. In order to do this, the field will build on two of the great contributions of astrobiology: studies of the origin of life and life in extreme environments.

synthetic biology↗
NASA NTRS1998

The universal ancestor

A genetic annealing model for the universal ancestor of all extant life is presented; the name of the model derives from its resemblance to physical annealing. The scenario pictured starts when "genetic temperatures" were very high, cellular entities (progenotes) were very simple, and information processing systems were inaccurate. Initially, both mutation rate and lateral gene transfer levels were elevated. The latter was pandemic and pervasive to the extent that it, not vertical inheritance, defined the evolutionary dynamic. As increasingly complex and precise biological structures and processes evolved, both the mutation rate and the scope and level of lateral gene transfer, i.e., evolutionary temperature, dropped, and the evolutionary dynamic gradually became that characteristic of modern cells. The various subsystems of the cell "crystallized," i.e., became refractory to lateral gene transfer, at different stages of "cooling," with the translation apparatus probably crystallizing first. Organismal lineages, and so organisms as we know them, did not exist at these early stages. The universal phylogenetic tree, therefore, is not an organismal tree at its base but gradually becomes one as its peripheral branchings emerge. The universal ancestor is not a discrete entity. It is, rather, a diverse community of cells that survives and evolves as a biological unit. This communal ancestor has a physical history but not a genealogical one. Over time, this ancestor refined into a smaller number of increasingly complex cell types with the ancestors of the three primary groupings of organisms arising as a result.

NASA Discipline Exobiology↗
NASA NTRS1992

Biodiversity: molecular biological domains, symbiosis and kingdom origins

The number of extant species of organisms is estimated to be from fewer than 3 to more than 30 x 10(6) (May, 1992). Molecular biology, comparative genetics and ultrastructural analyses provide new insights into evolutionary relationships between these species, including increasingly precise ideas of how species and higher taxa have evolved from common ancestors. Accumulation of random mutations and large macromolecular sequence change in all organisms since the Proterozoic Eon has been importantly supplemented by acquisition of inherited genomes ('symbiogenesis'). Karyotypic alterations (polyploidization and karyotypic fissioning) have been added to these other mechanisms of species origin in plants and animals during the Phanerozoic Eon. The new evolution concepts (coupled with current rapid rates of species extinction and ignorance of the extent of biodiversity) prompted this analysis of the field of systematic biology and its role in the reorganization of extant species into higher taxa. Two superkingdoms (= Domains: Prokaryotae and Eukaryotae) and five kingdoms (Monera = Procaryotae or Bacteria; Protoctista: algae, amoebae, ciliates, foraminifera, oomycetes, slime molds, etc.; Mychota: 'true' fungi; Plantae: one phylum (division) of bryophytes and nine phyla of tracheophytes; and Animalia) are recognized. Two subkingdoms comprise the monera: the great diverse lineages are Archaebacteria and Eubacteria. The criteria for classification using molecular, ultrastructural and genetic data for this scheme are mentioned. For the first time since the nineteenth century, logical, technical definitions for each group are given with their time of appearance as inferred from the fossil record in the primary scientific literature. This classification scheme, which most closely reflects the evolutionary history, molecular biology, genetics and ultrastructure of extant life, requires changes in social organization of biologists, many of whom as botanists and zoologists, still behave as if there were only two important kingdoms (plants and animals).

Non-NASA Center↗
NASA NTRS2000

Detection of Extraterrestrial Ecology (Exoecology)

Researchers in the Astrobiology Technology Branch at Ames Research Center have begun investigating alternate concepts for the detection of extraterrestrial life. We suggest searching for extraterrestrial ecology, exoecology, as well as for extraterrestrial biology, exobiology. Ecology describes the interactions of living things with their environment. All ecosystems are highly constrained by their environment and are constrained by well-known system design principles. Ecology could exist wherever there is an energy source and living I things have discovered some means to capture, store, and use the available energy. Terrestrial ecosystems use as energy sources, light, organic molecules, and in thermal vents and elsewhere, simple inorganic molecules. Ecosystem behavior is controlled by matter and energy conservation laws and can be described by linear and nonlinear dynamic systems theory. Typically in an ecosystem different molecules are not in chemical equilibrium and scarce material is conserved, stored, or recycled. Temporal cycles and spatial variations are often observed. These and other -eneral principles of exoecology can help guide the search for extraterrestrial life. The chemical structure observed in terrestrial biology may be highly contingent on evolutionary accidents. Oxygen was not always abundant on Earth. Primitive sulfur bacteria use hydrogen sulfide and sulfur to perform photosynthesis instead of water and oxygen. Astrobiologists have assumed, for the sake of narrowing and focusing our life detection strategies, that extraterrestrial life will have detailed chemical similarities with terrestrial life. Such assumptions appear very reasonable and they allow us to design specific and highly sensitive life detection experiments. But the fewer assumptions we make, the less chance we have of being entirely wrong The best strategy for the detection of extraterrestrial life could be a mixed strategy. We should use detailed assumptions based on terrestrial biology to guide some but not all future searches for alien life. The systems principles of exoecology seem much more fundamental and inescapable than the terrestrial biology analogies of exobiology. We should search for exoecology as well as exobiology.

