20 results on '"Cole Mathis"'
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2. A robotic prebiotic chemist probes long term reactions of complexifying mixtures
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Silke Asche, Geoffrey J. T. Cooper, Graham Keenan, Cole Mathis, and Leroy Cronin
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Science - Abstract
The transition of prebiotic chemistry to present-day chemistry lasted a very long period of time, but the current laboratory investigations of this process are mostly limited to a couple of days. Here, the authors develop a fully automated robotic prebiotic chemist designed for long-term chemical experiments exploring unconstrained multicomponent reactions, which can run autonomously and uses simple chemical inputs.
- Published
- 2021
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3. Identifying molecules as biosignatures with assembly theory and mass spectrometry
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Stuart M. Marshall, Cole Mathis, Emma Carrick, Graham Keenan, Geoffrey J. T. Cooper, Heather Graham, Matthew Craven, Piotr S. Gromski, Douglas G. Moore, Sara. I. Walker, and Leroy Cronin
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Science - Abstract
The search for life in the universe is difficult due to issues with defining signatures of living systems. Here, the authors present an approach based on the molecular assembly number and tandem mass spectrometry that allows identification of molecules produced by biological systems, and use it to identify biosignatures from a range of samples, including ones from outer space.
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- 2021
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4. Exploring the sequence space of unknown oligomers and polymers
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David Doran, Emma Clarke, Graham Keenan, Emma Carrick, Cole Mathis, and Leroy Cronin
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oligomers ,sequencing ,tandem mass spectrometry ,MS2 fragmentation ,depsipeptides ,polyimines ,Physics ,QC1-999 - Abstract
Summary: The characterization of the chemistry of life on earth has been facilitated by developments in analysis and sequencing of bio-oligomers using tandem mass spectrometry (MS/MS). Bio-oligomers can be identified with sequence-level resolution in analytes more complex than any synthetic mixture, enabled by well-established knowledge of fragmentation properties and extensive MS/MS databases built up over decades. However, unknown oligomer systems remain difficult to characterize, as no comparable databases exist, partly because of the vast chemical diversity and fragmentation pathways. Here, we present oligomer-soup-sequencing (OLIGOSS), a new approach to the sequencing of unknown oligomer systems. Using a novel set of backbone-agnostic abstract properties to define fragmentation, OLIGOSS is capable of sequencing any linear oligomer class amenable to MS/MS, regardless of backbone chemistry. We validated OLIGOSS by sequencing synthetic peptides, polyesters, polyimines and depsipeptide oligomers, mapped RNA methylation sites, and a ribosomally synthesized peptide, thioholgamide, directly from a cell lysate without purification.
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- 2021
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5. Prebiotic RNA Network Formation: A Taxonomy of Molecular Cooperation
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Cole Mathis, Sanjay N. Ramprasad, Sara Imari Walker, and Niles Lehman
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cooperation ,prebiotic chemistry ,taxonomy ,ribozymes ,RNA ,origin of life ,Science - Abstract
Cooperation is essential for evolution of biological complexity. Recent work has shown game theoretic arguments, commonly used to model biological cooperation, can also illuminate the dynamics of chemical systems. Here we investigate the types of cooperation possible in a real RNA system based on the Azoarcus ribozyme, by constructing a taxonomy of possible cooperative groups. We construct a computational model of this system to investigate the features of the real system promoting cooperation. We find triplet interactions among genotypes are intrinsically biased towards cooperation due to the particular distribution of catalytic rate constants measured empirically in the real system. For other distributions cooperation is less favored. We discuss implications for understanding cooperation as a driver of complexification in the origin of life.
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- 2017
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6. Autocatalysis in a Hierarchically Organized Inorganic Chemical Network.
- Author
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Cole Mathis, Haralampos N. Miras, and Leroy Cronin
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- 2019
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7. Individual perception dynamics in drunk games.
