scholarly journals Self-Reproduction and Darwinian Evolution in Autocatalytic Chemical Reaction Systems

Life ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 308
Author(s):  
Sandeep Ameta ◽  
Yoshiya J. Matsubara ◽  
Nayan Chakraborty ◽  
Sandeep Krishna ◽  
Shashi Thutupalli
Keyword(s):  
Experimental Evolution ◽  
Experimental Studies ◽  
Theoretical Work ◽  
Living System ◽  
Darwinian Evolution ◽  
Chemical System ◽  
Chemical Systems ◽  
Open Questions ◽  
Scientific Questions ◽  
Emergence Of Life

Understanding the emergence of life from (primitive) abiotic components has arguably been one of the deepest and yet one of the most elusive scientific questions. Notwithstanding the lack of a clear definition for a living system, it is widely argued that heredity (involving self-reproduction) along with compartmentalization and metabolism are key features that contrast living systems from their non-living counterparts. A minimal living system may be viewed as “a self-sustaining chemical system capable of Darwinian evolution”. It has been proposed that autocatalytic sets of chemical reactions (ACSs) could serve as a mechanism to establish chemical compositional identity, heritable self-reproduction, and evolution in a minimal chemical system. Following years of theoretical work, autocatalytic chemical systems have been constructed experimentally using a wide variety of substrates, and most studies, thus far, have focused on the demonstration of chemical self-reproduction under specific conditions. While several recent experimental studies have raised the possibility of carrying out some aspects of experimental evolution using autocatalytic reaction networks, there remain many open challenges. In this review, we start by evaluating theoretical studies of ACSs specifically with a view to establish the conditions required for such chemical systems to exhibit self-reproduction and Darwinian evolution. Then, we follow with an extensive overview of experimental ACS systems and use the theoretically established conditions to critically evaluate these empirical systems for their potential to exhibit Darwinian evolution. We identify various technical and conceptual challenges limiting experimental progress and, finally, conclude with some remarks about open questions.

scholarly journals A mechanism of abiogenesis based on complex reaction networks organized by seed-dependent autocatalytic systems

2021 ◽  
Author(s):  
Zhen Peng ◽  
Jeff Linderoth ◽  
David Baum
Keyword(s):  
Reaction Networks ◽  
Food Utilization ◽  
Complex Reaction ◽  
Chemical Systems ◽  
Promising Strategy ◽  
Underlying Basis ◽  
Scientific Questions ◽  
Emergence Of Life

The complexity gap between the biotic and abiotic worlds has made explaining abiogenesis one of the hardest scientific questions. A promising strategy for addressing this problem is to identify features shared by abiotic and biotic chemical systems that permit the stepwise accretion of complexity. Therefore, we compared abiotic and biotic reaction networks in order to evaluate the presence of autocatalysis, the underlying basis of biological self-propagation, and to see if the organization of autocatalytic motifs permits stepwise complexification. We provide an algorithm to detect seed-dependent autocatalytic systems (SDASs), namely subnetworks that can use food chemicals to self-propagate but must be seeded by some non-food chemicals to become activated. We show that serial activation of SDASs can cause incremental complexification. Furthermore, we identify life-like features that emerge during the accretion of SDASs, including the emergence of new ecological opportunities and improvements in the efficiency of food utilization. The SDAS concept explains how driven abiotic environments, namely ones receiving an ongoing flux of food chemicals, can incrementally complexify without the need for genetic polymers. This framework also suggests experiments that have the potential to detect the spontaneous emergence of life-like features, such as self-propagation and adaptability, in driven chemical systems.

scholarly journals Conceptualizing the origin of life in terms of evolution

2017 ◽  
Vol 375 (2109) ◽  
pp. 20160346 ◽  
Author(s):  
N. Takeuchi ◽  
P. Hogeweg ◽  
K. Kaneko
Keyword(s):  
Origin Of Life ◽  
Origins Of Life ◽  
Darwinian Evolution ◽  
Chemical System ◽  
Crucial Question ◽  
Opinion Piece ◽  
Ongoing Work ◽  
The Origin Of Life ◽  
Multi Level ◽  
Emergence Of Life

