The nasa biosatellite program.
NASA biosatellite program to study physiological, evolutionary and genetic effects of weightlessness, radiation and removal from Earth rotation
BIOSATELLITE↗
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Biology and the Exploration of Mars
Until recent years the origin of life and its possible occurrence elsewhere in the universe have been matters for speculation only. The rapid growth of molecular biology since 1940 has, to be sure, made it possible to discuss life's origins in far more precise and explicit terms than was possible earlier; and the subject entered a new experimental phase in the 1950's with successful abiogenic synthesis of important biochemical substances in conditions simulating the presumptive environment of the primitive Earth. But the real transformation that the subject has undergone stems from the spectacular growth of space technology in the last decade. The possibility of life's origin and occurrence on planets other than ours is no longer limited to idle speculation: it has entered the realm of the testable, of science in the strict sense. Given the rockets now available, and especially those available by 1969, it has become fully realistic to consider plans for the biological exploration of Mars. The study that this report seeks to interpret was initiated in June, 1964, by the Space Science Board of the National Academy of Sciences to examine this possibility. The working group comprised 36 people representing a broad spectrum of scientific interests: evolutionary biology, genetics, microbiology, biochemistry and molecular biology, animal physiology, soil chemistry, organic chemistry, planetary astronomy, geochemistry, and theoretical physics. The participants included some with considerable prior involvement in problems of space exploration and others with none. Advice was also sought outside the group of immediate participants on the potentialities of selected analytical methods for the experimental study of extraterrestrial life and its environment. More than 30 individuals contributed in this fashion written assessments of techniques in which they were particularly well versed. Our task was to examine the scientific foundations and merits of the proposal to undertake a biological exploration of Mars. What are the potential scientific yields? How valuable, if attained, would they be? What, in fact, is the possibility of life occurring on Mars? And of our detecting it with available and foreseeable technology? What could be achieved by further astronomical work from Earth? by Martian fly-by missions? by Martian orbiters? and Martian Landers? What payloads would we recommend for planetary missions? What timing and over-all strategy would we recommend for Martian exploration were we to consider it worthwhile at all? In brief, the over-all purpose was to recommend to. the government, through the Academy's Space Science Board, whether or not a biological exploration of Mars should be included in the nation's space program over the next few decades; and, further, to outline what that program, if any, should be.
CONFERENCE↗
Identifying Organic Molecules in Space: The AstroBiology Explorer (ABE) MIDEX Mission Concept
Infrared spectroscopy in the 2.5-16 micron range is a principle means by which organic compounds are detected and identified in space. Ground-based, airborne, and spaceborne IR spectral studies have already demonstrated that a significant fraction of the carbon in the interstellar medium (ISM) resides in the form of complex organic molecular species. Unfortunately, neither the distribution of these materials nor their genetic and evolutionary relationships with each other or their environments are well understood. The Astrobiology Explorer (ABE) is a MIDEX mission concept currently under study at NASA's Ames Research Center in collaboration with Ball Aerospace and Technologies Corporation. ABE will conduct IR spectroscopic observations to address outstanding important problems in astrobiology, astrochemistry, and astrophysics. The core observational program would make fundamental scientific progress in understanding (1) the evolution of ices and organic matter in dense molecular clouds and young forming stellar systems, (2) the chemical evolution of organic molecules in the ISM as they transition from AGB outflows to planetary nebulae to the general diffuse ISM to H II regions and dense clouds, (3) the distribution of organics in the diffuse ISM, (4) the nature of organics in the Solar System (in comets, asteroids, satellites), and (5) the nature and distribution of organics in local galaxies. The technical considerations of achieving these science objectives in a MIDEX-sized mission will be described.
