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Dual Role of Hydrophobic Racemic Thioesters of alpha-Amino Acids in the Generation of Isotactic Peptides and Co-peptides in Water; Implications for the Origin of Homochirality.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Thioesters of alpha-amino acids are considered as plausible monomers for the generation of the primeval peptides. DL-Leucine-thioethyl esters (LeuSEt), where the L-enantiomer was tagged with deuterium atoms, undergo polycondensation in water or in bicarbonate or imidazole buffer solutions to yield mainly heterochiral (atactic) peptides and diketopiperazine, as analyzed by MALDI-TOF and ESI mass-spectrometry. In variance, when polymerization of DL(d(10))-Leu, first activated with N,N'-carbonyldiimidazole, then initiated with ethanethiol or with DL(d(3))-LeuSEt yielded a library of peptides up to 30 detectable residues w...
Source: Origins of Life and Evolution of the Biosphere - November 13, 2009 Category: Molecular Biology Authors: Illos RA, Clodic G, Bolbach G, Weissbuch I, Lahav M Tags: Orig Life Evol Biosph Source Type: journals

Amplification of Chirality at Solid Surfaces.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Symmetry-breaking phenomena in two-dimensional crystallization at surfaces are reviewed and the potential impact to chiral amplification in three-dimensional systems in connection with the origin of homochirality in the biomolecular world is discussed. Adsorption of prochiral molecules leads to two-dimensional conglomerates, i.e., on a local scale spontaneously to homochiral crystal structures. Small enantiomeric excess or chiral impurities in this environment install homochirality on a global scale, that is, on the entire surface. PMID: 19911299 [PubMed - as supplied by publisher] (Source: Origins of Life and Evol...
Source: Origins of Life and Evolution of the Biosphere - November 13, 2009 Category: Molecular Biology Authors: Ernst KH Tags: Orig Life Evol Biosph Source Type: journals

Asymmetric Autocatalysis Induced by Chiral Crystals of Achiral Tetraphenylethylenes.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The achiral hydrocarbon tetraphenylethylene crystallizes in enantiomorphous forms (chiral space group: P2(1)) to afford right- and left-handed hemihedral crystals, which can be recognized by solid-state circular dichroism spectroscopic analysis. Chiral organic crystals of tetraphenylethylene mediated enantioselective addition of diisopropylzinc to pyrimidine-5-carbaldehyde to give, in conjunction with asymmetric autocatalysis with amplification of chirality, almost enantiomerically pure (S)- and (R)-5-pyrimidyl alkanols whose absolute configurations were controlled efficiently by the crystalline chirality of the tetrap...
Source: Origins of Life and Evolution of the Biosphere - November 13, 2009 Category: Molecular Biology Authors: Kawasaki T, Nakaoda M, Kaito N, Sasagawa T, Soai K Tags: Orig Life Evol Biosph Source Type: journals

Homochirality and the Need for Energy.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The mechanisms for explaining how a stable asymmetric chemical system can be formed from a symmetric chemical system, in the absence of any asymmetric influence other than statistical fluctuations, have been developed during the last decades, focusing on the non-linear kinetic aspects. Besides the absolute necessity of self-amplification processes, the importance of energetic aspects is often underestimated. Going down to the most fundamental aspects, the distinction between a single object-that can be intrinsically asymmetric-and a collection of objects-whose racemic state is the more stable one-must be emphasized. A ...
Source: Origins of Life and Evolution of the Biosphere - November 13, 2009 Category: Molecular Biology Authors: Plasson R, Brandenburg A Tags: Orig Life Evol Biosph Source Type: journals

Homochirality in Life: Two Equal Runners, One Tripped.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Strong arguments can be found in the literature addressed to the question of the origin of homochirality in life, supporting the hypothesis that primordial life could have evolved in both homochiral forms and that early on when life was still rarely found, random events led to the survival of only one of these living mirror images. This proposal is an alternative to the generally accepted view that small enantiomeric excesses of biologically important molecules were amplified to homochirality prior to life's origin. Acceptance of the possibility of "two equal runners" leads to the importance of research investigations ...
Source: Origins of Life and Evolution of the Biosphere - November 13, 2009 Category: Molecular Biology Authors: Green MM, Jain V Tags: Orig Life Evol Biosph Source Type: journals

Imitating Prebiotic Homochirality on Earth.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We show how the amino acids needed on prebiotic earth in their homochiral L form can be produced by a reaction of L-alpha-methyl amino acids-that have been identified in the Murchison meteorite-with alpha-keto acids under credible prebiotic conditions. When they are simply heated together they perform a process of decarboxylative transamination but with almost no chiral transfer, and that in the wrong direction, producing D-amino acids from the L-alpha-methyl amino acids. With copper ion a square planar complex with two of the reaction intermediates is formed, and now there is the desired L to L transformation, produci...
Source: Origins of Life and Evolution of the Biosphere - November 13, 2009 Category: Molecular Biology Authors: Breslow R, Levine M, Cheng ZL Tags: Orig Life Evol Biosph Source Type: journals

