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NASA NTRS1995

The RNA World and its origins

The theory of the "RNA World" states that the first molecular systems to display the properties of self-replication and evolution were RNA molecules. The origin of life not only depended crucially upon this event, but RNA molecules can even be viewed as the first "living" things. In recent years this theory has gained ascendancy over competing ideas and is now largely accepted by biologists as the most satisfactory explanation for the origin of life. The reasons for this development will be reviewed and the problem of the origin of the first RNA molecules will be discussed.

RNA/analysis/genetics/physiology↗

NASA NTRS1975

Replica grating study

Methods are outlined which were used to test the response of replica diffraction gratings to a space environment, specifically the response of the replica gratings to thermal-vacuum and electron irradiation stress. It is concluded that there probably is some degradation to thermal stress, but that there is probably no significant degradation due to a vacuum environment. It is further concluded that the degradation of performance of replica gratings because of electron irradiation is due to the interaction of the electrons and the replica grating substrate and not to the replication material itself. Replica and original gratings on the same substrate material should thus respond to particle irradiation in the same manner. A study is presented on the variation of refraction index of a space-related material, Nd:CaF2, with wavelength, percent neodymium doping, and temperature.

Gunter, R. C., Jr.↗

NASA NTRS2000

Modular Low-Heater-Power Cathode/Electron Gun Assembly for Microwave and Millimeter Wave Traveling Wave Tubes

A low-cost, low-mass, electrically efficient, modular cathode/electron gun assembly has been developed by FDE Inc. of Beaverton, Oregon, under a Small Business Innovation Research (SBIR) contract with the NASA Glenn Research Center at Lewis Field. This new assembly offers significant improvements in the design and manufacture of microwave and millimeter wave traveling-wave tubes (TWT's) used for radar and communications. It incorporates a novel, low-heater-power, reduced size and mass, high-performance barium dispenser type thermionic cathode and provides for easy integration of the cathode into a large variety of conventional TWT circuits. Among the applications are TWT's for Earth-orbiting communication satellites and for deep space communications, where future missions will require smaller spacecraft, higher data transfer rates (higher frequencies and radiofrequency output power), and greater electrical efficiency. A particularly important TWT application is in the microwave power module (a hybrid microwave/millimeter wave amplifier consisting of a low-noise solid-state driver, a small TWT, and an electronic power conditioner integrated into a single compact package), where electrical efficiency and thermal loading are critical factors and lower cost is needed for successful commercialization. The design and fabrication are based on practices used in producing cathode ray tubes (CRT's), which is one of the most competitive and efficient manufacturing operations in the world today. The approach used in the design and manufacture of thermionic cathodes and electron guns for CRT's has been optimized for fully automated production, standardization of parts, and minimization of costs. It is applicable to the production of similar components for microwave tubes, with the additional benefits of low mass and significantly lower cathode heater power (less than half that of dispenser cathodes presently used in TWT s). Modular cathode/electron gun assembly. The modular cathode/electron gun assembly consists of four subassemblies the cathode, the focus electrode, the header (including the electrical feedthroughs), and the gun envelope (including the anode) a diagram of which is shown. The modular construction offers a number of significant advantages, including flexibility of design, interchangeability of parts, and a drop-in final assembly procedure for quick and accurate alignment. The gun can accommodate cathodes ranging in size from 0.050 to 0.250-in. in diameter and is applicable to TWT's over a broad range of sizes and operating parameters, requiring the substitution of only a few parts: that is, the cathode, focus electrode, and anode. The die-pressed cathode pellets can be made with either flat or concave (Pierce gun design) emitting surfaces. The gun can be either gridded (pulse operation) or ungridded (continuous operation). Important factors contributing to low cost are the greater use of CRT materials and parts, the standardization of processes (welding and mechanical capture), and tooling amenable to automated production. Examples are the use of simple shapes, drawn or stamped metal parts, and parts joined by welding or mechanical capture. Feasibility was successfully demonstrated in the retrofit and testing of a commercial Kaband (22-GHz) TWT. The modular cathode/electron gun assembly was computer modeled to replicate the performance of the original electron gun and fabricated largely from existing CRT parts. Significant test results included demonstration of low heater power (1.5-W, 1010 C brightness temperature for a 0.085-in.-diameter cathode), mechanical ruggedness (100g shock and vibration tests in accordance with military specifications (MIL specs)), and a very fast warmup. The results of these tests indicate that the low-cost CRT manufacturing approach can be used without sacrificing performance and reliability.

