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Life, Volume 2, Issue 1 (March 2012) – 6 articles , Pages 1-214

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129 KiB

Open AccessEditorial

Publication of Controversial Papers in Life

by Shu-Kun Lin

Life 2012, 2(1), 213-214; https://doi.org/10.3390/life2010213 - 3 Feb 2012

Viewed by 21565

Abstract

Life (ISSN 2075-1729, https://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. [...] Full article

768 KiB

Open AccessEssay

Primal Eukaryogenesis: On the Communal Nature of Precellular States, Ancestral to Modern Life

by Richard Egel

Life 2012, 2(1), 170-212; https://doi.org/10.3390/life2010170 - 23 Jan 2012

Cited by 18 | Viewed by 18242

Abstract

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. Full article

(This article belongs to the Special Issue Origin of Life - Feature Papers)

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Full article ">Figure 1
Recasting the early phylogenetic tree of life. The diagram emphasizes an unbroken chain of communal evolution from photo-geochemical reactors and organic molecular ecosystems to complex eukaryotic macro-cells. From the common matrix of communal ancestor states (here conceived as syncytial-like super-cells), prokaryotic micro-cells and acellular viral lineages "escaped" multiple times, as based on partly overlapping sampling of unified genomes from a highly redundant communal gene pool and subsequent clonal propagation. The primal dichotomy between bacterial and archaeal/protoeukaryotic stemlines occurred at the level of communal ancestors. All the composite modern eukaryotes descend from an ancestor that had already adopted some fairly advanced bacteria as permanently integrated mitochondrial endosymbionts. Similarly, cyanobacterial endosymbionts were acquired as plastids by the diverging lineage of green plants. Full article ">Figure 2
Porespace and mineral-facilitated biogenesis. In the multiply connected porespace between sedimented mineral grains (left panel), water can flow in various directions. Confluent layers of biogenic organic hydrogels (right panel, green) accumulate and progressively cover much of the mineral surface, whilst water can still move back and forth through most channels in the porespace network. The organic matrix does not only spread by incremental growth, but also by turbulent currents that redistribute the upper layers of the sediment. This diagram emphasizes the connectivity throughout a contiguous porespace. It does not, however, represent the nanoscale roughness and heterogeneity of the catalytically important mineral grains. Full article ">Figure 3
Photochemical charge separation, coupled to redox reactions. In a colloidal MeS particle (center), absorption of a UVB photon mobilizes an electron (e-) of the crystalline lattice into the energetic conductance band (CB). This leaves a complementary void in the lattice, which is conductable, too, as a hole (h+) in the valence band (VB). Both these 'bands' represent different levels on an energy scale. Upon reaching the particle surface, e- and h+ can initiate reductive and oxidative biochemical reaction pathways, respectively. Figure modified from Refs. [<a href="#B9-life-02-00170" class="html-bibr">9</a>,<a href="#B82-life-02-00170" class="html-bibr">82</a>]. Full article ">Figure 4
Tentative transition of energized electron transfer from mineral grains to membrane assemblages. (a) Peptide-rich micellar patches (pink), together with a rudimentary electron transfer chain, can have assembled at the substratum surface, between the precellular organic matrix (light green) and a larger external photoactive particle (grey), or in close contact with colloidal grains inside. (b) Fully enclosing such colloidal particles in membrane-bounded vesicles could render charge separation more effective. (c) Incorporating organic pigments (green) in the peptide-rich reaction centers could shift the effective bandwidth into the visible part of the sunlight spectrum. Full article ">

171 KiB

Open AccessCommunication

The Capricious Character of Nature

by Jaana Keto and Arto Annila

Life 2012, 2(1), 165-169; https://doi.org/10.3390/life2010165 - 11 Jan 2012

Cited by 3 | Viewed by 6275

Abstract

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. Full article

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623 KiB

Open AccessArticle

Life Origination Hydrate Hypothesis (LOH-Hypothesis)

by Victor Ostrovskii and Elena Kadyshevich

Life 2012, 2(1), 135-164; https://doi.org/10.3390/life2010135 - 4 Jan 2012

Cited by 5 | Viewed by 8963

Abstract

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. Full article

(This article belongs to the Special Issue Origin of Life - Feature Papers)

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454 KiB

Open AccessReview

Is Life Unique?

by David L. Abel

Life 2012, 2(1), 106-134; https://doi.org/10.3390/life2010106 - 30 Dec 2011

Cited by 14 | Viewed by 21947

Abstract

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. Full article

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1937 KiB

Open AccessArticle

Theory of the Origin, Evolution, and Nature of Life

by Erik D. Andrulis

Life 2012, 2(1), 1-105; https://doi.org/10.3390/life2010001 - 23 Dec 2011

Cited by 12 | Viewed by 116877

Abstract

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. Full article

(This article belongs to the Special Issue Origin of Life - Feature Papers)

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