Astrobiology Research Program - Details

Our long range goal for the astrobiology research programme is to chart the formation of life - from the formation of planetary systems and creation of biomolecules and habitable conditions - to the characteristics of the first organisms that appeared on the Earth and possibly other planets. The people that we have assembled as co-applicants have the broad range of interests necessary to achieve these goals, including observational, experimental, theoretical, and computational experts which provide a complementary set of state-of-the-art labs and experiments, observing programmes, and theoretical modeling efforts.

We highlight, in point form, our proposed research programmes (documented below) in 3 basic and related directions:

  1. Conditions for Life
  2. Origins of Life
  3. Extremophiles

 

1. Conditions for Life

In order to get planet formation theory -- especially the formation of Terrestrial planets -- right, one needs to start with convincing initial conditions that are closely related to observed properties of protostellar disks. R. Pudritz, and postdoc R. Banerjee (2005, ApJ) have extended the FLASH Adaptive Mesh Refinement code to allow one to study the collapse of magnetized protostellar cores (including cooling processes in molecular gas that contains dust) from initial turbulent conditions in a molecular cloud, and to the stellar surface. This provides excellent simulations of protostellar disks that can be constrained by astronomical observations (by R. Jayawarhana, and J. Di Francesco) data, and which would allow authoritative computations of astrochemistry and the formation of biomolecules in protoplanetary environments to be carried out.
With the ability to rigourously compute the properties of such protoplanetary disks, we are prepared to address some very important astrobiological questions. The foremost of these is - are the biomolecules that were critical for the first cells produced primarily in interstellar space, or through geochemical processes in hydrothermal vents in the Earth's young oceans? Pudritz and his group will collaborate with M. Bernstein's lab at NASA Ames, whose experiments focus on the formation of amino acids and fatty acids (amphiphiles) on the surfaces of UV irradiated, the ice-coated grains under typical conditions found in molecular clouds. The experimental data on the UV irradiation of ice-covered grains will be used to constrain astrochemistry calculations that will be incorporated into our existing code. This will allow us to make quantitative predictions of amino acid synthesis. This can be compared with the increasing data on the abundance of amino acids in cometary as well as meteoritic samples. Our new models of planet formation that predict "dead zones" in the interior of such protostellar disks (Matsumura & Pudritz 2005, MNRAS )can also be used to compute -- through dynamical --> -- simulations -- the rate at which these may be delivered to young planets. Our work will be compared with studies of amino acid content in meteorite data, such as the famous Murchison's meteorite, as well as searches for amino acids such as glycine in molecular gas. These earliest stages of the formation of terrestrial planets involve a detailed understanding of how dust can build planetesimals. It may be that organic molecules will be needed as the sticky glue that will help small dust particles to bind in the early phases of planetesimal formation.

The environments where planets form are dynamic, with spiralling gas flows and perturbations from nearby stars in the form of gravitational tugs and intense ultraviolet radiation. J. Wadsley will extend current gaseous planetary disk simulations to demonstrate how these effects modify the old simple scenario where dust accumulates very slowly to form asteroids, comets and ultimately planets. Recent results indicate that gas drag (Tanga et al. 2004) and turbulence (Anders et al. 2005) greatly enhance dust accumulation. The emerging picture is that an evolving gaseous disk is important to the evolution of planets of all sizes (Mayer, Wadsley, Quinn & Stadel 2005, Thommes 2005) and for the formation of potentially life-bearing moon systems (e.g. Europa) around giant planets (Yann et al. 2005). These detailed planet formation scenarios indicate how common such systems are, how early they might be ready to support life, which elements are present and the potential for pre-biotic chemical synthesis.

Using state-of-the art instruments on many of the world's largest telescopes, R. Jayawardhana explores how these extrasolar planetary systems form and evolve. He studies the timescales and processes related to building planets out of dust and gas in protoplanetary disks around young Sun-like stars as well as much lower mass M dwarfs and `failed stars' known as brown dwarfs. He is also searching for newborn planets around young stars, so that we can learn about the initial configurations and long-term stability of planetary systems, especially with regard to planets in the habitable zone. He plans to investigate the structure of disks in the terrestrial planet region as well as the changes in mineralogy and chemistry as these disks build up plantesimals. There is great potential for collaboration here with theorists at the OI, particularly J. Wadsley and R. Pudritz, whose disk models will complement Jayawardhana's observations.

