scholarly journals Prebiotic chemistry: a new modus operandi

2011 ◽  
Vol 366 (1580) ◽  
pp. 2870-2877 ◽  
Author(s):  
Matthew W. Powner ◽  
John D. Sutherland
Keyword(s):  
Origin Of Life ◽  
Early Life ◽  
Rna World ◽  
Origins Of Life ◽  
Geochemical Conditions ◽  
Systems Chemistry ◽  
Novel Approach ◽  
Sequential Addition ◽  
World Hypothesis ◽  
Emergence Of Life

A variety of macromolecules and small molecules—(oligo)nucleotides, proteins, lipids and metabolites—are collectively considered essential to early life. However, previous schemes for the origin of life—e.g. the ‘RNA world’ hypothesis—have tended to assume the initial emergence of life based on one such molecular class followed by the sequential addition of the others, rather than the emergence of life based on a mixture of all the classes of molecules. This view is in part due to the perceived implausibility of multi-component reaction chemistry producing such a mixture. The concept of systems chemistry challenges such preconceptions by suggesting the possibility of molecular synergism in complex mixtures. If a systems chemistry method to make mixtures of all the classes of molecules considered essential for early life were to be discovered, the significant conceptual difficulties associated with pure RNA, protein, lipid or metabolism ‘worlds’ would be alleviated. Knowledge of the geochemical conditions conducive to the chemical origins of life is crucial, but cannot be inferred from a planetary sciences approach alone. Instead, insights from the organic reactivity of analytically accessible chemical subsystems can inform the search for the relevant geochemical conditions. If the common set of conditions under which these subsystems work productively, and compatibly, matches plausible geochemistry, an origins of life scenario can be inferred. Using chemical clues from multiple subsystems in this way is akin to triangulation, and constitutes a novel approach to discover the circumstances surrounding the transition from chemistry to biology. Here, we exemplify this strategy by finding common conditions under which chemical subsystems generate nucleotides and lipids in a compatible and potentially synergistic way. The conditions hint at a post-meteoritic impact origin of life scenario.

Understanding Life: A Bioinformatics Perspective

2016 ◽  
Vol 25 (2) ◽  
pp. 231-245 ◽  
Author(s):  
Natalia Szostak ◽  
Szymon Wasik ◽  
Jacek Blazewicz
Keyword(s):  
Origin Of Life ◽  
Rna World ◽  
Origins Of Life ◽  
Life Itself ◽  
Wet Lab ◽  
The Origin Of Life ◽  
To Come ◽  
World Hypothesis ◽  
Definition Of ◽  
Rna World Hypothesis

According to some hypotheses, from a statistical perspective the origin of life seems to be a highly improbable event. Although there is no rigid definition of life itself, life as it is, is a fact. One of the most recognized hypotheses for the origins of life is the RNA world hypothesis. Laboratory experiments have been conducted to prove some assumptions of the RNA world hypothesis. However, despite some success in the ‘wet-lab’, we are still far from a complete explanation. Bioinformatics, supported by biomathematics, appears to provide the perfect tools to model and test various scenarios of the origins of life where wet-lab experiments cannot reflect the true complexity of the problem. Bioinformatics simulations of early pre-living systems may give us clues to the mechanisms of evolution. Whether or not this approach succeeds is still an open question. However, it seems likely that linking efforts and knowledge from the various fields of science into a holistic bioinformatics perspective offers the opportunity to come one step closer to a solution to the question of the origin of life, which is one of the greatest mysteries of humankind. This paper illustrates some recent advancements in this area and points out possible directions for further research.

scholarly journals The difficult case of an RNA-only origin of life

2019 ◽  
Vol 3 (5) ◽  
pp. 469-475 ◽  
Author(s):  
Kristian Le Vay ◽  
Hannes Mutschler
Keyword(s):  
Origin Of Life ◽  
Rna World ◽  
Large Body ◽  
Difficult Case ◽  
Experimental Approaches ◽  
World Hypothesis ◽  
Life On Earth ◽  
Self Replication ◽  
Emergence Of Life ◽  
Rna World Hypothesis

The RNA world hypothesis is probably the most extensively studied model for the emergence of life on Earth. Despite a large body of evidence supporting the idea that RNA is capable of kick-starting autocatalytic self-replication and thus initiating the emergence of life, seemingly insurmountable weaknesses in the theory have also been highlighted. These problems could be overcome by novel experimental approaches, including out-of-equilibrium environments, and the exploration of an early co-evolution of RNA and other key biomolecules such as peptides and DNA, which might be necessary to mitigate the shortcomings of RNA-only systems.

scholarly journals Investigating Prebiotic Protocells for a Comprehensive Understanding of the Origins of Life: A Prebiotic Systems Chemistry Perspective

Life ◽  
2019 ◽  
Vol 9 (2) ◽  
pp. 49 ◽  
Author(s):  
Augustin Lopez ◽  
Michele Fiore
Keyword(s):  
Thin Films ◽  
Synthetic Biology ◽  
Chemical Compounds ◽  
Origins Of Life ◽  
Supramolecular Systems ◽  
Comprehensive Understanding ◽  
Giant Vesicles ◽  
Relevant Concept ◽  
Systems Chemistry ◽  
Emergence Of Life

Protocells are supramolecular systems commonly used for numerous applications, such as the formation of self-evolvable systems, in systems chemistry and synthetic biology. Certain types of protocells imitate plausible prebiotic compartments, such as giant vesicles, that are formed with the hydration of thin films of amphiphiles. These constructs can be studied to address the emergence of life from a non-living chemical network. They are useful tools since they offer the possibility to understand the mechanisms underlying any living cellular system: Its formation, its metabolism, its replication and its evolution. Protocells allow the investigation of the synergies occurring in a web of chemical compounds. This cooperation can explain the transition between chemical (inanimate) and biological systems (living) due to the discoveries of emerging properties. The aim of this review is to provide an overview of relevant concept in prebiotic protocell research.

