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2000 Annual Science Report

Scripps Research Institute Reporting  |  JUL 1999 – JUN 2000

Benner's Laboratory

4 Institutions
3 Teams
0 Publications
0 Field Sites
Field Sites

Project Progress

In the past year, the Florida Astrobiology Group has made five major contributions towards the goals set forward by the NASA Astrobiology road map. We have: (a) assigned structures to organic molecules from the near-surface of Mars; (b) Provided evidence against peptide-linked nucleic acid analogs (PNA) being a prebiotic genetic molecule; (c) Advanced efforts to do in vitro selection with functionalized nucleic acids; (d) Assembled the Master Catalog, an evolutionarily organized database of protein sequences containing a complete history of macromolecular life on Earth (as it can be presently inferred from genomic sequence data, and (e) Analyzed the size of microfossils in Mars-derived meteorites.
1. Organic Molecules on Mars. The NASA Planetary Exploration Missions. Entirely funded by the NAI, the Florida Astrobiology sub-node has combined theoretical and experimental work to suggest that, contrary to the widely held interpretation of experiments from the Viking 1976 landers, organic molecules should be present on the surface of Mars. This work is influencing the design of Mars probes. After extensive discussions with scientists involved in the 1976 Viking mission, a paper describing this result appeared in Proc. Natl. Acad. Sci. USA. Within the month, Luann Becker (Univ. Hawaii) delivered to us her laser desorption mass spectra from Allan Hills and Nakhla meteorites, both derived from Mars. These spectra show the presence of organic matter in these meteorites. C12-C13 isotope ratio measurements suggest that this organic material was delivered to the rocks while they were on Mars, from kerogen contained in meteorites that landed on Mars.
Interestingly, both meteorites generate a mass spectrum with a peak at 288. This is the mass of the trianhydride of benzenehexacarboxylic acid, which is expected to be the principal compound observed by laser desorption mass spectrometry in any sample containing benzenehexacarboxylic acid. Benzenehexacarboxylic acid is the principal organic compound that we predicted should be present on the surface of Mars.
While one is obligated to distrust any experimental result that one wants to believe, if the 288 peak turns out to arise from benzenehexacarboxylic acid, this will be a very short turn-around between prediction and verification. It also serves as a nice illustration of how a broad understanding of organic chemical reactivity can be useful to NASA in general and to the NAI in particular.
More importantly, however, close inspection of the mass spectra of the high molecular weight material from ALH and Nakhla reveals significant differences. Naively, these differences suggest that the organics in ALH were exposed to molecular oxygen over very long periods of time, while those from Nakhla were not. ALH is a much older rock, formed over 4 billion years ago. Nakhla is much younger, perhaps less than 2 billion years old. While speculative, it is intriguing to note the possibility that the differences in the high mass organic products may indicate the presence of oxygen in the atmosphere of Mars in a time when oxygen was appearing first on Earth as a result of biogenesis.
At this early stage, we certainly do not suggest that this can be interpreted as evidence for life on Mars 3 billion years ago. These experiments have, however, opened up a line of reasoning that might conclude this, especially if more SNC meteorites are investigated, and if samples ultimately become available from Mars. In the next year (see below) we plan to start to build the organic chemical tools that will enable such a conclusion to be drawn.

2. Universal Chemical Features of Genetic Biopolymers. Consistent with our focus as stated in the last report, and partly funded from Astrobiology sources, the Florida Astrobiology sub-node has developed further its “second generation” model of nucleic acids that emphasizes the importance of the polyanionic nature of DNA as a genetic biopolymer. The concept of a biopolymer that is Capable of Suffering Mutation Independent of Concern over Loss Of Properties Essential for Replication (COSMIC-LOPER) has been adopted by other authors in their effort to understand self-organization and self-replication in molecular systems. COSMIC-LOPERness permits a biopolymer to support a Darwinian search for function. A polyelectrolyte structure (polyanionic or polycationic) is proposed to be a universal feature of the genetic molecules of life, regardless of genesis. This work all but excludes peptide nucleic acid analogs (PNAs) as the original genetic material. A probe to search for such structures in planetary missions is being designed.

3. Darwinian Chemistry. Also consistent with our focus as stated in the last report, we further developed functionalized standard and non-standard DNA molecules as the starting point for generating biological function. The goal continues to be to develop molecular systems that can direct the synthesis of replicates with the possibility of mutation, selection, and therefore evolution, and to quantitatively analyze their performance in in vitro selection experiments. Largely funded from non-Astrobiology sources, but central to the Astrobiology program’s goal of obtaining self-replicating systems in the laboratory, the work from the Florida Astrobiology sub-node that examined in vitro selection “structure space” in both functionalized and non-functionalized nucleic acids. These studies represent a substantial step in our progress towards self-replicating systems in the laboratory.
Battersby, T. R., Ang, D. N., Burgstaller, P., Jurczyk, S., Bowser, M. T., Buchanan, D. D., Kennedy, R. T., Benner, S. A. In vitro selection of an adenosine receptor from a library incorporating a cationic nucleotide analog. J. Am. Chem. Soc. 121, 9781-9789 (1999)
4. The Master Catalog, a Comprehensive Model for Life in the Terrean Biosphere. Largely funded from non-Astrobiology sources, but central to the Astrobiology goal of describing the history of life on Earth, the Florida “Master Catalog” has identified all of the independently evolving modules from completed microbial genomes, and built for each an evolutionary history, an analysis of the evolution of function, and a preliminary secondary structural model. The dataset is now being analyzed to better understand the microscopic processes by which proteins evolve. At present, the Master Catalog is accessible free of charge to interested scientists, and soon will be offered as a commercial product by the company EraGen Biosciences. This tool underlies our strategy of “working backwards in time”, a stepwise approach that proceeds from more highly validatable models of the history of Earth to more controversial ones farther back in time.

5. Structures in the Alan Hills Martian Meteorite. Not too Small to be Living Cells. Entirely funded by the Astrobiology program, the Florida Astrobiology sub-node has joined theory and experiment to show that the structures in the Allan Hills meteorite are not too small to be remnants of life, if that life is based on a single biopolymer capable of both genetics and catalysis. Such biopolymers are believed to have enabled the origin of life on Earth. A 50-step metabolism for small cells has been proposed from an understanding of organic reactivity. The paper has now appeared.

    Steven Benner
    Project Investigator

    Objective 3.0
    Replicating, catalytic systems capable of evolution, and construct laboratory models of metabolism in primitive living systems.