Spontaneous Mirror Symmetry Breaking in the Aldol Reaction and its Potential Relevance in Prebiotic Chemistry.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The origin of the single chirality of most biomolecules is still a great puzzle. Carbohydrates could form in the formose reaction, which is proposed to be autocatalytic and contains aldol reaction steps. Based on our earlier observation of organoautocatalysis and spontaneous enantioenrichment in absence of deliberate chiral influences in the aldol reaction of acetone and p-nitrobenzaldehyde we suggest that a similar effect might be present also in the aldol reactions involved in gluconeogenesis. Herein we show that reactant precipitation observed in our earlier reported experiments does not affect the asymmetric autoca...
Source: Origins of Life and Evolution of the Biosphere - November 13, 2009 Category: Molecular Biology Authors: Mauksch M, Wei S, Freund M, Zamfir A, Tsogoeva SB Tags: Orig Life Evol Biosph Source Type: journals

Stereoselective Syntheses of Pentose Sugars Under Realistic Prebiotic Conditions.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Glycolaldehyde and DL: -glyceraldehyde reacted in a water-buffered solution under mildly acidic conditions and in the presence of chiral dipeptide catalysts produced pentose sugars whose configuration is affected by the chirality of the catalyst. The chiral effect was found to vary between catalysts and to be largest for di-valine. Lyxose, arabinose, ribose and xylose are formed in different amounts, whose relative proportions do not change significantly with the varying of conditions. With LL: -peptide catalysts, ribose was the only pentose sugar to have a significant D: -enantiomeric excess (ee) (</=44%), lyxose d...
Source: Origins of Life and Evolution of the Biosphere - November 10, 2009 Category: Molecular Biology Authors: Pizzarello S, Weber AL Tags: Orig Life Evol Biosph Source Type: journals

Erratum to: Origins of Life and Evolution of Biospheres.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
PMID: 19898951 [PubMed - as supplied by publisher] (Source: Origins of Life and Evolution of the Biosphere)
Source: Origins of Life and Evolution of the Biosphere - November 7, 2009 Category: Molecular Biology Authors: Macdermott AJ Tags: Orig Life Evol Biosph Source Type: journals

On the Emergence of Biochemical Homochirality: An Elusive Beginning.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
PMID: 19890734 [PubMed - as supplied by publisher] (Source: Origins of Life and Evolution of the Biosphere)
Source: Origins of Life and Evolution of the Biosphere - November 6, 2009 Category: Molecular Biology Authors: Pizzarello S, Lahav M Tags: Orig Life Evol Biosph Source Type: journals

Life Began When Evolution Began: A Lipidic Vesicle-Based Scenario.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The research on the origin of life, as such, seems to have reached an impasse as a clear and universal scientific definition of life is probably impossible. On the contrary, the research on the origin of evolution may provide a clue. But it is necessary to identify the minimum requirements that allowed evolution to emerge on early Earth. The classical approach, the 'RNA world hypothesis' is one way, but an alternative based on nonlinear dynamics dealing with far-from-equilibrium self-organization and dissipative structures can also be proposed. The conditions on early Earth, near deep-sea hydrothermal sites, were favor...
Source: Origins of Life and Evolution of the Biosphere - October 14, 2009 Category: Molecular Biology Authors: Tessera M Tags: Orig Life Evol Biosph Source Type: journals

Editorial note--Darwin and the origin of life.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
PMID: 19760521 [PubMed - in process] (Source: Origins of Life and Evolution of the Biosphere)
Source: Origins of Life and Evolution of the Biosphere - September 20, 2009 Category: Molecular Biology Authors: Schwartz AW Tags: Orig Life Evol Biosph Source Type: journals

Special issue: abstracts from the 2008 issol meeting.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Authors: PMID: 19468860 [PubMed - in process] (Source: Origins of Life and Evolution of the Biosphere)
Source: Origins of Life and Evolution of the Biosphere - June 12, 2009 Category: Molecular Biology Tags: Orig Life Evol Biosph Source Type: journals

Simple Formation of an Abiotic Porphyrinogen in Aqueous Solution.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Porphyrins have long been proposed as key ingredients in the emergence of life yet plausible routes for forming their essential pyrrole precursor have heretofore not been identified. Here we show that the anaerobic reaction of delta-aminolevulinic acid (ALA, 1-5 mM) with the beta-ketoester methyl 4-methoxyacetoacetate (2-40 mM) in water (pH 5-7) at 70-100 degrees C for >6 h affords the porphyrinogen, which upon chemical oxidation gives the corresponding porphyrin in overall yield of up to 10%. The key intermediate is the alpha-methoxymethyl-substituted pyrrole, which undergoes tetramerization and macrocycle formatio...
Source: Origins of Life and Evolution of the Biosphere - May 27, 2009 Category: Molecular Biology Authors: Lindsey JS, Ptaszek M, Taniguchi M Tags: Orig Life Evol Biosph Source Type: journals

