Should the teaching of biological evolution include the origin of life?

The development of mainstream research on the origin of life as an outcome of Darwinian evolution is discussed. It is argued that prebiotic evolution and the origin of life should not be excluded from the syllabus and should be part of classes on biological evolution, and that the transition from non-living to living matter is best understood when seen as part of evolutionary biology. The wide acceptance of evolutionary approaches to the study of the emergence of life in European and Latin American countries is discussed

Geostatistical modeling and spatial distribution analysis of porosity and permeability in the Shurijeh-B reservoir of Khangiran gas field in Iran

The main objectives of this study are analysis of spatial behavior of the porosity and permeability, presenting direction of anisotropy for each variable and describing variation of these parameters in Shurijeh B gas reservoir in Khangiran gas field. Porosity well log data of 32 wells are available for performing this geostatistical analysis. A univariate statistical analysis is done on both porosity and permeability to provide a framework for geostatistical analysis and modeling. For spatial analysis of these parameters, the experimental semivariogram of each variable in different direction as well as their variogram map plotted to find out the direction of anisotropy and their geostatistical parameters such as range, sill, and nugget effect for later geostatistical work and finally for geostatistical modeling, two approaches kriging and Sequential Gaussian Simulation are used to get porosity and permeability maps through the entire reservoir. All of statistical and geostatistical analysis has been done using GSLIB and PETREL software. Maximum and minimum direction of continuity are found to be N75W and N15E, respectively. Geostatistical parameters of calculated semivariogram in this direction like range of 7000 m and nugget of 0.2 are used for modeling. Both kriging and SGS method used for modeling but kriging tends to smooth out estimates but on the other hand SGS method tends to show up details. Cross-validation also used to validate the generated modeling

Codon Size Reduction as the Origin of the Triplet Genetic Code

The genetic code appears to be optimized in its robustness to missense errors and frameshift errors. In addition, the genetic code is near-optimal in terms of its ability to carry information in addition to the sequences of encoded proteins. As evolution has no foresight, optimality of the modern genetic code suggests that it evolved from less optimal code variants. The length of codons in the genetic code is also optimal, as three is the minimal nucleotide combination that can encode the twenty standard amino acids. The apparent impossibility of transitions between codon sizes in a discontinuous manner during evolution has resulted in an unbending view that the genetic code was always triplet. Yet, recent experimental evidence on quadruplet decoding, as well as the discovery of organisms with ambiguous and dual decoding, suggest that the possibility of the evolution of triplet decoding from living systems with non-triplet decoding merits reconsideration and further exploration. To explore this possibility we designed a mathematical model of the evolution of primitive digital coding systems which can decode nucleotide sequences into protein sequences. These coding systems can evolve their nucleotide sequences via genetic events of Darwinian evolution, such as point-mutations. The replication rates of such coding systems depend on the accuracy of the generated protein sequences. Computer simulations based on our model show that decoding systems with codons of length greater than three spontaneously evolve into predominantly triplet decoding systems. Our findings suggest a plausible scenario for the evolution of the triplet genetic code in a continuous manner. This scenario suggests an explanation of how protein synthesis could be accomplished by means of long RNA-RNA interactions prior to the emergence of the complex decoding machinery, such as the ribosome, that is required for stabilization and discrimination of otherwise weak triplet codon-anticodon interactions

The Rodin-Ohno hypothesis that two enzyme superfamilies descended from one ancestral gene: an unlikely scenario for the origins of translation that will not be dismissed

Background Because amino acid activation is rate-limiting for uncatalyzed protein synthesis, it is a key puzzle in understanding the origin of the genetic code. Two unrelated classes (I and II) of contemporary aminoacyl-tRNA synthetases (aaRS) now translate the code. Observing that codons for the most highly conserved, Class I catalytic peptides, when read in the reverse direction, are very nearly anticodons for Class II defining catalytic peptides, Rodin and Ohno proposed that the two superfamilies descended from opposite strands of the same ancestral gene. This unusual hypothesis languished for a decade, perhaps because it appeared to be unfalsifiable. Results The proposed sense/antisense alignment makes important predictions. Fragments that align in antiparallel orientations, and contain the respective active sites, should catalyze the same two reactions catalyzed by contemporary synthetases. Recent experiments confirmed that prediction. Invariant cores from both classes, called Urzymes after Ur = primitive, authentic, plus enzyme and representing ~20% of the contemporary structures, can be expressed and exhibit high, proportionate rate accelerations for both amino-acid activation and tRNA acylation. A major fraction (60%) of the catalytic rate acceleration by contemporary synthetases resides in segments that align sense/antisense. Bioinformatic evidence for sense/antisense ancestry extends to codons specifying the invariant secondary and tertiary structures outside the active sites of the two synthetase classes. Peptides from a designed, 46-residue gene constrained by Rosetta to encode Class I and II ATP binding sites with fully complementary sequences both accelerate amino acid activation by ATP ~400 fold. Conclusions Biochemical and bioinformatic results substantially enhance the posterior probability that ancestors of the two synthetase classes arose from opposite strands of the same ancestral gene. The remarkable acceleration by short peptides of the rate-limiting step in uncatalyzed protein synthesis, together with the synergy of synthetase Urzymes and their cognate tRNAs, introduce a new paradigm for the origin of protein catalysts, emphasize the potential relevance of an operational RNA code embedded in the tRNA acceptor stems, and challenge the RNA-World hypothesis. Reviewers This article was reviewed by Dr. Paul Schimmel (nominated by Laura Landweber), Dr. Eugene Koonin and Professor David Ardell