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2012 Annual Science Report

NASA Ames Research Center Reporting  |  SEP 2011 – AUG 2012

Executive Summary

The Ames Team 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 start by tracking 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. The work focuses on characterizing carbon-rich species that are interesting from a biogenic perspective and on understanding their possible roles in the origin of life on habitable worlds. We do this by measuring the spectra and chemistry of analog materials in the laboratory, remote sensing with small spacecraft, and analysis 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.

Several published papers describe the production of prebiotic compounds by UV irradiation of cosmic ices. For example, we demonstrated that the photolysis of pyrimidine in astrophysical ices produces a host of new compounds, including the nucleobases uracil and cytosine. Additional papers describe modeling of photolytic production of organics in the protosolar disk and analyses of the recently fallen Almahata Sitta and Sutter’s Mill meteorites.

Figure 1. Breakdown of the 5 – 15 µm PAH emission spectrum at one position in the diffuse region of Reflection Nebula NGC 7023 into PAH subclasses by size (top), charge (middle) and composition (bottom). Our PAHdb helps to correlate the growth, evolution and destruction of PAH and fullerene with local conditions within the nebula.

We substantially expanded content and capabilities of the PAH IR spectroscopic database (PAHdb) to support Spitzer, SOFIA, Herschel and JWST. A major highlight is the inclusion of the capability to directly import astronomical spectra and fit them with database spectra, providing deep new insight into the evolution of PAHs in different environments spanning the universe. We have routinely assisted users develop new PAHdb applications to PAH-related problems (PAHs in Titan or in interstellar ices, etc.). We are creating 2d-maps from Spitzer observations, showing UV-driven spatial evolution of PAH subpopulations broken down by size, charge and composition (Fig. 1), and we are relating these variations to changes in an object’s morphology, radiation field, PDR boundary, etc. We published four papers on the following topics: i – extension of spectra in PAHdb from C130H28 to C384H48 with astronomical applications, ii – long wavelength (15 to 20 µm) IR PAH emission based on spectra in PAHdb, iii – spectral changes along 11 lines-of-sight in Orion PDR, tracking stepwise evolution of PAHs and fullerenes (Fig. 2), and iv – photochemistry of PAHs in NH3 and mixed H2O/NH3 ices.

Figure 2. HST-ACS visible (left) and Spitzer IRAC false color IR (right) images of a 12 square-arcsecond region southwest of the ionization ridge in Orion (top right both images). The red star shows the position of the exciting star, theta1 C Orion. The “+” symbols indicate the 11 positions probing PAHs and fullerenes using PAHdb.

Evolution of protoplanetary disks. 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.

A submitted manuscript describes the location of water ice in the protoplanetary nebula using a new model that takes into account the evolution of the Sun (luminosity and temperature) over the million or so years that the disk is active. Included for the first time are the effects on disk opacity of grains as they evolve and grow from micron to millimeter sizes. The “ice line” (the boundary within the disk beyond which ice can form and accumulate) is not a simple curve, but a two-branched line with a cusp that defines the innermost location of water ice (Fig. 3). The changing shape of the ice line over time gives some indication of the ultimate location of the HZ.

Figure 3. Effect of solar luminosity on the ice line: The left panel indicates the ice line assuming an evolving sun. The right panel shows the ice line assuming current and constant solar luminosity.

We have enhanced our disk evolution models that explore the effects of photoevaporation and dust grain growth and settling. The disk evolution models now include viscous accretion and photoevaporation by ultraviolet and X-ray photons from the central star. These models allow for the redistribution of angular momentum and disk surface density due to the influence of any embedded planets. We find that the inclusion of dust evolution does not significantly influence the timescale over which the disk disperses, however it might have implications for the solid content of the disk that is left behind as well as the accretion of planets. Thermochemical modeling of Spitzer and Herschel line emission data from evolved transition disks around GM Aur and T Cha, both of which are suspected to harbor embedded planets, indicates that significant amounts of gas occur in their inner dust holes and therefore is consistent with the early onset of planet formation.

Origins of functional proteins. The main goal of this project is 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 and thus demonstrate key steps in the earliest evolution of protein functions.