J. Di Francesco (Herzberg Institute of Astrophysics) is involved in astronomical observations of organic molecules associated with the formation of protostars and their disklike proto-solar-systems. Such molecules. through chemical reactions within proto- solar-systems, could form the more complex molecules required for Earth-based life such as amino acids, the building blocks of proteins. Indeed. life here may have been strongly influenced if such molecules were introduced to Earth during its formative period. Ident- ification of biomolecules from proto-solar-system disks will soon be probable with the high sensitivities expected from next generation telescopes like the Atacama Large Milli- meter Array (ALMA). For example, the simplest amino acid, glycine, has several emission signatures at the high radio frequency ranges for which ALMA was designed. Di Francesco plans to observe proto-solar-system disks for traces of glycine and other amino acids to understand better the development of biomolecules in extrasolar planetary environments.

J. Fiege has developed an extremely general genetic algorithm (see Goldberg 1989, 2002 for example) which is designed for problems requiring massive- scale parameter exploration and optimization. This code can be viewed as an interdisciplinary data-modeling tool, which provides a powerful methodology, based loosely on biological evolution, to understand complex problems that may be intractable otherwise. This tool would find many interesting new applications to problems including the authoritative modeling of the structure of Europa.
Jupiter's moon Europa is one of the most intriguing planetary bodies in the solar system. A crust of water ice covers Europa, whose surface is dominated by innumerable cracks, fissures and "ice rafts" , where the crust appears to have broken and shifted, forming a jigsaw puzzle of ice fragments. Measurements of Europa's magnetic field from NASA's Galileo Orbiter provide additional evidence of a global ocean of liquid water containing dissolved mineral salts (Kivelson et al. 2000). J. Fiege is developing a global model of Europa that accounts for its layered density structure, heat transport through its outer layers of water and ice, and the possibility of liquid and solid-state ice convection in these outer layers. The model parameters are explored fully and well-constrained, thanks to the genetic algorithm discussed above. This work also includes a physical model of the tidal stresses in the ice, due to interactions with Jupiter, and the physical processes that regularly crack Europa's icy surface. This will help provide constraints for the availability of sunlight to microbes living beneath the ice, and the transport of potential raw materials for biology between the surface and the ocean.

 

2. Origins of Life

Prebiotic conditions for life may involve the delivery of biomolecules such as amino acids and fatty acids (amphiphiles). Many of the 20 amino acids for current life are found in meteorites, although the frequencies seen in extraterrestrial sources do not match those in modern proteins. The meteorite data, plus the results of simulations on interstellar biomolecule production, give an idea of the composition of the prebiotic soup at the time life appeared. There have also been attempts to predict the frequencies of amino acids formed abiotically in deep sea vent conditions. When new biochemical synthesis pathways evolved, the composition of proteins was no longer constrained by the thermodynamics of the prebiotic environment. A good deal is known about the pathways and energetic costs for amino acid synthesis in modern cells. Bacteria are sensitive to energetic constraints - low cost amino acids are found to be more abundant specifically in the most abundant proteins. Higgs and Pudritz will combine all these lines of evidence to form a coherent picture of the factors that influence the change of amino acid frequency over time.

We also propose two new studies related to this. Firstly, recent sequence analysis studies claim to detect systematic trends of increase/decrease in amino acid frequencies dating from the earliest life forms. We are somewhat skeptical of this, because it is known that base frequencies in DNA vary greatly between organisms, and amino acid frequencies respond to this mutation pressure despite selection acting at the protein level (Higgs form 100, ref J1). We will apply this method to bacterial sequences, and ask whether any trends observed are really due to long-lasting effects dating from the origin of life or due to more recent changes in mutation or selection processes in individual lineages. Secondly, the frequencies of amino acids used in proteins depend on the genetic code. Our recent theoretical model (Higgs form 100 ref J2) studies codon reassignments that create modified codes from the canonical code. We will now develop this to study the origin of the canonical code. Early codes probably had few amino acids, each with many codons. Greater specificity of the code evolved as new amino acids were added. Amino acids that were prebiotically common were presumably the earliest to be added. The order of addition is also influenced by biochemical pathway constraints. Selection rules in the model (based on minimization of the effects of translational and mutational errors) will determine the likelihood of addition of any new amino acid in any trial codon block. We will compare the relative error rates of simulated codes, random codes and the real code in order to understand the processes leading to selection of the real code.

