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Project Reports

• Biosphere-Geosphere Stability and the Evolution of Complex Life

  Both the rise of complex life and the Phanerozoic mass extinctions are accompanied by significant perturbations of the carbon cycle. Attention is usually focused on causality, and environmental change is almost always considered the driver. Yet the co-evolution of life and the environment suggests that the fundamental issue is not causality but rather stability. This project seeks to develop a theory of biosphere-geosphere stability and to test it using the geochemical and fossil records.

  ROADMAP OBJECTIVES: 4.2 4.3 5.2 6.1

• Project 1: Dynamics of Self-Programming Systems

  This project is a theoretical attempt to understand how evolution can arise from inanimate physical systems. The key idea is that matter can organize into structures that not only replicate and carry information, but are able to program and reprogram themselves functionally. We have already been able to construct simple computer programs that can increase their complexity in an open-ended way, but in this grant period we have been building a mathematical formulation of how this arises using recursive function theory. We have also been trying to develop cellular automata meta-programming pairs that can co-evolve complexity.

  ROADMAP OBJECTIVES: 3.2 4.1 4.2 5.3 6.2

• Biosignatures in Ancient Rocks – Kump Group

  We are analyzing FAR-DEEP cores that span the putative “oxygen overshoot” associated with the termination of the Great Oxidation Event, 2.0 billion years ago. The volcanic rocks in question are highly oxidized. Our hypothesis is that oxygen-enriched groundwaters altered these rocks during a time interval when atmospheric oxygen concentrations approached modern levels, falling subsequently to lower values characteristic of the ensuing billion years. Kump has also proposed a new explanation for the “second rise of atmospheric oxygen” in the Neoproterozoic (ca. 850 Ma).

  ROADMAP OBJECTIVES: 1.1 4.1 4.2 4.3 5.2 6.1

• Early Animals: Lipid Biomarkers as the Earliest Evidence of Metazoans

  A complex hydrocarbon, 24-isopropylcholestane, has been proposed as a biomarker for a particular group of sponges—the earliest-branching animals—and found in Neoproterozoic rocks. However, a particular group of marine algae, the pelagophytes, can also produce the precursor to this compound, and it has not been known whether this ability is more widespread within the eukaryotes. We have used genomic data combined with time-calibrated phylogenies to approach this question and find that pelagophytes did not evolve this ability until the Paleozoic, while in sponges it evolved in the Neoproterozoic. This work supports the conclusion that this sterane is a true sponge biomarker.

  ROADMAP OBJECTIVES: 4.1 4.2

• 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

• Early Animals: Modeling the Biotic-Abiotic Interface in the Early Evolution of Multicellular Form

  The size of early multicellular organisms was sufficint to modify their local environment. Our initial work modeling of Neoproterozoic frond-like forms in the earliest-known communities of multicellular organisms demonstrates they were of sufficient scale and density to generate a distinctive canopy flow-regime. This modified environment yielded a selective advantage towards large eukaryotic forms that evolved at this time. This result is a function of limits imposed by diffusion at the surface of organisms, and how height and attendant velocity exposure escape these limits. Building on these results, we are now developing additional models of abiotic/biotic interactions at organismal surfaces, which are implicit in the morphology, development and orientation of other Neoproterozoic fossils. Ultimately, this work will help illuminate how forms initialy dependent on passive diffusion became more trophically complex, yielding a transition to the animal radiation.

  ROADMAP OBJECTIVES: 4.1 4.2 5.2 6.1

• Early Animals: Predation, Oxygen and Preservation in Early Animal Evolution

  Research in the Knoll lab has focused on three major issues relevant to early animal evolution. First, Knoll and colleagues developed a hypothesis to explain the mid-Neoproterozoic diversification of eukaryotes by invoking the evolution of eukaryote-eating protists (analogous to the evolution of carnivores driving the Cambrian diversification of animals). Second, work to integrate ecological data from modern oxygen-minimum zones with paleontological and geochemical data has yielded insights on early animal evolution. Finally, collaborations with other groups have focused on a variety of topics including the preservation of tiny animals in phosphate in the earliest Cambrian, a new Neoproterozoic record of vase-shaped protists.