A Specific Scenario for the Origin of Life and the Genetic Code Based on Peptide/Oligonucleotide Interdependence.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Among various scenarios that attempt to explain how life arose, the RNA world is currently the most widely accepted scientific hypothesis among biologists. However, the RNA world is logistically implausible and doesn't explain how translation arose and DNA became incorporated into living systems. Here I propose an alternative hypothesis for life's origin based on cooperation between simple nucleic acids, peptides and lipids. Organic matter that accumulated on the prebiotic Earth segregated into phases in the ocean based on density and solubility. Synthesis of complex organic monomers and polymerization reactions occurr...
Source: Origins of Life and Evolution of the Biosphere - May 26, 2009 Category: Molecular Biology Authors: Griffith RW Tags: Orig Life Evol Biosph Source Type: journals

Survival of Akinetes (Resting-State Cells of Cyanobacteria) in Low Earth Orbit and Simulated Extraterrestrial Conditions.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Cyanobacteria are photosynthetic organisms that have been considered for space applications, such as oxygen production in bioregenerative life support systems, and can be used as a model organism for understanding microbial survival in space. Akinetes are resting-state cells of cyanobacteria that are produced by certain genera of heterocystous cyanobacteria to survive extreme environmental conditions. Although they are similar in nature to endospores, there have been no investigations into the survival of akinetes in extraterrestrial environments. The aim of this work was to examine the survival of akinetes from Anabae...
Source: Origins of Life and Evolution of the Biosphere - April 22, 2009 Category: Molecular Biology Authors: Olsson-Francis K, de la Torre R, Towner MC, Cockell CS Tags: Orig Life Evol Biosph Source Type: journals

Toward Homochiral Protocells in Noncatalytic Peptide Systems.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The activation-polymerization-epimerization-depolymerization (APED) model of Plasson et al. has recently been proposed as a mechanism for the evolution of homochirality on prebiotic Earth. The dynamics of the APED model in two-dimensional spatially-extended systems is investigated for various realistic reaction parameters. It is found that the APED system allows for the formation of isolated homochiral proto-domains surrounded by a racemate. A diffusive slowdown of the APED network induced, for example, through tidal motion or evaporating pools and lagoons leads to the stabilization of homochiral bounded structures as ...
Source: Origins of Life and Evolution of the Biosphere - April 16, 2009 Category: Molecular Biology Authors: Gleiser M, Walker SI Tags: Orig Life Evol Biosph Source Type: journals

Parity-Violating Energy Shifts of Murchison L-Amino Acids are Consistent with an Electroweak Origin of Meteorite L-Enantiomeric Excesses.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In 1996, four alpha-methyl amino acids in the Murchison meteorite-L-isovaline, L-alpha-methylnorvaline, L-alpha-methyl-allo-isoleucine and L-alpha-methyl-isoleucine-were found to show significant enantiomeric excesses of the L form, ranging from 2% to 9%. Their deuterium to hydrogen isotope ratios suggest they formed in the pre-solar interstellar gas cloud rather than during a later aqueous processing phase on the asteroid parent body. In this paper we apply the techniques of the preceding two papers to compute the parity-violating energy shifts of these amino acids. We find that, in the gas phase, the PVESs of the neu...
Source: Origins of Life and Evolution of the Biosphere - March 24, 2009 Category: Molecular Biology Authors: Macdermott AJ, Fu T, Nakatsuka R, Coleman AP, Hyde GO Tags: Orig Life Evol Biosph Source Type: journals

Self-Propagating beta-Sheet Polypeptide Structures as Prebiotic Informational Molecular Entities: The Amyloid World.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The idea is advanced that under the extreme earth conditions for ~3.9 billions years ago, protein-based beta-sheet molecular structures were the first self-propagating and information-processing biomolecules that evolved. The amyloid structure of these aggregates provided an effective protection against the harsh conditions known to decompose both polyribonucleotides and natively folded polypeptides. In the prebiotic amyloid world, both the replicative and informational functions were carried out by structurally stable beta-sheet protein aggregates in a prion-like mode involving templated self-propagation and storage o...
Source: Origins of Life and Evolution of the Biosphere - March 20, 2009 Category: Molecular Biology Authors: Maury CP Tags: Orig Life Evol Biosph Source Type: journals

Electroweak Parity-Violating Energy Shifts of Amino Acids: The "Conformation Problem"Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We present new computations of gas-phase amino acids PVESs, using partial optimizations with small basis sets, and the results agree well with those from higher level techniques. In the following paper we apply these less costly techniques to larger amino acids. The "conformation problem" has led some to dismiss the PVES as the source of life's handedness, but we believe this is premature: we show here that amino acids are a special case because their favoured conformations are almost achiral. PMID: 19291419 [PubMed - as supplied by publisher] (Source: Origins of Life and Evolution of the Biosphere)
Source: Origins of Life and Evolution of the Biosphere - March 17, 2009 Category: Molecular Biology Authors: Macdermott AJ, Fu T, Hyde GO, Nakatsuka R, Coleman AP Tags: Orig Life Evol Biosph Source Type: journals