Wintucky, Edwin G.↗

NASA NTRS1995

Unnatural selection in chemical systems

The theory of evolution through natural selection was proposed by Darwin and Wallace to explain how the characteristics of populations of animals change with time. An examination of their assumptions shows that the theory has much broader application than they originally envisaged. We now know that in appropriate environments RNA molecules or computer viruses, for example, can evolve. The adventure with which we are concerned is the quest for chemical systems that undergo processes analogous to Darwinian selection in the test tube. The search is not restricted to systems that are closely related to nucleic acids, although most of the available experimental evidence concerns such systems. A population of molecules satisfies all the requirements of the theory is there are different kinds of molecules in the population and if each individual molecule can direct the formation of copies of itself, then a population of molecules will adapt to a varying environment by changing its composition so as to maintain as high as possible a rate of replication. Sol Spiegelman is the inventor of 'unnatural selection'. He showed clearly that populations of RNA molecules evolve when replicated repeatedly by Q beta RNA polymerase under a chosen set of adverse reaction conditions. In the systems that he studied, the initial population was fairly homogeneous and much of the variation was created during the course of the experiment by mutation, that is, error of replication. The term 'unnatural selection' will be used loosely to describe evolution of nucleic acids or other replicatable polymers in vitro. The term 'Natural Selection' will be reserved for the evolution of living organisms and their viruses. Natural Section usually involves the coevolution of nucleic acids and proteins, while 'unnatural selection', as practiced so far, allows replicating nucleic acids to evolve but hold constant the enzymes that catalyze replication. It is widely believed that biology based on DNA, RNA, and proteins was preceded by the biology of an 'RNA world' in which enzymes were composed of RNA alone. The origin of RNA replication is thus the central puzzle of the origins of life. Consequently, RNA-catalyzed RNA replication is presently one of the main goals of experimental work on unnatural selection. However, there is also a more distant goal, namely, to achieve replication and selection in systems unrelated to RNA. These different systems are discussed in this article.

Orgel, Leslie E.↗

NASA NTRS2000

Viral carcinogenesis: revelation of molecular mechanisms and etiology of human disease

The RNA and DNA tumor viruses have made fundamental contributions to two major areas of cancer research. Viruses were vital, first, to the discovery and analysis of cellular growth control pathways and the synthesis of current concepts of cancer biology and, second, to the recognition of the etiology of some human cancers. Transforming retroviruses carry oncogenes derived from cellular genes that are involved in mitogenic signalling and growth control. DNA tumor viruses encode oncogenes of viral origin that are essential for viral replication and cell transformation; viral oncoproteins complex with cellular proteins to stimulate cell cycle progression and led to the discovery of tumor suppressors. Viral systems support the concept that cancer development occurs by the accumulation of multiple cooperating events. Viruses are now accepted as bona fide etiologic factors of human cancer; these include hepatitis B virus, Epstein-Barr virus, human papillomaviruses, human T-cell leukemia virus type I and hepatitis C virus, plus several candidate human cancer viruses. It is estimated that 15% of all human tumors worldwide are caused by viruses. The infectious nature of viruses distinguishes them from all other cancer-causing factors; tumor viruses establish long-term persistent infections in humans, with cancer an accidental side effect of viral replication strategies. Viruses are usually not complete carcinogens, and the known human cancer viruses display different roles in transformation. Many years may pass between initial infection and tumor appearance and most infected individuals do not develop cancer, although immunocompromised individuals are at elevated risk of viral-associated cancers. Variable factors that influence viral carcinogenesis are reviewed, including possible synergy between viruses and environmental cofactors. The difficulties in establishing an etiologic role for a virus in human cancer are discussed, as well as the different approaches that proved viral links to cancer. Future directions for tumor virus studies are considered.

NASA Program Biomedical Research and Countermeasur↗

NASA NTRS2001

Models of Protocellular Structure, Function and Evolution

In the absence of any record of protocells, the most direct way to test our understanding of the origin of cellular life is to construct laboratory models that capture important features of protocellular systems. Such efforts are currently underway in a collaborative project between NASA-Ames, Harvard Medical School and University of California. They are accompanied by computational studies aimed at explaining self-organization of simple molecules into ordered structures. The centerpiece of this project is a method for the in vitro evolution of protein enzymes toward arbitrary catalytic targets. A similar approach has already been developed for nucleic acids in which a small number of functional molecules are selected from a large, random population of candidates. The selected molecules are next vastly multiplied using the polymerase chain reaction. A mutagenic approach, in which the sequences of selected molecules are randomly altered, can yield further improvements in performance or alterations of specificities. Unfortunately, the catalytic potential of nucleic acids is rather limited. Proteins are more catalytically capable but cannot be directly amplified. In the new technique, this problem is circumvented by covalently linking each protein of the initial, diverse, pool to the RNA sequence that codes for it. Then, selection is performed on the proteins, but the nucleic acids are replicated. Additional information is contained in the original extended abstract.

