Toy trains, loaded dice and the origin of life: dimerization on mineral surfaces under periodic drive with Gaussian inputs

In a major extension of previous work, we model the putative hydrothermal rock pore setting for the origin of life on Earth as a series of coupled continuous flow units (the toy train ). Perfusing through this train are reactants that set up thermochemical and pH oscillations, and an activated nucleotide that produces monomer and dimer monophosphates. The dynamical equations that model this system are thermally self-consistent. In an innovative step that breaks some new ground, we build stochasticity of the inputs into the model. The computational results infer various constraints and conditions on, and insights into, chemical evolution and the origin of life and its physical setting: long, interconnected porous structures with longitudinal non-uniformity would have been favourable, and the ubiquitous pH dependences of biology may have been established in the prebiotic era. We demonstrate the important role of Gaussian fluctuations of the inputs in driving polymerization, evolution and diversification. In particular, we find that the probability distribution of the resulting output fluctuations is left-skewed and right-weighted (the loaded dice ), which could favour chemical evolution towards a living RNA world. We tentatively name this distribution ‘Goldilocks’. These results also vindicate the general approach of constructing and running a simple model to learn important new information about a complex system.

Download Full-text

Chemical evolution toward the origin of life

Pure and Applied Chemistry ◽

10.1351/pac200779122101 ◽

2007 ◽

Vol 79 (12) ◽

pp. 2101-2117 ◽

Cited By ~ 26

Author(s):

Daniel Fitz ◽

Hannes Reiner ◽

Bernd Michael Rode

Keyword(s):

Chemical Evolution ◽

Rna World ◽

Early Stage ◽

Building Blocks ◽

Point Of View ◽

Peptide Formation ◽

The Origin Of Life ◽

Life On Earth ◽

Primordial Earth ◽

Rna And Dna

Numerous hypotheses about how life on earth could have started can be found in the literature. In this article, we give an overview about the most widespread ones and try to point out which of them might have occurred on the primordial earth with highest probability from a chemical point of view. The idea that a very early stage of life was the "RNA world" encounters crucial problems concerning the formation of its building blocks and their stability in a prebiotic environment. Instead, it seems much more likely that a "peptide world" originated first and that RNA and DNA took up their part at a much later stage. It is shown that amino acids and peptides can be easily formed in a realistic primordial scenario and that these biomolecules can start chemical evolution without the help of RNA. The origin of biohomochirality seems strongly related to the most probable formation of the first peptides via the salt-induced peptide formation (SIPF) reaction.

Download Full-text

Origins of Life

Sciential - McMaster Undergraduate Science Journal ◽

10.15173/sciential.v1i4.2241 ◽

2020 ◽

pp. 2-7

Author(s):

Hannah Mahoney

Keyword(s):

Origin Of Life ◽

Hydrothermal Vents ◽

Rna World ◽

Relevant Information ◽

Future Research ◽

Specific Chemical ◽

Scientific Disciplines ◽

Earth Environment ◽

The Origin Of Life ◽

Life On Earth

When, where, and how did life on Earth originate? The origin of life problem involves multiple scientific disciplines and has spanned multiple decades. It can be summarized into three stages: (1) the origin of biological monomers, (2) the origin of biological polymers, and (3) the emergence and evolution of cells. While highly speculative, the connections between these stages are theorized by attempting to determine the geochemical situations which could have driven chemical evolution and allow for the emergence of specific chemical functions of biological systems. This review summarizes reported findings relevant to the early Earth environment and the main theories in the origin of life subject. Specific focus is placed on the metabolism first, RNA world, and compartmentalization first theories as they are involved in the origin of life paradox. The review then discusses submarine hydrothermal vents as a possible location for which life could have occurred. Understanding of information pertaining to the origin of life is important as it allows for advancement and discoveries in other fields of science and medicine. Overall, the aim of this review is to display the relevant information about the origin of life theory and highlight the importance of future research.