scholarly journals Life Emerged as the “Protein/Metabolism-First” Theory Expects

2018 ◽  
Author(s):  
Kenji Ikehara
Keyword(s):  
Protein Metabolism ◽  
Rna World ◽  
Order Structure ◽  
Protein World ◽  
Weak Points ◽  
The Origin Of Life ◽  
World Hypothesis ◽  
Emergence Of Life ◽  
Gadv Hypothesis ◽  
Rna World Hypothesis

The origin of life has not been solved as yet, in spit of the time passage more than thirty years from publication of RNA world hypothesis by W. Gilbert (1986), which is based on the “gene/replicator--first” theory. On the contrary, I have proposed [GADV]-protein world hypothesis (GADV hypothesis), assuming that life emerged from [GADV]-protein world, which is grounded on the “protein/metabolism-first” theory. However, two weak points of protein world hypothesis, (i) protein cannot be produced without gene, and (ii) protein cannot be self-replicated, have been frequently pointed out by supporters of RNA world hypothesis. Then, I examined whether the two weak points could be overcome by GADV hypothesis or not. From the results, it was confirmed that (i) [GADV]-protein could be pseudo-replicated in the absence of gene owing to protein 0th-order structure or [GADV]-amino acids, and (ii) the replication ability is not always required from the beginning but it is sufficient to acquire it at some time point until the emergence of life. Thus, it was concluded that life emerged as [GADV]-protein world hypothesis, which is grounded on the “protein/metabolism-first” theory, expects.

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

Sci ◽  
2020 ◽  
Vol 3 (1) ◽  
pp. 2
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 ◽  
Logical Sense ◽  
Simpson's Paradox ◽  
Emergence Of Life

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 interrelated points, namely: (i) Models are valuable tools for understanding both the processes and intricacies of origin-of-life issues, and (ii) Insights from models also help us to evaluate the core objection to origin-of-life theories, called “the inefficiency objection”, which is commonly raised by proponents of both the Metabolism First theory and the RNA World theory against each other. We use Simpson’s Paradox (SP) 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 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 first two senses but it is not feasible to test it using current technology.

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

Elements ◽  
2017 ◽  
Vol 13 (4) ◽  
pp. 261-265 ◽  
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.

Pyrite and the Origins of Life

Pyrite ◽  
2015 ◽  
Author(s):  
David Rickard
Keyword(s):  
Origin Of Life ◽  
Early Life ◽  
Life Forms ◽  
Origins Of Life ◽  
Sources Of Information ◽  
Ancient India ◽  
Pyrite Formation ◽  
The Origin Of Life ◽  
Life On Earth ◽  
The Relationship

If you have been reading this book since the beginning, you will not be surprised by now to find that you have come across a chapter documenting the involvement of pyrite in the origin of life. This is because you will have read in this book how pyrite has been at the root of many fundamental discoveries about the nature of our world. So you do not suffer more than eyebrow-raising surprise and maybe a gentle throat-clearing in learning that pyrite is contributing to our current understanding of the origins of life. By contrast, if you have dived in at Chapter 9 you probably look at the title of this chapter with disbelief. After all, what could be the connection between a common glitzy mineral and the origin of life? The more diligent reader will have already learned that pyrite formation is intimately associated with biology because most of it is produced by bacteria that extract their oxygen from sulfate and produce hydrogen sulfide. This relationship is so overweening today that pyrite formation controls many fundamental aspects of the Earth’s environment. So what happens if we extend this line of inquiry back to the beginnings of geologic time? We have already seen that the characteristics of ancient pyrite are one of the main sources of information about the nature of the early Earth. The consequence of this is that we know quite a bit about the relationship between pyrite and early life on Earth. In this chapter, we further explore this and review the laboratory work that implicates pyrite itself in the original syntheses of the self-replicating biomolecules that assembled to produce Earth’s first life forms. The thesis that life developed from nonbiological chemistry is a very old idea stretching back through Anaximander in 6th-century BCE Greece to the Vedic writings of ancient India around 1500 BCE and is often called abiogenesis.

scholarly journals Origins of Life and the RNA World: Evolution of RNA-Replicase Recognition

2004 ◽  
Vol 213 ◽  
pp. 321-324 ◽  
Author(s):  
Laura Guogas ◽  
James Hogle ◽  
Lee Gehrke
Keyword(s):  
Origin Of Life ◽  
Protein Complex ◽  
Rna Viruses ◽  
Rna World ◽  
Rna Virus ◽  
Genetic Material ◽  
Virus Family ◽  
The Origin Of Life ◽  
World Hypothesis ◽  
Rna World Hypothesis

Central to understanding the origin of life is the elucidation of the first replication mechanism. The RNA World hypothesis suggests that the first self-replicating molecules were RNAs and that DNA later superceded RNA as the genetic material. RNA viruses were not subjected to the same evolutionary pressures as cellular organisms; consequently, they likely possess remnants of earlier replication strategies. Our laboratory investigates how members of the RNA virus family Bromoviridae can have structurally distinct 3' end tags yet are specifically recognized by conserved replication enzymes. This work addresses the idea that 3' tRNA tails were functionally replaced in some viruses by an RNA-protein complex. These viruses may serve as a timeline for the transition from the RNA world to DNA and protein based life.

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.

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