scholarly journals The automatic parameter-exploration with a machine-learning-like approach: Powering the evolutionary modeling on the origin of life

2021 ◽  
Vol 17 (12) ◽  
pp. e1009761
Author(s):  
Yuzhen Liang ◽  
Chunwu Yu ◽  
Wentao Ma
Keyword(s):  
Machine Learning ◽  
Origin Of Life ◽  
Parameter Space ◽  
Prebiotic Chemistry ◽  
Theoretical Research ◽  
Parameter Setting ◽  
Evolutionary Modeling ◽  
Complex Models ◽  
The Origin Of Life ◽  
Parameter Values

The origin of life involved complicated evolutionary processes. Computer modeling is a promising way to reveal relevant mechanisms. However, due to the limitation of our knowledge on prebiotic chemistry, it is usually difficult to justify parameter-setting for the modeling. Thus, typically, the studies were conducted in a reverse way: the parameter-space was explored to find those parameter values “supporting” a hypothetical scene (that is, leaving the parameter-justification a later job when sufficient knowledge is available). Exploring the parameter-space manually is an arduous job (especially when the modeling becomes complicated) and additionally, difficult to characterize as regular “Methods” in a paper. Here we show that a machine-learning-like approach may be adopted, automatically optimizing the parameters. With this efficient parameter-exploring approach, the evolutionary modeling on the origin of life would become much more powerful. In particular, based on this, it is expected that more near-reality (complex) models could be introduced, and thereby theoretical research would be more tightly associated with experimental investigation in this field–hopefully leading to significant steps forward in respect to our understanding on the origin of life.

scholarly journals Prebiotic Chemistry in the Wild: How Geology Interferes with the Origins of Life

2020 ◽  
Author(s):  
Craig Walton ◽  
Paul B. Rimmer ◽  
Helen Williams ◽  
Oliver Shorttle
Keyword(s):  
Origin Of Life ◽  
Water Activity ◽  
Parameter Space ◽  
Prebiotic Chemistry ◽  
Effective Means ◽  
Adenosine Monophosphate ◽  
Experimental Models ◽  
Dehydration Reactions ◽  
The Origin Of Life ◽  
Reaction Schemes

A plausible explanation for the origin of life must satisfy constraints imposed by both organic chemistry and early Earth geochemistry. However, the full scope of geochemical parameter space is rarely considered by either theoretical or experimental models of abiogenesis. Here we propose a novel approach, which can make maximum use of available data. We posit that constructive and destructive geochemical interferences with proposed prebiotic reaction schemes can be used to restrict plausible environmental parameter space for the origin of life. Our approach is demonstrated by exploring parameter space for dehydration reactions. Such reactions are universally important in extant biochemistry and all proposed prebiotic reaction schemes, yet challenging to perform under plausible conditions. We specifically explore a minimal pathway for RNA synthesis (formaldehyde; ribose; ribose phosphate; adenosine monophosphate; RNA). Based on assembled thermodynamic and geochemical constraints, we identify that low water activity is a key constructive interference in prebiotic chemistry. Critically, the manner in which low water activity is achieved can strongly discriminate between different environmental scenarios. Exploring interference chemistry is hence an effective means of discriminating between competing origin of life scenarios.

scholarly journals Prebiotic Chemistry in the Wild: How Geology Interferes with the Origins of Life

2020 ◽  
Author(s):  
Craig Walton ◽  
Paul B. Rimmer ◽  
Helen Williams ◽  
Oliver Shorttle
Keyword(s):  
Origin Of Life ◽  
Water Activity ◽  
Parameter Space ◽  
Prebiotic Chemistry ◽  
Effective Means ◽  
Adenosine Monophosphate ◽  
Experimental Models ◽  
Dehydration Reactions ◽  
The Origin Of Life ◽  
Reaction Schemes

A plausible explanation for the origin of life must satisfy constraints imposed by both organic chemistry and early Earth geochemistry. However, the full scope of geochemical parameter space is rarely considered by either theoretical or experimental models of abiogenesis. Here we propose a novel approach, which can make maximum use of available data. We posit that constructive and destructive geochemical interferences with proposed prebiotic reaction schemes can be used to restrict plausible environmental parameter space for the origin of life. Our approach is demonstrated by exploring parameter space for dehydration reactions. Such reactions are universally important in extant biochemistry and all proposed prebiotic reaction schemes, yet challenging to perform under plausible conditions. We specifically explore a minimal pathway for RNA synthesis (formaldehyde; ribose; ribose phosphate; adenosine monophosphate; RNA). Based on assembled thermodynamic and geochemical constraints, we identify that low water activity is a key constructive interference in prebiotic chemistry. Critically, the manner in which low water activity is achieved can strongly discriminate between different environmental scenarios. Exploring interference chemistry is hence an effective means of discriminating between competing origin of life scenarios.

