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Juli Peretó
Synthetic Biology is currently presented as an emergent field involving the application of engineering principles to living matter. However, the scientific pursuit of making life in a laboratory is not new and has been the ultimate, if somewhat distant, aim of the origin-of-life research program for many years. Actually, over a century ago, the idea that the synthesis of life was indispensable to fully understand its nature already appealed to material scientists and evolutionists alike. Jacques Loeb proposed a research program from an engineering standpoint, following a synthetic method (experimental abiogenesis) and based on his mechanist vision of living beings, which he considered true chemical machines...
December 2016: Journal of Molecular Evolution
Kathrin I Mohr
For thousands of years people were delivered helplessly to various kinds of infections, which often reached epidemic proportions and have cost the lives of millions of people. This is precisely the age since mankind has been thinking of infectious diseases and the question of their causes. However, due to a lack of knowledge, the search for strategies to fight, heal, and prevent the spread of communicable diseases was unsuccessful for a long time. It was not until the discovery of the healing effects of (antibiotic producing) molds, the first microscopic observations of microorganisms in the seventeenth century, the refutation of the abiogenesis theory, and the dissolution of the question "What is the nature of infectious diseases?" that the first milestones within the history of antibiotics research were set...
2016: Current Topics in Microbiology and Immunology
Caleb Scharf, Leroy Cronin
A simple, heuristic formula with parallels to the Drake Equation is introduced to help focus discussion on open questions for the origins of life in a planetary context. This approach indicates a number of areas where quantitative progress can be made on parameter estimation for determining origins of life probabilities, based on constraints from Bayesian approaches. We discuss a variety of "microscale" factors and their role in determining "macroscale" abiogenesis probabilities on suitable planets. We also propose that impact ejecta exchange between planets with parallel chemistries and chemical evolution could in principle amplify the development of molecular complexity and abiogenesis probabilities...
July 19, 2016: Proceedings of the National Academy of Sciences of the United States of America
Bruce Damer
Charles Darwin's original intuition that life began in a "warm little pond" has for the last three decades been eclipsed by a focus on marine hydrothermal vents as a venue for abiogenesis. However, thermodynamic barriers to polymerization of key molecular building blocks and the difficulty of forming stable membranous compartments in seawater suggest that Darwin's original insight should be reconsidered. I will introduce the terrestrial origin of life hypothesis, which combines field observations and laboratory results to provide a novel and testable model in which life begins as protocells assembling in inland fresh water hydrothermal fields...
2016: Life
Loris Serafino
In this paper I will reflect on the intellectual rationale underlying the origin of life scientific research efforts by reconsidering some of its conceptual premises and difficulties.
August 7, 2016: Journal of Theoretical Biology
Bhakti Niskama Shanta
In the past, philosophers, scientists, and even the general opinion, had no problem in accepting the existence of consciousness in the same way as the existence of the physical world. After the advent of Newtonian mechanics, science embraced a complete materialistic conception about reality. Scientists started proposing hypotheses like abiogenesis (origin of first life from accumulation of atoms and molecules) and the Big Bang theory (the explosion theory for explaining the origin of universe). How the universe came to be what it is now is a key philosophical question...
September 2015: Communicative & Integrative Biology
Theodor O Diener
The discovery of the viroid in 1971, which initiated the third major expansion of the biosphere towards smaller living entities-after discovery of the "subvisual" microorganisms in 1675 and that of the "submicroscopic" viruses in 1892-has been officially endorsed by the International Committee on Virus Taxonomy as a new order called subviral agents.In 1989, I proposed that, based on their respective molecular properties, viroids are more plausible "living fossils" of the hypothetical RNA World (widely assumed to have existed prior to the evolution of DNA or proteins) than are intron-derived RNAs, which were, at that time, suggested as putative survivors...
March 25, 2016: Biology Direct
Dmitry Yu Zubarev, Leonardo A Pachón
It is generally recognized that a distinguishing feature of life is its peculiar capability to avoid equilibration. The origin of this capability and its evolution along the timeline of abiogenesis is not yet understood. We propose to study an analog of this phenomenon that could emerge in non-biological systems. To this end, we introduce the concept of sustainability of transient kinetic regimes. This concept is illustrated via investigation of cooperative effects in an extended system of compartmentalized chemical oscillators under batch and semi-batch conditions...
February 8, 2016: Scientific Reports
Sukrit Ranjan, Dimitar D Sasselov
Ultraviolet radiation is common to most planetary environments and could play a key role in the chemistry of molecules relevant to abiogenesis (prebiotic chemistry). In this work, we explore the impact of UV light on prebiotic chemistry that might occur in liquid water on the surface of a planet with an atmosphere. We consider effects including atmospheric absorption, attenuation by water, and stellar variability to constrain the UV input as a function of wavelength. We conclude that the UV environment would be characterized by broadband input, and wavelengths below 204 nm and 168 nm would be shielded out by atmospheric CO2 and water, respectively...
January 2016: Astrobiology
Sarah E Maurer, Gunarso Nguyen
Self-assembly is considered one of the driving forces behind abiogenesis and would have been affected by the environmental conditions of early Earth. The formation of membranes is a key step in this process, and unlike large dialkyl membranes of modern cells the first membranes were likely formed from small single-chain amphiphiles, which are environment-sensitive. Fatty acids and their derivatives have been previously characterized in this role without concern for the concentrations of ionic solutes in the suspension...