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Alberto Antonioni, Luis A. Martinez-Vaquero, Cole Mathis, Leto Peel, and Massimo Stella
- Published
- 2018
8. Identifying molecules as biosignatures with assembly theory and mass spectrometry
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Piotr S. Gromski, Douglas Moore, Stuart M. Marshall, Sara Imari Walker, Heather Graham, Geoffrey J. T. Cooper, Graham Keenan, Emma Carrick, Matthew Craven, Cole Mathis, and Leroy Cronin
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0301 basic medicine ,Extraterrestrial Environment ,Computer science ,media_common.quotation_subject ,Science ,Planets ,General Physics and Astronomy ,Outer space ,01 natural sciences ,Measure (mathematics) ,Article ,General Biochemistry, Genetics and Molecular Biology ,Astrobiology ,03 medical and health sciences ,Abiogenesis ,Origin of life ,Exobiology ,0103 physical sciences ,010303 astronomy & astrophysics ,media_common ,Multidisciplinary ,Mass spectrometry ,Cheminformatics ,Scale (chemistry) ,Computational Biology ,General Chemistry ,Living systems ,Identification (information) ,030104 developmental biology ,Molecular Diagnostic Techniques ,Extraterrestrial life ,Algorithms - Abstract
The search for alien life is hard because we do not know what signatures are unique to life. We show why complex molecules found in high abundance are universal biosignatures and demonstrate the first intrinsic experimentally tractable measure of molecular complexity, called the molecular assembly index (MA). To do this we calculate the complexity of several million molecules and validate that their complexity can be experimentally determined by mass spectrometry. This approach allows us to identify molecular biosignatures from a set of diverse samples from around the world, outer space, and the laboratory, demonstrating it is possible to build a life detection experiment based on MA that could be deployed to extraterrestrial locations, and used as a complexity scale to quantify constraints needed to direct prebiotically plausible processes in the laboratory. Such an approach is vital for finding life elsewhere in the universe or creating de-novo life in the lab., The search for life in the universe is difficult due to issues with defining signatures of living systems. Here, the authors present an approach based on the molecular assembly number and tandem mass spectrometry that allows identification of molecules produced by biological systems, and use it to identify biosignatures from a range of samples, including ones from outer space.
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- 2021
9. Exploring and mapping chemical space with molecular assembly trees
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Michał Dariusz Bajczyk, Stuart M. Marshall, Leroy Cronin, Yu Liu, Liam Wilbraham, and Cole Mathis
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Network Science ,Multidisciplinary ,Theoretical computer science ,Computer science ,Drug discovery ,SciAdv r-articles ,Function (mathematics) ,Space (mathematics) ,Tree (graph theory) ,Chemical space ,Set (abstract data type) ,Chemistry ,Fragment (logic) ,Cheminformatics ,Physical and Materials Sciences ,Research Article - Abstract
Description, Assembly theory is used to map molecular and gene assembly pathways exploring evolutionary trajectories looking for novelty., The rule-based search of chemical space can generate an almost infinite number of molecules, but exploration of known molecules as a function of the minimum number of steps needed to build up the target graphs promises to uncover new motifs and transformations. Assembly theory is an approach to compare the intrinsic complexity and properties of molecules by the minimum number of steps needed to build up the target graphs. Here, we apply this approach to prebiotic chemistry, gene sequences, plasticizers, and opiates. This allows us to explore molecules connected to the assembly tree, rather than the entire space of molecules possible. Last, by developing a reassembly method, based on assembly trees, we found that in the case of the opiates, a new set of drug candidates could be generated that would not be accessible via conventional fragment-based drug design, thereby demonstrating how this approach might find application in drug discovery.