New, Michael H.↗

NASA NTRS1986

Did template-directed nucleation precede molecular replication?

It is proposed that mononucleotides incorporated into the surfaces of microcrystals of inorganic phosphates such as hydroxyapatite can act as templates to assemble complementary mononucleotides from solution, and that the phosphate groups of the assembled nucleotides can facilitate nucleation of a second hydroxyapatite crystal. This would provide a mechanism of replication that is subject to natural selection. The possible role of a replicating system of this kind in the origins of life on the earth is discussed.

Orgel, Leslie E.↗

NASA NTRS2017

CME Velocity and Acceleration Error Estimates Using the Bootstrap Method

The bootstrap method is used to determine errors of basic attributes of coronal mass ejections (CMEs) visually identified in images obtained by the Solar and Heliospheric Observatory (SOHO) mission's Large Angle and Spectrometric Coronagraph (LASCO) instruments. The basic parameters of CMEs are stored, among others, in a database known as the SOHO/LASCO CME catalog and are widely employed for many research studies. The basic attributes of CMEs (e.g. velocity and acceleration) are obtained from manually generated height-time plots. The subjective nature of manual measurements introduces random errors that are difficult to quantify. In many studies the impact of such measurement errors is overlooked. In this study we present a new possibility to estimate measurements errors in the basic attributes of CMEs. This approach is a computer-intensive method because it requires repeating the original data analysis procedure several times using replicate datasets. This is also commonly called the bootstrap method in the literature. We show that the bootstrap approach can be used to estimate the errors of the basic attributes of CMEs having moderately large numbers of height-time measurements. The velocity errors are in the vast majority small and depend mostly on the number of height-time points measured for a particular event. In the case of acceleration, the errors are significant, and for more than half of all CMEs, they are larger than the acceleration itself.

Michalek, Grzegorz↗

NASA NTRS1986

The principle of cooperation and life's origin and evolution

In simple terms a living entity is a negentropic system that replicates, mutates and evoluves. A number of suggestions have been made, such as directed panspermia, atmospheric photosynthesis, genetic overtaking from inorganic processes, etc., as alternative models to the accepted Oparin-Haldane-Urey model of the origin of life on Earth. This has probably occurred because in spite of tremendous advances in the prebiotic synthesis of biochemical compounds, the fundamental problem of the appearance of the first life--a primordial replicating cell-ancestral to all other forms of extant life, has remained elusive. This is indeed a reflection on the different fundamental nature of the problem involved. Regardless of which were the fundamental processes which occurred on the primitive Earth, it has to end up with the fundamental characteristics of an ancestral protocell. The problem of the emergence of the first ancestral cell was one of synergistic macromolecular cooperation, as it has been discussed by authors recently (COSPAR XXV Plenary Meeting). An analogous situation must have occurred at the time of the appearance of the first eucaryotic organism. Procaryotic life appeared probably during the first 600 million years of Earth history when the Earth was sufficiently cool and continually bombarded (in the late accretion period) by comets and minor bodies of the solar system, when the sea had not yet acquired its present form.

Oro, J.↗

NASA NTRS2002

Some Like It Hot, But Not the First Biomolecules

Ever since the pioneering work of Aleksandr Oparin and John Haldane nearly a century ago, the prebiotic soup theory has dominated thinking about how life emerged on Earth. According to the modern version of this theory, organic compounds accumulated in the primordial oceans and underwent polymerization, producing increasingly complex macromolecules that eventually evolved the ability to catalyze their own replication (see the figure). But is this really how life originated? And what were the conditions that favored its emergence?

Bada, Jeffrey L.↗

NASA NTRS1987

The triose model - Glyceraldehyde as a source of energy and monomers for prebiotic condensation reactions

Glyceraldehyde acts as a source of energy and monomers in a new model of the origin of life. The simplest form of the model functions by converting formaldehyde from the environment into glyceraldehyde which spontaneously forms hemiacetal adducts that are oxidized to polyglyceric acid. Polyglyceric acid, in turn, acts as an autocatalyst with a rudimentary replicating ability. A unique property of the model is its ability to unite the origin of metabolism and the origin of polymer synthesis into a single process. Furthermore, the chemical resemblance of the model to glycolysis gives it the potential to develop a biological metabolism in a straightforward manner.