Evaluation of Coupled Perturbed and Density Functional Methods of Computing the Parity-Violating Energy Difference between Enantiomers.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We present new coupled-perturbed Hartree-Fock (CPHF) and density functional theory (DFT) computations of the parity-violating energy difference (PVED) between enantiomers for H(2)O(2) and H(2)S(2). Our DFT PVED computations are the first for H(2)S(2) and the first with the new HCTH and OLYP functionals. Like other "second generation" PVED computations, our results are an order of magnitude larger than the original "first generation" uncoupled-perturbed Hartree-Fock computations of Mason and Tranter. We offer an explanation for the dramatically larger size in terms of cancellation of contributions of opposing signs, which a...
Source: Origins of Life and Evolution of the Biosphere - March 17, 2009 Category: Molecular Biology Authors: Macdermott AJ, Hyde GO, Cohen AJ Tags: Orig Life Evol Biosph Source Type: journals

Energy Transduction Inside of Amphiphilic Vesicles: Encapsulation of Photochemically Active Semiconducting Particles.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Amphiphilic bilayer membrane structures (vesicles) have been postulated to have been abiotically formed and spontaneously assemble on the prebiotic Earth, providing compartmentalization for the origin of life. These vesicles are similar to modern cellular membranes and can serve to contain water-soluble species, concentrate species, and have the potential to catalyze reactions. The origin of the use of photochemical energy in metabolism (i.e. energy transduction) is one of the central issues in the origin of life. This includes such questions as how energy transduction may have occurred before complex enzymatic systems...
Source: Origins of Life and Evolution of the Biosphere - March 4, 2009 Category: Molecular Biology Authors: Summers DP, Noveron J, Basa RC Tags: Orig Life Evol Biosph Source Type: journals

Special Issue: Abstracts from the Eighth European Workshop on Astrobiology, Neuchâtel, Switzerland, 1-3 September, 2008.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Special Issue: Abstracts from the Eighth European Workshop on Astrobiology, Neuchâtel, Switzerland, 1-3 September, 2008. Orig Life Evol Biosph. 2009 Jan 31; Authors: PMID: 19184520 [PubMed - as supplied by publisher] (Source: Origins of Life and Evolution of the Biosphere)
Source: Origins of Life and Evolution of the Biosphere - January 31, 2009 Category: Molecular Biology Tags: Orig Life Evol Biosph Source Type: journals

Metabolic Constraints on the Eukaryotic Transition.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Mutualism, obligate mutualism, symbiosis, and the eukaryotic 'fusion' of Serial Endosymbiosis Theory represent progressively more rapid and less distorted real-time communication between biological structures instantiating information sources. Such progression in accurate information transmission requires, in turn, progressively greater channel capacity that, through the homology between information source uncertainty and free energy density, requires ever more energetic metabolism. The eukaryotic transition, according to this model, may have been entrained by an ecosystem resilience shift from anaerobic to aerobic met...
Source: Origins of Life and Evolution of the Biosphere - January 21, 2009 Category: Molecular Biology Authors: Wallace R Tags: Orig Life Evol Biosph Source Type: journals

A Possible Evolutionary Origin for the Mn(4) Cluster in Photosystem II: From Manganese Superoxide Dismutase to Oxygen Evolving Complex.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The recently published X-ray absorption fine structure of photosystem II provides a more detailed architecture of the oxygen-evolving complex (OEC) and the surrounding amino acids. In this paper, a comparison between manganese superoxide dismutase, dinuclear manganese catalase enzymes and the oxygen evolving complex in photosystem II is reported. The author suggests that the development of oxygenic photosynthesis occurred in steps, the first of which involved only one manganese ion (Mn(II)) that oxidized two water molecules to hydrogen peroxide and then oxygen. PMID: 19148771 [PubMed - as supplied by publisher] (So...
Source: Origins of Life and Evolution of the Biosphere - January 16, 2009 Category: Molecular Biology Authors: Najafpour MM Tags: Orig Life Evol Biosph Source Type: journals

An Evaluation of the Critical Parameters for Abiotic Peptide Synthesis in Submarine Hydrothermal Systems.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
It has been proposed that oligopeptides may be formed in submarine hydrothermal systems (SHSs). Oligopeptides have been synthesized previously under simulated SHS conditions which are likely geochemically implausible. We have herein investigated the oligomerization of glycine under SHS-like conditions with respect to the limitations imposed by starting amino acid concentration, heating time, and temperature. When 10(-1) M glycine solutions were heated at 250 degrees C for < 20 min glycine oligomers up to tetramers and diketopiperazine (DKP) were detectable. At 200 degrees C, less oligomerization was noted. Peptides ...
Source: Origins of Life and Evolution of the Biosphere - November 27, 2008 Category: Molecular Biology Authors: Cleaves HJ, Aubrey AD, Bada JL Tags: Orig Life Evol Biosph Source Type: journals