Mathematical and computational models play a key role in evolutionary biology because they allow testing of the logic of evolutionary arguments, and they allow simulation of complex systems which are not tractable analytically. Kauffman and Higgs will develop a range of models to test ideas related to the earliest cells on Earth. Gene replication and cell division in the first cells are unlikely to have been well controlled. We envisage proto-cells containing separate unlinked genes that divide with random segregation of the genes between the two daughter cells. This would lead to the occasional creation of inviable cells that lack essential genes. Another hazard is that proto-cells are vulnerable to invasion by parasitic replicators that do not contribute to cell fitness. It has been shown that cells containing moderate copy numbers of each essential gene can survive despite both these problems (known as the Stochastic Corrector Mechanism - SCM). We will use mathematical models to investigate whether the SCM can explain the possible survival of populations in the presence of both parasites and HGT, and if so, to ask whether barriers to HGT would be selected in order to reduce the transfer of parasites. In this way we will determine whether the picture of very high HGT rate between early cells is theoretically feasible.

S. Kauffman has previously developed models for the origin of life based on the idea of autocatalytic sets of chemical reactions. Autocatalysis is a key requirement for life. The argument is that in any sufficiently diverse mixture of reactants, the chance of a connected autocatalytic set arising becomes large. So far, models of this type are ' continuous medium' models, in the sense that they do not consider spatial compartments for reactions. We will develop models of autocatalytic reaction sets that are enclosed in many separate compartments. Lipids can spontaneously form vesicles and micelles, hence it is likely that compartments were present at the earliest stages of life. Additionally, the presence of many small compartments allows for competition between them, which is a prerequisite for natural selection and evolution. If compartments are small, then key molecules will only be present in small numbers. Therefore, stochastic dynamics is likely to be important. Autocatalytic sets will be in danger of losing components by chance and this will limit the complexity of sets that is possible. Autocatalytic sets are also subject to being invaded by parasitic molecules. Both these features link the autocatalytic set models with the SCM above. All cells need to work within the constraints imposed by thermodynamics. Reactions can be exergonic or endergonic, but a life-form with an autocatalytic cycle can never be perfectly efficient and is bound to be a net consumer of energy. It therefore requires an external energy source. One specific model of an organism that considers energetic constraints in the work-cycle model discussed in Kauffman's book Investigations. We would like to build on this idea by combining it with the autocatalytic set model. This will involve coupling certain reactions to an external energy source, and assigning free energy changes to individual reactions, so that any autocatalytic set that develops is abiding by the laws of thermodynamics.

 

3. Extremophiles

In order to get planet formation theory -- especially the formation of Terrestrial planets -- right, one needs to start with convincing initial conditions that are closely related to observed properties of protostellar disks. R. Pudritz, and postdoc R. Banerjee (2005, ApJ) have extended the FLASH Adaptive Mesh Refinement code to allow one to study the collapse of magnetized protostellar cores (including cooling processes in molecular gas that contains dust) from initial turbulent conditions in a molecular cloud, and to the stellar surface. This provides excellent simulations of protostellar disks that can be constrained by astronomical observations (by R. Jayawarhana, and J. Di Francesco) data, and which would allow authoritative computations of astrochemistry and the formation of biomolecules in protoplanetary environments to be carried out.
With the ability to rigourously compute the properties of such protoplanetary disks, we are prepared to address some very important astrobiological questions. The foremost of these is - are the biomolecules that were critical for the first cells produced primarily in interstellar space, or through geochemical processes in hydrothermal vents in the Earth's young oceans? Pudritz and his group will collaborate with M. Bernstein's lab at NASA Ames, whose experiments focus on the formation of amino acids and fatty acids (amphiphiles) on the surfaces of UV irradiated, the ice-coated grains under typical conditions found in molecular clouds. The experimental data on the UV irradiation of ice-covered grains will be used to constrain astrochemistry calculations that will be incorporated into our existing code. This will allow us to make quantitative predictions of amino acid synthesis. This can be compared with the increasing data on the abundance of amino acids in cometary as well as meteoritic samples. Our new models of planet formation that predict "dead zones" in the interior of such protostellar disks (Matsumura & Pudritz 2005, MNRAS )can also be used to compute -- through dynamical --> -- simulations -- the rate at which these may be delivered to young planets. Our work will be compared with studies of amino acid content in meteorite data, such as the famous Murchison's meteorite, as well as searches for amino acids such as glycine in molecular gas. These earliest stages of the formation of terrestrial planets involve a detailed understanding of how dust can build planetesimals. It may be that organic molecules will be needed as the sticky glue that will help small dust particles to bind in the early phases of planetesimal formation.

