Macroevolution simulated with autonomously replicating computer programs

The process of adaptation occurs on two timescales. In the short term, natural selection merely sorts the variation already present in a population, whereas in the longer term genotypes quite different from any that were initially present evolve through the cumulation of new mutations. The first process is described by the mathematical theory of population genetics. However, this theory begins by defining a fixed set of genotypes and cannot provide a satisfactory analysis of the second process because it does not permit any genuinely new type to arise. The evolutionary outcome of selection acting on novel variation arising over long periods is therefore difficult to predict. The classical problem of this kind is whether 'replaying the tape of life' would invariably lead to the familiar organisms of the modern biota. Here we study the long-term behaviour of populations of autonomously replicating computer programs and find that the same type, introduced into the same simple environment, evolves on any given occasion along a unique trajectory towards one of many well-adapted end points.     

Evidence from detrital zircons for the existence of continental crust and oceans on the Earth 4.4 Gyr ago

No crustal rocks are known to have survived since the time of the intense meteor bombardment that affected Earth between its formation about 4,550 Myr ago and 4,030 Myr, the age of the oldest known components in the Acasta Gneiss of northwestern Canada. But evidence of an even older crust is provided by detrital zircons in metamorphosed sediments at Mt Narryer and Jack Hills in the Narryer Gneiss Terrane, Yilgarn Craton, Western Australia, where grains as old as approximately 4,276 Myr have been found. Here we report, based on a detailed micro-analytical study of Jack Hills zircons, the discovery of a detrital zircon with an age as old as 4,404+/-8 Myr--about 130 million years older than any previously identified on Earth. We found that the zircon is zoned with respect to rare earth elements and oxygen isotope ratios (delta18O values from 7.4 to 5.0%), indicating that it formed from an evolving magmatic source. The evolved chemistry, high delta18O value and micro-inclusions of SiO2 are consistent with growth from a granitic melt with a delta18O value from 8.5 to 9.5%. Magmatic oxygen isotope ratios in this range point toward the involvement of supracrustal material that has undergone low-temperature interaction with a liquid hydrosphere. This zircon thus represents the earliest evidence for continental crust and oceans on the Earth.     

Developing a genome-wide selection model for genetic improvement of residual feed intake and carcass merit in a beef cattle breeding program

Residual feed intake (RFI) and carcass merit (CM) are both complex traits emerging as critical targets for beef genetic improvement.RFI and CM traits are difficult and expensive to measure and genetic improvement for these traits through traditional selection methods is not very effective.Therefore,genome-wide selection using DNA markers may be a potential alternative for genetic improvement of these traits.In this study,the efficiency of a genome-wide selection model for genetic improvement of RFI and CM was assessed.The Illumina Bovine50K bead chip was used to genotype 922 beef cattle from the Kinsella Beef Research Ranch of the University of Alberta.A Bayes model and multiple marker regression using a stepwise method were used to conduct the association test.The number of significant SNP markers for carcass weight (CWT),carcass back fat (BF),carcass rib eye area (REA),carcass grade fat (GDF),lean meat yield (LMY),and residual feed intake (RFI) were 75,54,67,57,44 and 50,respectively.Bi-variate analysis of marker scores and phenotypes for all traits were made using DMU Software.The genetic parameter for each trait was estimated.The genetic correlations of marker score and phenotype for CWT,BF,REA,GDF,LMY and RFI were 0.75,0.69,0.87,0.77,0.78,and 0.85,respectively.The average prediction accuracies of phenotypic EBV for the six traits were increased by 0.05,0.16,0.24,0.23,0.17 and 0.19,respectively.The results of this study indicated that the two-trait marker-assisted evaluation model used was a suitable alternative of genetic evaluation for these traits in beef cattle.     

Diverse mechanisms of feeding and movement in Cyclorrhaphan larvae (Diptera)

Direct observation, filmed behaviour and morphological analysis were used to investigate mechanisms of larval feeding and movement in 20 species of Cyclorrhapha (Diptera). Feeding mechanisms refer to techniques of gathering food close to the pharynx entrance prior to sucking it in. A total of 12 mechanisms were recorded. Contrasting mechanisms were associated with saprophagy, phytophagy, mycophagy and zoophagy. Larvae had role-specific, compartmentalised bodies. The rear compartment grips substrates enabling the front ones to scan for food by sweeping from side to side or up and down. The front compartments extend or lunge to gather food or grip substrates during locomotion. Lower cyclorrhaphans had more disparate mechanisms than higher cyclorrhaphans. In the latter, the size, shape and movements of the thorax, pseudocephalon and head skeleton are diverse. Influences on this diversity are food quality and access conditions at development sites. Movement capabilities and functions were established for many components.     

