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Project Reports

• Project 2: Cells as Engines and the Serpentinization Hypothesis for the Origin of Life

  All life is, and must be, “powered” since all of its most essential and distinguishing processes have to be driven “up-hill” against their natural thermodynamic direction. By the 2nd law of thermodynamics, however, a process can only be made to proceed up-hill by being mechanistically linked, via a molecular device functioning as an engine, to another, more powerful, process that is moving in its natural, down-hill direction. On fundamental principles, we argue, such engine-mediated conversion activities must also have been operating at, and indeed have been the cause of, life’s emergence. But what then were life’s birthing engines, what sources of power drove them, what did they need to produce, and how did they arise in an entirely lifeless world? Promising potential answers to these and other questions related to the emergence of life are provided by the Alkaline Hydrothermal Vent/serpentinization (“AHV”) hypothesis, whose original propounder and lead proponent, Dr. Michael Russell of JPL, is a co-investigator on this project. The goal of the project is specifically to clarify the essential mechanistic modus operandi of all molecular engines that power life, and to see how the most fundamental and prerequisite of these could have arisen, and operated, in the structures and flows produced by the serpentinization process. Importantly, candidate answers to these questions can be put to definitive laboratory tests.

  ROADMAP OBJECTIVES: 1.1 2.1 3.1 3.2 3.3 3.4

• Project 3: The Origin of Homochirality

  A universal aspect of living systems on Earth is their homochirality: Life uses dextrorotary sugars and levorotary amino acids. The reasons for this are hotly debated and not close to being settled. However, the leading idea is that autocatalytic reactions grew exponentially fast at the origin of life, and whatever chiral symmetry breaking was accidentally present became amplified subsequently. We are calculating the way in which this can take place using statistical mechanics, and also trying to see how a uniform homochirality could be stable to spatial fluctuations.

  ROADMAP OBJECTIVES: 3.2 3.4 4.1 4.2 5.1 5.2 7.1 7.2

• Origins of Functional Proteins and the Early Evolution of Metabolism

  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. Applying a combination of experimental and theoretical methods, we investigate whether protein functionality can arise from an inventory of polypeptides that might have naturally existed in habitable environments, investigate how primordial proteins could evolve through the diversification of their structure and function and determine how simple proteins could carry out seemingly complex functions that are essential to life. This work offers unique information about the earliest evolution of cellular systems that has not been available from other studies.

  ROADMAP OBJECTIVES: 3.2 3.4

• Biosignatures of Ancient Rocks – Hedges Group

  Our work involves the design, assembly, and release to the public of a tree of life calibrated to geologic time (timetree). It is needed by astrobiologists to help determine the source of biomarkers for the presence of life in the geologic record.

  ROADMAP OBJECTIVES: 3.3 3.4 4.1 4.2 7.1 7.2

• Project 5: The Origins of Life’s Diversity

  The huge diversity of life poses a major challenge to ecological theory and a major source of optimism for astrobiology. Ecological theory argues that a single environmental niche should be colonized by a single species of organism, or perhaps a small community, and so the diversity of life should be essentially a measure of the number of niches present. The huge diversity of life does suggest, however, that the ability of life to explore, colonize and especially create environmental niches has been drastically underestimated. Accordingly, the likelihood of extraterrestrial life arising is also underestimated, or at least inadequately estimated, by our present understanding of biological evolution. This project attempts to solve this problem by developing a new theory for niche diversity.

  ROADMAP OBJECTIVES: 3.4 4.1 4.2 5.1 5.2 5.3 6.1 6.2

• Project 6. Mining Archaeal Genomes for Signatures of Early Life: Comparison of Metabolic Genes in Methanogens

  Methanogenic archaea derive energy from simple starting materials, producing methane and carbon dioxide in the process. The chemical simplicity of the growth substrates and versatility of the organisms in extreme environments provide for a possibility that they could exist on other planets. By characterizing the evolution of methanogens from the most simple to most complex organism as well as their growth characteristics under controlled environments, we hope to address the question as to whether they could exist on planets such as Mars, where bursts of methane have been seen, yet no source has yet been identified.

  ROADMAP OBJECTIVES: 1.1 2.1 3.1 3.2 3.3 3.4 4.1 4.2 5.1 5.2 5.3 6.1 6.2 7.1 7.2

• Biosignatures of Life in Ancient Stratified Ocean Analogs

  Instigated by Macalady and Kump in 2010, this project investigates biosignatures of life in modern analogs for stratified ancient and/or extraterrestrial oceans. The primary field site is a sinkhole in Florida. Other field site include stratified ocean analogs in the Bahamas, New York State, and the Dominican Republic. A website monitoring the activities of an informal working group on Early Earth Photosynthesis is maintained by Macalady (http://www.geosc.psu.edu/~jlm80/EEP.html).

