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Life
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From Messy Chemistry to the Origin of Life
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From Messy Chemistry to the Origin of Life

A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Origin of Life".

Deadline for manuscript submissions: closed (29 January 2021) | Viewed by 30896

Special Issue Editors

Prof. Dr. Irena Mamajanov

E-Mail Website
Guest Editor
Earth-Life Science Institute (ELSI), Tokyo Institute of Technology, 2-12-1-I7E-313 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
Interests: origin of life; prebiotic chemistry; systems chemistry; protoenzymes; functional polymers; hyperbranched polymers; chemical evolution
Dr. Tony Z. Jia

E-Mail Website
Guest Editor
Earth-Life Science Institute (ELSI), Tokyo Institute of Technology, 2-12-1-IE-32 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
Interests: origin of life; prebiotic chemistry; protocells; phase separation; compartmentalization; chemical evolution
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The origin of life is an unsolved scientific question and an area of active research. In recent years, many chemical systems with promising hints of life-like processes have been discovered. One such set of discoveries involves the ability to produce biologically relevant or precursor molecules in a wide variety of environments. Beyond the question of just producing particular precursor molecules, some studies investigate “life-like” processes in examples of functioning autocatalysis, non-enzymatic RNA replication, and biomimetic catalysis. One of the characteristics of life, as we know it, is a complex but highly organized metabolic reaction network. Such a network is markedly different from the chemistry observed in model prebiotic and abiotic chemical systems, which yields an apparently disorganized vast and complex mixture of chemical materials with an end product, often being a polymeric tar. Understanding the mechanisms of organization in these messy chemical systems, and how such systems eventually transitioned into or contributed to primitive biochemistries, is crucial to solving the question of the origin of life. This Special Issue welcomes submissions of original research papers, comprehensive reviews, and perspectives that demonstrate or summarize advances related, but not limited, to the following fields:

Experimental and computational studies of autocatalytic sets;

Information flows in complex chemical systems;

Selective chemical processes in prebiotic chemistry;

Chemical evolution in complex chemical systems;

Chemical characterization of complex chemical systems;

Advances in the analytical methodology applied to studies of complex chemical systems.

Prof. Dr. Irena Mamajanov
Dr. Tony Z. Jia
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Life is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • origin of life
  • autocatalysis
  • complex chemical systems
  • chemical evolution
  • prebiotic chemistry

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Published Papers (4 papers)

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Research

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9 pages, 765 KiB  
Article
Quantifying Mineral-Ligand Structural Similarities: Bridging the Geological World of Minerals with the Biological World of Enzymes
by Daniel Zhao, Stuart Bartlett and Yuk L. Yung
Life 2020, 10(12), 338; https://doi.org/10.3390/life10120338 - 10 Dec 2020
Cited by 11 | Viewed by 3717
Abstract
Metal compounds abundant on Early Earth are thought to play an important role in the origins of life. Certain iron-sulfur minerals for example, are proposed to have served as primitive metalloenzyme cofactors due to their ability to catalyze organic synthesis processes and facilitate [...] Read more.
Metal compounds abundant on Early Earth are thought to play an important role in the origins of life. Certain iron-sulfur minerals for example, are proposed to have served as primitive metalloenzyme cofactors due to their ability to catalyze organic synthesis processes and facilitate electron transfer reactions. An inherent difficulty with studying the catalytic potential of many metal compounds is the wide range of data and parameters to consider when searching for individual minerals and ligands of interest. Detecting mineral-ligand pairs that are structurally analogous enables more relevant selections of data to study, since structural affinity is a key indicator of comparable catalytic function. However, current structure-oriented approaches tend to be subjective and localized, and do not quantify observations or compare them with other potential targets. Here, we present a mathematical approach that compares structural similarities between various minerals and ligands using molecular similarity metrics. We use an iterative substructure search in the crystal lattice, paired with benchmark structural similarity methods. This structural comparison may be considered as a first stage in a more advanced analysis tool that will include a range of chemical and physical factors when computing mineral-ligand similarity. This approach will seek relationships between the mineral and enzyme worlds, with applications to the origins of life, ecology, catalysis, and astrobiology. Full article
(This article belongs to the Special Issue From Messy Chemistry to the Origin of Life)
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10 pages, 1268 KiB  
Article
The Messy Alkaline Formose Reaction and Its Link to Metabolism
by Arthur Omran, Cesar Menor-Salvan, Greg Springsteen and Matthew Pasek
Life 2020, 10(8), 125; https://doi.org/10.3390/life10080125 - 28 Jul 2020
Cited by 49 | Viewed by 7576
Abstract
Sugars are essential for the formation of genetic elements such as RNA and as an energy/food source. Thus, the formose reaction, which autocatalytically generates a multitude of sugars from formaldehyde, has been viewed as a potentially important prebiotic source of biomolecules at the [...] Read more.
Sugars are essential for the formation of genetic elements such as RNA and as an energy/food source. Thus, the formose reaction, which autocatalytically generates a multitude of sugars from formaldehyde, has been viewed as a potentially important prebiotic source of biomolecules at the origins of life. When analyzing our formose solutions we find that many of the chemical species are simple carboxylic acids, including α-hydroxy acids, associated with metabolism. In this work we posit that the study of the formose reaction, under alkaline conditions and moderate hydrothermal temperatures, should not be solely focused on sugars for genetic materials, but should focus on the origins of metabolism (via metabolic molecules) as well. Full article
(This article belongs to the Special Issue From Messy Chemistry to the Origin of Life)
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Review