The structure and dynamics of a small enzyme capable of ligating two RNA fragments with the rate of 106 above background was fully characterized. This enzyme was evolved in vitro from a vast library of randomized proteins based on a scaffold. It does not resemble any contemporary protein – it consists of a flexible loop, a part of which is responsible for catalytic activity, a small, rigid core containing two zinc ions coordinated by neighboring amino acids and two highly flexible tails that might affect the catalytic activity. In contrast to other zinc finger proteins, this enzyme does not contain any ordered secondary structure elements such as helices or sheets. The ends of the loop are kept in direct proximity just through interactions of a charged residue and a histidine with a zinc ion. The high flexibility of the protein facilitates its structural adjustments.

A similar picture emerges from studies of simple transmembrane channels that mimic those in ancestral cells. One such channel is an aggregation of an antiamoebin peptide that consists of only 16 amino acids. In contrast to all known genomically coded, well-structured channels, this channel is extremely flexible and does not form a conventional pore (Fig. 4), yet it efficiently mediates ion transport.

Figure 4. Top view of the antiamoebin channel that is formed through aggregation of 6 monomers (yellow, gold, gray, green, white and pink) surrounding a water-filled pore embedded in the membrane. Water molecules were removed for clarity. This picture is a snapshot from molecular dynamics computer simulations. Note the highly irregular, asymmetric shape of the channel.

Our findings indicate that highly flexible proteins or protein assemblies that do not resemble their contemporary counterparts could carry out functions quite efficiently. These might be points on a continuous evolutionary trajectory that form the “missing link” between simple, but only weakly active, oligopeptides and well-folded proteins similar to those found in modern organisms.

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, in order to support 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.

This year we conducted an intensive characterization of the newly established borehole observatories at McLaughlin Natural Reserve. We examined rock cores from new wells, specifically using a commercial analog of CheMin. This effort specifically supports MSL by identifying mineral assemblages characteristic of active serpentinization and linking them to the observed geochemistry. An important focus of this work was to quantify the abundance of magnetite as a proxy the production of the microbe-sustaining substrate H2 during serpentinization.

We completed a yearlong program of seasonal monitoring of newly drilled wells that charted the recovery of subsurface environmental conditions from the effects of drilling. Analyses focused on (i) abundances of potential metabolites and other chemical species necessary to construct models for metabolism; (ii) isotopic measurements designed to indicate CH4 sources; and (iii) process rate measurements to document any microbial consumption of H2 and CO.

Figure 5. Microbial consumption of both hydrogen and carbon monoxide is demonstrated in well waters at pH 11.5, from pre-existing wells at the McLaughlin Natural Reserve.

We conducted tag-based deep sequencing analyses of microbial community composition in water and rock cores from new boreholes. These analyses will provide the basis for comparing community compositions across McLaughlin samples and with other serpentinizing systems worldwide. Results indicate a low diversity serpentinite biosphere consisting largely of Betaproteobacteria and Clostridiales. We obtained the first of several metagenomes from new near-surface well samples at McLaughlin. Early findings reveal areas of marked similarity in metagenome content to those at other serpentinizing sites, such as the Tablelands ophiolite in Newfoundland.

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.

Figure 6. Postdoctoral associate Sanjoy Som talks to a class of elementary school students about Mars.

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. Interns examined hydrothermal features, collected field data and generated a database of 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 being located at sites that illustrate astrobiology research at Lassen. Park staff installed the first in a series of all-weather trailside signs.

Figure 7. Red Bluff High School students who participate in NASA’s Astrobiology Intern Program work with Terra, the field-based version of the CheMin instrument on the Mars Science Laboratory Curiosity rover, currently operating successfully on Mars. CheMin, which stands for Chemistry and Mineralogy, was designed by Ames Team member David Blake to identify minerals and rocks on Mars, similar to what the Astrobiology interns are doing at Lassen Volcanic National Park.

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. is also Chair of MEPAG (NASA’s Mars Exploration Program Analysis Group). One Co-I is P.I. of the MSL Curiosity CheMin team. Another Co-I is currently serving as the P.I. 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.