The dead-end elimination theorem and its use in protein side-chain positioning

The prediction of a protein's tertiary structure is still a considerable problem because the huge amount of possible conformational space1 makes it computationally difficult. With regard to side-chain modelling, a solution has been attempted by the grouping of side-chain conformations into representative sets of rotamers2??. Nonetheless, an exhaustive combinatorial search is still limited to carefully indentified packing units?? containing a limited number of residues. For larger systems other strategies had to be developed, such as the Monte Carlo Procedure?? and the genetic algorithm and clustering approach?. Here we present a theorem, referred to as the 'dead-end elimination' theorem, which imposes a suitable condition to identify rotamers that cannot be members of the global minimum energy conformation. Application of this theorem effectively controls the computational explosion of the rotamer combinatorial problem, thereby allowing the determination of the global minimum energy conformation of a large collection of side chains.     

Evolution of the atmosphere and oceans

The residence times of most constituents of the atmosphere and oceans are small fractions of the age of the Earth and, in general, their rate of output has been nearly equal to their rate of input. We are disturbing a number of these dynamic equilibria quite severely. The mineralogy of marine evaporites rules out drastic changes in the composition of sea water during the last 900 Myr. The chemistry of soils formed more than 1,000 Myr ago suggests that the atmosphere then contained significantly more CO2 and less O2 than at present. Hydrogen peroxide may well have been the principal oxidant and formaldehyde the main reductant in rain water between 3,000 and 1,000 Myr ago. Major changes in atmospheric chemistry since that time are almost certainly related to the evolution of the biosphere.     

Inner ear of the coelacanth fish Latimeria has tetrapod affinities

Auditory reception in elasmobranchs, teleosts and amphibians may be mediated by various inner-ear sensory epithelia 1–3, including the basilar papilla, which seems to be the precursor of the cochlea in mammals. The origin of the basilar papilla remains a major unsolved problem for understanding the evolution of hearing in terrestrial vertebrates4–6. Study of living species indicates that the basilar papilla is a unique feature of tetrapods 6,7, but palaeonto-logical data indicate that this epithelium as well as a middle ear, is already present in crossopterygian fish 8–10. However, no basilar papilla has been found in the only living crossopterygian species, the coelacanth Latimeria chalumnae 11. I have re-examined the inner ear of adult and embryonic Latimeria and find a membranous specialization which resembles in structure, position and innerva-tion pattern the basilar papilla of tetrapods, in particular amniotes. No epithelium comparable to the basilar papilla was found in lungfish. I suggest that the basilar papillae of Latimeria and tetrapods are homologous and evolved only once in their common ancestor.     

Symmetry perception in an insect

Symmetrical visual patterns have a salient status in human perception, as evinced by their prevalent occurrence in art, and also in animal perception, where they may be an indicator of phenotypic and genotypic quality. Symmetry perception has been demonstrated in humans, birds, dolphins and apes. Here we show that bees trained to discriminate bilaterally symmetrical from non-symmetrical patterns learn the task and transfer it appropriately to novel stimuli, thus demonstrating a capacity to detect and generalize symmetry or asymmetry. We conclude that bees, and possibly flower-visiting insects in general, can acquire a generalized preference towards symmetrical or, alternatively, asymmetrical patterns depending on experience, and that symmetry detection is preformed or can be learned as perceptual category by insects, because it can be extracted as an independent visual pattern feature. Bees show a predisposition for learning and generalized symmetry because, if trained to it, they choose it more frequently, come closer to and hover longer in front of the novel symmetrical stimuli than the bees trained for asymmetry do for the novel asymmetrical stimuli. Thus, even organisms with comparatively small nervous systems can generalize about symmetry, and favour symmetrical over asymmetrical patterns.     

A massive phytoplankton bloom induced by an ecosystem-scale iron fertilization experiment in the equatorial Pacific Ocean

The seeding of an expanse of surface waters in the equatorial Pacific Ocean with low concentrations of dissolved iron triggered a massive phytoplankton bloom which consumed large quantities of carbon dioxide and nitrate that these microscopic plants cannot fully utilize under natural conditions. These and other observations provide unequivocal support for the hypothesis that phytoplankton growth in this oceanic region is limited by iron bioavailability.     

Pulsating aurora induced by upper atmospheric barium releases

An effect which appeared to be pulsating aurora was observed to be associated with explosive releases of barium vapour near 250 km altitude, but only when the explosions were in the path of precipitating electrons associated with the visible aurora.