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- 2021
10. Mapping the Molecular Tree of Life using Assembly Spaces
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Yu Liu, Cole Mathis, stuart Marshall, and Leroy Cronin
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The mapping of chemical space by the enumeration of graphs generates an infinite number of molecules, yet the experimental exploration of known chemical space shows that it appears to become sparser as the molecular weight of the compounds increases. What is needed is a way to explore chemical space that exploits the information encoded in known molecules to give access to unknown chemical space by building on the common conserved structures found in related families of molecules. Molecular assembly theory provides an approach to explore and compare the intrinsic complexity of molecules by the minimum number of steps needed to build up the target graphs, and here we show this can be applied to networks of molecules to explore the assembly properties of common motifs, rather than just focusing on molecules in isolation. This means molecular assembly theory can be used to define a tree of assembly spaces, allowing us to explore the accessible molecules connected to the tree, rather than the entire space of possible molecules. This approach provides a way to map the relationship between the molecules and their common fragments and thus measures the distribution of structural information collectively embedded in the molecules. We apply this approach to prebiotic chemistry, specifically the construction of RNA, and a family of opiates and plasticizers, as well as to gene sequences. This analysis allows us to quantify the amount of external information needed to assemble the tree and identify and predict new components in this family of molecules, based on the contingent information in the assembly spaces.
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- 2020
11. Identifying Molecules as Biosignatures with Assembly Theory and Mass Spectrometry
- Author
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stuart Marshall, Cole Mathis, Emma Carrick, Graham Keenan, Geoffrey Cooper, Heather Graham, Jessica Bame, Matthew Craven, Nicola Bell, Piotr S. Gromski, Marcel Swart, Douglas G. Moore, Sara Walker, and Leroy Cronin
- Abstract
The search for evidence of life elsewhere in the universe is hard because it is not obvious what signatures are unique to life. Here we postulate that complex molecules found in high abundance are universal biosignatures as they cannot form by chance. To explore this, we developed the first intrinsic measure of molecular complexity that can be experimentally determined, and this is based upon a new approach called assembly theory which gives the molecular assembly number (MA) of a given molecule. MA allows us to compare the intrinsic complexity of molecules using the minimum number of steps required to construct the molecular graph starting from basic objects, and a probabilistic model shows how the probability of any given molecule forming randomly drops dramatically as its MA increases. To map chemical space, we calculated the MA of ca. 2.5 million compounds, and collected data which showed the complexity of a molecule can be experimentally determined by using three independent techniques including infra-red spectroscopy, nuclear magnetic resonance, and by fragmentation in a mass spectrometer, and this data has an excellent corelation with the values predicted from our assembly theory. We then set out to see if this approach could allow us to identify molecular biosignatures with a set of diverse samples from around the world, outer space, and the laboratory including prebiotic soups. The results show that there is a non-living to living threshold in MA complexity and the higher the MA for a given molecule, the more likely that it had to be produced by a biological process. This work demonstrates it is possible to use this approach to build a life detection instrument that could be deployed on missions to extra-terrestrial locations to detect biosignatures, map the extent of life on Earth, and be used as a molecular complexity scale to quantify the constraints needed to direct prebiotically plausible processes in the laboratory. Such an approach is vital if we are going to find new life elsewhere in the universe or create de-novo life in the lab.
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- 2020
12. A Universal Sequencing System for Unknown Oligomers
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David Doran, Emma Carrick, Graham Keenan, Emma Clarke, Cole Mathis, and Leroy Cronin
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Resolution (mass spectrometry) ,Computer science ,Sequence (biology) ,Computational biology ,Tandem mass spectrometry - Abstract
No synthetic chemical system can produce complex oligomers with fidelities comparable to biological systems. To bridge this gap, chemists must be able to characterise synthetic oligomers. Currently there are no tools for identifying synthetic oligomers with sequence resolution. Herein, we present a system that allows us to do omics-level sequencing for synthetic oligomers and use this to explore unconstrained complex mixtures. The system, Oligomer-Soup-Sequencing (OLIGOSS), can sequence individual oligomers in heterogeneous and polydisperse mixtures from tandem mass spectrometry (MS/MS) data. Unlike existing software, OLIGOSS can sequence oligomers with different backbone chemistries. Using an input file format, OLIG, that formalizes the set of abstract properties, any MS/MS fragmentation pathway can be defined. This has been demonstrated on four model systems of linear oligomers. OLIGOSS can screen large sequence spaces, enabling reliable sequencing of synthetic oligomeric mixtures, with false discovery rates (FDRs) of 0-1.1%, providing sequence resolution comparable to bioinformatic tools.
