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2013 Annual Science Report

NASA Ames Research Center Reporting  |  SEP 2012 – AUG 2013

Executive Summary

The Ames Team of the NAI investigates the physical, chemical and biological processes that combined to create early habitable environments. We trace the cosmic evolution of organic molecules from the interstellar medium, through protoplanetary disks and planetesimals, and ultimately to potentially habitable planets. We characterize the diversity of planetary systems that might emerge from protoplanetary disks. We identify diverse scenarios for the origins and early evolution of catalytic functionality and metabolic reaction networks. We develop and test a methodology for assessing quantitatively the habitability of early planetary environments – particularly Mars – via capabilities that could be deployed in situ. Our ongoing active involvement in multiple NASA missions provides context, incentives and collaborative opportunities for our research and education and public outreach programs. Please visit

Cosmic distribution of chemical complexity. This project explores the connections between chemistry in space and the origins of life. We track the formation and evolution of chemical complexity in space, from simple carbon-rich molecules such as formaldehyde and acetylene to complex species including amino acids, nucleic acids and polycyclic aromatic hydrocarbons. We characterize carbon-rich species that are interesting biologically and we explore their possible roles in the origins of life on habitable worlds. We do this by measuring the spectra and chemistry of analog materials in the laboratory, by remote sensing with small spacecraft, and by analyses of extraterrestrial samples returned by spacecraft or that fall to Earth as meteorites. We use these results to interpret astronomical observations made with ground-based and orbiting telescopes.

We have published several papers that describe the production of prebiotic compounds by UV irradiation of cosmic ices. We showed that the photolysis of pyrimidine in astrophysical ices produces a host of new compounds, including all of the pyrimidine-based nucleobases (Figure 1). We described organic nanoglobules found in carbonaceous meteorites. We published analyses of the recently fallen Sutter’s Mill meteorite. We analyzed Spitzer spectral data cubes on the reflection nebula, NGC 7023, exclusively using polycyclic aromatic hydrocarbon (PAH) spectra and tools in the PAH database (PAHdb) generated in the Ames Astrochemistry Laboratory. 2D-maps of the region show, for the first time, UV-driven, spatial evolution of PAH subpopulations broken down by size, charge (Figure 2), and composition, variations that probe subtle changes in the morphology, radiation field, photodissociation region (PDR) boundary, etc. This work marks a number of 'firsts.’ We published another study that also marks a number of 'firsts’ and illustrates the global interest for PAHdb. It represents an unusual application to data returned by the Cassini spacecraft as it reports the presence of PAHs in the atmosphere of Saturn’s largest moon, Titan. Finally, the content and capabilities of PAHdb have been substantially expanded and will be made publicly available by the end of 2013 in a version 2.00 release, timed to coincide with a coupled publication.

Figure 1. UV photolysis of pyrimidine in mixed molecular ices leads to the formation of all three of the pyrimidine-based nucleobases - uracil, cytosine, and thymine (Materese et al. 2013).
Figure 2. Northwest PDR in Reflection Nebula NGC 7023. Left: Fraction of total PAH surface brightness from neutral PAHs. Right: Fraction of total PAH surface brightness from PAH cations. The PAH breakdown maps were made by blind algorithm-driven-machine analyses of 300 spectra using PAHdb.

Evolution of protoplanetary disks and early planetary environments. We explore evolving protoplanetary disks to understand the formation of primitive planetary bodies that ultimately could host habitable environments. The disk is in many ways an astrochemical “primeval soup” in which abundant elements are assembled into increasingly complex organic compounds and mixed in the disk’s dust and gas envelope. We also investigate planetary processes that can influence early habitable environments.

We enhanced our models of large-scale transport in protoplanetary disks. We contributed to a paper that treats the foundational problem of modeling opacity in protoplanetary disks and exoplanet atmospheres. We included into a model for the first time the effect of grain evolution from micron to millimeter sizes and the effect on disk opacity. These concepts will enable models to include predicting habitability zones in extra-solar planetary systems. We also used the opacity models to study tenuous atmospheres of the Moon and similar bodies.We continued our study of how planets beyond the ice line affect the accretion of volatiles by rocky planets in circumstellar habitable zones (CHZ). We found that giant planets are not required to provide CHZ planets with several oceans worth of water.