Weber, Arthur L.↗

NASA NTRS2017

Exploring Connectivity in Sequence Space of Functional RNA

Emergence of replicable genetic molecules was one of the marking points in the origin of life, evolution of which can be conceptualized as a walk through the space of all possible sequences. A theoretical concept of fitness landscape helps to understand evolutionary processes through assigning a value of fitness to each genotype. Then, evolution of a phenotype is viewed as a series of consecutive, single-point mutations. Natural selection biases evolution toward peaks of high fitness and away from valleys of low fitness. whereas neutral drift occurs in the sequence space without direction as mutations are introduced at random. Large networks of neutral or near-neutral mutations on a fitness landscape, especially for sufficiently long genomes, are possible or even inevitable. Their detection in experiments, however, has been elusive. Although a few near-neutral evolutionary pathways have been found, recent experimental evidence indicates landscapes consist of largely isolated islands. The generality of these results, however, is not clear, as the genome length or the fraction of functional molecules in the genotypic space might have been insufficient for the emergence of large, neutral networks. Thorough investigation on the structure of the fitness landscape is essential to understand the mechanisms of evolution of early genomes. RNA molecules are commonly assumed to play the pivotal role in the origin of genetic systems. They are widely believed to be early, if not the earliest, genetic and catalytic molecules, with abundant biochemical activities as aptamers and ribozymes, i.e. RNA molecules capable, respectively, to bind small molecules or catalyze chemical reactions. Here, we present results of our recent studies on the structure of the sequence space of RNA ligase ribozymes selected through in vitro evolution. Several hundred thousands of sequences active to a different degree were obtained by way of deep sequencing. Analysis of these sequences revealed several large clusters defined such that every sequence in a cluster can be reached from any other sequence in the same cluster through a series of single point mutations. Sequences in a single cluster appear to adopt more than one secondary structure. The mechanism of refolding within a single cluster was examined. To shed light on possible evolutionary paths in the space of ribozymes, the connectivity between clusters was investigated. The effect of length of RNA molecules on the structure of the fitness landscape and possible evolutionary paths was examined by way of comparing functional sequences of 20 and 80 nucleobases in length. It was found that sequences of different lengths shared secondary structure motifs that were presumed responsible for catalytic activity, with increasing complexity and global structural rearrangements emerging in longer molecules.

Wei, Chenyu↗

NASA NTRS1986

Origin of life and iron-rich clays

The premise that life began with self-replicating iron-rich clays is explored. In association with these clays and UV light, polar organic molecules, such as oxalic acid, were synthesized. The carbonaceous chondrites have both iron-rich clays and organic molecules. It is convenient to classify meteoritic organic matter into 3 categories: insoluble polymer, hydrocarbons and polar organics (soluble in water). Recent work on the delta D, delta N-15 and delta C-13 has made it clear that these three fractions have been made by three different mechanisms. A significant fraction of the insoluble polymer has a delta-D which suggests that it was made in an interstellar medium. The hydrocarbons seem to have been made on a parent body by a Fischer-Tropsch mechanism. The polar organics were probably synthesized in a mixture of carbonate (NH4)2CO3, Fe(++) ion and liquid water by radiolysis. In a set of experiments the radiolysis of (NH4)2CO3 in the presence and absence of Fe(++) ion has been examined. The synthesis of glycine in the presence of Fe(++) ion is 3-4 times that in the absence of ferrous ion. The effects of the addition of hydrocarbons to this mixture are explored. Iron-rich clays at low temperature and pressure are synthesized. So far the results are not sufficiently crystalline to look for replication. It should be noted that organic chelating agents such as oxalic acid do increase the crystallinity of the clays but not sufficiently. The hydrothermal synthesis of iron-rich clays is being examined.