Sandford, Scott A.↗
Detecting and Identifying Organic Molecules in Space: The AstroBiology Explorer (ABE) MIDEX Mission Concept
Infrared spectroscopy in the 2.5-16 microns (4000-625/cm) range is a principle means by which organic compounds are detected and identified in space. Ground-based, airborne, and spaceborne IR spectral studies have already demonstrated that a significant fraction of the carbon in the interstellar medium (ISM) resides in the form of complex organic molecular species. Unfortunately, neither the distribution of these materials nor their genetic and evolutionary relationships with each other or their environments are well understood. The Astrobiology Explorer (ABE) is a MIDEX (Medium-class Explorer) mission concept currently under study at NASA's Ames Research Center in collaboration with Ball Aerospace and Technologies Corporation. ABE will conduct IR spectroscopic observations to address outstanding important problems in astrobiology, astrochemistry, and astrophysics. The core observational program would make fundamental scientific progress in understanding (1) the evolution of ices and organic matter in dense molecular clouds and young forming stellar systems, (2) the chemical evolution of organic molecules in the ISM as they transition from AGB outflows to planetary nebulae to the general diffuse ISM to H II regions and dense clouds, (3) the distribution of organics in the diffuse ISM, (4) the nature of organics in the Solar System (in comets, asteroids, satellites), and (5) the nature and distribution of organics in local galaxies. Both the scientific goals of the mission and how they would be achieved will be discussed.
Sandford, Scott A.↗
The AstroBiology Explorer (ABE) MIDEX Mission Concept: Exploring the Links Between the Interstellar Medium and Meteorites
Infrared spectroscopy in the 2.5-16 micron range is a principle means by which organic compounds can be detected and identified in space via their vibrational transitions. Ground-based, airborne, and spaceborne IR spectral studies have already demonstrated that a significant fraction of the carbon in the interstellar medium (ISM) resides in the form of complex organic molecular species. Furthermore, the presence of D-enriched organics in meteorites suggests that a portion of these materials survives incorporation into protosolar nebulae. Unfortunately, neither the distribution of these materials nor their genetic and evolutionary relationships with each other or their environments are well understood. The Astrobiology Explorer (ABE) is a MIDEX mission concept currently under study at NASA's Ames Research Center in collaboration with Ball Aerospace and Technologies Corporation. ABE will conduct IR spectroscopic observations to address outstanding important problems in astrobiology, astrochemistry, and astrophysics. The core observational program would make fundamental scientific progress in understanding (1) the evolution of ices and organic matter in dense molecular clouds and young forming stellar systems, (2) the chemical evolution of organic molecules in the ISM as they transition from AGB outflows to planetary nebulae to the general diffuse ISM to HII regions and dense clouds, (3) the distribution of organics in the diffuse ISM, (4) the nature of organics in the Solar System (in comets, asteroids, satellites), and (5) the nature and distribution of organics in local galaxies. In addition, ABE will attempt to detect and quantify deuterium enrichments in a select set of these materials and environments. This should assist both with understanding the chemical processes that occur in these environments and with establishing any links that exist between interstellar and meteoritic organics.
Sandford, Scott A.↗
Detecting and Identifying Organic Molecules in Space - The AstroBiology Explorer (ABE) MIDEX Mission Concept
Infrared spectroscopy in the 2.5-16 micron (4000-625/cm) range is a principle means by which organic compounds are detected and identified in space. Ground-based, airborne, and spaceborne IR spectral studies have already demonstrated that a significant fraction of the carbon in the interstellar medium (ISM) resides in the form of complex organic molecular species. Unfortunately, neither the distribution of these materials nor their genetic and evolutionary relationships with each other or their environments are well understood. The Astrobiology Explorer (ABE) is a MIDEX (Medium-class Explorer) mission concept currently under study at NASA's Ames Research Center in collaboration with Ball Aerospace and Technologies Corporation. ABE will conduct IR spectroscopic observations to address outstanding important problems in astrobiology, astrochemistry, and astrophysics. The core observational program would make fundamental scientific progress in understanding (1) the evolution of ices and organic matter in dense molecular clouds and young forming stellar systems, (2) the chemical evolution of organic molecules in the ISM as they transition from AGB outflows to planetary nebulae to the general diffuse ISM to H II regions and dense clouds, (3) the distribution of organics in the diffuse ISM, (4) the nature of organics in the Solar System (in comets, asteroids, satellites), and (5) the nature and distribution of organics in local galaxies. Both the scientific goals of the mission and how they would be achieved will be discussed.
Sandford, Scott A.↗
Automatic Evolution of Molecular Nanotechnology Designs
This paper describes strategies for automatically generating designs for analog circuits at the molecular level. Software maps out the edges and vertices of potential nanotechnology systems on graphs, then selects appropriate ones through evolutionary or genetic paradigms.