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32 pages, 3254 KiB  
Review
Self-Reproduction and Darwinian Evolution in Autocatalytic Chemical Reaction Systems
by Sandeep Ameta, Yoshiya J. Matsubara, Nayan Chakraborty, Sandeep Krishna and Shashi Thutupalli
Life 2021, 11(4), 308; https://doi.org/10.3390/life11040308 - 1 Apr 2021
Cited by 22 | Viewed by 8807
Abstract
Understanding the emergence of life from (primitive) abiotic components has arguably been one of the deepest and yet one of the most elusive scientific questions. Notwithstanding the lack of a clear definition for a living system, it is widely argued that heredity (involving [...] Read more.
Understanding the emergence of life from (primitive) abiotic components has arguably been one of the deepest and yet one of the most elusive scientific questions. Notwithstanding the lack of a clear definition for a living system, it is widely argued that heredity (involving self-reproduction) along with compartmentalization and metabolism are key features that contrast living systems from their non-living counterparts. A minimal living system may be viewed as “a self-sustaining chemical system capable of Darwinian evolution”. It has been proposed that autocatalytic sets of chemical reactions (ACSs) could serve as a mechanism to establish chemical compositional identity, heritable self-reproduction, and evolution in a minimal chemical system. Following years of theoretical work, autocatalytic chemical systems have been constructed experimentally using a wide variety of substrates, and most studies, thus far, have focused on the demonstration of chemical self-reproduction under specific conditions. While several recent experimental studies have raised the possibility of carrying out some aspects of experimental evolution using autocatalytic reaction networks, there remain many open challenges. In this review, we start by evaluating theoretical studies of ACSs specifically with a view to establish the conditions required for such chemical systems to exhibit self-reproduction and Darwinian evolution. Then, we follow with an extensive overview of experimental ACS systems and use the theoretically established conditions to critically evaluate these empirical systems for their potential to exhibit Darwinian evolution. We identify various technical and conceptual challenges limiting experimental progress and, finally, conclude with some remarks about open questions. Full article
(This article belongs to the Special Issue From Messy Chemistry to the Origin of Life)
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22 pages, 1651 KiB  
Review
Origin of Species before Origin of Life: The Role of Speciation in Chemical Evolution
by Tony Z. Jia, Melina Caudan and Irena Mamajanov
Life 2021, 11(2), 154; https://doi.org/10.3390/life11020154 - 17 Feb 2021
Cited by 14 | Viewed by 9229
Abstract
Speciation, an evolutionary process by which new species form, is ultimately responsible for the incredible biodiversity that we observe on Earth every day. Such biodiversity is one of the critical features which contributes to the survivability of biospheres and modern life. While speciation [...] Read more.
Speciation, an evolutionary process by which new species form, is ultimately responsible for the incredible biodiversity that we observe on Earth every day. Such biodiversity is one of the critical features which contributes to the survivability of biospheres and modern life. While speciation and biodiversity have been amply studied in organismic evolution and modern life, it has not yet been applied to a great extent to understanding the evolutionary dynamics of primitive life. In particular, one unanswered question is at what point in the history of life did speciation as a phenomenon emerge in the first place. Here, we discuss the mechanisms by which speciation could have occurred before the origins of life in the context of chemical evolution. Specifically, we discuss that primitive compartments formed before the emergence of the last universal common ancestor (LUCA) could have provided a mechanism by which primitive chemical systems underwent speciation. In particular, we introduce a variety of primitive compartment structures, and associated functions, that may have plausibly been present on early Earth, followed by examples of both discriminate and indiscriminate speciation affected by primitive modes of compartmentalization. Finally, we discuss modern technologies, in particular, droplet microfluidics, that can be applied to studying speciation phenomena in the laboratory over short timescales. We hope that this discussion highlights the current areas of need in further studies on primitive speciation phenomena while simultaneously proposing directions as important areas of study to the origins of life. Full article
(This article belongs to the Special Issue From Messy Chemistry to the Origin of Life)
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