The Role of Submarine Hydrothermal Systems in the Synthesis of Amino Acids.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We report here the results of experiments exploring the potential for amino acid synthesis at high temperature from synthetic seawater solutions of varying composition. The synthesis of amino acids was examined as a function of temperature, heating time, starting material composition and concentration. Using very favorable reactant conditions (high concentrations of reactive, reduced species), small amounts of a limited set of amino acids are generated at moderate temperature conditions ( approximately 125-175 degrees C) over short heating times of a few days, but even these products are significantly decomposed after expo...
Source: Origins of Life and Evolution of the Biosphere - November 26, 2008 Category: Molecular Biology Authors: Aubrey AD, Cleaves HJ, Bada JL Tags: Orig Life Evol Biosph Source Type: journals

Prebiotic Synthesis of Simple Sugars by an Interstellar Formose Reaction.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The prebiotic possibilities for the synthesis of interstellar carbohydrates through a protic variant of the formose reaction under gas phase conditions were studied. Ab initio calculations were used to evaluate potential mechanisms. Based on considerations of barrier heights and temperature variations in the Interstellar Medium the plausibility of extended sugar synthesis will be discussed. PMID: 18998238 [PubMed - as supplied by publisher] (Source: Origins of Life and Evolution of the Biosphere)
Source: Origins of Life and Evolution of the Biosphere - November 8, 2008 Category: Molecular Biology Authors: Jalbout AF Tags: Orig Life Evol Biosph Source Type: journals

Results of the Second Stage of the Investigation of the Radiation Mechanism of Chiral Influence (RAMBAS-2 Experiment).Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Results of the second stage of the RAMBAS (RAdiation Mechanism of Biomolecular ASymmetry) experiment on investigation of the radiation mechanism of the influence on chiral molecules are presented. Optical activity of samples of racemic mixtures of amino acids with heavy metals was compared prior to and after irradiation by electron flux from a radioactive source. It is found that the irradiation results in asymmetric degradation of both complexes and amino acids and in production of chiral asymmetry of the samples under study. These results confirm the conclusions inferred from the first stage of the RAMBAS experiment ...
Source: Origins of Life and Evolution of the Biosphere - November 1, 2008 Category: Molecular Biology Authors: Gusev GA, Kobayashi K, Moiseenko EV, Poluhina NG, Saito T, Ye T, Tsarev VA, Xu J, Huang Y, Zhang G Tags: Orig Life Evol Biosph Source Type: journals

Which Amino Acids Should Be Used in Prebiotic Chemistry Studies?Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The adsorption of amino acids on minerals and their condensation under conditions that resemble those of prebiotic earth is a well studied subject. However, which amino acids should be used in these experiments is still an open question. The main goal of this review is to attempt to answer this question. There were two sources of amino acids for the prebiotic earth: (1) exogenous-meaning that the amino acids were synthesized outside the earth and delivered to our planet by interplanetary dust particles (IDPs), meteorites, comets, etc. and (2) endogenous-meaning that they were synthesized on earth in atmospheric mixture...
Source: Origins of Life and Evolution of the Biosphere - October 17, 2008 Category: Molecular Biology Authors: Zaia DA, Zaia CT, De Santana H Tags: Orig Life Evol Biosph Source Type: journals

Astrobiological Phase Transition: Towards Resolution of Fermi's Paradox.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Can astrophysics explain Fermi's paradox or the "Great Silence" problem? If available, such explanation would be advantageous over most of those suggested in literature which rely on unverifiable cultural and/or sociological assumptions. We suggest, instead, a general astrobiological paradigm which might offer a physical and empirically testable paradox resolution. Based on the idea of James Annis, we develop a model of an astrobiological phase transition of the Milky Way, based on the concept of the global regulation mechanism(s). The dominant regulation mechanisms, arguably, are gamma-ray bursts, whose properties and...
Source: Origins of Life and Evolution of the Biosphere - October 15, 2008 Category: Molecular Biology Authors: Cirković MM, Vukotić B Tags: Orig Life Evol Biosph Source Type: journals

The Most Conserved Genome Segments for Life Detection on Earth and Other Planets.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We present here a computational comparison of full genomes from 13 diverse organisms from the Archaea, Bacteria, and Eucarya to identify genetic sequences conserved across the widest divisions of life. Our results identify the 16S and 23S ribosomal RNA genes as well as other universally conserved nucleotide sequences in genes encoding particular classes of transfer RNAs and within the nucleotide binding domains of ABC transporters as the most conserved DNA sequence segments across phylogeny. This set of sequences defines a core set of DNA regions that have changed the least over billions of years of evolution and provides ...
Source: Origins of Life and Evolution of the Biosphere - October 14, 2008 Category: Molecular Biology Authors: Isenbarger TA, Carr CE, Johnson SS, Finney M, Church GM, Gilbert W, Zuber MT, Ruvkun G Tags: Orig Life Evol Biosph Source Type: journals