Globus, Al↗
The AstroBiology Explorer (ABE) Mission
Introduction: Infrared spectroscopy in the 2.5- 16 micron range is a principle means by which organic compounds can be detected and identified in space via their vibrational transitions. Ground-based, airborne, and spaceborne IR spectral studies have already demonstrated that a significant fraction of the carbon in the interstellar medium (ISM) resides in the form of complex organic molecular species. Furthermore, the presence of D-enriched organics in meteorites suggests that a portion of these materials survives incorporation into protosolar nebulae. Unfortunately, neither the distribution of these materials in space nor their genetic and evolutionary relationships with each other or their environments are currently well understood. The Astrobiology Explorer (ABE) is a MIDEX mission concept designed to use infrared spectroscopy to address outstanding problems in Astrochemistry which are particularly relevant to Astrobiology and are amenable to astronomical observation. ABE is currently under study at NASA's Ames Research Center in collaboration with Ball Aerospace and Technologies Corporation and the Jet Propulsion Laboratory. ABE was selected for Phase A study during the last MIDEX AO round, but has yet to be selected for flight.
Sandford, S. A.↗
The AstroBiology Explorer (ABE) Mission Concept
Infrared spectroscopy in the 2.5-16 micron range is a principle means by which organic compounds can be detected and identified in space via their vibrational transitions. Ground-based, airborne, and spaceborne IR spectral studies have already demonstrated that a significant fraction of the carbon in the interstellar medium (ISM) resides in the form of complex organic molecular species. Unfortunately, neither the distribution of these materials nor their genetic and evolutionary relationships with each other or their environments are well understood. The Astrobiology Explorer (ABE) is a MIDEX mission concept currently under study by a team of partners: NASA's Ames Research Center, Ball Aerospace and Technologies Corporation, and the Jet Propulsion Laboratory. ABE will conduct IR spectroscopic observations to address outstanding important problems in astrobiology, astrochemistry, and astrophysics. The core observational program would make fundamental scientific progress in understanding (1) The evolution of ices and organic matter in dense molecular clouds and young forming stellar systems, (2) The chemical evolution of organic molecules in the ISM as they transition from AGB outflows to planetary nebulae to the general diffuse ISM to HII regions and dense clouds, (3) The distribution of organics in the diffuse ISM, (4) The nature of organics in the Solar System (in comets, asteroids, satellites), and (5) The nature and distribution of organics in local galaxies. The technical considerations of achieving these science objectives in a MIDEX-sized mission will be presented.
Sandford, Scott A.↗
Towards a Universal Biology: Is the Origin and Evolution of Life Predictable?
The origin and evolution of life seems an unpredictable oddity, based on the quirks of contingency. Celebrated by the late Stephen Jay Gould in several books, "evolution by contingency" has all the adventure of a thriller, but lacks the predictive power of the physical sciences. Not necessarily so, replied Simon Conway Morris, for convergence reassures us that certain evolutionary responses are replicable. The outcome of this debate is critical to Astrobiology. How can we understand where we came from on Earth without prophesy? Further, we cannot design a rational strategy for the search for life elsewhere - or to understand what the future will hold for life on Earth and beyond - without extrapolating from pre-biotic chemistry and evolution. There are several indirect approaches to understanding, and thus describing, what life must be. These include philosophical approaches to defining life (is there even a satisfactory definition of life?), using what we know of physics, chemistry and life to imagine alternate scenarios, using different approaches that life takes as pseudoreplicates (e.g., ribosomal vs non-ribosomal protein synthesis), and experimental approaches to understand the art of the possible. Given that: (1) Life is a process based on physical components rather than simply an object; (2). Life is likely based on organic carbon and needs a solvent for chemistry, most likely water, and (3) Looking for convergence in terrestrial evolution we can predict certain tendencies, if not quite "laws", that provide predictive power. Biological history must obey the laws of physics and chemistry, the principles of natural selection, the constraints of an evolutionary past, genetics, and developmental biology. This amalgam creates a surprising amount of predictive power in the broad outline. Critical is the apparent prevalence of organic chemistry, and uniformity in the universe of the laws of chemistry and physics. Instructive is the widespread occurrence of convergent or parallel evolution, which suggests that under certain conditions similar solutions are arrived at independently.
