Clara Blättler, Phil
Education: University of Oxford, DPhil., Earth Sciences
Institution: Princeton University (laboratory of John Higgins)
Project: Ca and Mg Isotopic Indicators in Ancient Carbonates
This proposal introduces two new geochemical tools to the search for evidence of the earliest life on Earth and the environments it may have inhabited. The tools for this research will be the stable isotope ratios of calcium and magnesium, which are major components of limestone and dolomite rocks and hold promise as proxies for recording early microbial activity and marine conditions. Substantial work on both modern analogue environments and theoretical considerations suggests that this approach can introduce valuable new dimensions to long-debated problems on the chemical composition of seawater during the early evolution of life and the biogenicity of minerals in the ancient (> 2.5 billion year old) rock record. This work is directed at answering two major questions: 1) did the earliest oceans resemble modern soda lakes, rather than the sodium-chloride-rich oceans of today, and 2) can the presence of microbial activity be identified through a characteristic isotope signal in ancient sedimentary deposits.
Alexandria Johnson, Ph.D.
Education: Purdue University, Ph.D., Atmospheric Sciences
Institution: Massachusetts Institute of Technology (laboratory of Daniel Cziczo)
Project: Clouds in Exoplanet Atmospheres – Are They Blocking our View of Life Below?
The identification and characterization of extra solar planets, or exoplanets, has given context to Earth and the potential for analogs orbiting other stars. However, one long-standing question remains – Can these planets sustain life as we know it? A first step in the search for life beyond our solar system is the detection of biosignature gases; known to be produced when Earth based life metabolizes. Yet a fundamental uncertainty remains in just how easily these gases can be detected through constituents in exoplanet atmospheres such as clouds.
In this project we will use theory and laboratory based experiments to determine how cloud particles interact with light across the visible spectrum and under a wide range of atmospheric compositions, pressures, and temperatures. The aim of this project is two fold. First, to better understand the role and properties of clouds in exoplanet atmospheres. Second, use of this information to determine how clouds will directly limit our ability to detect biosignature gases. We believe this work is critical for recognizing biosignatures in the very different environments on exoplanets and that cutting edge laboratory research on exoplanet atmospheres and clouds is the best way to approach this problem. The results of this work will aid with observations of exoplanet atmospheres and biosignatures through direct imaging or transmission spectroscopy, as well as exoplanet atmospheric and radiative balance models which can give valuable information on the surface habitability of exoplanets.
Claudia El Nachef, Ph.D.
Education: University of Florida, Ph.D., Organic Chemistry
Institution: University of Ottawa (laboratory of André M. Beauchemin)
Project: Simple Aldehydes and Carbohydrates as Prebiotic Catalysts
Over decades, scientists have been trying to understand how life as we know it today emerged from simpler molecules. From a chemical evolution perspective, the molecular complexity of life is daunting. Building on the key Miller experiment, scientists have attempted to rationalize how simple molecular building blocks (HCN, NH3, CH4, aldehydes, etc.) have led to more complex structures such as: purines, pyrimidines, amino acids, and eventually to self replicating machinery. By definition, these structures must form through intermolecular reactions, for which there is an entropic penalty. Intermolecular reactions are also inherently slow at low concentrations. Catalysis of difficult intermolecular reactions is very important, as it could have dictated how chemical evolution occurred.
This proposal aims at investigating the roles of simple aldehydes and carbohydrates as catalysts in chemical evolution (prebiotic chemistry). An important goal is to establish that aldehydes could have acted as “simple enzymes” for many reactions involving water, which were crucial to form the building blocks of life (amino acids and base pairs). Second, it will show that these aldehydes can operate as catalysts under dilute aqueous conditions, through a pre-concentration mechanism that avoids most of the entropic penalty associated with intermolecular reactions. In parallel, studies will focus on possible mechanisms through which aldehydes and carbohydrates could have induced homochirality under prebiotic conditions, and create the single handedness observed in organic molecules. Overall, this work will establish that several prebiotic aldehydes and carbohydrates are “sweet” catalysts, thus addressing important void in the prebiotic chemistry literature.