June 2016: Origins of Life and Evolution of the Biosphere
Anna Grochmal, Luba Prout, Robert Makin-Taylor, Rafel Prohens, Salvador Tomas
In living cells, reactions take place in membrane-bound compartments, often in response to changes in the environment. Learning how the reactions are influenced by this compartmentalization will help us gain an optimal understanding of living organisms at the molecular level and, at the same time, will offer vital clues on the behavior of simple compartmentalized systems, such as prebiotic precursors of cells and cell-inspired artificial systems. In this work we show that a reactive building block (an activated amino acid derivative) trapped in the cavity of a liposome is protected against hydrolysis and reacts nearly quantitatively with another building block, which is membrane-permeable and free in solution, to form the dipeptide...
September 30, 2015: Journal of the American Chemical Society
James A Coffman
Chance has somewhat different meanings in different contexts, and can be taken to be either ontological (as in quantum indeterminacy) or epistemological (as in stochastic uncertainty). Here I argue that, whether or not it stems from physical indeterminacy, chance is a fundamental biological reality that is meaningless outside the context of knowledge. To say that something happened by chance means that it did not happen by design. This of course is a cornerstone of Darwin's theory of evolution: random undirected variation is the creative wellspring upon which natural selection acts to sculpt the functional form (and hence apparent design) of organisms...
December 1, 2014: Biosemiotics
Brian C Larson, R Paul Jensen, Niles Lehman
We describe the initial realization of behavior in the biosphere, which we term behavioral chemistry. If molecules are complex enough to attain a stochastic element to their structural conformation in such as a way as to radically affect their function in a biological (evolvable) setting, then they have the capacity to behave. This circumstance is described here as behavioral chemistry, unique in its definition from the colloquial chemical behavior.  This transition between chemical behavior and behavioral chemistry need be explicit when discussing the root cause of behavior, which itself lies squarely at the origins of life and is the foundation of choice...
2012: Life
James Attwater, Philipp Holliger
Synthetic biology seeks to probe fundamental aspects of biological form and function by construction (resynthesis) rather than deconstruction (analysis). Here we discuss how such an approach could be applied to assemble synthetic quasibiological systems able to replicate and evolve, illuminating universal properties of life and the search for its origins.
May 2014: Nature Methods
Laura M Barge, Terence P Kee, Ivria J Doloboff, Joshua M P Hampton, Mohammed Ismail, Mohamed Pourkashanian, John Zeytounian, Marc M Baum, John A Moss, Chung-Kuang Lin, Richard D Kidd, Isik Kanik
In this paper, we discuss how prebiotic geo-electrochemical systems can be modeled as a fuel cell and how laboratory simulations of the origin of life in general can benefit from this systems-led approach. As a specific example, the components of what we have termed the "prebiotic fuel cell" (PFC) that operates at a putative Hadean hydrothermal vent are detailed, and we used electrochemical analysis techniques and proton exchange membrane (PEM) fuel cell components to test the properties of this PFC and other geo-electrochemical systems, the results of which are reported here...
March 2014: Astrobiology
Ian S Dunn
Terrestrial biosystems depend on macromolecules, and this feature is often considered as a likely universal aspect of life. While opinions differ regarding the importance of small-molecule systems in abiogenesis, escalating biological functional demands are linked with increasing complexity in key molecules participating in biosystem operations, and many such requirements cannot be efficiently mediated by relatively small compounds. It has long been recognized that known life is associated with the evolution of two distinct molecular alphabets (nucleic acid and protein), specific sequence combinations of which serve as informational and functional polymers...
December 2013: Origins of Life and Evolution of the Biosphere
Doriano Brogioli
The mass-action law, which predicts the rates of chemical reactions, is widely used for modeling the kinetics of the chemical reactions and their stationary states, also for complex chemical reaction networks. However, violations of the mass-action equations have been reported in various cases: in confined systems with a small number of molecules, in non-ideally-stirred systems, when the reactions are limited by the diffusion, at high concentrations of reactants, or in chemical reaction networks with marginally stable mass-action equations...
November 14, 2013: Journal of Chemical Physics
Addy Pross
The identification of dynamic kinetic stability (DKS) as a stability kind that governs the evolutionary process for both chemical and biological replicators, opens up new avenues for uncovering the chemical basis of biological phenomena. In this paper, we utilize the DKS concept to explore the chemical roots of two of biology's central concepts--function and complexity. It is found that the selection rule in the world of persistent replicating systems--from DKS less stable to DKS more stable--is the operational law whose very existence leads to the creation of function from of a world initially devoid of function...
April 2013: Journal of Molecular Evolution
Addy Pross, Robert Pascal
The origin of life (OOL) problem remains one of the more challenging scientific questions of all time. In this essay, we propose that following recent experimental and theoretical advances in systems chemistry, the underlying principle governing the emergence of life on the Earth can in its broadest sense be specified, and may be stated as follows: all stable (persistent) replicating systems will tend to evolve over time towards systems of greater stability. The stability kind referred to, however, is dynamic kinetic stability, and quite distinct from the traditional thermodynamic stability which conventionally dominates physical and chemical thinking...
March 2013: Open Biology
Alexey A Novoselov, Paloma Serrano, Mírian Liza Alves Forancelli Pacheco, Michael Scott Chaffin, Jack Thomas O'Malley-James, Susan Carla Moreno, Filipe Batista Ribeiro
Early in its history, Earth's surface developed from an uninhabitable magma ocean to a place where life could emerge. The first organisms, lacking ion transporters, fixed the composition of their cradle environment in their intracellular fluid. Later, though life adapted and spread, it preserved some qualities of its initial environment within. Modern prokaryotes could thus provide insights into the conditions of early Earth and the requirements for the emergence of life. In this work, we constrain Earth's life-forming environment through detailed analysis of prokaryotic intracellular fluid...
March 2013: Astrobiology
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