Download Full-text

Borate and the Origin of RNA: A Model for the Precursors to Life

Elements ◽

10.2138/gselements.13.4.261 ◽

2017 ◽

Vol 13 (4) ◽

pp. 261-265 ◽

Cited By ~ 13

Author(s):

Yoshihiro Furukawa ◽

Takeshi Kakegawa

Keyword(s):

Origin Of Life ◽

Chemical Evolution ◽

Ribonucleic Acid ◽

Rna World ◽

Critical Role ◽

Formose Reaction ◽

Strong Affinity ◽

The Origin Of Life ◽

World Hypothesis ◽

Rna World Hypothesis

According to the RNA World hypothesis, ribonucleic acid (RNA) played a critical role in the origin of life. However, ribose, an essential component of RNA, is easily degraded: finding a way to stabilize it is critical to the viability of the hypothesis. Borate has been experimentally shown to have a strong affinity for ribose, and, thus, could have protected ribose from degradation in the formose reaction, a potential process for prebiotic ribose formation. Accumulation of borate on Hadean Earth (prior to ~4,000 Ma) might have been a key step in the chemical evolution of the biotic sugar. Proto-arcs are suggested as a geological setting sufficiently rich in borate to stabilize ribose during the Hadean.

Download Full-text

Are Scientific Models of Life Testable? A Lesson from Simpson’s Paradox

Sci ◽

10.3390/sci2030073 ◽

2020 ◽

Vol 2 (3) ◽

pp. 73

Author(s):

Prasanta S. Bandyopadhyay ◽

Nolan Grunska ◽

Don Dcruz ◽

Mark C. Greenwood

Keyword(s):

Origin Of Life ◽

Rna World ◽

Scientific Models ◽

Scientific Model ◽

Simpson’S Paradox ◽

World Theory ◽

Life Issues ◽

The Origin Of Life ◽

Logical Sense ◽

Simpson's Paradox

We address the need for a model by considering two competing theories regarding the origin of life: (i) the Metabolism First theory and (ii) the RNA World theory. We discuss two inter-related points. (I) Models are valuable tools in understanding both the processes and intricacies of the origin of life issues. (II) Insights from models also help us to evaluate the core objection to origin of life theories called “the inefficiency objection” commonly raised by proponents of both the Metabolism First theory and the RNA World theory against each other. We use Simpson’s paradox as a tool for challenging this objection. We will use models in various senses ranging from taking them as representations of reality to treating them as theories/accounts that provide heuristics for probing reality. In this paper, we will frequently use models and theories interchangeably. Additionally, we investigate Conway’s Game of Life and contrast it with our Simpson’s Paradox (SP)-based approach to emergence of life issues. Finally, we discuss some of the consequences of our view. A scientific model is testable in three senses: (i) a logical sense, (ii) a nomological sense, and (iii) a current technological sense. The SP-based model is testable in the logical sense. It is also testable nomologically. However, it is not currently feasible to test it.

Download Full-text

‘Whole Organism’, Systems Biology, and Top-Down Criteria for Evaluating Scenarios for the Origin of Life

Life ◽

10.3390/life11070690 ◽

2021 ◽

Vol 11 (7) ◽

pp. 690

Author(s):

Clifford F. Brunk ◽

Charles R. Marshall

Keyword(s):

Origin Of Life ◽

Top Down ◽

Chemical Systems ◽

Biochemical Pathways ◽

The Origin Of Life ◽

Energy And Material Flows ◽

Complex Scenario ◽

Life On Earth ◽

Physical Laws ◽

Equilibrium Chemical

While most advances in the study of the origin of life on Earth (OoLoE) are piecemeal, tested against the laws of chemistry and physics, ultimately the goal is to develop an overall scenario for life’s origin(s). However, the dimensionality of non-equilibrium chemical systems, from the range of possible boundary conditions and chemical interactions, renders the application of chemical and physical laws difficult. Here we outline a set of simple criteria for evaluating OoLoE scenarios. These include the need for containment, steady energy and material flows, and structured spatial heterogeneity from the outset. The Principle of Continuity, the fact that all life today was derived from first life, suggests favoring scenarios with fewer non-analog (not seen in life today) to analog (seen in life today) transitions in the inferred first biochemical pathways. Top-down data also indicate that a complex metabolism predated ribozymes and enzymes, and that full cellular autonomy and motility occurred post-LUCA. Using these criteria, we find the alkaline hydrothermal vent microchamber complex scenario with a late evolving exploitation of the natural occurring pH (or Na+ gradient) by ATP synthase the most compelling. However, there are as yet so many unknowns, we also advocate for the continued development of as many plausible scenarios as possible.

Download Full-text