Education: University of Missouri-Columbia, Ph.D., Biochemistry
Institution: The Pennsylvania State University (laboratory of Philip Bevilacqua)
Project: The RNA World inside compartments: A study of formation and functions
The RNA World hypothesis posits that Ribonucleic acid (RNA) molecules were among the primordial catalysts. Over the last two decades, many labs have isolated both natural and artificial catalytic RNAs through comparative genomics and in vitro selection experiments. While the catalytic repertoire of RNA is well established, the formation of these biopolymers and acquisition of functions by RNA molecules in prebiotic microenvironment are not well understood. Compartmentalization of molecules is ubiquitous in modern biology and certainly was very important during the early evolution of life to circumvent infinite dilution of functional molecules. Proposed work will study the conditions that favor both non-enzymatic and RNA catalyzed formation of RNA in novel coacervate compartments. We will also determine the effects of microenvironments and cosolutes in the activity and fitness landscape of the naturally occurring ribozyme. It has been shown previously that Magnesium (Mg2+), nucleotides and other molecules can partition at very high concentrations inside coacervates, thus favoring high activity of catalytic RNAs inside compartments. Through cutting-edge high throughput sequencing, changes in the local fitness landscapes of naturally occurring ribozyme will be determined and correlated to mechanistic studies obtained from classical biophysical techniques. This study will vastly increase our understanding of factors that influence formation of RNA and its ability to catalyze chemical reactions; both of which will have an enduring impact in the field of origins of life.
Sarah Rugheimer, Ph.D.
Education: Harvard University, Ph.D., Astronomy and Astrophysics
Institution: University of St. Andrews (laboratory of Mark Claire)
Project: Modeling Atmospheres: Warming Archean Earth to Detecting Biosignatures
Atmospheric modeling allows us to examine two key areas of interest in origins research – the remote detection of life on an exoplanet and the atmospheric conditions of early Earth that gave rise to the origin of life. Theoretical modeling of atmospheres is essential in determining the size, resolution, and observing time required for a telescope to detect signs of life, or biosignatures, around an Earth-like planet orbiting a distant star. Currently all observing strategies for rocky planets rely on the ability to add multiple observations of a planet to detect atmospheric gases. This inherently assumes the planet’s atmosphere is constant in the months or years it takes for these multiple observations. However, stars can have variations in their output of high-energy light over that time. I propose to examine how the atmosphere might change due to this variation in high-energy light from the host star. I will then test how averaging multiple observations from a changing atmosphere might confuse our search for biosignatures in the future.
I also am interested in understanding the early Earth conditions that gave rise to the origin of life. We have geological evidence for warm climates and liquid water on the surface of Earth 4.4 billion years ago, yet it is difficult for current climate models to predict above freezing temperatures. This is called the Faint Young Sun Paradox. I propose to look at a potential solution to the paradox by including clouds in our climate model. In addition, a natural output of my models is the amount of high-energy light reaching the surface of a planet. This high-energy light can have both positive and negative effects on early life and chemistry. I propose to collaborate with other Simons teams to model the amount of high-energy light reaching the surface at the geological times of interest to them in their experiments.
Teresa Ruiz Herrero, Ph.D.
Education: Autonomous University of Madrid, Ph.D., Soft Matter Physics
Institution: Harvard University (laboratory of Mahadevan Lakshminarayanan)
Project: Dynamics of growth and division in prebiotic vesicles
Self-replicating vesicles serve as a model for prebiotic cells, the precursors of life. These originated when a self-replicating biomolecule was separated from its environment by a permeable barrier able to grow and divide. This compartmentalization allowed for different chemical properties between the interior and the exterior media and eventually for specialization and competition between cells, which is the basis for Darwinian evolution. How these early cells could grow and divide without complex machinery remains an open question. The growth, shape and dynamics of these primitive vesicles can shed light on the ways modern cells have evolved by exploiting those characteristics to develop their replication mechanisms. Using a combination of theoretical and computational tools, we will investigate these questions with the aim of characterizing the conditions that allow these systems to replicate and evolve.