Jones, Harry↗
NASA NTRS2012

From Extremophiles to Star Trek, The Use of Synthetic Biology in Astrobiology

Synthetic biology – the design and construction of new biological parts and systems and the redesign of existing ones for useful purposes – has the potential to transform fields from pharmaceuticals to fuels. Our lab has focused on the potential of synthetic biology to revolutionize all three major parts of astrobiology: Where do we come from? Where are we going? and Are we alone? For the first and third, synthetic biology is allowing us to answer whether the evolutionary narrative that has played out on planet earth is likely to have been unique or universal. For example, in our lab we are re-evolving biotic functions using only the most thermodynamically stable amino acids in order to understand potential capabilities of an early organism with a limited repertoire of amino acids. In the future synthetic biology will play an increasing role in human activities both on earth, in fields as diverse as bio-mining, human health and the industrial production of novel bio-composites. Beyond earth, we will rely increasingly on biologically-provided life support, as we have throughout our evolutionary history. In order to do this, the field will build on two of the great contributions of astrobiology: studies of the origin of life and life in extreme environments.

Life in Extreme Environments↗
NASA NTRS2016

Where Synthetic Biology Meets ET

Synthetic biology - the design and construction of new biological parts and systems and the redesign of existing ones for useful purposes - has the potential to transform fields from pharmaceuticals to fuels. Our lab has focused on the potential of synthetic biology to revolutionize all three major parts of astrobiology: Where do we come from? Where are we going? and Are we alone? For the first and third, synthetic biology is allowing us to answer whether the evolutionary narrative that has played out on planet earth is likely to have been unique or universal. For example, in our lab we are re-evolving the biosynthetic pathways of amino acids in order to understand potential capabilities of an early organism with a limited repertoire of amino acids and developing techniques for the recovery of metals from spent electronics on other planetary bodies. And what about the limits for life? Can we create organisms that expand the envelope for life? In the future synthetic biology will play an increasing role in human activities both on earth, in fields as diverse as human health and the industrial production of novel bio-composites. Beyond earth, we will rely increasingly on biologically-provided life support, as we have throughout our evolutionary history. In order to do this, the field will build on two of the great contributions of astrobiology: studies of the origin of life and life in extreme environments.

life in extreme environments↗
NASA NTRS2015

Synthetic Astrobiology

Synthetic biology - the design and construction of new biological parts and systems and the redesign of existing ones for useful purposes - has the potential to transform fields from pharmaceuticals to fuels. Our lab has focused on the potential of synthetic biology to revolutionize all three major parts of astrobiology: Where do we come from? Where are we going? and Are we alone? For the first and third, synthetic biology is allowing us to answer whether the evolutionary narrative that has played out on planet earth is likely to have been unique or universal. For example, in our lab we are re-evolving the biosynthetic pathways of amino acids in order to understand potential capabilities of an early organism with a limited repertoire of amino acids and developing techniques for the recovery of metals from spent electronics on other planetary bodies. In the future synthetic biology will play an increasing role in human activities both on earth, in fields as diverse as human health and the industrial production of novel bio-composites. Beyond earth, we will rely increasingly on biologically-provided life support, as we have throughout our evolutionary history. In order to do this, the field will build on two of the great contributions of astrobiology: studies of the origin of life and life in extreme environments.

Potential Fields↗
NASA NTRS1980

From inanimate matter to living systems

Since the early part of this century, the Genesis account of the origin and evolution of life has been explained as an extrapolation of astronomical and geochemical processes. The essence of the answer to date is a protoreproductive protocell of much biochemical and cytophysical competance. The processes of its origin, molecular ordering, and its functions are described. A crucial understanding is that of the nonrandomness of evolutionary processes at all stages (with perhaps a minor statistical component). In this way, evolution conflicts with statistical randomness; the latter is a favorite assumption of both scientific and creationistic critics of the proteinoid theory. The principle contribution of the proteinoid theory to the understanding of general biology is to particularize the view that evolutionary direction is rooted in the shapes of molecules, in stereochemistry. After molecules of the right kind first assembled to protocells, life in its various stages of evolution was an inevitable consequence. It is molecules that continue to assemble as part of living process and, in the role of enzymes, continue to direct life cycle of the cell.

