Special Issue "Molecules to Microbes"

A special issue of Sci (ISSN 2413-4155).

Deadline for manuscript submissions: closed (31 August 2019).

Special Issue Editor

Dr. Sohan Jheeta
Website
Guest Editor
NoR HGT & LUCA*, 1 Scott Hall Crescent, Leeds, LS7 3RB, UK
Interests: origin of life; RNA world; panspermia; hydrothermal vent; horizontal gene transfer; tree of life; phylogenetics; extraterrestrial life; astrochemistry
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Special Issue Information

Dear Colleagues,

A discussion meeting on the origin of life and life elsewhere in the Universe took place at the Eugenides Hall Foundation, in association with the National Technical University of Athens on 4th, 5th, and 6th November 2018. This meeting is a biennial event that brings together scientists from different disciplines, including those who are not necessarily working directly on the questions of the origin of life. The reasoning behind this collaboration between scientists from “outside” and those directly involved in the origin of life sphere is that the question is just too darned difficult to answer, and this approach certainly maximises the array of perspective and input. How can this alliance help to answer these questions? This is best illustrated with an example; scientists (e.g., virologists) investigating the RNA viruses (primarily Retroviruses) discovered that the retroviral enzyme, reverse transcriptase (RT), can bring about the synthesis of DNA from an RNA template. It is inaccurate to describe RT as reverse, because the formation of DNA from an RNA is, in fact, a forward reaction as far as the origin of life is concerned, thus illustrating that DNA came after RNA—i.e., an RNA ‘invented’ DNA, also noting that DNA is primarily RNA without deoxy ribose sugar (as below) and methylated uracil base. The DNA synthesis reaction, in the presence of RT, could be more accurately written as RNA à DNA, and so it should be labelled forward transcriptase or real transcriptase, as announced by Professor Karin Moelling, a virologist, in her book (page 61) entitled “Viruses—More Friends than Foes” (2017). Moelling, who is a virologist turned advocate of the origin of life, is a typical example of an “outside” scientist.

The reason DNA came after RNA concerns ribose sugar and uracil. In RNA, ribose is a five-carbon “normal” sugar; in DNA, this sugar is deoxy, meaning that there is a conspicuous absence of the oxygen [O] atom at carbon atom number two (C2) in the pentose ring of ribose. There is no known natural mechanism by which [O] could be removed from the hydroxyl (OH) group at C2; this is because [O] is highly electronegative and is tightly bound to C2. Although it is possible to make 2-deoxyribose sugar experimentally from acetaldehyde and glyceraldehyde-5-phosphate, this is unlikely to have occurred in nature. The removal of [O] from the C2 hydroxyl group is still an open-ended question. The absence of [O] makes a DNA molecule more stable compared to an RNA molecule as a repository of genomes. So, it can be surmised that RNA with its hydroxylated C2 came first with DNA making its appearance later. The other difference—methylated uracil—is relatively easy to synthesise from uracil by adding methyl group (CH3) to it.

To elucidate the exact routes of the emergence of life requires a multifaceted approach; that is, the input of scientists working in a wide spectrum of fields of research, including general practitioners in biology, chemistry, and physics; systems biology and chemistry; synthetics biology; virology pertaining to all three domains of life, including palaeontology and medical virologists; metagenomic and horizontal gene transfer specialists; pathogen scientists working with food poisoning microbes; bioinformatics; and geneticists. Scientists from these fields, as well as computer modelers and even mathematicians, are invited to submit articles of interest to this Special Issue.

Dr. Sohan Jheeta
Guest Editor

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Published Papers (8 papers)