Three stages of the origin of life process: bifurcation, stabilization and inversion

2008 ◽  
Vol 7 (1) ◽  
pp. 27-46 ◽  
Author(s):  
V.N. Kompanichenko
Keyword(s):  
Free Energy ◽  
Origin Of Life ◽  
Bifurcation Point ◽  
Stable State ◽  
Theoretical Research ◽  
Unstable State ◽  
Heterogeneous Structure ◽  
Biological Organization ◽  
The Origin Of Life ◽  
Transformation Of Organic Matter

AbstractThe principal succession of transformations of a prebiotic microsystem leading to its transition into the primary living state is theoretically substantiated. For the first stage of the succession, a significant change in the external conditions constrains an organic microsystem to leave the current stable state with the following transition into a new stable state through the unstable critical (bifurcation) point. At the bifurcation point the microsystem acquires the original properties without which life cannot exist (self-maintaining heterogeneous structure, incessant fluctuations and rearrangement of molecules, exchange with the surroundings by matter and energy, etc.). During the second stage its unstable state stabilizes relatively by means of the balanced oscillations around the bifurcation point (the paradoxical state of ‘stabilized instability’ appears). The third stage is characterized with the radical turn in the network of chemical reactions: the free energy contribution begins to prevail over the entropy contribution. As a result, constructive transformations proceed faster than destructive transformations. At this stage the key properties of biological organization appear: the ability to concentrate free energy and information, intensified counteraction to external influences, expedient behaviour and persistent self-renovation. On the early Earth, such successive transformation of organic matter occurred in the changeable conditions of a hydrothermal medium. Some new methods for experimental and theoretical research in the origin of life field are suggested.

scholarly journals Scum of the Earth: A Hypothesis for Prebiotic Multi-Compartmentalised Environments

Life ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 976
Author(s):  
Craig Robert Walton ◽  
Oliver Shorttle
Keyword(s):  
Origin Of Life ◽  
Prebiotic Chemistry ◽  
Near Surface ◽  
Microbial Biofilms ◽  
The Earth ◽  
Rock Record ◽  
Universal Feature ◽  
The Origin Of Life ◽  
New Hypothesis ◽  
Surface Environment

Compartmentalisation by bioenergetic membranes is a universal feature of life. The eventual compartmentalisation of prebiotic systems is therefore often argued to comprise a key step during the origin of life. Compartments may have been active participants in prebiotic chemistry, concentrating and spatially organising key reactants. However, most prebiotically plausible compartments are leaky or unstable, limiting their utility. Here, we develop a new hypothesis for an origin of life environment that capitalises upon, and mitigates the limitations of, prebiotic compartments: multi-compartmentalised layers in the near surface environment—a ’scum’. Scum-type environments benefit from many of the same ensemble-based advantages as microbial biofilms. In particular, scum layers mediate diffusion with the wider environments, favouring preservation and sharing of early informational molecules, along with the selective concentration of compatible prebiotic compounds. Biofilms are among the earliest traces imprinted by life in the rock record: we contend that prebiotic equivalents of these environments deserve future experimental investigation.

scholarly journals Scum of the Earth: a hypothesis for prebiotic multi-compartmentalised environments}

2021 ◽  
Author(s):  
Craig Walton ◽  
Oliver Shorttle
Keyword(s):  
Origin Of Life ◽  
Prebiotic Chemistry ◽  
Near Surface ◽  
Microbial Biofilms ◽  
The Earth ◽  
Rock Record ◽  
Universal Feature ◽  
The Origin Of Life ◽  
New Hypothesis ◽  
Surface Environment

Compartmentalisation by bioenergetic membranes is a universal feature of life. The eventual compartmentalisation of prebiotic systems is therefore often argued to comprise a key step during the origin of life. Compartments may have been active participants in prebiotic chemistry, concentrating and spatially organising key reactants. However, most prebiotically plausible compartments are leaky or unstable, limiting their utility. Here, we develop a new hypothesis for an origin of life environment, that capitalises upon, and mitigates the limitations of, prebiotic compartments: multi-compartmentalised layers in the near surface environment --- a 'scum'. Scum-type environments benefit from many of the same ensemble-based advantages as microbial biofilms. In particular, scum layers mediate diffusion with the wider environment, favouring preservation and sharing of early informational molecules, along with the selective concentration of compatible prebiotic compounds. Biofilms are among the earliest traces imprinted by life in the rock record: we contend that prebiotic equivalents of these environments deserve future experimental investigation.

scholarly journals Meteor Storms as a Window on the Delivery of Extraterrestrial Organic Matter to the Early Earth

2004 ◽  
Vol 213 ◽  
pp. 281-288
Author(s):  
P. Jenniskens
Keyword(s):  
Organic Matter ◽  
Origin Of Life ◽  
Prebiotic Chemistry ◽  
Early Earth ◽  
Rarefied Flow ◽  
Physical Conditions ◽  
Prebiotic Molecules ◽  
The Origin Of Life ◽  
Recent Insight