A non representationalist view of model explanation

In this paper, I examine two idealized models in astrophysics, with the aim of showing that the idealizations in these models play an important explanatory role. I argue, against many representationalists, that it is because of the idealizations in these models, rather than in spite of them, that the models turn out to have explanatory power. In many cases, this claim can be extended to the use of idealized models in the sciences more generally, and thus it gives important insight into the nature of model explanation.     

Atomism and ‘subtlety’ in Francis Bacon's philosophy

Francis Bacon's reflections on atomism have generally been misunderstood because they have never been systematically studied in relation to the speculative chemical philosophy which he developed in the interval between about 1592 and his death in 1626. This philosophy, in many respects unknown to historians until quite recently, was the only body of positive science which Bacon ever accepted. The speculative philosophy was, on the whole, chemical and non-mechanical, and consequently not consistent with atomist doctrines. In fact, Bacon never at any time accepted the principal atomist tenets. It is therefore necessary to explain why he was interested in atomism at all. Of the several reasons for his interest one (hitherto unrecognised) is especially important—namely, his belief that the speculative and atomic philosophies had affinities. In particular, he believed that of all the ancient philosophies atomism alone approached the ideals associated with the key notion of ‘subtlety’—ideals represented in their highest form (as he imagined) in the speculative philosophy.     

Variation in styles of rifting in the Gulf of California

Constraints on the structure of rifted continental margins and the magmatism resulting from such rifting can help refine our understanding of the strength of the lithosphere, the state of the underlying mantle and the transition from rifting to seafloor spreading. An important structural classification of rifts is by width, with narrow rifts thought to form as necking instabilities (where extension rates outpace thermal diffusion) and wide rifts thought to require a mechanism to inhibit localization, such as lower-crustal flow in high heat-flow settings. Observations of the magmatism that results from rifting range from volcanic margins with two to three times the magmatism predicted from melting models to non-volcanic margins with almost no rift or post-rift magmatism. Such variations in magmatic activity are commonly attributed to variations in mantle temperature. Here we describe results from the PESCADOR seismic experiment in the southern Gulf of California and present crustal-scale images across three rift segments. Over short lateral distances, we observe large differences in rifting style and magmatism--from wide rifting with minor synchronous magmatism to narrow rifting in magmatically robust segments. But many of the factors believed to control structural evolution and magmatism during rifting (extension rate, mantle potential temperature and heat flow) tend to vary over larger length scales. We conclude instead that mantle depletion, rather than low mantle temperature, accounts for the observed wide, magma-poor margins, and that mantle fertility and possibly sedimentary insulation, rather than high mantle temperature, account for the observed robust rift and post-rift magmatism.     

Chemical reduction of three-dimensional silica micro-assemblies into microporous silicon replicas

The carbothermal reduction of silica into silicon requires the use of temperatures well above the silicon melting point (> or =2,000 degrees C). Solid silicon has recently been generated directly from silica at much lower temperatures (< or =850 degrees C) via electrochemical reduction in molten salts. However, the silicon products of such electrochemical reduction did not retain the microscale morphology of the starting silica reactants. Here we demonstrate a low-temperature (650 degrees C) magnesiothermic reduction process for converting three-dimensional nanostructured silica micro-assemblies into microporous nanocrystalline silicon replicas. The intricate nanostructured silica microshells (frustules) of diatoms (unicellular algae) were converted into co-continuous, nanocrystalline mixtures of silicon and magnesia by reaction with magnesium gas. Selective magnesia dissolution then yielded an interconnected network of silicon nanocrystals that retained the starting three-dimensional frustule morphology. The silicon replicas possessed a high specific surface area (>500 m(2) g(-1)), and contained a significant population of micropores (< or =20 A). The silicon replicas were photoluminescent, and exhibited rapid changes in impedance upon exposure to gaseous nitric oxide (suggesting a possible application in microscale gas sensing). This process enables the syntheses of microporous nanocrystalline silicon micro-assemblies with multifarious three-dimensional shapes inherited from biological or synthetic silica templates for sensor, electronic, optical or biomedical applications.