We continued to investigate protoplanetary disk conditions that lead to planet formation. We studied lifetimes of disks acting under the influence of photoevaporation from the central star, and we modeled observations of disks with planets to determine their physical and chemical evolution. We reported the first direct measurement of the gas mass of a protoplanetary disk using emission lines from HD, detected for the first time from a disk. (Figure 3) Although TW Hydrae is an old system (~10 Myrs), its disk is surprisingly massive at ~50 Jupiter masses. This study may indicate that gas in disks may survive long enough to form gas giant planets and circularize terrestrial planet orbits like those in our solar system. In other related work, we examined emission line diagnostics of winds from disks (Hubble Space Telescope data), and concluded that disk winds due to photoevaporation may not be as vigorous as once believed. We examined high-resolution data of optical forbidden lines from a small sample of protoplanetary disks and found that more than half the emission—-previously attributed to winds—- actually arises from bound gas at the disk surface. These results indicate that mass loss rates from photoevaporating disks are low and suggest that gas disk lifetimes may typically be sufficiently long to allow planets to form.

Figure 3. The left panel shows the first detection of hydrogen deuteride, the main isotopologue of molecular hydrogen, which is the primary constituent of planet-forming disks. The HD 1-0 line was detected using NASA’s Herschel Space Observatory and enabled the first determination of the mass of a disk. The right panel shows an image release (NASA JPL) depicting the result---the mass of gas in the 10 million-year old disk that surrounds TW Hydrae is still sufficient to form 50 Jupiters.

We continue to spearhead the development of the publicly available Systemic Console software for the analysis of radial velocity and photometric data sets for extrasolar planets. We continued to investigate the statistical nature of the galactic planetary census and we are studying the ramifications that the latest results from the Kepler Mission have for the formation and evolution of planetary systems. We conclude that the dominant population of planets observed by the Kepler Mission (“super-Earth” type planets, often in multiple-planet systems, and with orbital periods P<100 days) formed in situ and did not require extensive planetary migration to arrive at their current locations. This work introduced and quantified the concept of a Minimum-Mass Extrasolar Nebula (MMEN), which describes the default mode of planet formation in the galaxy, and which we believe will have broad ramifications for the study of planetary origins.

We contributed to a review paper addressing the effects of large body impacts on the climates of Earth, Titan, Mars, and Venus. We also completed two manuscripts addressing the hypothesis that Earth was oxygenated by hydrogen escape. We argue that the advent of an O2-rich atmosphere depended both upon the advent of oxygenic photosynthesis and the preparation of an oxygen-friendly surface environment by a history of hydrogen escape from Earth. In another study, we used detailed radiative transfer models to address whether a runaway greenhouse is possible on Earth today.

Origins of functional proteins. We seek to identify critical requirements for the emergence of biological complexity in early habitable environments by examining key steps in the origins and early evolution of functional proteins and metabolic reaction networks. We investigate whether protein functionality can arise from an inventory of polypeptides that might have naturally existed in habitable environments. We attempt the first demonstration of multiple origins of a single enzymatic function. We investigate experimentally how primordial proteins could evolve through the diversification of their structure and function. We determine how simple proteins could carry out seemingly complex functions.

The structure and dynamics of a model primordial enzyme capable of ligating two RNA fragments was published in a journal and featured on a number of science news websites. Through a combination of computer simulations and molecular biology methods we showed that mutations of several amino acids that appeared to be key for structural integrity of the enzyme did not reduce its activity, thus demonstrating a remarkable functional robustness of the ligase. We continue to seek the most primitive version of this enzyme by selecting for activity using a ligase library with random deletions (Figure 4).

Figure 4. Identification of minimal amino acid sequence needed for enzymatic activity. We developed a method to create a library of all possible deletion variants of the ligase 10C gene. We first generated random interruptions of the original gene using a transposon reaction. The resulting fragments were re-assembled in a random fashion to yield the library of deletion variants. This library will be subjected to our previously described in vitro selection process to identify active enzymes of reduced size.

With the goal of isolating alternative RNA ligase enzymes from a library consisting of random polypeptides, we performed 13 rounds of in vitro selection but were unable to detect ligase activity. We will repeat the selection under conditions modified to include transition metal ions. These cofactors could participate in catalysis or support the three- dimensional protein structure, as we demonstrated for the previously identified ligase, which utilizes zinc.

In order to understand how primordial proteins could have mediated a key cellular function – proton transport across membranous cell walls – we conducted extensive computer simulations of a simple ion channel from influenza A virus. The membrane core of the channel consists of just four identical helices (Figure 5). Protons transported through the channel must navigate two gates formed by valine and histidine/tryptophan amino acids, respectively; the second gate is pH-sensitive. The channel opens at this gate only when at least three of four histidines at the gate become protonated. Histidines actively participate in the transport through shuttling protons across the gate. A similar mechanism of directional proton transport might have been used in the earliest ion pumps if they contained the properly placed, photo-activated proton source.