Fox, S. W.↗
NASA NTRS1995

Taphonomic and evolutionary changes across the Mesoproterozoic-Neoproterozoic transition

The principal biological distinction between Mesoproterozoic and Neoproterozoic is the abundance and diversity of eukaryotic fossils in the Neoproterozoic rocks, but the two eras also differ in the composition of preserved cyanobacterial assemblages. Evolving eukaryotes provide a partial explanation for observed differences in prokaryotic fossils, but the taphonomic and environmental influences of shifting carbonate depositional pattern are also important.

Non-NASA Center↗
NASA NTRS1998

Phylogenetic mapping of bacterial morphology

The availability of a meaningful molecular phylogeny for bacteria provides a context for examining the historical significance of various developments in bacterial evolution. Herein, the classical morphological descriptions of selected members of the domain Bacteria are mapped upon the genealogical ancestry deduced from comparison of small-subunit rRNA sequences. For the species examined in this study, a distinct pattern emerges which indicates that the coccus shape has arisen and accumulated independently multiple times in separate lineages and typically survived as a persistent end-state morphology. At least two other morphologies persist but have evolved only once. This study demonstrates that although bacterial morphology is not useful in defining bacterial phylogeny, it is remarkably consistent with that phylogeny once it is known. An examination of the experimental evidence available for morphogenesis as well as microbial fossil evidence corroborates these findings. It is proposed that the accumulation of persistent morphologies is a result of the biophysical properties of peptidoglycan and their genetic control, and that an evolved body-plan strategy based on peptidoglycan may have been a fate-sealing step in the evolution of Bacteria. More generally, this study illustrates that significant evolutionary insights can be obtained by examining biological and biochemical data in the context of a reliable phylogenetic structure.

NASA Discipline Exobiology↗
NASA NTRS2011

Evolutionary Computational Methods for Identifying Emergent Behavior in Autonomous Systems

A technique based on Evolutionary Computational Methods (ECMs) was developed that allows for the automated optimization of complex computationally modeled systems, such as autonomous systems. The primary technology, which enables the ECM to find optimal solutions in complex search spaces, derives from evolutionary algorithms such as the genetic algorithm and differential evolution. These methods are based on biological processes, particularly genetics, and define an iterative process that evolves parameter sets into an optimum. Evolutionary computation is a method that operates on a population of existing computational-based engineering models (or simulators) and competes them using biologically inspired genetic operators on large parallel cluster computers. The result is the ability to automatically find design optimizations and trades, and thereby greatly amplify the role of the system engineer.

Terrile, Richard J.↗
NASA NTRS1989

From non-random molecular structure to life and mind

The evolutionary hierarchy molecular structure-->macromolecular structure-->protobiological structure-->biological structure-->biological functions has been traced by experiments. The sequence always moves through protein. Extension of the experiments traces the formation of nucleic acids instructed by proteins. The proteins themselves were, in this picture, instructed by the self-sequencing of precursor amino acids. While the sequence indicated explains the thread of the emergence of life, protein in cellular membrane also provides the only known material basis for the emergence of mind in the context of emergence of life.

Non-NASA Center↗
NASA NTRS2021

An Evolutionary System of Mineralogy. Part III: Primary Chondrule Mineralogy (4566 to 4561 Ma)

Information-rich attributes of minerals reveal their physical, chemical, and biological modes of origin in the context of planetary evolution, and thus they provide the basis for an evolutionary system of mineralogy. Part III of this system considers the formation of 43 different primary crystalline and amorphous phases in chondrules, which are diverse igneous droplets that formed in environments with high dust/gas ratios during an interval of planetesimal accretion and differentiation between 4566 and 4561 Ma. Chondrule mineralogy is complex, with several generations of initial droplet formation via various proposed heating mechanisms, followed in many instances by multiple episodes of reheating and partial melting. Primary chondrule mineralogy thus reflects a dynamic stage of mineral evolution, when the diversity and distribution of natural condensed solids expanded significantly.

Classification↗
NASA NTRS1995

Primate Language and Cognition: Common Ground

Research of the past decade has served to underscore the close psychological relationship between humans, chimpanzees, and the other great apes. In his evolutionary theory, Darwin (1860, 1871) posited both psychological and biological continuities between animals and humans. Although the evidence for biological continuity has been strong for decades, the evidence necessary for affirmation of psychological continuity is recent.

