Alternative bases in the RNA world: The prebiotic synthesis of urazole and its ribosides

1994 ◽  
Vol 38 (6) ◽  
Author(s):  
V.M. Kolb ◽  
J.P. Dworkin ◽  
S.L. Miller
Keyword(s):  
Rna World ◽  
Prebiotic Synthesis

scholarly journals A model for the emergence of RNA from a prebiotically plausible mixture of ribonucleotides, arabinonucleotides and 2’-deoxynucleotides

2019 ◽  
Author(s):  
Seohyun Chris Kim ◽  
Lijun Zhou ◽  
Wen Zhang ◽  
Derek K. O’Flaherty ◽  
Valeria Rondo-Brovetto ◽  
...  
Keyword(s):  
Rna Synthesis ◽  
Rna World ◽  
Random Sequence ◽  
Prebiotic Synthesis ◽  
Primer Extension ◽  
Complex Mixtures ◽  
Essential Step ◽  
Simultaneous Synthesis ◽  
The Difference ◽  
Chimeric Oligonucleotides

AbstractThe abiotic synthesis of ribonucleotides is thought to have been an essential step towards the emergence of the RNA world. However, it is likely that the prebiotic synthesis of ribonucleotides was accompanied by the simultaneous synthesis of arabinonucleotides, 2′-deoxyribonucleotides, and other variations on the canonical nucleotides. In order to understand how relatively homogeneous RNA could have emerged from such complex mixtures, we have examined the properties of arabinonucleotides and 2′-deoxyribonucleotides in nonenzymatic template-directed primer extension reactions. We show that nonenzymatic primer extension with activated arabinonucleotides is much less efficient than with activated ribonucleotides, and furthermore that once an arabinonucleotide is incorporated, continued primer extension is strongly inhibited. As previously shown, 2′-deoxyribonucleotides are also less efficiently incorporated in primer extension reactions, but the difference is more modest. Experiments with mixtures of nucleotides suggest that the coexistence of ribo- and arabino-nucleotides does not impede the copying of RNA templates. Moreover, chimeric oligoribonucleotides containing 2′-deoxy- or arabino-nucleotides are effective templates for RNA synthesis. We propose that the initial genetic polymers were random sequence chimeric oligonucleotides formed by untemplated polymerization, but that template copying chemistry favored RNA synthesis; multiple rounds of replication may have led to pools of oligomers composed mainly of RNA.

Randomness and Complexity

2018 ◽  
Author(s):  
Steven E. Vigdor
Keyword(s):  
Quantum Mechanics ◽  
Natural Selection ◽  
Rna World ◽  
Biological Evolution ◽  
Variable Theory ◽  
Cosmological Natural Selection ◽  
Einstein Podolsky Rosen ◽  
World Hypothesis ◽  
Rna World Hypothesis

Chapter 7 describes the fundamental role of randomness in quantum mechanics, in generating the first biomolecules, and in biological evolution. Experiments testing the Einstein–Podolsky–Rosen paradox have demonstrated, via Bell’s inequalities, that no local hidden variable theory can provide a viable alternative to quantum mechanics, with its fundamental randomness built in. Randomness presumably plays an equally important role in the chemical assembly of a wide array of polymer molecules to be sampled for their ability to store genetic information and self-replicate, fueling the sort of abiogenesis assumed in the RNA world hypothesis of life’s beginnings. Evidence for random mutations in biological evolution, microevolution of both bacteria and antibodies and macroevolution of the species, is briefly reviewed. The importance of natural selection in guiding the adaptation of species to changing environments is emphasized. A speculative role of cosmological natural selection for black-hole fecundity in the evolution of universes is discussed.

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

Sci ◽  
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.

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