http://www.mdpi.com/journal/life Latest open access articles published in Life at http://www.mdpi.com/journal/life http://www.mdpi.com/2075-1729/2/1/213 Life (ISSN 2075-1729, http://www.mdpi.com/journal/life/) is a new journal that deals with new and sometime difficult interdisciplinary matters. Consequently, the journal will occasionally be presented with submitted articles that are controversial and/or outside conventional scientific views. Some papers recently accepted for publication in Life have attracted significant attention. Moreover, members of the Editorial Board have objected to these papers; some have resigned, and others have questioned the scientific validity of the contributions. In response I want to first state some basic facts regarding all publications in this journal. All papers are peer-reviewed, although it is often difficult to obtain expert reviewers for some of the interdisciplinary topics covered by this journal. I feel obliged to stress that although we will strive to guarantee the scientific standard of the papers published in this journal, all the responsibility for the ideas contained in the published articles rests entirely on their authors. Discussions on previously published articles are welcome and I hope that, by fostering discussion and by keeping an open-minded attitude towards new ideas, the journal will spur progress in this little explored, difficult and very exciting area of knowledge. [...] http://www.mdpi.com/2075-1729/2/1/213 Fri, 03 Feb 2012 00:00:00 CET Life 2012-02-03 2 1 Editorial 213 214 2075-1729 Publication of Controversial Papers in Life 2012-02-03 doi: 10.3390/life2010213 Shu-Kun Lin http://www.mdpi.com/2075-1729/2/1/170 This problem-oriented, exploratory and hypothesis-driven discourse toward the unknown combines several basic tenets: (i) a photo-active metal sulfide scenario of primal biogenesis in the porespace of shallow sedimentary flats, in contrast to hot deep-sea hydrothermal vent conditions; (ii) an inherently complex communal system at the common root of present life forms; (iii) a high degree of internal compartmentalization at this communal root, progressively resembling coenocytic (syncytial) super-cells; (iv) a direct connection from such communal super-cells to proto-eukaryotic macro-cell organization; and (v) multiple rounds of micro-cellular escape with streamlined reductive evolution—leading to the major prokaryotic cell lines, as well as to megaviruses and other viral lineages. Hopefully, such nontraditional concepts and approaches will contribute to coherent and plausible views about the origins and early life on Earth. In particular, the coevolutionary emergence from a communal system at the common root can most naturally explain the vast discrepancy in subcellular organization between modern eukaryotes on the one hand and both archaea and bacteria on the other. http://www.mdpi.com/2075-1729/2/1/170 Mon, 23 Jan 2012 00:00:00 CET Life 2012-01-23 2 1 Essay 170 212 2075-1729 Primal Eukaryogenesis: On the Communal Nature of Precellular States, Ancestral to Modern Life 2012-01-23 doi: 10.3390/life2010170 Richard Egel http://www.mdpi.com/2075-1729/2/1/165 The on-going whole genome sequencing and whole cell assays of metabolites and proteins imply that complex systems could ultimately be mastered by perfecting knowledge into great detail. However, courses of nature are inherently intractable because flows of energy and their driving forces depend on each other. Thus no data will suffice to predict precisely the outcomes of e.g., engineering experiments. All path-dependent processes, most notably evolution in its entirety, display this capricious character of nature. http://www.mdpi.com/2075-1729/2/1/165 Wed, 11 Jan 2012 00:00:00 CET Life 2012-01-11 2 1 Communication 165 169 2075-1729 The Capricious Character of Nature 2012-01-11 doi: 10.3390/life2010165 Jaana Keto Arto Annila http://www.mdpi.com/2075-1729/2/1/135 The paper develops the Life Origination Hydrate Hypothesis (LOH-hypothesis), according to which living-matter simplest elements (LMSEs, which are N-bases, riboses, nucleosides, nucleotides), DNA- and RNA-like molecules, amino-acids, and proto-cells repeatedly originated on the basis of thermodynamically controlled, natural, and inevitable processes governed by universal physical and chemical laws from CH4, niters, and phosphates under the Earth's surface or seabed within the crystal cavities of the honeycomb methane-hydrate structure at low temperatures; the chemical processes passed slowly through all successive chemical steps in the direction that is determined by a gradual decrease in the Gibbs free energy of reacting systems. The hypothesis formulation method is based on the thermodynamic directedness of natural movement and consists ofan attempt to mentally backtrack on the progression of nature and thus reveal principal milestones alongits route. The changes in Gibbs free energy are estimated for different steps of the living-matter origination process; special attention is paid to the processes of proto-cell formation. Just the occurrence of the gas-hydrate periodic honeycomb matrix filled with LMSEs almost completely in its final state accounts for  size limitation in the DNA functional groups and the nonrandom location