Punctuated Chirality.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Most biomolecules occur in mirror, or chiral, images of each other. However, life is homochiral: proteins contain almost exclusively L-amino acids, while only D-sugars appear in RNA and DNA. The mechanism behind this fundamental asymmetry of life remains an open problem. Coupling the spatiotemporal evolution of a general autocatalytic polymerization reaction network to external environmental effects, we show through a detailed statistical analysis that high intensity and long duration events may drive achiral initial conditions towards chirality. We argue that life's homochirality resulted from sequential chiral symmet...
Source: Origins of Life and Evolution of the Biosphere - October 8, 2008 Category: Molecular Biology Authors: Gleiser M, Thorarinson J, Walker SI Tags: Orig Life Evol Biosph Source Type: journals

On the Spectrum of Prebiotic Chemical Systems : An Information Theory Treatment of Eigen's Paradox.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We reexamine Eigen's paradox using the asymptotic limit theorems of information theory. Applying the homology between information source uncertainty and free energy density, under rate distortion constraints, the error catastrophe emerges as the lowest energy state for simple prebiotic systems without error correction. Invoking the usual compartmentalization - i.e., 'vesicles' - and using a Red Queen argument, suggests that information crosstalk between two or more properly interacting structures can initiate a coevolutionary dynamic having at least two quasi-stable states. The first is a low energy realm near the erro...
Source: Origins of Life and Evolution of the Biosphere - September 6, 2008 Category: Molecular Biology Authors: Wallace R, Wallace RG Tags: Orig Life Evol Biosph Source Type: journals

Stanley L. Miller (1930-2007): Reflections and Remembrances.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
An appreciation of Stanley L. Miller, the pioneer prebiotic chemist, who died last year. PMID: 18726708 [PubMed - as supplied by publisher] (Source: Origins of Life and Evolution of the Biosphere)
Source: Origins of Life and Evolution of the Biosphere - August 26, 2008 Category: Molecular Biology Authors: Lazcano A, Bada JL Tags: Orig Life Evol Biosph Source Type: journals

Compositional Inheritance: Comparison of Self-assembly and Catalysis.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Genetic inheritance in modern cells is due to template-directed replication of nucleic acids. However, the difficulty of prebiotic synthesis of long information-carrying polymers like RNA raises the question of whether some other form of heredity is possible without polymers. As an alternative, the lipid world theory has been proposed, which considers non-covalent assemblies of lipids, such as micelles and vesicles. Assemblies store information in the form of a non-random molecular composition, and this information is passed on when the assemblies divide, i.e. the assemblies show compositional inheritance. Here, we var...
Source: Origins of Life and Evolution of the Biosphere - July 18, 2008 Category: Molecular Biology Authors: Wu M, Higgs PG Tags: Orig Life Evol Biosph Source Type: journals

Sugar-Driven Prebiotic Synthesis of 3,5(6)-Dimethylpyrazin-2-one: A Possible Nucleobase of a Primitive Replication Process.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Reaction of glyceraldehyde with alanine amide (or ammonia) under anaerobic aqueous conditions yielded 3,5(6)-dimethylpyrazin-2-one that is considered a possible complementary residue of a primitive replicating molecule that preceded RNA. Synthesis of the dimethylpyrazin-2-one isomers under mild aqueous conditions (65 degrees C, pH 5.5) from 100 mM glyceraldehyde and alanine amide (or ammonia) was complete in about 5 days. This synthesis using 25 mM glyceraldehyde and alanine amide gave a total pyrazinone yield of 9.3% consisting of 42% of the 3,5-dimethylprazin-2-one isomer and 58% of the 3,6-dimethylpyrazin-2-one isom...
Source: Origins of Life and Evolution of the Biosphere - June 26, 2008 Category: Molecular Biology Authors: Weber AL Tags: Orig Life Evol Biosph Source Type: journals

Thermodynamic Potential for the Abiotic Synthesis of Adenine, Cytosine, Guanine, Thymine, Uracil, Ribose, and Deoxyribose in Hydrothermal Systems.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The thermodynamic potential for the abiotic synthesis of the five common nucleobases (adenine, cytosine, guanine, thymine, and uracil) and two monosaccharides (ribose and deoxyribose) from formaldehyde and hydrogen cyanide has been quantified under temperature, pressure, and bulk composition conditions that are representative of hydrothermal systems. The activities of the precursor molecules (formaldehyde and hydrogen cyanide) required to evaluate the thermodynamics of biomolecule synthesis were computed using the concentrations of aqueous N(2), CO, CO(2) and H(2) reported in the modern Rainbow hydrothermal system. The...
Source: Origins of Life and Evolution of the Biosphere - June 24, 2008 Category: Molecular Biology Authors: Larowe DE, Regnier P Tags: Orig Life Evol Biosph Source Type: journals