Vlada Stamenkovic, Ph.D.
Education: University of Muenster, Ph.D., Earth, Atmospheric, and Planetary Sciences
Institution: California Institute of Technology (laboratories of Woodward W. Fischer and Joseph Kirschvink)
Project: Life From Inside Out: Connecting Geodynamics to the Origins of Life
All life we know occupies mostly the surface, oceans, and shallow crust of our planet – not reaching more than a few kilometers into the planet’s interior.
However, this inhabited environment is only a small part of our whole planet. The planet interior from rocky crust and mantle to the metallic core is the largest heat and nutrient reservoir that life can access. Tectonic forces and heat transport deep within the planet control what kind of nutrients reach the surface and what kind of nutrients are being removed from our atmosphere and oceans.
Therefore, the planet interior does significantly impact the origins of life and moreover all biogeochemical processes that determine the habitability of Earth and any rocky planet in our solar system and beyond.
In this proposal, I suggest to explore “Life from inside out”, or in other words the geodynamical connections to the origins of life. To achieve this goal, we must fully connect the interior evolution of planets with biogeochemical cycles occurring in oceans and on land. To get closer to this goal, the best approach is to 1) start exploring the geodynamically driven emergence of hydrogen, a first nutrient for life, as well as 2) to determine the potential of a geodynamic regulation of the atmospheric oxygen concentration, an element necessary for the emergence of complex life.
The oxygen and the hydrogen cycles are the key to explore the connections between planet interiors and the origins of life because oxygen and hydrogen significantly affect interior dynamics.
Answering both questions will allow us to explore the geodynamical drivers for the origin of life, to start uniting geodynamics with biogeochemistry, and to unveil whether or not Earth is a rare oasis for life in the Galaxy.
Stephanie Valleau, Ph.D.
Education: Harvard University, Ph.D., Chemical Physics
Institution: Stanford University (laboratory of Todd J. Martinez)
Project: Atomistic exploration of abiogenesis with a nanoreactor
In this project, we aim to understand how life-essential molecules were formed using a theoretical lens. We will investigate how atoms and molecules could have combined in the presence of carbon-nitrogen and sulfur compounds to produce the fundamental building blocks of life: amino acids, nucleotides and lipids. This will be carried out on video cards and large computer clusters using the laws of classical and quantum mechanics to follow the movement of all atoms. We will define a bubble of life containing the initial molecules in a specific environment, for instance in a water pool. The compounds will interact and collide, bonds will be broken and new bonds formed. Hundreds of picoseconds later we will examine what has been created. We will look at the time-dependent evolution of this bubble to find intermediate structures and determine how fast the whole process occurred. We will also investigate the influence of external factors such as temperature and pressure and whether adding/removing specific compounds strongly influences the reactions. Ultimately we will see whether the products can combine to form long chains, the ancestors and precursors of RNA.
Education: Harvard University, Ph.D., Astronomy and Astrophysics
Institution: Harvard University (laboratory of Stein Jacobson)
Project: Uncovering the Chemistry of Earth-like Planets
We propose to use evidence from our solar system to understand exoplanets, and in particular, to predict their surface chemistry and thereby the possibility of life.
An Earth-like planet, born from the same nebula as its host star, is composed primarily of silicate rocks and an iron-nickel metal core, and depleted in volatile content in a systematic manner. The more volatile (easier to vaporize or dissociate into gas form) an element is in an Earth-like planet, the more depleted the element is compared to its host star.
After depletion, an Earth-like planet would go through the process of core formation due to heat from radioactive decay and collisions. Core formation depletes a planet’s rocky mantle of siderophile (iron-loving) elements, in addition to the volatile depletion.
After that, Earth-like planets likely accrete some volatile-rich materials, called “late veneer”. The late veneer could be essential to the origins of life on Earth and Earth-like planets, as it also delivers the volatiles such as nitrogen, sulfur, carbon and water to the planet’s surface, which are crucial for life to occur. These volatiles would be lost in the earlier stages (volatile depletion and core formation), rendering them absent on the planet’s surface, until delivered later when the planet’s surface cooled down enough to retain them.