The environments where planets form are dynamic, with spiralling gas flows and perturbations from nearby stars in the form of gravitational tugs and intense ultraviolet radiation. J. Wadsley will extend current gaseous planetary disk simulations to demonstrate how these effects modify the old simple scenario where dust accumulates very slowly to form asteroids, comets and ultimately planets. Recent results indicate that gas drag (Tanga et al. 2004) and turbulence (Anders et al. 2005) greatly enhance dust accumulation. The emerging picture is that an evolving gaseous disk is important to the evolution of planets of all sizes (Mayer, Wadsley, Quinn & Stadel 2005, Thommes 2005) and for the formation of potentially life-bearing moon systems (e.g. Europa) around giant planets (Yann et al. 2005). These detailed planet formation scenarios indicate how common such systems are, how early they might be ready to support life, which elements are present and the potential for pre-biotic chemical synthesis.

Using state-of-the art instruments on many of the world's largest telescopes, R. Jayawardhana explores how these extrasolar planetary systems form and evolve. He studies the timescales and processes related to building planets out of dust and gas in protoplanetary disks around young Sun-like stars as well as much lower mass M dwarfs and `failed stars' known as brown dwarfs. He is also searching for newborn planets around young stars, so that we can learn about the initial configurations and long-term stability of planetary systems, especially with regard to planets in the habitable zone. He plans to investigate the structure of disks in the terrestrial planet region as well as the changes in mineralogy and chemistry as these disks build up plantesimals. There is great potential for collaboration here with theorists at the OI, particularly J. Wadsley and R. Pudritz, whose disk models will complement Jayawardhana's observations.

J. Di Francesco (Herzberg Institute of Astrophysics) is involved in astronomical observations of organic molecules associated with the formation of protostars and their disklike proto-solar-systems. Such molecules. through chemical reactions within proto- solar-systems, could form the more complex molecules required for Earth-based life such as amino acids, the building blocks of proteins. Indeed. life here may have been strongly influenced if such molecules were introduced to Earth during its formative period. Ident- ification of biomolecules from proto-solar-system disks will soon be probable with the high sensitivities expected from next generation telescopes like the Atacama Large Milli- meter Array (ALMA). For example, the simplest amino acid, glycine, has several emission signatures at the high radio frequency ranges for which ALMA was designed. Di Francesco plans to observe proto-solar-system disks for traces of glycine and other amino acids to understand better the development of biomolecules in extrasolar planetary environments.

J. Fiege has developed an extremely general genetic algorithm (see Goldberg 1989, 2002 for example) which is designed for problems requiring massive- scale parameter exploration and optimization. This code can be viewed as an interdisciplinary data-modeling tool, which provides a powerful methodology, based loosely on biological evolution, to understand complex problems that may be intractable otherwise. This tool would find many interesting new applications to problems including the authoritative modeling of the structure of Europa.
Jupiter's moon Europa is one of the most intriguing planetary bodies in the solar system. A crust of water ice covers Europa, whose surface is dominated by innumerable cracks, fissures and "ice rafts" , where the crust appears to have broken and shifted, forming a jigsaw puzzle of ice fragments. Measurements of Europa's magnetic field from NASA's Galileo Orbiter provide additional evidence of a global ocean of liquid water containing dissolved mineral salts (Kivelson et al. 2000). J. Fiege is developing a global model of Europa that accounts for its layered density structure, heat transport through its outer layers of water and ice, and the possibility of liquid and solid-state ice convection in these outer layers. The model parameters are explored fully and well-constrained, thanks to the genetic algorithm discussed above. This work also includes a physical model of the tidal stresses in the ice, due to interactions with Jupiter, and the physical processes that regularly crack Europa's icy surface. This will help provide constraints for the availability of sunlight to microbes living beneath the ice, and the transport of potential raw materials for biology between the surface and the ocean.