Hartman, H. H.↗

NASA NTRS1991

Controlled evolution of an RNA enzyme

It is generally thought that prior to the origin of protein synthesis, life on earth was based on self-replicating RNA molecules. This idea has become especially popular recently due to the discovery of catalytic RNA (ribozymes). RNA has both genotypic and phenotypic properties, suggesting that it is capable of undergoing Darwinian evolution. RNA evolution is likely to have played a critical role in the early history of life on earth, and thus is important in considering the possibility of life elsewhere in the solar system. We have constructed an RNA-based evolving system in the laboratory, combining amplification and mutation of an RNA genotype with selection of a corresponding RNA phenotype. This system serves as a functional model of a primitive organism. It can also be used as a tool to explore the catalytic potential of RNA. By altering the selection constraints, we are attempting to modify the substrate specificity of an existing ribozyme in order to develop ribozymes with novel catalytic function. In this way, we hope to gain a better understanding of RNA's catalytic versatility and to assess its suitability for the role of primordial catalyst. All of the RNA enzymes that are known to exist in contemporary biology carry out cleavage/ligation reactions involving RNA substrates. The Tetrahymena ribozyme, for example, catalyzes phosphoester transfer between a guanosine containing and an oligopyrimidine containing substrate. We tested the ability of mutant forms of the Tetrahymena ribozyme to carry out a comparable reaction using DNA, rather than RNA substrate. An ensemble of structural variants of the ribozyme was prepared and tested for their ability to specifically cleave d(GGCCCTCT-A3TA3TA) at the phosphodiester bond following the sequence CCCTCT. We recovered a mutant form of the enzyme that cleaves DNA more efficiently than does the wild-type. Beginning with this selected mutant we have now scattered random mutations throughout the ribozyme and have begun an evolutionary search to further expand the catalytic repertoire of RNA.

Joyce, G. F.↗

NASA NTRS1994

A novel computational method to simulate non-enzymatic self-replication

Non-enzymatic, template-directed synthesis of oligonucleotides has been extensively studied in the laboratory as a model to understand the kind of chemical processes that might have contributed to the origin of life on Earth. Several oligonucleotides have been shown to catalyze the synthesis of their complements from activated mononucleotides; however, a restricted number of them have been found to self-replicate. Recently we developed an efficient modified cellular automata method that supports the study of self-replicating oligonucleotides. With this method the oligonucleotide molecules are represented as active cells imbedded in a two-dimensional array of inactive cells symbolizing the environment. Random movements and probability-governed chemical reactions occurring in a cellular space can effectively simulate the experimental behavior observed in self-directed replication of oligonucleotides.

Navarro-Gonzalez, Rafael↗

NASA NTRS1994

ISSOL Meeting, 7th, Barcelona, Spain, July 4-9, 1993

The journal issue consists of abstracts presented at the International Society for the Study of the Origins of Life (ISSOL) conference. Topics include research on biological and chemical evolution including prebiotic evolution: cosmic and terrestrial; mechanisms of abiogenesis including synthesis and reactions of biomonomers; and analysis of cometary matter and its possible relationship to organic compounds on Earth. Theories and research on origins of ribonucleic acids (RNA), deoxyribonucleic acid (DNA), and other amino acids and complex proteins including their autocatalysis, replication, and translation are presented. Abiotic synthesis of biopolymers, mechanisms of the Genetic Code, precellular membrane systems and energetics are considered. Earth planetary evolution including early microfossils and geochemical conditions and simulations to study these conditions are discussed. The role of chirality in precellular evolution and the taxonomy and phylogeny of very simple organisms are reported. Past and future explorations in exobiology and space research directed toward study of the origins of life and solar system evolution are described.

Ferris, James P.↗

NASA NTRS1992

The origin and early evolution of nucleic acid polymerases

The hypothesis that vestiges of the ancestral RNA-dependent RNA polymerase involved in the replication of RNA genomes of Archean cells are present in the eubacterial RNA-polymerase beta-prime subunit and its homologues is discussed. It is shown that, in the DNA-dependent RNA polymerases from three cellular lineages, a very conserved sequence of eight amino acids, also found in a small RNA-binding site previously described for the E. coli polynucleotide phosphorylase and the S1 ribosomal protein, is present. The optimal conditions for the replicase activity of the avian-myeloblastosis-virus reverse transcriptase are presented. The evolutionary significance of the in vitro modifications of substrate and template specificities of RNA polymerases and reverse transcriptases is discussed.

Lazcano, A.↗

NASA NTRS2015

The Ribofilm as a Concept for Life’s Origins

Recent phylogenetic data indicating that the first archaea were methane-producing galvanizes cross-disciplinary evidence supporting the hypothesis that life arose via thermodynamically directed events at hydrothermal vents. The new developments lead us to propose the concept of a ribofilm in which RNA’s origin-of-life role is more akin to a slowly changing platform than a spontaneous self-replicator.

John A Baross↗