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- 2020
13. Meaning of the Living State
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Cole Mathis
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State (polity) ,media_common.quotation_subject ,Sociology ,Meaning (existential) ,Epistemology ,media_common - Abstract
This chapter draws inspiration from statistical physics to describe a statistical category that can be termed the “living state.” References to a living state can be found throughout origin of life and astrobiology science. Some researchers have used the concept of the living state to explicitly place biological phenomena within the epistemological scope of statistical physics. Within this framework, biological phenomena at a given scale of organization are explained and understood by appealing to the statistical properties of the dynamics of the smaller and larger scales. This is analogous to how distinct states of matter are understood by appealing to the statistical properties of atoms, with the important distinction that statistical physicists have historically not included constraints from larger levels of organization, which are essential in determining the properties of living systems. This conception of the living state may enable astrobiologists to integrate progress from different disciplinary perspectives into a quantitative theory of life.
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- 2020
14. Spontaneous Formation of Autocatalytic Sets with Self-Replicating Inorganic Metal Oxide Clusters
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Cole Mathis, De-Liang Long, Robert Pow, Leroy Cronin, Weimin Xuan, and Haralampos N. Miras
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Materials science ,Nanostructure ,Oxide ,origin of life ,Metal ,Autocatalysis ,chemistry.chemical_compound ,Molecular recognition ,Abiogenesis ,Saturation (graph theory) ,autocatalysis ,autocatalytic sets ,Cluster (physics) ,Molecule ,Multidisciplinary ,molecular replication ,self-assembly ,Crystallography ,Chemistry ,chemistry ,Self-replication ,Chemical physics ,visual_art ,Physical Sciences ,visual_art.visual_art_medium ,Self-assembly - Abstract
Significance Self-replication is an important property of life, yet no one knows how it arose, and the machinery found in modern cells is far too complex to have formed by chance. One suggestion is that simple networks may become able to cooperate and hence replicate together forming autocatalytic sets, but no simple systems have been found. Here we present an inorganic autocatalytic, based on molybdenum blue, that is formed spontaneously when a simple inorganic salt of sodium molybdate is reduced under acidic conditions. This study demonstrates how autocatalytic sets, based on simple inorganic salts, can lead to the spontaneous emergence of self-replicating systems and solves the mystery of how gigantic molecular nanostructures of molybdenum blue can form in the first place., Here we show how a simple inorganic salt can spontaneously form autocatalytic sets of replicating inorganic molecules that work via molecular recognition based on the {PMo12} ≡ [PMo12O40]3– Keggin ion, and {Mo36} ≡ [H3Mo57M6(NO)6O183(H2O)18]22– cluster. These small clusters are able to catalyze their own formation via an autocatalytic network, which subsequently template the assembly of gigantic molybdenum-blue wheel {Mo154} ≡ [Mo154O462H14(H2O)70]14–, {Mo132} ≡ [MoVI72MoV60O372(CH3COO)30(H2O)72]42– ball-shaped species containing 154 and 132 molybdenum atoms, and a {PMo12}⊂{Mo124Ce4} ≡ [H16MoVI100MoV24Ce4O376(H2O)56 (PMoVI10MoV2O40)(C6H12N2O4S2)4]5– nanostructure. Kinetic investigations revealed key traits of autocatalytic systems including molecular recognition and kinetic saturation. A stochastic model confirms the presence of an autocatalytic network involving molecular recognition and assembly processes, where the larger clusters are the only products stabilized by the cycle, isolated due to a critical transition in the network.