Finally, the materials delivered to the surface of the planet would be gradually mixed into the planet’s mantle through mantle convection.
By parameterizing and modeling each of these steps properly, we plan to build an integrative model of Earth-like planets from the bottom up. We would like to infer their chemical compositions from their mass-radius relations and their host stars’ elemental abundances, and understand the origins of volatile contents (especially water) on their surfaces, and thereby shed light on the origins of life on them.
Elizabeth Bell, Ph.D.
Education: University of California, Los Angeles, Ph.D. Geochemistry
Institution: University of California, Los Angeles, Earth and Space Sciences (laboratory of Mark Harrison)
Project: A Search for Isotopic Traces of Life in 4.0 to 4.4-Billion-Year-Old Minerals
Because Earth’s surface is continually scoured by water and other agents of erosion, our geologic record becomes increasingly sparse with age. Although the planet is over 4.5 billion years (Ga) old, rocks older than 4 Ga are currently unknown. This makes the earliest history of Earth, and any possible biosphere older than 4 billion years, largely inaccessible.
However, tiny grains of the mineral zircon (approximately the width of a human hair) from the Jack Hills in Western Australia range as old as 4.4 Ga, constituting the oldest known materials on the planet. These zircons contain abundant inclusions of earlier minerals, some of them carbon-bearing, that were enclosed in the zircon during its formation.
Since biologically-derived carbon tends to have characteristically low ratios of the isotope C-13 compared to C-12, carbon isotope ratios can be proxies for the presence of life even when direct fossils are not available. Bell intends to analyze a significant number of carbon-bearing inclusions in Jack Hills zircons in order to constrain the over-4-Ga carbon isotope record and determine whether it is consistent with the presence of life. This would constitute the oldest known evidence of life on Earth.
Ziwei Liu, Ph.D.
Education: State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, Jilin University, Ph.D. Inorganic Chemistry
Institution: University Montpellier, Institut des Biomolécules Max Mousseron (laboratory of Robert Pascal)
Project: Coevolution of RNA and Peptides — Connecting the Activation Processes
The observation that amino acids are easily available in abiotic environments suggests that RNA coevolved with peptides in an RNA world. In other words, the carriers of information may have coexisted with short polymers of amino acids built by chemical pathways predating the translation of nucleic acid sequences into proteins. This possibility makes the subsequent transition to an RNA-protein world logical.
Ziwei Liu’s work is aimed at precisely identifying chemical pathways potentially responsible for the connection of peptide and RNA chemistries. The present-day biosynthesis of peptides, through elongation of peptide chains by the stepwise addition of activated amino acids in the ribosome, was probably preceded by simpler chemical processes involving activated amino acid building blocks and adducts with short RNA strands.
Beginning with previous work in his advisor’s lab, which showed that intermediates made of amino acid and nucleotide moieties can be easily formed, Liu will work to enlarge the scope of the process to the formation of peptide chains connected to simple nucleotides.
He will study the chemical and kinetic properties of these activated intermediates for their role in the elongations of both peptides and nucleotides. He will also study the stereochemistry of the reactions as a potential process leading to mirror symmetry breaking.
These investigations are part of an ongoing research program based on the physicochemical view that self-organization in the emergence of life process requires both a far-from-equilibrium state and the replication of chemical entities. Introducing free energy through activated amino acid monomers or activated peptides as a means to drive the replication of an information support and the selection of the more efficient sequences may thus be considered an essential step in the evolutionary process leading to life.
Irena Mamajanov, Ph.D.
Education: Brandeis University, Ph.D. Physical Chemistry
Institution: Carnegie Institution of Washington, Geophysical Laboratory (laboratory of George D. Cody)
Project: Potential Protoenzymes: Structure and Function of Hyperbranched Polyesters
Enzymes are biopolymers responsible for the catalysis of chemical conformations that sustain life. Modern enzymes are comprised of complex protein or RNA structures unlikely to be present on prebiotic Earth. Enzymatic molecules through tree-dimensional folding create compartments that bind and orient specific reactions. Moreover, enzymes can create local environments with polarity different from water to augment the reaction rate. These properties of enzymes can be approximated by synthetically accessible polymers.
