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Life, Volume 1, Issue 1 (December 2011), Pages 1-48

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Editorial

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Open AccessEditorial Origin of Life and Birth of Life ― An Open Access Journal
Life 2011, 1(1), 1-2; doi:10.3390/life1010001
Received: 19 August 2011 / Accepted: 23 August 2011 / Published: 23 August 2011
Cited by 1 | PDF Full-text (150 KB) | HTML Full-text | XML Full-text
Abstract
Our publishing company MDPI (Multidisciplinary Digital Publishing Institute) planned to launch this journal Life (ISSN 2075-1729) since June 2009. Life science as a topic covers a very broad area. We decided to focus the scope of this new journal on the origin [...] Read more.
Our publishing company MDPI (Multidisciplinary Digital Publishing Institute) planned to launch this journal Life (ISSN 2075-1729) since June 2009. Life science as a topic covers a very broad area. We decided to focus the scope of this new journal on the origin of life and the evolution of biosystems such as molecular evolution. Of course any fundamental theoretical topics and experimental discoveries in biology, biochemistry and biophysics will be welcomed also. [...] Full article
Open AccessEditorial Emergence of Life
Life 2011, 1(1), 7-8; doi:10.3390/life1010007
Received: 13 September 2011 / Accepted: 15 September 2011 / Published: 29 September 2011
Cited by 1 | PDF Full-text (146 KB) | HTML Full-text | XML Full-text
Abstract
Indeed, even if we know that many individual components are necessary for life to exist, we do not yet know what makes life emerge. One goal of this journal Life is to juxtapose articles with multidisciplinary approaches and perhaps to answer in [...] Read more.
Indeed, even if we know that many individual components are necessary for life to exist, we do not yet know what makes life emerge. One goal of this journal Life is to juxtapose articles with multidisciplinary approaches and perhaps to answer in the near future this question of the emergence of life. Different subjects and themes will be developed, starting of course with the multiple definitions of life and continuing with others such as: life diversity and universality; characteristics of living systems; thermodynamics with energy and entropy; kinetics and catalysis; water in its different physical states; circulation of sap and blood and its origin; the first blood pump and first heart; the first exchange of nutrients between cells, sap and blood; essential molecules of living systems; chirality; molecular asymmetry and its origin; formation of enantiomer excess and amplification; microscopic observations on a micrometer and sub-micrometer scales, at molecular and atomic levels; the first molecules at the origin of genetic information, viroids, circular RNA; regions of space or the area inside membranes and cells capable of initiating and maintaining life; phenomena at the origin of the emergence of life; molecules studied in the traditional field of chemistry and in the recent field of nanoscience governed by new laws; interaction between the individual molecules and components of living systems; interaction between living systems and the environment; transfer of information through generations; continuation of life from one generation to the next; prebiotic chemistry and prebiotic signatures on Earth, on Mars, on other planets; biosignatures of the first forms of life; fossils and pseudofossils dating 3.5 Ga ago and more recent ones; experimental fossilization; pluricellular eukaryotes dating 2.1 Ga ago; sudden increase in oxygen in the atmosphere around 2.0 to 2.5 Ga ago and its relation to geology; shell symmetry; aging with transformation of molecules, of their symmetry, their interactions, their exchanges. [...] Full article