In this opinion piece, we discuss how to place evolution in the context of origin-of-life research. Our discussion starts with a popular definition: ‘life is a self-sustained chemical system capable of undergoing Darwinian evolution’. According to this definition, the origin of life is the same as the origin of evolution: evolution is the ‘end’ of the origin of life. This perspective, however, has a limitation, in that the ability of evolution in and of itself is insufficient to explain the origin of life as we know it, as indicated by Spiegelman’s and Lincoln and Joyce’s experiments. This limitation provokes a crucial question: What conditions are required for replicating systems to evolve into life? From this perspective, the origin of life includes the emergence of life through evolution: evolution is a ‘means’ of the origin of life. After reviewing Eigen’s pioneering work on this question, we mention our ongoing work suggesting that a key condition might be conflicting multi-level evolution. Taken together, there are thus two questions regarding the origin of life: how evolution gets started, and how evolution produces life. Evolution is, therefore, at the centre of the origin of life, where the two lines of enquiry must meet. This article is part of the themed issue ‘Reconceptualizing the origins of life’.

scholarly journals A mechanism of abiogenesis based on complex reaction networks organized by seed-dependent autocatalytic systems

2021 ◽  
Author(s):  
Zhen Peng ◽  
Jeff Linderoth ◽  
David Baum
Keyword(s):  
Reaction Networks ◽  
Food Utilization ◽  
Complex Reaction ◽  
Chemical Systems ◽  
Promising Strategy ◽  
Underlying Basis ◽  
Scientific Questions ◽  
Emergence Of Life

The complexity gap between the biotic and abiotic worlds has made explaining abiogenesis one of the hardest scientific questions. A promising strategy for addressing this problem is to identify features shared by abiotic and biotic chemical systems that permit the stepwise accretion of complexity. Therefore, we compared abiotic and biotic reaction networks in order to evaluate the presence of autocatalysis, the underlying basis of biological self-propagation, and to see if the organization of autocatalytic motifs permits stepwise complexification. We provide an algorithm to detect seed-dependent autocatalytic systems (SDASs), namely subnetworks that can use food chemicals to self-propagate but must be seeded by some non-food chemicals to become activated. We show that serial activation of SDASs can cause incremental complexification. Furthermore, we identify life-like features that emerge during the accretion of SDASs, including the emergence of new ecological opportunities and improvements in the efficiency of food utilization. The SDAS concept explains how driven abiotic environments, namely ones receiving an ongoing flux of food chemicals, can incrementally complexify without the need for genetic polymers. This framework also suggests experiments that have the potential to detect the spontaneous emergence of life-like features, such as self-propagation and adaptability, in driven chemical systems.

scholarly journals Photoionization Cross-Sections of Carbon-Like N+ Near the K-Edge (390–440 eV)

Atoms ◽  
2021 ◽  
Vol 9 (2) ◽  
pp. 27
Author(s):  
Jean-Paul Mosnier ◽  
Eugene T. Kennedy ◽  
Jean-Marc Bizau ◽  
Denis Cubaynes ◽  
Ségolène Guilbaud ◽  
...  
Keyword(s):  
High Resolution ◽  
Cross Section ◽  
Cross Sections ◽  
Experimental Studies ◽  
Photoionization Cross Section ◽  
Theoretical Work ◽  
Rydberg Series ◽  
R Matrix ◽  
Resonance Strengths ◽  
Nitrogen Ion

High-resolution K-shell photoionization cross-sections for the C-like atomic nitrogen ion (N+) are reported in the 398 eV (31.15 Å) to 450 eV (27.55 Å) energy (wavelength) range. The results were obtained from absolute ion-yield measurements using the SOLEIL synchrotron radiation facility for spectral bandpasses of 65 meV or 250 meV. In the photon energy region 398–403 eV, 1s⟶2p autoionizing resonance states dominated the cross section spectrum. Analyses of the experimental profiles yielded resonance strengths and Auger widths. In the 415–440 eV photon region 1s⟶(1s2s22p2 4P)np and 1s⟶(1s2s22p2 2P)np resonances forming well-developed Rydberg series up n=7 and n=8 , respectively, were identified in both the single and double ionization spectra. Theoretical photoionization cross-section calculations, performed using the R-matrix plus pseudo-states (RMPS) method and the multiconfiguration Dirac-Fock (MCDF) approach were bench marked against these high-resolution experimental results. Comparison of the state-of-the-art theoretical work with the experimental studies allowed the identification of new resonance features. Resonance strengths, energies and Auger widths (where available) are compared quantitatively with the theoretical values. Contributions from excited metastable states of the N+ ions were carefully considered throughout.

scholarly journals Autocatalytic and oscillatory reaction networks that form guanidines and products of their cyclization

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Alexander I. Novichkov ◽  
Anton I. Hanopolskyi ◽  
Xiaoming Miao ◽  
Linda J. W. Shimon ◽  
Yael Diskin-Posner ◽  
...  
Keyword(s):  
Chemical Cues ◽  
Native Chemical Ligation ◽  
Reaction Networks ◽  
Oscillatory Reaction ◽  
Experimental Conditions ◽  
Chemical Ligation ◽  
Chemical Systems ◽  
Life On Earth ◽  
Emergence Of Life ◽  
Equilibrium Chemical