One such class of macromolecules is hyperbranched polymers, structures with a high degree of branching that possess globular structures similar to biological enzymes. Mamajanov will study the formation, structure and catalytic properties of hyperbranched polymers under prebiotically plausible conditions. A successful experimental demonstration of such approach would provide a valuable model of how the first enzyme-like systems could have arisen on Earth.
James Saenz, Ph.D.
Education: Massachusetts Institute of Technology, Ph.D., Chemical Oceanography
Institution: Max-Planck-Institut fuer Molekulare Zellbiologie u. Genetik (laboratory of Tony Hyman)
Project: The Emergence and Evolution of Molecular Order in the Cell Membrane
One of the most interesting and elusive problems in science has been to understand how life emerged on earth. This is intricately linked to the question: How did the first cells arise? Modern life employs a complex and highly interconnected chemical system to assemble its parts and replicate. However, life did not start with these advanced biochemical tools and would have relied on simple systems that 1) could self assemble from preexisting molecules available on early Earth and 2) segregate biomolecules from the environment by some means of compartmentalization. Encapsulation by lipid membranes is one mechanism to compartmentalize primitive biomolecules.
In the scope of this proposal I want to ask: what were the early Earth membranes like? Membranes are thought to have emerged from the self-assembly of primitive lipids that were present on early Earth. The properties of early membranes would have been dependent on the structure of these primitive lipids. Over time, evolution would then have selected more specialized membrane compositions ultimately leading to the first cellular membranes. In this context, the interactions between membranes and early biomolecules (e.g. RNA) may even have served as a primitive form of heredity before a formalized genetic code emerged.
I will examine the properties of membranes that could have emerged from potential early Earth lipids. In particular I will test how aromatic hydocarbons that are thought to have been present on early Earth can modulate the thermodynamic order of membrane lipids. I will approach this through a comprehensive range of classical and modern biophysical tools in model membrane systems aimed at mimicking the complexity of primitive membranes.
By understanding the potential distribution of properties of primitive membranes, I aim to excavate the fundamental principles that allowed life to emerge, bringing us closer to understanding how modern membranes function and how to engineer functional membranes from the bottom up.
Kartik Temburnikar, Ph.D.
Education: University of Maryland, Baltimore County, Ph.D. Organic Chemistry
Institution: Arizona State University, the Biodesign Institute (laboratory of John C. Chaput)
Project: Investigating TNA as a Candidate RNA Progenitor
The RNA world hypothesis postulates that cellular life based on DNA genomes
and protein enzymes was preceded in evolutionary history by RNA-based life forms that stored information and catalyzed chemical reactions. This hypothesis is supported by many lines of evidence, including the existence of RNA enzymes in nature.
Whether RNA was the first genetic material of life or an important evolutionary intermediate is not yet known. Problems associated with the prebiotic synthesis of ribose and non-enzymatic replication of RNA suggest that simpler genetic polymers whose structures were more accessible on the early Earth may have preceded RNA.
One possible candidate is threose nucleic acid, or TNA. TNA is a synthetic genetic polymer that contains a four-carbon threose sugar in place of nature’s five-carbon ribose sugar found in RNA. TNA is an attractive candidate for an RNA progenitor, because threose is chemically much simpler than ribose, and TNA can exchange genetic information with RNA. This latter observation provides a plausible mechanism for passing information between successive genetic systems. In addition to information storage and chemical simplicity, early genetic polymers would have also needed to fold into shapes with catalytic activity.
Kartik Temburnikar aims to explore the functional properties of TNA as an RNA progenitor by evolving a TNA enzyme capable of joining two strands of TNA together to form longer TNA polymers. If successful, this template-copying reaction will provide new insights into mechanisms that could have given rise to early self-replicating genetic polymers.
Falk Wachowius, Ph.D.