  ROADMAP OBJECTIVES: 4.1 4.2

• Project 4: Rapid Evolution in Stressed Populations: Theory

  Evolution is typically thought of as occurring over millions of years. But recently it has become clear that we have grossly over-estimated this time scale. Perhaps the most famous example of this is the rapid evolution of resistance of bacteria, worldwide, to modern antibiotics. Similarly, early life has an evolution time scale problem: given the age of the Earth and the known age of the Last Universal Common Ancestor, life must have arisen and evolved the majority of the complexity of the modern cell in less than a billion years. This project is a theoretical attempt to understand how a fluctuating environment can accelerate evolution rate, and lead to evolution on ecosystem time scales. Eventually, this work will join up with the experimental work being done by our team, using the GeoBioCell, in Project 8.

  ROADMAP OBJECTIVES: 4.1 4.2 5.1 5.2 5.3 6.1

• Early Animals: Sensory Systems and Combinatorial Codes

  Understanding the evolution of integrated sensory organs—such as the eyes, ears and nose that develop in concert on our heads—is fundamental to understanding animal complexity. These are the features that permit movement and the environmental responses that characterize animals. We examine understudied early branches of the animal family tree, with a focus on the jellyfish Aurelia, to understand how the genetic regulation of sensory organs is conserved in some cases and evolves in others. Comparison of developmental regulation reveals how similar gene networks can be differentially modified and deployed, permitting the evolution of complex sensory systems. Jellyfish provide an ideal study system for the examination of the evolution of such sensory systems in animal evolution, as they are the most basal branch the animal tree with multiple sensory modes, and these develop at multiple stages in a complex life history. This provides us the ability to compare and contrast within the broader cnidarian group to which jellyfish belong, and to the bilaterians, the broad group containing humans and most other animals. The application of genomic methods greatly enhances our ability to pursue these questions.

  ROADMAP OBJECTIVES: 4.1 4.2

• 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

• 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

• Early Animals: Taphonomic Controls on the Early Animal Fossil Record

  We have been carrying out a number of studies in support of our objective to investigate the controls on the preservation of complex life on earth, with the ultimate aim of allowing the fossil evidence for the succession of events to be constrained and interpreted. These studies include investigating the connections between taphonomy and ecology of the Ediacara Biota based on the collection of fossil specimens and their careful examination, laboratory experiments designed to better understand how these fossils became preserved in different settings, and investigations of how Proterozoic eukaryotic microfossils are preserved, again from studying both new fossil material through a variety of approaches, and performing analog experiments in the laboratory.

  ROADMAP OBJECTIVES: 4.1 4.2

• Project 1F: Chemolithotrophic Microbial Communities in Subglacial Sediments

  Recent interpretation of Yellowknife Bay, Gale Crater, Mars as an ancient lake basin characterized by low salinity, circumneutral pH, and Fe and S compounds in a range of redox states (1) motivates inquiry into the capability of analogous Earth systems to support microbiomes founded on Fe and S chemolithoautotrophy. The research progress outlined herein was conducted to improve understanding of the microbial metabolisms that promote Fe and S redox transformation in an analogous system – the subglacial environment Robertson Glacier (RG), Peter Loughleed Provincial Park, Alberta, Canada. We seek to better understand the mechanisms by which chemolithoautotrophs access mineral-bound electron donors and acceptors and the potential for biosignature preservation associated with this type of life. Geochemical attributes of the RG subglacial environment that are consistent with the former aqueous habitat at Yellowknife Bay include circumneutral pH, low salinity, and sulfur (S) and iron (Fe) existing in a range of oxidation states. Further, the structure, composition, and function of the endogenous subglacial microbiome at RG is largely shaped by redox transformation of pyrite (FeS₂) and chemolithoautotrophic growth on released Fe and/or S intermediates. To achieve these goals we have assembled a collaborative, multidisciplinary team with expertise in molecular biology, microbial physiology, geochemistry, and thermodynamics.

  ROADMAP OBJECTIVES: 4.2 5.3 7.2

• 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

• Early Animals: The Genomic Origins of Morphological Complexity

  The Peterson lab has continued its focus on micro-RNAs (miRNA) in order to better understand the relationship between genetic and phenotypic diversity. Toward this goal, they have established a new database of miRNA genes (as opposed to sequences) assembled under strict quality control and an entirely novel nomenclature, bridging the different names previously given to the same gene across taxa. This database allows the evolution of miRNA genes to be studied across the animal kingdom. Such study shows that miRNA evolution is not correlated to the duplication of genetic material, but shaped by periods of intense miRNA innovation.