Habitability of Enceladus: Planetary Conditions for Life.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The prolific activity and presence of a plume on Saturn's tiny moon Enceladus offers us a unique opportunity to sample the interior composition of an icy satellite, and to look for interesting chemistry and possible signs of life. Based on studies of the potential habitability of Jupiter's moon Europa, icy satellite oceans can be habitable if they are chemically mixed with the overlying ice shell on Myr time scales. We hypothesize that Enceladus' plume, tectonic processes, and possible liquid water ocean may create a complete and sustainable geochemical cycle that may allow it to support life. We discuss evidence for s...
Source: Origins of Life and Evolution of the Biosphere - June 20, 2008 Category: Molecular Biology Authors: Parkinson CD, Liang MC, Yung YL, Kirschivnk JL Tags: Orig Life Evol Biosph Source Type: journals

Stability of Model Membranes in Extreme Environments.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The first forms of cellular life required a source of amphiphilic compounds capable of assembling into stable boundary structures. Membranes composed of fatty acids have been proposed as model systems of primitive membranes, but their bilayer structure is stable only within a narrow pH range and low ionic strength. They are particularly sensitive to aggregating effects of divalent cations (Mg(+2), Ca(+2), Fe(+2)) that would be present in Archaean sea water. Here we report that mixtures of alkyl amines and fatty acids form vesicles at strongly basic and acidic pH ranges which are resistant to the effects of divalent cat...
Source: Origins of Life and Evolution of the Biosphere - June 17, 2008 Category: Molecular Biology Authors: Namani T, Deamer DW Tags: Orig Life Evol Biosph Source Type: journals

Life at the Limits: Capacities of Isolated and Cultured Lichen Symbionts to Resist Extreme Environmental Stresses.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Lichens are described as a symbiosis formed by a myco- and photobiont, capable of colonizing habitats where their separate symbionts would not be able to survive. Space simulation studies on the separated symbionts of the lichen Xanthoria elegans have been performed to test their capacity to resist the most extreme conditions. The isolated cultured symbiont cells were exposed to different doses of the UV spectrum, and to vacuum. Cultures of both symbionts were analysed by specific vitality tests (LIVE/DEAD-staining detected by Confocal Laser Scanning Microscopy). Growth capacity of symbiont cultures on different media ...
Source: Origins of Life and Evolution of the Biosphere - June 4, 2008 Category: Molecular Biology Authors: de Vera JP, Rettberg P, Ott S Tags: Orig Life Evol Biosph Source Type: journals

Early Stages of the Evolution of Life: a Cybernetic Approach.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Early stages of the evolution of life are considered in terms of control theory. A model is proposed for the transport of substances in a protocell possessing the property of robustness with regard to changes in the environmental concentration of a substance. PMID: 18521718 [PubMed - as supplied by publisher] (Source: Origins of Life and Evolution of the Biosphere)
Source: Origins of Life and Evolution of the Biosphere - June 3, 2008 Category: Molecular Biology Authors: Melkikh AV, Seleznev VD Tags: Orig Life Evol Biosph Source Type: journals

Isotope Chirality and Asymmetric Autocatalysis: A Possible Entry to Biological Chirality.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Natural-abundance isotopic substitution in isotopically prochiral groups of otherwise achiral molecules can provide stochastically formed enantiomeric excesses which exceed the sensitivity threshold of sensitive asymmetric autocatalytic (Soai-type) reactions. This kind of induction of chirality should be taken into consideration in in vitro model experiments and offer a new kind of entry into primary prebiotic or early biotic enantioselection in the earliest stages of molecular evolution. PMID: 18521719 [PubMed - as supplied by publisher] (Source: Origins of Life and Evolution of the Biosphere)
Source: Origins of Life and Evolution of the Biosphere - June 3, 2008 Category: Molecular Biology Authors: Barabás B, Caglioti L, Micskei K, Zucchi C, Pályi G Tags: Orig Life Evol Biosph Source Type: journals

An Extended Model for the Evolution of Prebiotic Homochirality: A Bottom-Up Approach to the Origin of Life.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A generalized autocatalytic model for chiral polymerization is investigated in detail. Apart from enantiomeric cross-inhibition, the model allows for the autogenic (non-catalytic) formation of left and right-handed monomers from a substrate with reaction rates epsilon ( L ) and epsilon ( R ), respectively. The spatiotemporal evolution of the net chiral asymmetry is studied for models with several values of the maximum polymer length, N. For N = 2, we study the validity of the adiabatic approximation often cited in the literature. We show that the approximation obtains the correct equilibrium values of the net chirality...
Source: Origins of Life and Evolution of the Biosphere - May 9, 2008 Category: Molecular Biology Authors: Gleiser M, Walker SI Tags: Orig Life Evol Biosph Source Type: journals