Universal biology; life everywhere↗
Targeted genetic manipulation and yeast-like evolutionary genomics in the green alga Auxenochlorella
Auxenochlorella spp. are diploid oleaginous green algae whose streamlined genomes can be readily manipulated by homologous recombination, making them highly amenable to discovery research and bioengineering. Vegetatively diploid organisms experience specific evolutionary phenomena, including allodiploid hybridization, mitotic recombination, loss-of-heterozygosity, and aneuploidy; however, studies of these forces have largely focused on yeasts. Here, we present a telomere-to-telomere phased diploid genome assembly of Auxenochlorella UTEX 250-A (haploid length 22 Mb) and introduce a genetic toolkit for site-specific manipulation of the nuclear genome in multiple strains, featuring several selectable markers, inducible promoters, and fluorescent reporters for protein localization. UTEX 250-A is an allodiploid hybrid of Auxenochlorella protothecoides and Auxenochlorella symbiontica, two species differentiated by extensive chromosomal rearrangements. UTEX 250-A haplotypes are a mosaic of each parental species following mitotic recombination, and two chromosomes are trisomic. Loss-of-heterozygosity events are pervasive across Auxenochlorella and can evolve rapidly in the laboratory. High-quality structural annotation yielded ∼7,500 genes per haplotype. Auxenochlorella have experienced gene family loss and reduction, including core photosynthesis genes, and exhibit periodic adenine and cytosine methylation at promoters and gene bodies, respectively. Approximately 10% of genes, especially those involved in DNA repair and sex, overlap antisense long noncoding RNAs, which may participate in a regulatory mechanism. We demonstrate the utility of Auxenochlorella for fundamental research by knockout of a chlorophyll biosynthesis enzyme, and confirm one trisomy by allele-specific transformation. These results demonstrate the generality of several evolutionary forces associated with vegetative diploidy and provide a foundation for the use of Auxenochlorella as a reference organism.
CHL27↗
The evolution of transcriptional regulation in eukaryotes
Gene expression is central to the genotype-phenotype relationship in all organisms, and it is an important component of the genetic basis for evolutionary change in diverse aspects of phenotype. However, the evolution of transcriptional regulation remains understudied and poorly understood. Here we review the evolutionary dynamics of promoter, or cis-regulatory, sequences and the evolutionary mechanisms that shape them. Existing evidence indicates that populations harbor extensive genetic variation in promoter sequences, that a substantial fraction of this variation has consequences for both biochemical and organismal phenotype, and that some of this functional variation is sorted by selection. As with protein-coding sequences, rates and patterns of promoter sequence evolution differ considerably among loci and among clades for reasons that are not well understood. Studying the evolution of transcriptional regulation poses empirical and conceptual challenges beyond those typically encountered in analyses of coding sequence evolution: promoter organization is much less regular than that of coding sequences, and sequences required for the transcription of each locus reside at multiple other loci in the genome. Because of the strong context-dependence of transcriptional regulation, sequence inspection alone provides limited information about promoter function. Understanding the functional consequences of sequence differences among promoters generally requires biochemical and in vivo functional assays. Despite these challenges, important insights have already been gained into the evolution of transcriptional regulation, and the pace of discovery is accelerating.
Review, Academic↗
Metabolic and evolutionary responses of Clostridium thermocellum to genetic interventions aimed at improving ethanol production
Engineering efforts targeted at increasing ethanol by modifying the central fermentative metabolism of Clostridium thermocellum have been variably successful. Here, we aim to understand this variation by a multifaceted approach including genomic and transcriptomic analysis combined with chemostat cultivation and high solids cellulose fermentation. Three strain lineages comprising 16 strains total were examined. Two strain lineages in which genes involved in pathways leading to organic acids and/or sporulation had been knocked out resulted in four end-strains after adaptive laboratory evolution (ALE). A third strain lineage recapitulated mutations involving adhE that occurred spontaneously in some of the engineered strains.
Biotechnology & Applied Microbiology↗
Century-long timelines of herbarium genomes predict plant stomatal response to climate change
Abstract Dissecting plant responses to the environment is key to understanding whether and how plants adapt to anthropogenic climate change. Stomata, plants’ pores for gas exchange, are expected to decrease in density following increased CO 2 concentrations, a trend already observed in multiple plant species. However, it is unclear whether such responses are based on genetic changes and evolutionary adaptation. Here we make use of extensive knowledge of 43 genes in the stomatal development pathway and newly generated genome information of 191 Arabidopsis thaliana historical herbarium specimens collected over 193 years to directly link genetic variation with climate change. While we find that the essential transcription factors SPCH, MUTE and FAMA, central to stomatal development, are under strong evolutionary constraints, several regulators of stomatal development show signs of local adaptation in contemporary samples from different geographic regions. We then develop a functional score based on known effects of gene knock-out on stomatal development that recovers a classic pattern of stomatal density decrease over the past centuries, suggesting a genetic component contributing to this change. This approach combining historical genomics with functional experimental knowledge could allow further investigations of how different, even in historical samples unmeasurable, cellular plant phenotypes may have already responded to climate change through adaptive evolution.