AbstractAutocatalytic and oscillatory networks of organic reactions are important for designing life-inspired materials and for better understanding the emergence of life on Earth; however, the diversity of the chemistries of these reactions is limited. In this work, we present the thiol-assisted formation of guanidines, which has a mechanism analogous to that of native chemical ligation. Using this reaction, we designed autocatalytic and oscillatory reaction networks that form substituted guanidines from thiouronium salts. The thiouronium salt-based oscillator show good stability of oscillations within a broad range of experimental conditions. By using nitrile-containing starting materials, we constructed an oscillator where the concentration of a bicyclic derivative of dihydropyrimidine oscillates. Moreover, the mixed thioester and thiouronium salt-based oscillator show unique responsiveness to chemical cues. The reactions developed in this work expand our toolbox for designing out-of-equilibrium chemical systems and link autocatalytic and oscillatory chemistry to the synthesis of guanidinium derivatives and the products of their transformations including analogs of nucleobases.

scholarly journals THE QUANTIZED HALL INSULATOR: A "QUANTUM" SIGNATURE OF A "CLASSICAL" TRANSPORT REGIME?

2004 ◽  
Vol 18 (18) ◽  
pp. 923-943 ◽  
Author(s):  
EFRAT SHIMSHONI
Keyword(s):  
Quantum Interference ◽  
Random Network ◽  
Experimental Studies ◽  
Localization Length ◽  
Theoretical Studies ◽  
Hall Resistivity ◽  
Transport Regime ◽  
Open Questions ◽  
Weakly Coupled ◽  
Classical Transport

Experimental studies of the transitions from a primary quantum Hall (QH) liquid at filling factor ν=1/k (with k an odd integer) to the insulator have indicated a "quantized Hall insulator" (QHI) behavior: while the longitudinal resistivity diverges with decreasing temperature and current bias, the Hall resistivity remains quantized at the value kh/e2. We review the experimental results and the theoretical studies addressing this phenomenon. In particular, we discuss a theoretical approach which employs a model of the insulator as a random network of weakly coupled puddles of QH liquid at fixed ν. This model is proved to exhibit a robust quantization of the Hall resistivity, provided the electron transport on the network is incoherent. Subsequent theoretical studies have focused on the controversy whether the assumption of incoherence is necessary. The emergent conclusion is that in the quantum coherent transport regime, quantum interference destroys the QHI as a consequence of localization. Once the localization length becomes much shorter than the dephasing length, the Hall resistivity diverges. We conclude by mentioning some recent experimental observations and open questions.

scholarly journals Planet forming disks, debris disks and the Solar System

2019 ◽  
Vol 15 (S350) ◽  
pp. 207-215
Author(s):  
Inga Kamp
Keyword(s):  
Chemical Composition ◽  
Solar System ◽  
Planetary Systems ◽  
Theoretical Work ◽  
Structure Evolution ◽  
Debris Disks ◽  
Physical Processes ◽  
Disk Structure ◽  
Open Questions ◽  
Evolution Modeling

AbstractVLT instruments and ALMA with their high spatial resolution have revolutionized in the past five years our view and understanding of how disks turn into planetary systems. This talk will briefly outline our current understanding of the physical processes occurring and chemical composition evolving as these disks turn into debris disks and eventually planetary systems like our own solar system. I will especially focus on the synergy between disk structure/evolution modeling and astrochemical laboratory/theoretical work to highlight the most recent advances, and open questions such as (1) how much of the chemical composition in disks is inherited from molecular clouds, (2) the relevance of snowlines for planet formation, and (3) what is the origin of the gas in debris disks and what can we learn from it. For each of the three, I will outline briefly how the combination of theory/lab astrochemistry, astrophysical models and observations are required to advance our understanding.