Rumbaugh, Duane↗
NASA NTRS1995

Advanced Biotelemetry Systems for Space Life Sciences: PH Telemetry

The SENSORS 2000! (S2K!) program at NASA's Ames Research Center is currently developing a biotelemetry system for monitoring pH and temperature in unrestrained subjects. This activity is part of a broader scope effort to provide an Advanced Biotelemetry System (ABTS) for use in future space life sciences research. Many anticipated research endeavors will require biomedical and biochemical sensors and related instrumentation to make continuous inflight measurements in a variable-gravity environment. Since crew time is limited, automated data acquisition, data processing, data storage, and subject health monitoring are required. An automated biochemical and physiological data acquisition system based on non invasive or implantable biotelemetry technology will meet these requirements. The ABTS will ultimately acquire a variety of physiological measurands including temperature, biopotentials (e.g. ECG, EEG, EMG, EOG), blood pressure, flow and dimensions, as well as chemical and biological parameters including pH. Development activities are planned in evolutionary, leveraged steps. Near-term activities include 1) development of a dual channel pH/temperature telemetry system, and 2) development of a low bandwidth, 4-channel telemetry system, that measures temperature, heart rate, pressure, and pH. This abstract describes the pH/temperature telemeter.

Hines, John W.↗
NASA NTRS1992

On the nature of global classification

Molecular sequencing technology has brought biology into the era of global (universal) classification. Methodologically and philosophically, global classification differs significantly from traditional, local classification. The need for uniformity requires that higher level taxa be defined on the molecular level in terms of universally homologous functions. A global classification should reflect both principal dimensions of the evolutionary process: genealogical relationship and quality and extent of divergence within a group. The ultimate purpose of a global classification is not simply information storage and retrieval; such a system should also function as an heuristic representation of the evolutionary paradigm that exerts a directing influence on the course of biology. The global system envisioned allows paraphyletic taxa. To retain maximal phylogenetic information in these cases, minor notational amendments in existing taxonomic conventions should be adopted.

NASA Program Exobiology↗
NASA NTRS1993

Calibrating rates of early Cambrian evolution

An explosive episode of biological diversification occurred near the beginning of the Cambrian period. Evolutionary rates in the Cambrian have been difficult to quantify accurately because of a lack of high-precision ages. Currently, uranium-lead zircon geochronology is the most powerful method for dating rocks of Cambrian age. Uranium-lead zircon data from lower Cambrian rocks located in northeast Siberia indicate that the Cambrian period began about 544 million years ago and that its oldest (Manykaian) stage lasted no less than 10 million years. Other data indicate that the Tommotian and Atdabanian stages together lasted only 5 to 10 million years. The resulting compression of Early Cambrian time accentuates the rapidity of both the faunal diversification and subsequent Cambrian turnover.

Bowring, Samuel A.↗
NASA NTRS1997

Isolation of novel ribozymes that ligate AMP-activated RNA substrates

BACKGROUND: The protein enzymes RNA ligase and DNA ligase catalyze the ligation of nucleic acids via an adenosine-5'-5'-pyrophosphate 'capped' RNA or DNA intermediate. The activation of nucleic acid substrates by adenosine 5'-monophosphate (AMP) may be a vestige of 'RNA world' catalysis. AMP-activated ligation seems ideally suited for catalysis by ribozymes (RNA enzymes), because an RNA motif capable of tightly and specifically binding AMP has previously been isolated. RESULTS: We used in vitro selection and directed evolution to explore the ability of ribozymes to catalyze the template-directed ligation of AMP-activated RNAs. We subjected a pool of 10(15) RNA molecules, each consisting of long random sequences flanking a mutagenized adenosine triphosphate (ATP) aptamer, to ten rounds of in vitro selection, including three rounds involving mutagenic polymerase chain reaction. Selection was for the ligation of an oligonucleotide to the 5'-capped active pool RNA species. Many different ligase ribozymes were isolated; these ribozymes had rates of reaction up to 0.4 ligations per hour, corresponding to rate accelerations of approximately 5 x10(5) over the templated, but otherwise uncatalyzed, background reaction rate. Three characterized ribozymes catalyzed the formation of 3'-5'-phosphodiester bonds and were highly specific for activation by AMP at the ligation site. CONCLUSIONS: The existence of a new class of ligase ribozymes is consistent with the hypothesis that the unusual mechanism of the biological ligases resulted from a conservation of mechanism during an evolutionary replacement of a primordial ribozyme ligase by a more modern protein enzyme. The newly isolated ligase ribozymes may also provide a starting point for the isolation of ribozymes that catalyze the polymerization of AMP-activated oligonucleotides or mononucleotides, which might have been the prebiotic analogs of nucleoside triphosphates.

NASA Discipline Exobiology↗