The unique rarefied flow and flash heating in meteors creates physical conditions that can change exogenous organic matter into unique prebiotic molecules. with the exception of rare giant comet impacts, most infalling matter at the time of the origin of life was deposited in the atmosphere during the meteor phase. Much new data has been obtained from observations in the Leonid Multi-Instrument Aircraft Campaign; a series of NASA and USAF sponsored Astrobiology missions that explored the 1998–2002 Leonid meteor storms. Here, we provide an overview of some of this recent insight, which provides a framework in which the prebiotic chemistry can be studied.

scholarly journals Chemical Diversity of Metal Sulfide Minerals and Its Implications for the Origin of Life

Life ◽  
2018 ◽  
Vol 8 (4) ◽  
pp. 46 ◽  
Author(s):  
Yamei Li ◽  
Norio Kitadai ◽  
Ryuhei Nakamura
Keyword(s):  
Origin Of Life ◽  
Prebiotic Chemistry ◽  
Metal Sulfide ◽  
Sulfide Minerals ◽  
Chemical Diversity ◽  
Metal Sulfides ◽  
Learning Approaches ◽  
Wide Range ◽  
The Origin Of Life ◽  
Catalytic Functions

Prebiotic organic synthesis catalyzed by Earth-abundant metal sulfides is a key process for understanding the evolution of biochemistry from inorganic molecules, yet the catalytic functions of sulfides have remained poorly explored in the context of the origin of life. Past studies on prebiotic chemistry have mostly focused on a few types of metal sulfide catalysts, such as FeS or NiS, which form limited types of products with inferior activity and selectivity. To explore the potential of metal sulfides on catalyzing prebiotic chemical reactions, here, the chemical diversity (variations in chemical composition and phase structure) of 304 natural metal sulfide minerals in a mineralogy database was surveyed. Approaches to rationally predict the catalytic functions of metal sulfides are discussed based on advanced theories and analytical tools of electrocatalysis such as proton-coupled electron transfer, structural comparisons between enzymes and minerals, and in situ spectroscopy. To this end, we introduce a model of geoelectrochemistry driven prebiotic synthesis for chemical evolution, as it helps us to predict kinetics and selectivity of targeted prebiotic chemistry under “chemically messy conditions”. We expect that combining the data-mining of mineral databases with experimental methods, theories, and machine-learning approaches developed in the field of electrocatalysis will facilitate the prediction and verification of catalytic performance under a wide range of pH and Eh conditions, and will aid in the rational screening of mineral catalysts involved in the origin of life.

Histidine adsorption onto modified montmorillonite under prebiotic chemistry conditions: a thermodynamic and kinetic study

2020 ◽  
pp. 1-12
Author(s):  
Rafael Block Samulewski ◽  
Regiane Tamires Damasceno Guimarães ◽  
Dimas Augusto Morozin Zaia
Keyword(s):  
Gibbs Energy ◽  
Origin Of Life ◽  
Prebiotic Chemistry ◽  
Reaction Medium ◽  
Time Range ◽  
Slow Step ◽  
Essential Information ◽  
Pseudo Second Order ◽  
The Origin Of Life ◽  
Open Question

Abstract The origin of life from inanimate matter is still an open question, and our knowledge is still very limited. In this sense, prebiotic chemistry seeks to study and understand how chemical reactions may have contributed to the origin of life. Minerals are of great relevance to prebiotic chemistry, as they may have preconcentrated precursors of biomolecules or biomolecules from diluted solutions, provided protection for biomolecules against UV radiation and hydrolysis, catalysing their reactions and played the role of a primitive genetic code. Montmorillonite, a prebiotic mineral, was shown to be able to adsorb adenine and later also histidine. In addition, histidine adsorption did not displace adenine from the montmorillonite. Kinetic experiments showed that using a whole period of time (7 days) it was not possible to adjust the data to any mathematical kinetic model. Thus, the data were separated into four different adsorption ranges: range 1 (0–60 min), range 2 (60–4320 min), range 3 (4320–7200 min) and range 4 (7200–10 080 min). Range 1 showed adsorption that was too fast, meaning no variations in the adsorption data, and the data of range 3 did not fit in any model used in this work. Thus, range 2 (60–4320 min) and range 4 (7200–10 080 min) were analysed. The adsorption kinetics of histidine adsorption indicated two reaction steps, a quick step (60–4320 min), following the pseudo-first-order model, followed by a slower step (7200–10 080 min) of the pseudo-second order. With these results, isotherms were constructed with times of 1 h and 7 days. The results of the quick step (1 h) showed a reaction that was not thermodynamically favoured. For this time range, Gibbs energy values obtained ranged between 5 and 10 kJ mol−1 at temperatures of 20, 35 and 50°C, and the adsorption occurred due to the balance shift of increase in histidine concentrations. The isotherms of the slow step (7 days) presented negative values, showing a more favourable reaction with Gibbs energy values ranging between −5 and −11 kJ mol−1. The mathematical modelling of the data indicates that seawater ions are crucial in the adsorption process. Thus, the study provided essential information for prebiotic chemistry, showing that time and the reaction medium should always be taken into account.

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