  ROADMAP OBJECTIVES: 4.1 4.2

• Early Animals: The Origins of Biological Complexity

  The focus of the Erwin group remained on the origins of novelty and innovation, particularly associated with the origin and early diversification of animals during the Cryogenian, Ediacaran and early Cambrian. A field campaign in Namibia yielded new specimens, new fossil localities, and a potential new organism from the Ediacaran. Work on the phylogeny of early Cambrian lobopods was carried out to the hypothesis that arthropods evolved from this enigmatic group of organisms.

  ROADMAP OBJECTIVES: 4.1 4.2

• Early Animals: The Role of Biosignatures in Illuminating Homonin Diet

  Work conducted by Ainara Sistiaga, a student visitor from the University of La Laguna, Tenerife, Spain, aimed to evaluate the biomarker methodologies we typically apply to modern and ancient sediments to the issues surrounding the evolution of homo sapiens. Gas chromatography-mass spectrometry data on samples from El Salt (Spain), a Middle Palaeolithic site dating to ca. 50,000 yr. BP, represents the oldest positive identification of human faecal matter. We showed that Neanderthals, like anatomically modern humans, have a high rate of conversion of cholesterol to coprostanol related to the presence of specific gut flora. Analysis of five sediment samples from different occupation floors suggests that Neanderthals predominantly consumed meat, as indicated by high coprostanol proportions, but also had significant plant intake, as shown by the presence of 5β-stigmastanol.

  ROADMAP OBJECTIVES: 3.2 4.2

• Molecular Biosignatures of Redox-Sensitive Bacteria and Hyperthermophiles

  The Summons lab has been researching a range of molecular and isotopic phenomena aimed at shedding light on what controls Neoproterozoic ocean redox, evolutionary trends in the abundances of molecular fossils (biomarkers) and the enigmatic natural variability carbon isotopic compositions of organic and inorganic carbon at this time. Our studies of carotenoid pigment biomarkers for green and purple sulfur bacteria have revealed that they are ubiquitous in rock extracts of Proterozoic to Paleozoic age—implying that the shallow oceans became sulfidic more frequently than previously thought. Other projects focused on the biosynthesis of another important biomaker, the hopanoids, vesicles released from marine bacteria for interaction between cells and their environment, and the molecular signatures of microbial communities in hot springs in Yellowstone National Park.

  ROADMAP OBJECTIVES: 4.1 4.2 5.1 5.2 7.1

• 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

• Paleontological, Sedimentological, and Geochemical Investigations of the Mesoproterozoic-Neoproterozoic Transition

  As we learn more about the earliest evolutionary history of animals and other complex multicellular organisms, it becomes clearer that a satisfactory understanding of these events have to be set within the broader context of late Mesoproterozoic and early Neoproterozoic biological and environmental change. To this end, several labs within our team have focused research effort of Mesoproterozoic and Neoproterozoic sedimentary successions. Over the reporting period, this has included stratigraphic and sedimentological fieldwork on rocks of this age in northwestern Canada, Death Valley, Mongolia, and anaylsis of drill cores from Russia, Congo and Zambia. Progress has also been made in new techniques for the discovery and description of Proterozoic microfossils, the processes forming ooids and wrinkle structures, severalfold improvements in the precision of oxygen-17 measurements, which can record the balance of atmospheric oxygen and carbon dioxide, and in measurements of nitrogen isotopes in ancient pigments, a potential redox tracer for the Proterozoic.

  ROADMAP OBJECTIVES: 4.1 4.2

• 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

• The Long Wavelength Limit of Oxygenic Photosynthesis

  Oxygenic photosynthesis (OP) produces the strongest biosignatures at the planetary scale on Earth: atmospheric oxygen and the spectral reflectance of vegetation. Both are controlled by the properties of chlorophyll a (Chl a), its ability to perform the water-splitting to produce oxygen, and its spectral absorbance that is limited to red and shorter wavelength photons. We seek to answer what is the long wavelength limit at which OP might remain viable, and how. This would clarify whether and how to look for OP adapted to the light from stars redder than our Sun.

  Previously under this project, with other co-investigators we spectrally quantified the thermodynamic efficiency of photon energy use in the chlorophyll d utilizing cyanobacterium, Acaryochloris marina str. MBIC11017, determining that it is more efficient than a Chl a cyanobacterium. The current focus of the project is aimed at understanding the adaptations of far-red/near-infrared (NIR) oxygenic photosynthetic organisms in general: what is their ecological niche where they are competitive against chlorophyll a organisms in nature, and what energetic shifts have been made in their photosynthetic reactions centers to enable their use of far-red/NIR photons. Field sampling and measurements are being conducted to isolate new strains of far-red utilizing oxygenic photosynthetic organisms, to quantify the spectral and temporal light regime in which they and previously discovered strains live in nature, and use these light measurements to drive kinetic models of photon energy use to ascertain light thresholds of survival.