Environmental Sciences & Ecology↗
Design and Optimization of Low-thrust Orbit Transfers Using Q-law and Evolutionary Algorithms
Future space missions will depend more on low-thrust propulsion (such as ion engines) thanks to its high specific impulse. Yet, the design of low-thrust trajectories is complex and challenging. Third-body perturbations often dominate the thrust, and a significant change to the orbit requires a long duration of thrust. In order to guide the early design phases, we have developed an efficient and efficacious method to obtain approximate propellant and flight-time requirements (i.e., the Pareto front) for orbit transfers. A search for the Pareto-optimal trajectories is done in two levels: optimal thrust angles and locations are determined by Q-law, while the Q-law is optimized with two evolutionary algorithms: a genetic algorithm and a simulated-annealing-related algorithm. The examples considered are several types of orbit transfers around the Earth and the asteroid Vesta.
low-thrust orbit transfer↗
The effects of genetic change at different levels
Evolutionary selection process effect on existing genes
EVOLUTION↗
The estimation of genetic divergence
Consideration is given to the criticism of Nei and Tateno (1978) of the REH (random evolutionary hits) theory of genetic divergence in nucleic acids and proteins, and to their proposed alternative estimator of total fixed mutations designated X2. It is argued that the assumption of nonuniform amino acid or nucleotide substitution will necessarily increase REH estimates relative to those made for a model where each locus has an equal likelihood of fixing mutations, thus the resulting value will not be an overestimation. The relative values of X2 and measures calculated on the basis of the PAM and REH theories for the number of nucleotide substitutions necessary to explain a given number of observed amino acid differences between two homologous proteins are compared, and the smaller values of X2 are attributed to (1) a mathematical model based on the incorrect assumption that an entire structural gene is free to fix mutations and (2) the assumptions of different numbers of variable codons for the X2 and REH calculations. Results of a repeat of the computer simulations of Nei and Tateno are presented which, in contrast to the original results, confirm the REH theory. It is pointed out that while a negative correlation is observed between estimations of the fixation intensity per varion and the number of varions for a given pair of sequences, the correlation between the two fixation intensities and varion numbers of two different pairs of sequences need not be negative. Finally, REH theory is used to resolve a paradox concerning the high rate of covarion turnover and the nature of general function sites as permanent covarions.
Holmquist, R.↗
Reinforcement learning in discrete action space applied to inverse defect design
Abstract Reinforcement learning (RL) algorithms that include Monte Carlo Tree Search (MCTS) have found tremendous success in computer games such as Go, Shiga and Chess. Such learning algorithms have demonstrated super-human capabilities in navigating through an exhaustive discrete action search space. Motivated by their success in computer games, we demonstrate that RL can be applied to inverse materials design problems. We deploy RL for a representative case of the optimal atomic scale inverse design of extended defects via rearrangement of chalcogen (e.g. S) vacancies in 2D transition metal dichalcogenides (e.g. MoS 2 ). These defect rearrangements and their dynamics are important from the perspective of tunable phase transition in 2D materials i.e. 2H (semi-conducting) to 1T (metallic) in MoS 2 . We demonstrate the ability of MCTS interfaced with a reactive molecular dynamics simulator to efficiently sample the defect phase space and perform inverse design—starting from randomly distributed S vacancies, the optimal defect rearrangement of defects corresponds a line defect of S vacancies. We compare MCTS performance with evolutionary optimization i.e. genetic algorithms and show that MCTS converges to a better optimal solution (lower objective) and in fewer evaluations compared to GA. We also comprehensively evaluate and discuss the effect of MCTS hyperparameters on the convergence to solution. Overall, our study demonstrates the effectives of using RL approaches that operate in discrete action space for inverse defect design problems.
42 ENGINEERING↗