  ROADMAP OBJECTIVES: 2.1 3.3 3.4 4.1 5.2 5.3 6.1 7.1 7.2

• Titan as a Prebiotic Chemical System – Benner

  In 2007, NASA sponsored a committed of the National Academies of Science to explore whether life might exist in environments outside of the traditional habitable zone, defined as positions in a solar system where liquid surface water might be found. Alternative solvents which have analogous “habitable zones” farther away from their star include hydrocarbons, ammonia, and dinitrogen. The core question asked whether life having genetic biopolymers might exist in these solvents, which are in many cases (including methane) characterized by the need for “cold” (temperatures < 100K in the case of methane).

  These “weird” solvents would require “weird” genetic molecules, “weird” metabolic processes, and “weird” bio-structures. In pursuit of this “big picture” question, we turned to Titan, which has exotic solvents both on its surface (methane-hydrocarbon) and sub-surface (perhaps super-cooled ammonia-rich water). This work sought genetic molecules that might support Darwinian evolution in both environments, including non-ionic polyether molecules in the first and biopolymers linked by exotic oxyanions (such as phosphite, arsenate, arsenite, germanate) in the second.

  In the current year, we completed our studies that identified biopolymers that might work in hydrocarbon solvents. These studies have essentially ruled out biological processes in true cryosolvents. However, a series of hydrocarbons containing different numbers of carbon atoms (one, two, three, and four, for example, in methane, ethane, propane, and butane) cease to be cryosolvents as their chain lengths increase. These might be found on “warm Titans”. Further, they might exist deep in Titan’s hydrocarbon oceans, where heating from below would lead to warm hydrocarbon oceans.

  These studies showed that polyethers are insufficiently soluble in hydrocarbons at very low temperatures, such as the 90-100 K found on Titan’s surface where methane is a liquid at ambient pressures. However, we did show that “warm Titans” could exploit propane (and, of course, higher hydrocarbons) as a biosolvent for certain of these “weird” alternative genetic biopolymers; propane has a huge liquid range (far larger than water). Further, we integrated this work with mineralogy-based work that allows reduced molecules to appear as precursors for less “weird” genetic biomolecules, especially through interaction with various mineral species, including borates, molybdates, and sulfates.

  ROADMAP OBJECTIVES: 1.1 1.2 2.2 3.1 3.2 3.4 4.1 5.3 6.2 7.1 7.2

• Project 7: Microenvironmental Influences on Prebiotic Synthesis

  Before biotic, i.e., “biologically-derived” pathways for the formation of essential biological molecules such as RNA, DNA and proteins could commence, abiotic pathways were needed to form the molecules that were the basis for the earliest life. Much research has been done on possible non-biological routes to synthesis of RNA, thought by many to be the best candidate or model for the emergence of life. Our work focuses on possible physicochemical microenvironments and processes on early earth that could have influenced and even directed or templated the formation of RNA or its predecessors.

  ROADMAP OBJECTIVES: 3.1 3.2 3.3 3.4

• Project 10: Identifying Key Innovations in the Origin of the Cell

  Identifying essential functions of conserved hypothetical genes holds the key to understanding the origins of key innovations in the origin of the cell. Our goal is to take a comparative genomic approach to define the molecular machinery that differentiate the Bacterial from its sister lineage that later diverged to became the Archaea and Eukaryotes. One of the obstacles clouding our view of these early cells from a comparative approach is the large number of conserved hypothetical genes present in Archaeal and Eukaryote genomes whose cellular functions are unknown. Our approach is to identify which conserved hypothetical genes are essential to the function of the model crenarchaeon Sulfolobus islandicus. The Crenarchaea are one of the major lineages with in the Archaeal domain with close ties in function to the cellular biology of Eukaryotes. The essential gene profile has not been identified within any organism in this lineage and holds the key to understanding the origin of cellular features in central processing of genomic information through replication, recombination, repair and the shaping of the chromosome.

  ROADMAP OBJECTIVES: 3.4 4.2 5.1 6.1 6.2

• Project 11 Isolation and Genomic Sequencing

  This projects seeks to understand the early evolution of eukaryotic cells by comparing the genomes of diverse eukaryotic microbes and asking what genes are shared and when features of the eukaryotic cell evolved.

  ROADMAP OBJECTIVES: 3.4 4.2

• Project 12 Enrichment of Eukaryotic DNA

  This projects seeks to understand the early evolution of eukaryotic cells by comparing the genomes of diverse eukaryotic microbes and asking what genes are shared and when features of the eukaryotic cell evolved.

  ROADMAP OBJECTIVES: 3.4 4.2

• Project 13: Experimental Determination of the Existence of the Darwinian Transition

  Life on our planet can be divided into three domains: Archaea, Bacteria and Eukarya. While some genes may be shared among the domains of life, others especially those involved in information processing namely DNA replication, transcription and translation are often unique to a particular domain. It has, therefore, been proposed that the molecular machineries that carry out these processes (replication, transcription and translation) have crossed a so-called Darwinian threshold where the molecular machineries have become gelled and therefore intolerant of new components. This project is examining the Darwinian threshold hypothesis by testing the interchangeability of the components of the DNA replication machinery across the domains of life. Further experiments will examine the capacity of biomolecules involved in translation and transcription to substitute for their counterparts across the domains of life.

  ROADMAP OBJECTIVES: 3.2 3.4 4.2 5.3