Figure 5. A schematic of M2 ion channel from influenza A virus. Helical fragments of the protein are shown as red cylinders. The transmembrane core of the protein is formed by four helices in the center. Valine and histidine/tryptophan amino acids forming the gates to proton transport are shown at the atomic resolution (valine residues are located near the bottom).

Mineralogical Traces of Early Habitable Environments. We seek to understand how habitability (potential to support life) varies across a range of physical and chemical parameters. This supports a long-term goal of characterizing habitability of environments on Mars. The project consists of two main components: 1. Examine the interplay between physicochemical environments and associated microbial communities in a subsurface environment dominated by serpentinization (a reaction that involves water and crustal rocks, that can sustain life, and which occurred on Mars). 2. Determine how mineral assemblages can record prior environmental conditions and thereby indicate prior habitability. This work supports the CheMin XRD mineralogy instrument on MSL Curiosity.

Samples for aqueous geochemistry and molecular biology were collected and analyzed quarterly from the borehole observatories established in 2011, as part of a well recovery and seasonal monitoring campaign (Figure 6). We also established an initial suite of microbial colonization experiments within the boreholes. To our knowledge this is the first suite of time-resolved down-hole colonization experiments to have been deployed in actively serpentinizing subsurface. A first round of post-deployment monitoring has been conducted and publications prepared. We conducted an extensive metagenomic and pyrotag sequencing analysis of fluids and solid material from the new wells, and we compared these against in situ metabolic activity assays. Initial results demonstrate that, when arrayed against a series of other serpentinizing systems, the highest-pH wells in our field site have the lowest genetic diversity yet observed. The high pH samples also demonstrate very low to unmeasurable metabolic consumption of hydrogen and CO, suggesting that our sites span a gradient that may encompass marginally or uninhabitable conditions. Finally, we published our method for clean drilling (which utilized steam-sterilized drill bits and purified drinking water as drill fluid) and contamination monitoring (introduction of microbe-sized fluorescent spheres into the drill fluid).

Figure 6. A suite of samples for chemical and molecular biology analysis are collected and processed in the field at one of the CROMO borehole observatories.

We also developed a numerical model that determines the supply and demand of metabolic energy as a function of fluid composition, and ultimately as a function of host rock composition. The model is applied to demonstrate the range in habitability across a range of serpentinizing fluid chemistries, including those at our field site, and across the hypothetical chemical space represented by the range of naturally-occurring ultramafic rock compositions. Two manuscripts are currently in preparation based on these efforts. We also published a paper that surveys the current understanding of microbial life in very low energy surroundings – a conceptual link between the field work, the modeling effort, and attempts to understand the biological potential of the subsurface on Mars, Europa, and other bodies that might offer habitable subsurface niches.

Education and Public Outreach. Ames Team members pursued activities in education and public outreach (EPO) that included efforts in high-impact public venues. Team research efforts have contributed source material for the team’s EPO program. We maintain a graduate-level astrobiology course at the University of California at Santa Cruz. We conducted lab tours and demonstrations for students and educators. We delivered lectures to K-12 classrooms, universities, museums, planetariums, national park visitor centers, scientific conferences and the public media. The Ames Team maintained its strong partnership with Lassen Volcanic National Park by exploring astrobiological aspects of hydrothermal activity and microbiology. Ames team members collaborated with staff at Red Bluff High School and Lassen Park to offer the Lassen Astrobiology Student Intern Program to high school juniors and seniors. Each intern examined hydrothermal features, collected field data and wrote a report that presented and interpreted temperature, pH, GPS coordinates, photos, and geochemical and biological analyses. Ames team members continue to train Lassen Park interpretive staff and work with them to develop trailside signs that are being located at sites that illustrate astrobiology research at Lassen. Park staff installed the second in a series of all-weather trailside signs.

Mission involvement. The Ames NAI Team maintained its substantial presence in current and upcoming NASA missions. The P.I. is a member of the Mars Exploration Rover (MER) mission, the Mars Reconnaissance Orbiter (MRO) CRISM team and the Mars Science Laboratory (MSL) mission CheMin team. The P.I. also served as Chair of MEPAG (NASA’s Mars Exploration Program Analysis Group) for the third year. A Co-I is P.I. of the MSL Curiosity CheMin team. Another Co-I is currently serving as the PI on a Comet Surface Sample Return mission concept for the next New Frontiers AO. Other team members participate in the following missions: Kepler, Stardust, Stratospheric Observer for Infrared Astronomy, Mars Reconnaissance Orbiter, MSL, James Webb Space Telescope, Spitzer Space Telescope, Herschel, O/OREOS, ABE/ASPIRE, LCROSS, LADEE, and the Comet Coma Rendezvous Sample Return mission.