Education: Max Planck Institute for Biophysical Chemistry, Göttingen, Ph.D. Nucleic Acid Chemistry
Institution: Medical Research Council Laboratory of Molecular Biology (laboratory of Philipp Holliger)
Project: An RNA Polymerase Ribozyme With General Replication Capacity
One of the fundamental traits of life is self-replication. Therefore, the emergence of self-replication is closely linked to the origins of life itself. Several strands of compelling evidence strongly suggest that our current biology, which relies on DNA for information storage and proteins for catalysis, was preceded by a primordial biology that instead relied on DNA’s close chemical cousin, RNA, for both heredity and metabolism.
It is therefore widely believed that this ancestral biology, also referred to as the ‘RNA world’ began with an RNA molecule that acquired a capacity for self-replication and mutation and hence evolution towards ever more efficient self-replication.
Unfortunately, this primordial replicase appears to have been lost. However, we can reconstruct modern analogues and study the properties of these molecular ‘doppelgängers’ in order to better understand life’s first genetic system. Furthermore, using methods of evolution in the laboratory, we can retrace the first steps that this ancestral molecule must have taken and ultimately reconstruct an RNA world in the test-tube.
Rui Wang, Ph.D.
Education: Shanghai Institute of Organic Chemistry, Ph.D., Organic Chemistry
Institution: Research Foundation of SUNY – University at Albany (laboratory of Jia Sheng)
Project: Evolutionary Roles of RNA Aptamers in the Origin of Biological Catalysis
Most of chemical reactions in the current biological systems are catalyzed by enzymes, which can bind, orient and activate the substrates in specific ways. While these functions are highly integrated in enzyme systems, they could be separated as different modules in the prebiotic chemistry. Based on the RNA world hypothesis, RNA evolved first as both genetic information carrier and catalyst before DNA and protein. Therefore, studying the evolutionary roles of RNA in small molecule binding, orientating and activating will provide new insights to explain the origins of biological catalysis as well as certain metabolic networks in the prebiotic chemistry.
The major hypothesis of this project is: small RNA aptamers, which may exist in different variants (such as the hybrid forms of 2’-5’-linked, deoxyribo- and threose linked RNAs), could play important roles by binding substrates with diversified modes, therefore channeling their reactivity towards the most useful products as the potential metabolites. In other words, perhaps early protocells relied on the ambient chemistry for their sources of materials, but simple aptamers, instead of the structurally more complicated ribozymes, helped things along by making the chemistry proceed in a more specific manner, resulting in higher yields of the desired materials, which might facilitate the early metabolisms. Although they might have been inefficient, these aptamers might be able to gradually evolve into a special catalyst of the desired reaction, perhaps by docking into certain relatively nonspecific ribozyme domains and cooperating with other auxiliary domains, similar as the example of ribosome that could evolve by the docking of peptidyl-transferring ribozymes into the protein frames.
In this proposal, we will use phosphorylation, a universal and critical metabolic step in the extant biological systems, as the study model to explore the effects of aptamers in the regioselective phosphorylation of purine and pyrimidine nucleosides, as well as some amino acids, small peptides and other metabolites.
Dmitry Zubarev, Ph.D.
Education: Utah State University, Ph.D. Physical Chemistry
Institution: Harvard University, Chemistry and Chemical Biology (laboratory of Alán Aspuru-Guzik)
Project: Prebiotic Atlas: Exhaustive Exploration of Prebiotic Chemical Space
Advances in the investigation of the origins of life are associated with answers to the question: ‘Who was first?’ For example, we discuss which evolved first: metabolism, pre-RNA, RNA or DNA worlds. It is unclear to what extent chemistry of biological systems can be used to reconstruct early chemistries. This consideration makes it equally important to know: ‘What was there at all?’
The goal of Dmitry Zubarev’s research is to answer the latter question by using theoretical and computational approaches of the material design field to create a prebiotic atlas — a vast collection of reaction networks that cover prebiotic chemical space.
Zubarev will survey chemistries along the few known routes that connect simple molecules to biochemical systems. This will help to identify new routes and continue expansion into uncharted territories of the prebiotic world. The prebiotic chemical maps assembled into an atlas will be made available to scientists and the general public via Web interface with built-in research and educational tools.