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Open AccessArticlePost Publication Peer ReviewVersion 4, Approved
Organic Molecules: Is It Possible to Distinguish Aromatics from Aliphatics Collected by Space Missions in High-Speed Impacts?
Sci 2020, 2(3), 56; https://doi.org/10.3390/sci2030056 - 04 Aug 2020
Abstract
A prime site of astrobiological interest within the Solar System is the interior ocean of Enceladus. This ocean has already been shown to contain organic molecules, and is thought to have the conditions necessary for more complex organic biomolecules to emerge and potentially [...] Read more.
A prime site of astrobiological interest within the Solar System is the interior ocean of Enceladus. This ocean has already been shown to contain organic molecules, and is thought to have the conditions necessary for more complex organic biomolecules to emerge and potentially even life itself. This sub-surface ocean has been accessed by Cassini, an unmanned spacecraft that interacted with the water plumes ejected naturally from Enceladus. The encounter speed with these plumes and their contents, was between 5 and 15 km s−1. Encounters at such speeds allow analysis of vapourised material from submicron-sized particles within the plume, but sampling micron-sized particles remains an open question. The latter particles can impact metal targets exposed on the exterior of future spacecraft, producing impact craters lined with impactor residue, which can then be analysed. Although there is considerable literature on how mineral grains behave in such high-speed impacts, and also on the relationship between the crater residue and the original grain composition, far less is known regarding the behaviour of organic particles. Here we consider a deceptively simple yet fundamental scientific question: for impacts at speeds of around 5−6 kms−1 would the impactor residue alone be sufficient to enable us to recognise the signature conferred by organic particles? Furthermore, would it be possible to identify the organic molecules involved, or at least distinguish between aromatic and aliphatic chemical structures? For polystyrene (aromatic-rich) and polymethylmethacrylate (solely aliphatic) latex particles impinging at around 5 km s−1 onto metal targets, we find that sufficient residue is retained at the impact site to permit identification of a carbon-rich projectile, but not of the particular molecules involved, nor is it currently possible to discriminate between aromatic-rich and solely aliphatic particles. This suggests that an alternative analytical method to simple impacts on metal targets is required to enable successful collection of organic samples in a fly-by Enceladus mission, or, alternatively, a lower encounter speed is required. Full article
(This article belongs to the Special Issue Molecules to Microbes)
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Open AccessArticlePost Publication Peer ReviewVersion 3, Approved
Thermodynamic Jump from Prebiotic Microsystems to Primary Living Cells
Sci 2020, 2(1), 14; https://doi.org/10.3390/sci2010014 - 13 Mar 2020
Abstract
It is proposed that the primary living cells (“probionts”) cannot emerge of organic substance simply by continuous chemical complication of prebiotic macromolecules and microsystems. The complication must be accompanied by the radical thermodynamic transformation (“jump”) of prebiotic microsystems that resulted in the acquired [...] Read more.
It is proposed that the primary living cells (“probionts”) cannot emerge of organic substance simply by continuous chemical complication of prebiotic macromolecules and microsystems. The complication must be accompanied by the radical thermodynamic transformation (“jump”) of prebiotic microsystems that resulted in the acquired ability to extract free energy from the environment and export entropy. This transformation is called “the thermodynamic inversion” The inversion may occur by means of the efficient (intensified) response of the microsystems on the oscillations of physic-chemical parameters in hydrothermal environment. In this case the surplus available free energy within a microsystem, when combined with the informational modality, facilitates its conversion into a new microsystem—a living probiont. It is shown the schematic representation of an oscillating prebiotic microsystem that is transforming into a living probiont. A new kind of laboratory and computational experiments on prebiotic chemistry under oscillating conditions is offered to verify the inversion concept. Full article
(This article belongs to the Special Issue Molecules to Microbes)
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Open AccessArticlePost Publication Peer ReviewVersion 3, Revised
On Mautner-Type Probability of Capture of Intergalactic Meteor Particles by Habitable Exoplanets
Sci 2019, 1(3), 61; https://doi.org/10.3390/sci1030061 - 19 Oct 2019
Abstract
Both macro and microprojectiles (e.g., interplanetary, interstellar and even intergalactic material) are seen as important vehicles for the exchange of potential (bio)material within our solar system as well as between stellar systems in our Galaxy. Accordingly, this requires estimates of the impact probabilities [...] Read more.
Both macro and microprojectiles (e.g., interplanetary, interstellar and even intergalactic material) are seen as important vehicles for the exchange of potential (bio)material within our solar system as well as between stellar systems in our Galaxy. Accordingly, this requires estimates of the impact probabilities for different source populations of projectiles, including for intergalactic meteor particles which have received relatively little attention since considered as rare events (discrete occurrences that are statistically improbable due to their very infrequent appearance). We employ the simple but comprehensive model of intergalactic microprojectile capture by the gravity of exoplanets which enables us to estimate the map of collisional probabilities for an available sample of exoplanets in habitable zones around host stars. The model includes a dynamical description of the capture adopted from Mautner model of interstellar exchange of microparticles and changed for our purposes. We use statistical and information metrics to calculate probability map of intergalactic meteorite particle capture. Moreover, by calculating the entropy index map we estimate the concentration of these rare events. We further adopted a model from immigration theory, to show that the time dependent distribution of single molecule immigration of material indicates high survivability of the immigrated material taking into account birth and death processes on our planet. At present immigration of material can not be observationally constrained but it seems reasonable to think that it will be possible in the near future, and to use it along other proposed parameters for life sustainability on some planet. Full article
