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2002 Annual Science Report

Scripps Research Institute Reporting  |  JUL 2001 – JUN 2002

Benner - Self-Reproducing Molecular Systems and Darwinian Chemistry

4 Institutions
3 Teams
0 Publications
0 Field Sites
Field Sites

Project Progress

In the area of Darwinian Chemistry, our group has explored the possibility that alternative genetic systems might be built from non-ionic backbones and completed studies that tested the ability of alternative genetic systems to be supported without hydrogen bonding systems. We have also engaged in a program with Frank Grunthaner, of the Jet Propulsion Laboratory, developing chemical technology to detect benzenecarboxylic acids, the most likely Martian organic compounds on the accessible surface of the planet. Other studies include expanding the artificial genetic system to incorporate alternative genetic molecules and developing polymerases that incorporate thiol functionality in an artificial genetic system, thus setting the stage for in vitro evolution experiments with an unnatural genetic system.

Our efforts in the area of Evogenomics (through the NAI focus group and supplemental funding arranged by Blair Hedges) include: (1) developing examples coupling “nonstationary” divergent evolution of protein sequences to the three-dimensional structure of proteins, detecting functional change; (2) completing a comprehensive survey of adaptive evolution in the global proteome; (3) taking the first steps towards the “Phanaerozoic Project”; (4) exploiting reconstructed evolutionary intermediates to solve a long standing problem in protein structural biology, the search for compensatory changes in protein structure; (5) developing a new tool for dating events in the molecular record, and demonstrating its value to detect pathways from an in silico analysis of genomic/proteomic sequence data; and (6) developing a new metric for constructing and evaluating evolutionary trees.

    Steven Benner
    Project Investigator

    Ujjwal Das

    Ronald Geyer

    Photon Rao

    Eric Gaucher
    Graduate Student

    Alonso Ricardo
    Graduate Student

    J. Michael Thomson
    Graduate Student

    Objective 2.0
    Develop and test plausible pathways by which ancient counterparts of membrane systems, proteins and nucleic acids were synthesized from simpler precursors and assembled into protocells.

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

    Objective 4.0
    Expand and interpret the genomic database of a select group of key microorganisms in order to reveal the history and dynamics of evolution.

    Objective 5.0
    Describe the sequences of causes and effects associated with the development of Earth's early biosphere and the global environment.

    Objective 6.0
    Define how ecophysiological processes structure microbial communities, influence their adaptation and evolution, and affect their detection on other planets.

    Objective 7.0
    Identify the environmental limits for life by examining biological adaptations to extremes in environmental conditions.

    Objective 8.0
    Search for evidence of ancient climates, extinct life and potential habitats for extant life on Mars.

    Objective 9.0
    Determine the presence of life's chemical precursors and potential habitats for life in the outer solar system.

    Objective 12.0
    Define climatological and geological effects upon the limits of habitable zones around the Sun and other stars to help define the frequency of habitable planets in the universe.

    Objective 13.0
    Define an array of astronomically detectable spectroscopic features that indicate habitable conditions and/or the presence of life on an extrasolar planet.

    Objective 14.0
    Determine the resilience of local and global ecosystems through their response to natural and human-induced disturbances.

    Objective 16.0
    Understand the human-directed processes by which life can migrate from one world to another.

    Objective 17.0
    Refine planetary protection guidelines and develop protection technology for human and robotic missions.