- Published
- 2019
15. Individual perception dynamics in drunk games
- Author
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Leto Peel, Alberto Antonioni, Massimo Stella, Luis A. Martinez-Vaquero, and Cole Mathis
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FOS: Computer and information sciences ,Physics - Physics and Society ,Computer Science::Computer Science and Game Theory ,media_common.quotation_subject ,FOS: Physical sciences ,Physics and Society (physics.soc-ph) ,01 natural sciences ,010305 fluids & plasmas ,Game Theory ,Theoretical ,Computer Science - Computer Science and Game Theory ,Models ,SYSTEMS ,Perception ,0103 physical sciences ,Humans ,Narrative ,010306 general physics ,media_common ,COOPERATION ,Harmony (color) ,Polarization (politics) ,Prisoner's dilemma ,Prisoner Dilemma ,Models, Theoretical ,RECIPROCITY ,EVOLUTION ,Dilemma ,Psychology ,Game theory ,Cognitive psychology ,Social behavior ,Computer Science and Game Theory (cs.GT) - Abstract
We study the effects of individual perceptions of payoffs in two-player games. In particular we consider the setting in which individuals' perceptions of the game are influenced by their previous experiences and outcomes. Accordingly, we introduce a framework based on evolutionary games where individuals have the capacity to perceive their interactions in different ways. Starting from the narrative of social behaviors in a pub as an illustration, we first study the combination of the prisoner's dilemma and harmony game as two alternative perceptions of the same situation. Considering a selection of game pairs, our results show that the interplay between perception dynamics and game payoffs gives rise to non-linear phenomena unexpected in each of the games separately, such as catastrophic phase transitions in the cooperation basin of attraction, Hopf bifurcations and cycles of cooperation and defection. Combining analytical techniques with multi-agent simulations we also show how introducing individual perceptions can cause non-trivial dynamical behaviors to emerge, which cannot be obtained by analyzing the system as a whole. Specifically, initial heterogeneities at the microscopic level can yield a polarization effect that is unpredictable at the macroscopic level. This framework opens the door to the exploration of new ways of understanding the link between the emergence of cooperation and individual preferences and perceptions, with potential applications beyond social interactions., Comment: 13 pages, 8 figures
- Published
- 2019
16. Network Theory in Prebiotic Evolution
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Cole Mathis and Sara Imari Walker
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0301 basic medicine ,Structure (mathematical logic) ,Cognitive science ,Computer science ,Prebiotic evolution ,Complex system ,Statistical mechanics ,Systems approaches ,Network theory ,01 natural sciences ,Living systems ,03 medical and health sciences ,030104 developmental biology ,Component (UML) ,0103 physical sciences ,010306 general physics - Abstract
One of the most challenging aspect of origins of life research is that we do not know precisely what life is. In recent years, the use of network theory has revolutionized our understanding of living systems by permitting a mathematical framework for understanding life as an emergent, collective property of many interacting entities. So far, complex systems science has seen little direct application to the origins of life, particularly in laboratory science. Yet, networks are important mathematical descriptors in cases where the structure of interactions matters more than counting individual component parts—precisely what we envision happens as matter transitions to life. Here, we review a few notable examples of the use of network theory in prebiotic evolution, and discuss the promise of systems approaches to origins of life. The end goal is to develop a statistical mechanics useful to origins of life—that is, one that deals with interactions of system components (rather than merely counting them) and is therefore equipped to model life as an emergent phenomena.