Origins of Life: Open Questions and Debates

2017 ◽  
Author(s):  
André Brack
Keyword(s):  
Rna World ◽  
Stochastic Approach ◽  
Origins Of Life ◽  
Test Tube ◽  
Chemical System ◽  
Small Scale ◽  
Random Errors ◽  
Critical Feature ◽  
Open Questions ◽  
Simple Molecules

Stanley Miller demonstrated in 1953 that it was possible to form amino acids from methane, ammonia, and hydrogen in water, thus launching the ambitious hope that chemists would be able to shed light on the origins of life by recreating a simple life form in a test tube. However, it must be acknowledged that the dream has not yet been accomplished, despite the great volume of effort and innovation put forward by the scientific community. A minima, primitive life can be defined as an open chemical system, fed with matter and energy, capable of self-reproduction (i.e., making more of itself by itself), and also capable of evolving. The concept of evolution implies that chemical systems would transfer their information fairly faithfully but make some random errors. If we compared the components of primitive life to parts of a chemical automaton, we could conceive that, by chance, some parts self-assembled to generate an automaton capable of assembling other parts to produce a true copy. Sometimes, minor errors in the building generated a more efficient automaton, which then became the dominant species. Quite different scenarios and routes have been followed and tested in the laboratory to explain the origin of life. There are two schools of thought in proposing the prebiotic supply of organics. The proponents of a metabolism-first call for the spontaneous formation of simple molecules from carbon dioxide and water to rapidly generate life. In a second hypothesis, the primeval soup scenario, it is proposed that rather complex organic molecules accumulated in a warm little pond prior to the emergence of life. The proponents of the primeval soup or replication first approach are by far the more active. They succeeded in reconstructing small-scale versions of proteins, membranes, and RNA. Quite different scenarios have been proposed for the inception of life: the RNA world, an origin within droplets, self-organization counteracting entropy, or a stochastic approach merging chemistry and geology. Understanding the emergence of a critical feature of life, its one-handedness, is a shared preoccupation in all these approaches.

scholarly journals PhaSePro: the database of proteins driving liquid–liquid phase separation

2019 ◽  
Author(s):  
Bálint Mészáros ◽  
Gábor Erdős ◽  
Beáta Szabó ◽  
Éva Schád ◽  
Ágnes Tantos ◽  
...  
Keyword(s):  
Phase Separation ◽  
Liquid Phase ◽  
Ribosome Biogenesis ◽  
Weak Interactions ◽  
Experimental Studies ◽  
Rna Degradation ◽  
Liquid Phase Separation ◽  
General Mechanism ◽  
Open Questions ◽  
Liquid Liquid Phase Separation

Abstract Membraneless organelles (MOs) are dynamic liquid condensates that host a variety of specific cellular processes, such as ribosome biogenesis or RNA degradation. MOs form through liquid–liquid phase separation (LLPS), a process that relies on multivalent weak interactions of the constituent proteins and other macromolecules. Since the first discoveries of certain proteins being able to drive LLPS, it emerged as a general mechanism for the effective organization of cellular space that is exploited in all kingdoms of life. While numerous experimental studies report novel cases, the computational identification of LLPS drivers is lagging behind, and many open questions remain about the sequence determinants, composition, regulation and biological relevance of the resulting condensates. Our limited ability to overcome these issues is largely due to the lack of a dedicated LLPS database. Therefore, here we introduce PhaSePro (https://phasepro.elte.hu), an openly accessible, comprehensive, manually curated database of experimentally validated LLPS driver proteins/protein regions. It not only provides a wealth of information on such systems, but improves the standardization of data by introducing novel LLPS-specific controlled vocabularies. PhaSePro can be accessed through an appealing, user-friendly interface and thus has definite potential to become the central resource in this dynamically developing field.

Strength, fracture and erosion properties of CVD diamond

1993 ◽  
Vol 342 (1664) ◽  
pp. 261-275 ◽  
Keyword(s):  
Experimental Studies ◽  
Chemical Vapour ◽  
Theoretical Work ◽  
Cvd Diamond ◽  
Bulge Test ◽  
High Modulus ◽  
Free Standing ◽  
Multilayer Systems ◽  
Erosion Properties ◽  
Bulk Diamond

Theoretical and experimental studies have been made on the effect of high modulus coatings on the stress fields generated by indentation and impact onto a flat half-space. The theoretical work used finite-element techniques and it shows that a high modulus coating can have a significant effect on the maximum tensile stresses generated in the substrate providing there is a good bond at the coating/substrate interface. Because it is technically difficult to deposit layers of more than a few micrometres thickness without residual stresses causing debonding, double and multilayer systems have also been examined theoretically. A variety of techniques have been used to determine the strength, modulus, expansion coefficient, thermal conductivity and other physical properties of chemical vapour deposition CVD diamond layers. These are briefly reviewed and data from our own studies using such techniques as the vibrating reed, bulge test and indentation are present. The erosion properties of both CVD coated substrates and CVD free-standing layers are presented for both liquid drop and solid particle erosion. Finally, a study has also been made of the frictional properties of various CVD diamond layers in a range of environments; data are compared with our earlier work on bulk diamond.

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