Reduction of N(2) by Fe (2+) via Homogeneous and Heterogeneous Reactions Part 2: The Role of Metal Binding in Activating N(2) for Reduction; a Requirement for Both Pre-biotic and Biological Mechanisms.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Nitrogen reduction by ferrous iron has been suggested as an important mechanism in the formation of ammonia on pre-biotic Earth. This paper examines the effects of adsorption of ferrous iron onto a goethite (alpha-FeOOH) substrate on the thermodynamic driving force and rate of a ferrous iron-mediated reduction of N(2) as compared with the homogeneous aqueous reaction. Utilizing density functional theory and Marcus Theory of proton coupled electron transfer reactions, the following two reactions were studied: [Formula: see text]and [Formula: see text]Although the rates of both reactions were calculated to be approximate...
Source: Origins of Life and Evolution of the Biosphere - May 2, 2008 Category: Molecular Biology Authors: Wander MC, Kubicki JD, Schoonen MA Tags: Orig Life Evol Biosph Source Type: journals

Nucleic Acids Bind to Nanoparticulate iron (II) Monosulphide in Aqueous Solutions.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In the hydrothermal FeS-world origin of life scenarios nucleic acids are suggested to bind to iron (II) monosulphide precipitated from the reaction between hydrothermal sulphidic vent solutions and iron-bearing oceanic water. In lower temperature systems, the first precipitate from this process is nanoparticulate, metastable FeS(m) with a mackinawite structure. Although the interactions between bulk crystalline iron sulphide minerals and nucleic acids have been reported, their reaction with nanoparticulate FeS(m) has not previously been investigated. We investigated the binding of different nucleic acids, and their con...
Source: Origins of Life and Evolution of the Biosphere - April 13, 2008 Category: Molecular Biology Authors: Hatton B, Rickard D Tags: Orig Life Evol Biosph Source Type: journals

Abiogenic Photophosphorylation of ADP to ATP Sensitized by Flavoproteinoid Microspheres.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A model for abiogenic photophosphorylation of ADP by orthophosphate to yield ATP was studied. The model is based on the photochemical activity of flavoproteinoid microspheres that are formed by aggregation in an aqueous medium of products of thermal condensation of a glutamic acid, glycine and lysine mixture (8:3:1) and contain, along with amino acid polymers (proteinoids), abiogenic isoalloxazine (flavin) pigments. Irradiation of aqueous suspensions of microspheres with blue visible light or ultraviolet in the presence of ADP and orthophosphate resulted in ATP formation. The yield of ATP in aerated suspensions was 10-...
Source: Origins of Life and Evolution of the Biosphere - April 2, 2008 Category: Molecular Biology Authors: Kolesnikov MP, Telegina TA, Lyudnikova TA, Kritsky MS Tags: Orig Life Evol Biosph Source Type: journals

Comments in a Discussion: Differential Rates of D: - and L: -tyrosine Crystallization.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Discussion: Differential Rates of D: - and L: -tyrosine Crystallization. Orig Life Evol Biosph. 2008 Mar 20; Authors: Shinitzky M, Deamer D We earlier reported that we had observed quantifiable differences in crystallization rates of D: and L: tyrosine. It has been suggested that these results were due to the presence of impurities. Here we argue that it is premature to conclude that impurities entirely explain the results. More generally, there is an accumulating weight of evidence that D: and L: enantiomers display unexpected differences in their physical properties and behavior. These should be taken into ac...
Source: Origins of Life and Evolution of the Biosphere - March 20, 2008 Category: Molecular Biology Authors: Shinitzky M, Deamer D Tags: Orig Life Evol Biosph Source Type: journals

Adsorption and Polymerization of Amino Acids on Mineral Surfaces: A Review.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The present paper offers a review of recent (post-1980) work on amino acid adsorption and thermal reactivity on oxide and sulfide minerals. This review is performed in the general frame of evaluating Bernal's hypothesis of prebiotic polymerization in the adsorbed state, but written from a surface scientist's point of view. After a general discussion of the thermodynamics of the problem and exactly what effects surfaces should have to make adsorbed-state polymerization a viable scenario, we examine some practical difficulties in experimental design and their bearing on the conclusions that can be drawn from extant works...
Source: Origins of Life and Evolution of the Biosphere - March 15, 2008 Category: Molecular Biology Authors: Lambert JF Tags: Orig Life Evol Biosph Source Type: journals

First Results of the RAMBAS Experiment on Investigation of the Radiation Mechanism of Chiral Influence.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The first results of the RAdiation Mechanism of Biomolecular ASymmetry (RAMBAS) experiment on investigation of the radiation mechanism of the influence on chiral molecules, as a factor leading to origination of chiral asymmetry are presented. It was found that irradiation of simple achiral materials by a flux of electrons from radioactive source initiated the synthesis of amino acids, and it resulted in asymmetric degradation and chiral asymmetry in a racemic mixture of amino acids. The results obtained can be important for the solution of the origin-of-life and biological homochirality problems. PMID: 18302005 [Pu...
Source: Origins of Life and Evolution of the Biosphere - February 27, 2008 Category: Molecular Biology Authors: Burkov VI, Goncharova LA, Gusev GA, Kobayashi K, Moiseenko EV, Poluhina NG, Saito T, Tsarev VA, Xu J, Zhang G Tags: Orig Life Evol Biosph Source Type: journals