- Published
- 2018
17. Universal scaling across biochemical networks on Earth
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Hyunju Kim, Cole Mathis, Sara Imari Walker, Jason Raymond, and Harrison B. Smith
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Theoretical computer science ,Biochemical Phenomena ,Earth, Planet ,Computer science ,Systems biology ,Network science ,Computational biology ,Genome ,Catalysis ,Biochemical network ,Quantitative Biology::Subcellular Processes ,03 medical and health sciences ,Random Allocation ,0302 clinical medicine ,Three-domain system ,parasitic diseases ,Cluster Analysis ,Biochemical reactions ,Product (category theory) ,Scaling ,Ecosystem ,Research Articles ,Topology (chemistry) ,030304 developmental biology ,Structure (mathematical logic) ,0303 health sciences ,Multidisciplinary ,Bacteria ,urogenital system ,Scale (chemistry) ,Quantitative Biology::Molecular Networks ,Systems Biology ,food and beverages ,Computational Biology ,SciAdv r-articles ,Biosphere ,Archaea ,Biological Evolution ,Enzymes ,carbohydrates (lipids) ,Metagenomics ,Metagenome ,lipids (amino acids, peptides, and proteins) ,Astrophysics::Earth and Planetary Astrophysics ,030217 neurology & neurosurgery ,Metabolic Networks and Pathways ,Research Article - Abstract
Studying biochemical networks at a planetary scale reveals a deeper level of organization than what has been understood so far., The application of network science to biology has advanced our understanding of the metabolism of individual organisms and the organization of ecosystems but has scarcely been applied to life at a planetary scale. To characterize planetary-scale biochemistry, we constructed biochemical networks using a global database of 28,146 annotated genomes and metagenomes and 8658 cataloged biochemical reactions. We uncover scaling laws governing biochemical diversity and network structure shared across levels of organization from individuals to ecosystems, to the biosphere as a whole. Comparing real biochemical reaction networks to random reaction networks reveals that the observed biological scaling is not a product of chemistry alone but instead emerges due to the particular structure of selected reactions commonly participating in living processes. We show that the topology of biochemical networks for the three domains of life is quantitatively distinguishable, with >80% accuracy in predicting evolutionary domain based on biochemical network size and average topology. Together, our results point to a deeper level of organization in biochemical networks than what has been understood so far.
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- 2017
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18. Prebiotic RNA Network Formation: A Taxonomy of Molecular Cooperation
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Sanjay N. Ramprasad, Sara Imari Walker, Niles Lehman, and Cole Mathis
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0301 basic medicine ,prebiotic chemistry ,Theoretical computer science ,cooperation ,taxonomy ,ribozymes ,RNA ,origin of life ,01 natural sciences ,Article ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,Cooperative group ,Catalytic rate ,lcsh:Science ,Ecology, Evolution, Behavior and Systematics ,biology ,Game theoretic ,010405 organic chemistry ,Ecology ,Ribozyme ,Paleontology ,0104 chemical sciences ,Network formation ,Prebiotic chemistry ,030104 developmental biology ,Space and Planetary Science ,biology.protein ,Evolution of biological complexity ,lcsh:Q - Abstract
Cooperation is essential for evolution of biological complexity. Recent work has shown game theoretic arguments, commonly used to model biological cooperation, can also illuminate the dynamics of chemical systems. Here we investigate the types of cooperation possible in a real RNA system based on the Azoarcus ribozyme, by constructing a taxonomy of possible cooperative groups. We construct a computational model of this system to investigate the features of the real system promoting cooperation. We find triplet interactions among genotypes are intrinsically biased towards cooperation due to the particular distribution of catalytic rate constants measured empirically in the real system. For other distributions cooperation is less favored. We discuss implications for understanding cooperation as a driver of complexification in the origin of life.
- Published
- 2017
- Full Text
- View/download PDF
19. The Emergence of Life as a First Order Phase Transition
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Cole Mathis, Sara Imari Walker, and Tanmoy Bhattacharya
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0301 basic medicine ,Phase transition ,Time Factors ,Computer science ,Prebiotic evolution ,Origin of Life ,FOS: Physical sciences ,01 natural sciences ,Phase Transition ,03 medical and health sciences ,Abiogenesis ,0103 physical sciences ,Statistical physics ,Quantitative Biology - Populations and Evolution ,010303 astronomy & astrophysics ,Selection (genetic algorithm) ,Populations and Evolution (q-bio.PE) ,Evolutionary transitions ,Agricultural and Biological Sciences (miscellaneous) ,Nonlinear Sciences - Adaptation and Self-Organizing Systems ,030104 developmental biology ,13. Climate action ,Space and Planetary Science ,FOS: Biological sciences ,Adaptation and Self-Organizing Systems (nlin.AO) ,Life phase - Abstract
It is well known that life on Earth alters its environment over evolutionary and geological timescales. An important open question is whether this is a result of evolutionary optimization or a universal feature of life. In the latter case, the origin of life would be coincident with a shift in environmental conditions. Here we present a model for the emergence of life in which replicators are explicitly coupled to their environment through the recycling of a finite supply of resources. The model exhibits a dynamic, first-order phase transition from nonlife to life, where the life phase is distinguished by selection on replicators. We show that environmental coupling plays an important role in the dynamics of the transition. The transition corresponds to a redistribution of matter in replicators and their environment, driven by selection on replicators, exhibiting an explosive growth in diversity as replicators are selected. The transition is accurately tracked by the mutual information shared between replicators and their environment. In the absence of successfully repartitioning system resources, the transition fails to complete, leading to the possibility of many frustrated trials before life first emerges. Often, the replicators that initiate the transition are not those that are ultimately selected. The results are consistent with the view that life's propensity to shape its environment is indeed a universal feature of replicators, characteristic of the transition from nonlife to life. We discuss the implications of these results for understanding life's emergence and evolutionary transitions more broadly. Key Words: Origin of life-Prebiotic evolution-Astrobiology-Biopolymers-Life. Astrobiology 17, 266-276.