  ROADMAP OBJECTIVES: 3.2 4.2 5.1 5.3 6.2 7.2

• Understanding Past Earth Environments

  This year, this interdisciplinary effort continued on two major fronts. First, we furthered the development and use of new techniques that help us characterize environmental conditions on ancient Earth. This included progress on our development of a technique for estimating the atmospheric pressure on Archean Earth, and the development and use other techniques for analyzing the chemistry of Archean lakes. We also used our existing models of ancient Earth to simulate other conditions consistent with the conclusions reached from these laboratory analyses.

  ROADMAP OBJECTIVES: 1.1 1.2 4.1 4.2 5.1 5.2 6.1

• 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

• Taphonomy, Curiosity and Missions to Mars

  Members of our team continue to be involved in both the MER and MSL missions on Mars. On the latter mission, team members have recently documented a long-lived, habitable environment in Gale Crater dominated by rivers and lakes. Research on the mineralogy and geochemistry of rocks at the base of Mt Sharp has improved our understanding of their complex diagenetic history. Progress has also been made in linking orbital observations with those made by the rovers; this has been advanced particularly by field research at Rio Tinto and detailed laboratory experiments that constrain the relationship between mineral combinations and their signatures in infrared reflectance spectroscopy—and their effect on our ability to detect organics.

  ROADMAP OBJECTIVES: 2.1 4.1 4.2 6.1 7.1

• Task: 3a: Ancient Records – Geologic

  Among the fundamental questions in Earth history is when and where O2 first accumulated in the shallow ocean. These settings could have been ideal local ‘oases’ for initial O2 accumulation and for early eukaryotic life. Iodine geochemistry has emerged as an exciting possibility for exploring such settings characterized by carbonate deposition, but the proxy remains only rudimentarily known because of the lack of validation and calibration in modern shallow carbonate environments. Our work over the past year sought to remedy that situation while simultaneously exploring the proxy’s potential in deep time.

  ROADMAP OBJECTIVES: 4.1 4.2

• Task 4: Biogeochemical Impacts on Planetary Atmospheres

  Oxygenation of Earth’s early atmosphere must have involved an efficient mode of carbon burial. In the modern ocean, carbon export of primary production is dominated by fecal pellets and aggregates produced by the animal grazer community. But during most of Earth’s history the oceans were dominated by unicellular, bacteria-like organisms (prokaryotes) causing a substantially altered biogeochemistry. In this task we experiment with the marine cyanobacterium Synechococcus sp. as a model organism and test its aggregation and sinking speed as a function of nutrient (nitrogen, phosphorus, iron) limitation. We have found that these minute cyanobacteria form aggregates in conditions that mimic the open ocean and can sink gravitationally in the water column. Experiments with added clay minerals (bentonite and kaolinite) that might have been present in the Proterozoic ocean, show that these can accelerate aggregate sinking. In addition we find that Synechococcus could potentially export carbon 2–3 times of that contained in their cells via aggregation, likely due to the scavenging of transparent exopolymer particles and dissolved organic matter. Thus, aggregation and sinking by these small cyanobacteria could have constituted an important mode of carbon export in the Proterozoic ocean.

  ROADMAP OBJECTIVES: 4.1 4.2 5.2 6.1 7.2

• Project 3F — Apatitic Latest Precambrian and Early Cambrian Fossils Provide Direct Evidence of Concentrations of Environmental Oxygen

  Means are not currently available to asses either quantitatively or semi-quantitatively the concentration of oxygen in Earth’s atmosphere over geological time. Despite this, the environmental availability of O₂ has been repeatedly postulated to be a cause of major changes in Earth’s biota, most particularly at the Precambrian-Cambrian boundary-defining “Cambrian Explosion of Life,” a time in Earth history when large deposits of phosphate-rich apatite were deposited in shallow basins worldwide. This study shows that substitution of Sm⁺³ in the Ca I and Ca II sites of fossil-permineralizing, -infilling, and -encrusting apatite can differentiate between oxic, dysoxic, an anoxic settings of apatite formation. Further studies are to be undertaken to establish such REE-substitution as a quantitative O₂ paleobarometer.

  ROADMAP OBJECTIVES: 4.1 4.2 6.1 6.2 7.2