(This article belongs to the Special Issue Molecules to Microbes)
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Open AccessArticlePost Publication Peer ReviewVersion 2, Revised
Origin of the 16S Ribosomal Molecule from Ancestor tRNAs
Sci 2019, 1(2), 46; https://doi.org/10.3390/sci1020046 - 09 Aug 2019
Cited by 1
Abstract
We tested the hypothesis that concatemers of ancestral tRNAs gave rise to the 16S ribosomal RNA. We built an ancestral sequence of proto-tRNAs that showed a significant identity of 51.69% and a percentage of structural identity of 0.941 with the 16S ribosomal molecule. [...] Read more.
We tested the hypothesis that concatemers of ancestral tRNAs gave rise to the 16S ribosomal RNA. We built an ancestral sequence of proto-tRNAs that showed a significant identity of 51.69% and a percentage of structural identity of 0.941 with the 16S ribosomal molecule. We also propose a hypothesis for the emergence of translation. Full article
(This article belongs to the Special Issue Molecules to Microbes)
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Open AccessArticlePost Publication Peer ReviewVersion 1, Original
Influence of Gravitational Shielding on Time Dilation
Sci 2019, 1(2), 45; https://doi.org/10.3390/sci1020045 - 08 Aug 2019
Abstract
This research work investigates the possibility of shielding gravity. The ultimate purpose of this work is to understand the reality behind the concept of Gravitational Shielding (GS) and time dilation. Since the 19th century, scientists have tried to arrive at an understanding of [...] Read more.
This research work investigates the possibility of shielding gravity. The ultimate purpose of this work is to understand the reality behind the concept of Gravitational Shielding (GS) and time dilation. Since the 19th century, scientists have tried to arrive at an understanding of GS via the use of various experiments. Unfortunately, some experiments failed to prove the existence of gravitational shielding, whereas some results proclaimed the possibility of attaining GS. The original phenomenon exhibited by nature cannot easily be understood, but some experiments have demonstrated that the answer may lie behind the mysterious GS. If GS is proved, then in the future, it would be possible to travel across black holes by defying gravity or through any bigger mass having high gravitational field. To unravel the mystery of GS, this work investigates the history of GS and considers the future vision of technologically advanced spacecraft or other warp drive mechanisms with appropriate gravitational shielding. Though the problem is very complex, this research work tries to come to a deeper understanding and explanation of the complexity involved in achieving gravitational shielding. Full article
(This article belongs to the Special Issue Molecules to Microbes)
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Open AccessConference ReportPost Publication Peer ReviewVersion 2, Revised
Molecules to Microbes
Sci 2020, 2(2), 20; https://doi.org/10.3390/sci2020020 - 28 Mar 2020
Abstract
How did life begin on Earth? And is there life elsewhere in the Cosmos? Challenging questions, indeed. The series of conferences established by NoR CEL in 2013, addresses these very same questions. The basis for this paper is the summary report of oral [...] Read more.
How did life begin on Earth? And is there life elsewhere in the Cosmos? Challenging questions, indeed. The series of conferences established by NoR CEL in 2013, addresses these very same questions. The basis for this paper is the summary report of oral presentations that were delivered by NoR CEL’s network members during the 2018 Athens conference and, as such, disseminates the latest research which they have put forward. More in depth material can be found by consulting the contributors referenced papers. Overall, the outcome of this conspectus on the conference demonstrates a case for the existence of “probable chemistry” during the prebiotic epoch. Full article
(This article belongs to the Special Issue Molecules to Microbes)
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Open AccessEssayPost Publication Peer ReviewVersion 3, Revised
Mechanical Energy before Chemical Energy at the Origins of Life?
Sci 2020, 2(2), 19; https://doi.org/10.3390/sci2020019 - 25 Mar 2020
Abstract
Mechanical forces and mechanical energy are prevalent in living cells. This may be because mechanical forces and mechanical energy preceded chemical energy at life’s origins. Mechanical energy is more readily available in non-living systems than the various forms of chemical energy used by [...] Read more.
Mechanical forces and mechanical energy are prevalent in living cells. This may be because mechanical forces and mechanical energy preceded chemical energy at life’s origins. Mechanical energy is more readily available in non-living systems than the various forms of chemical energy used by living systems. Two possible prebiotic environments that might have provided mechanical energy are hot pools that experience wet/dry cycles and mica sheets as they move, open and shut, as heat pumps or in response to water movements. Full article
(This article belongs to the Special Issue Molecules to Microbes)
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Open AccessHypothesisPost Publication Peer ReviewVersion 1, Original
Are Scientific Models of Life Testable? A Lesson from Simpson’s Paradox
Sci 2019, 1(2), 54; https://doi.org/10.3390/sci1020054 - 16 Sep 2019
Abstract
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Molecules to Microbes)
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