- Published
- 2015
20. Environmental control programs the emergence of distinct functional ensembles from unconstrained chemical reactions
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Geoffrey J. T. Cooper, Piotr S. Gromski, Cole Mathis, Rebecca Turk-MacLeod, Leroy Cronin, Yousef M. Abul-Haija, Sara Imari Walker, Margaret Mullin, Andrew J. Surman, and Marc Rodriguez-Garcia
- Subjects
Chemical Phenomena ,Process (engineering) ,media_common.quotation_subject ,Origin of Life ,Combinatorial chemistry ,Environment ,01 natural sciences ,03 medical and health sciences ,Abiogenesis ,Origin of life ,0103 physical sciences ,Systems chemistry ,Molecule ,Amino Acids ,Function (engineering) ,010303 astronomy & astrophysics ,030304 developmental biology ,media_common ,Simple (philosophy) ,0303 health sciences ,Minerals ,Multidisciplinary ,Evolution, Chemical ,Primordial soup ,chemomics ,Living systems ,Chemistry ,Order (biology) ,Physical Sciences ,peptides ,Salts ,Biological system ,Peptides ,systems chemistry ,Chemomics ,combinatorial chemistry - Abstract
Significance We show that materials with different structure and function can emerge from the same starting materials under different environmental conditions, such as order of reactant addition or inclusion of minerals. The discoveries we report were made possible by using analytical tools more common in omics/systems biology for functional and structural characterization, retasked for exploring and manipulating complex reaction networks. We not only demonstrate that environments can differentiate fixed sets of starting materials (both mixtures of pure amino acids and the classic Miller–Urey “prebiotic soup” model), but that this has functional consequences. It has been often said that biology is “chemistry with history” and this work shows how this process can start., Many approaches to the origin of life focus on how the molecules found in biology might be made in the absence of biological processes, from the simplest plausible starting materials. Another approach could be to view the emergence of the chemistry of biology as process whereby the environment effectively directs “primordial soups” toward structure, function, and genetic systems over time. This does not require the molecules found in biology today to be made initially, and leads to the hypothesis that environment can direct chemical soups toward order, and eventually living systems. Herein, we show how unconstrained condensation reactions can be steered by changes in the reaction environment, such as order of reactant addition, and addition of salts or minerals. Using omics techniques to survey the resulting chemical ensembles we demonstrate there are distinct, significant, and reproducible differences between the product mixtures. Furthermore, we observe that these differences in composition have consequences, manifested in clearly different structural and functional properties. We demonstrate that simple variations in environmental parameters lead to differentiation of distinct chemical ensembles from both amino acid mixtures and a primordial soup model. We show that the synthetic complexity emerging from such unconstrained reactions is not as intractable as often suggested, when viewed through a chemically agnostic lens. An open approach to complexity can generate compositional, structural, and functional diversity from fixed sets of simple starting materials, suggesting that differentiation of chemical ensembles can occur in the wider environment without the need for biological machinery.
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