of N-bases in the DNA chains. The slowness of the low-temperature chemical transformations and their “thermodynamic front” guide the gross process of living matter origination and its successive steps. It is shown that the hypothesis is thermodynamically justified and testable and that many observed natural phenomena count in its favor. http://www.mdpi.com/2075-1729/2/1/135 Wed, 04 Jan 2012 00:00:00 CET Life 2012-01-04 2 1 Article 135 164 2075-1729 Life Origination Hydrate Hypothesis (LOH-Hypothesis) 2012-01-04 doi: 10.3390/life2010135 Victor Ostrovskii Elena Kadyshevich http://www.mdpi.com/2075-1729/2/1/106 Is life physicochemically unique? No. Is life unique? Yes. Life manifests innumerable formalisms that cannot be generated or explained by physicodynamics alone. Life pursues thousands of biofunctional goals, not the least of which is staying alive. Neither physicodynamics, nor evolution, pursue goals. Life is largely directed by linear digital programming and by the Prescriptive Information (PI) instantiated particularly into physicodynamically indeterminate nucleotide sequencing. Epigenomic controls only compound the sophistication of these formalisms. Life employs representationalism through the use of symbol systems. Life manifests autonomy, homeostasis far from equilibrium in the harshest of environments, positive and negative feedback mechanisms, prevention and correction of its own errors, and organization of its components into Sustained Functional Systems (SFS). Chance and necessity—heat agitation and the cause-and-effect determinism of nature’s orderliness—cannot spawn formalisms such as mathematics, language, symbol systems, coding, decoding, logic, organization (not to be confused with mere self-ordering), integration of circuits, computational success, and the pursuit of functionality. All of these characteristics of life are formal, not physical. http://www.mdpi.com/2075-1729/2/1/106 Fri, 30 Dec 2011 00:00:00 CET Life 2011-12-30 2 1 Review 106 134 2075-1729 Is Life Unique? 2011-12-30 doi: 10.3390/life2010106 David L. Abel http://www.mdpi.com/2075-1729/2/1/1 Life is an inordinately complex unsolved puzzle. Despite significant theoretical progress, experimental anomalies, paradoxes, and enigmas have revealed paradigmatic limitations. Thus, the advancement of scientific understanding requires new models that resolve fundamental problems. Here, I present a theoretical framework that economically fits evidence accumulated from examinations of life. This theory is based upon a straightforward and non-mathematical core model and proposes unique yet empirically consistent explanations for major phenomena including, but not limited to, quantum gravity, phase transitions of water, why living systems are predominantly CHNOPS (carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur), homochirality of sugars and amino acids, homeoviscous adaptation, triplet code, and DNA mutations. The theoretical framework unifies the macrocosmic and microcosmic realms, validates predicted laws of nature, and solves the puzzle of the origin and evolution of cellular life in the universe. http://www.mdpi.com/2075-1729/2/1/1 Fri, 23 Dec 2011 00:00:00 CET Life 2011-12-23 2 1 Article 1 105 2075-1729 Theory of the Origin, Evolution, and Nature of Life 2011-12-23 doi: 10.3390/life2010001 Erik D. Andrulis http://www.mdpi.com/2075-1729/1/1/34 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. http://www.mdpi.com/2075-1729/1/1/34 Fri, 18 Nov 2011 00:00:00 CET Life 2011-11-18 1 1 Article 34 48 2075-1729 Approaches to the Origin of Life on Earth 2011-11-18 doi: 10.3390/life1010034 Stuart A. Kauffman http://www.mdpi.com/2075-1729/1/1/19 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. http://www.mdpi.com/2075-1729/1/1/19 Fri, 18 Nov 2011 00:00:00 CET Life 2011-11-18 1 1 Article 19 33 2075-1729 The Apparent Involvement of ANMEs in Mineral Dependent Methane Oxidation, as an Analog for Possible Martian Methanotrophy 2011-11-18 doi: 10.3390/life1010019 Christopher H. House Emily J. Beal Victoria J. Orphan http://www.mdpi.com/2075-1729/1/1/9 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. http://www.mdpi.com/2075-1729/1/1/9 Thu, 20 Oct 2011 00:00:00 CEST Life 2011-10-20 1 1 Article 9 18 2075-1729 DNA Movies and Panspermia 2011-10-20 doi: 10.3390/life1010009 Victor Norris Yohann Grondin http://www.mdpi.com/2075-1729/1/1/7 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. [...] http://www.mdpi.com/2075-1729/1/1/7 Thu, 29 Sep 2011 00:00:00 CEST Life 2011-09-29 1 1 Editorial 7 8 2075-1729 Emergence of Life 2011-09-29 doi: 10.3390/life1010007 Marie-Paule Bassez http://www.mdpi.com/2075-1729/1/1/3 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”. http://www.mdpi.com/2075-1729/1/1/3 Thu, 29 Sep 2011 00:00:00 CEST Life 2011-09-29 1 1 Meeting Report 3 6 2075-1729 The Physics of Life and Quantum Complex Matter: A Case of Cross-Fertilization 2011-09-29 doi: 10.3390/life1010003 Nicola Poccia Antonio Bianconi http://www.mdpi.com/2075-1729/1/1/1 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. [...] http://www.mdpi.com/2075-1729/1/1/1 Tue, 23 Aug 2011 00:00:00 CEST Life 2011-08-23 1 1 Editorial 1 2 2075-1729 Origin of Life and Birth of Life ― An Open Access Journal 2011-08-23 doi: 10.3390/life1010001 Shu-Kun Lin