Research

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Open AccessArticle DNA Movies and Panspermia
Life 2011, 1(1), 9-18; doi:10.3390/life1010009
Received: 14 September 2011 / Revised: 8 October 2011 / Accepted: 18 October 2011 / Published: 20 October 2011
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Abstract
There are several ways that our species might try to send a message to another species separated from us by space and/or time. Synthetic biology might be used to write an epitaph to our species, or simply “Kilroy was here”, in the [...] Read more.
There are several ways that our species might try to send a message to another species separated from us by space and/or time. Synthetic biology might be used to write an epitaph to our species, or simply “Kilroy was here”, in the genome of a bacterium via the patterns of either (1) the codons to exploit Life's non-equilibrium character or (2) the bases themselves to exploit Life's quasi-equilibrium character. We suggest here how DNA movies might be designed using such patterns. We also suggest that a search for mechanisms to create and preserve such patterns might lead to a better understanding of modern cells. Finally, we argue that the cutting-edge microbiology and synthetic biology needed for the Kilroy project would put origin-of-life studies in the vanguard of research. Full article
(This article belongs to the Special Issue Origin of Life - Feature Papers)
Open AccessArticle The Apparent Involvement of ANMEs in Mineral Dependent Methane Oxidation, as an Analog for Possible Martian Methanotrophy
Life 2011, 1(1), 19-33; doi:10.3390/life1010019
Received: 25 August 2011 / Revised: 14 September 2011 / Accepted: 11 November 2011 / Published: 18 November 2011
Cited by 4 | PDF Full-text (2627 KB) | HTML Full-text | XML Full-text
Abstract
On Earth, marine anaerobic methane oxidation (AOM) can be driven by the microbial reduction of sulfate, iron, and manganese. Here, we have further characterized marine sediment incubations to determine if the mineral dependent methane oxidation involves similar microorganisms to those found for [...] Read more.
On Earth, marine anaerobic methane oxidation (AOM) can be driven by the microbial reduction of sulfate, iron, and manganese. Here, we have further characterized marine sediment incubations to determine if the mineral dependent methane oxidation involves similar microorganisms to those found for sulfate-dependent methane oxidation. Through FISH and FISH-SIMS analyses using 13C and 15N labeled substrates, we find that the most active cells during manganese dependent AOM are primarily mixed and mixed-cluster aggregates of archaea and bacteria. Overall, our control experiment using sulfate showed two active bacterial clusters, two active shell aggregates, one active mixed aggregate, and an active archaeal sarcina, the last of which appeared to take up methane in the absence of a closely-associated bacterial partner. A single example of a shell aggregate appeared to be active in the manganese incubation, along with three mixed aggregates and an archaeal sarcina. These results suggest that the microorganisms (e.g., ANME-2) found active in the manganese-dependent incubations are likely capable of sulfate-dependent AOM. Similar metabolic flexibility for Martian methanotrophs would mean that the same microbial groups could inhabit a diverse set of Martian mineralogical crustal environments. The recently discovered seasonal Martian plumes of methane outgassing could be coupled to the reduction of abundant surface sulfates and extensive metal oxides, providing a feasible metabolism for present and past Mars. In an optimistic scenario Martian methanotrophy consumes much of the periodic methane released supporting on the order of 10,000 microbial cells per cm2 of Martian surface. Alternatively, most of the methane released each year could be oxidized through an abiotic process requiring biological methane oxidation to be more limited. If under this scenario, 1% of this methane flux were oxidized by biology in surface soils or in subsurface aquifers (prior to release), a total of about 1020 microbial cells could be supported through methanotrophy with the cells concentrated in regions of methane release. Full article
(This article belongs to the Special Issue Origin of Life - Feature Papers)
Open AccessArticle Approaches to the Origin of Life on Earth
Life 2011, 1(1), 34-48; doi:10.3390/life1010034
Received: 16 September 2011 / Revised: 2 November 2011 / Accepted: 9 November 2011 / Published: 18 November 2011
Cited by 15 | PDF Full-text (193 KB) | HTML Full-text | XML Full-text
Abstract
I discuss briefly the history of the origin of life field, focusing on the “Miller” era of prebiotic synthesis, through the “Orgel” era seeking enzyme free template replication of single stranded RNA or similar polynucleotides, to the RNA world era with one [...] Read more.
I discuss briefly the history of the origin of life field, focusing on the “Miller” era of prebiotic synthesis, through the “Orgel” era seeking enzyme free template replication of single stranded RNA or similar polynucleotides, to the RNA world era with one of its foci on a ribozyme with the capacity to act as a polymerase able to copy itself. I give the history of the independent invention in 1971 by T. Ganti, M. Eigen and myself of three alternative theories of the origin of molecular replication: the Chemotron, the Hypercycle, and Collectively Autocatalytic Sets, CAS, respectively. To date, only collectively autocatalytic DNA, RNA, and peptide sets have achieved molecular reproduction of polymers. Theoretical work and experimental work on CAS both support their plausibility as models of openly evolvable protocells, if housed in dividing compartments such as dividing liposomes. My own further hypothesis beyond that of CAS in themselves, of their formation as a phase transition in complex chemical reaction systems of substrates, reactions and products, where the molecules in the system are candidates to catalyze the very same reactions, now firmly established as theorems, awaits experimental proof using combinatorial chemistry to make libraries of stochastic DNA, RNA and/or polypeptides, or other classes of molecules to test the hypothesis that molecular polymer reproduction has emerged as a true phase transition in complex chemical reaction systems. I remark that my colleague Marc Ballivet of the University of Geneva and I, may have issued the first publications discussing what became combinatorial chemistry, in published issued patents in 1987, 1989 and later, in this field. Full article
(This article belongs to the Special Issue Origin of Life - Feature Papers)

Other

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Open AccessMeeting Report The Physics of Life and Quantum Complex Matter: A Case of Cross-Fertilization
Life 2011, 1(1), 3-6; doi:10.3390/life1010003
Received: 30 August 2011 / Accepted: 31 August 2011 / Published: 29 September 2011
Cited by 2 | PDF Full-text (125 KB) | HTML Full-text | XML Full-text
Abstract
Progress in the science of complexity, from the Big Bang to the coming of humankind, from chemistry and biology to geosciences and medicine, and from materials engineering to energy sciences, is leading to a shift of paradigm in the physical sciences. The [...] Read more.
Progress in the science of complexity, from the Big Bang to the coming of humankind, from chemistry and biology to geosciences and medicine, and from materials engineering to energy sciences, is leading to a shift of paradigm in the physical sciences. The focus is on the understanding of the non-equilibrium process in fine tuned systems. Quantum complex materials such as high temperature superconductors and living matter are both non-equilibrium and fine tuned systems. These topics have been subbjects of scientific discussion in the Rome Symposium on the “Quantum Physics of Living Matter”. Full article

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