Problems with Using Evolutionary Theory in Philosophy

Does science move toward truths? Are present scientific theories (approximately) true? Should we invoke truths to explain the success of science? Do our cognitive faculties track truths? Some philosophers say yes, while others say no, to these questions. Interestingly, both groups use the same scientific theory, viz., evolutionary theory, to defend their positions. I argue that it begs the question for the former group to do so because their positive answers imply that evolutionary theory is warranted, whereas it is self-defeating for the latter group to do so because their negative answers imply that evolutionary theory is unwarranted

Estimating Effects and Making Predictions from Genome-Wide Marker Data

In genome-wide association studies (GWAS), hundreds of thousands of genetic markers (SNPs) are tested for association with a trait or phenotype. Reported effects tend to be larger in magnitude than the true effects of these markers, the so-called ``winner's curse.'' We argue that the classical definition of unbiasedness is not useful in this context and propose to use a different definition of unbiasedness that is a property of the estimator we advocate. We suggest an integrated approach to the estimation of the SNP effects and to the prediction of trait values, treating SNP effects as random instead of fixed effects. Statistical methods traditionally used in the prediction of trait values in the genetics of livestock, which predates the availability of SNP data, can be applied to analysis of GWAS, giving better estimates of the SNP effects and predictions of phenotypic and genetic values in individuals.Comment: Published in at http://dx.doi.org/10.1214/09-STS306 the Statistical Science (http://www.imstat.org/sts/) by the Institute of Mathematical Statistics (http://www.imstat.org

The Surveillance of Gastrointestinal Parasitic Nematodes of Northwest Arkansas Dairy Cattle Using Traditional and Genetic Parasitological Identification Procedures

Traditional and genetic parasitological identification procedures were compared using naturaland artificial nematode parasite infections in Holstein steer calves. The traditional parasitological procedures measured fecal egg counts, coprocultures with subsequent larval collection and adult nematodes collected at necropsy. The genetic identification procedures measured ITS-2 sequences extracted from different stages of nematode development: raw feces, concentrated nematode eggs, third stage larvae and adults. The primary nematodes observed were Cooperia oncophora, Cooperia punctata and Ostertagia ostertagi. The traditional techniques were not significantly different from one another, while the genetic sequencing showed variation amongst the different procedures. The raw feces sequences showed the most variation, displaying a wide array of sequences from nematode species that were not necessarily found in the other genetic procedures. There was good correlation between the traditional and genetic procedures as a whole, leading to the conclusion that traditional parasitological identification techniques are sufficient for the identification of parasitic nematodes of cattle

Charge collective modes in an incommensurately modulated cuprate

We report the first measurement of collective charge modes of insulating Sr14Cu24O41 using inelastic resonant x-ray scattering over the complete Brillouin zone. Our results show that the intense excitation modes at the charge gap edge predominantly originate from the ladder-containing planar substructures. The observed ladder modes (E vs. Q) are found to be dispersive for momentum transfers along the "legs" but nearly localized along the "rungs". Dispersion and peakwidth characteristics are similar to the charge spectrum of 1D Mott insulators, and we show that our results can be understood in the strong coupling limit (U >> t_{ladder}> t_{chain}). The observed behavior is in marked contrast to the charge spectrum seen in most two dimensional cuprates. Quite generally, our results also show that momentum-tunability of inelastic scattering can be used to resolve mode contributions in multi-component incommensurate systems.Comment: 4+ pages, 5 figure

The Shape, Multiplicity, and Evolution of Superclusters in LambdaCDM Cosmology

We determine the shape, multiplicity, size, and radial structure of superclusters in the LambdaCDM concordance cosmology from z = 0 to z = 2. Superclusters are defined as clusters of clusters in our large-scale cosmological simulation. We find that superclusters are triaxial in shape; many have flattened since early times to become nearly two-dimensional structures at present, with a small fraction of filamentary systems. The size and multiplicity functions are presented at different redshifts. Supercluster sizes extend to scales of ~ 100 - 200 Mpc/h. The supercluster multiplicity (richness) increases linearly with supercluster size. The density profile in superclusters is approximately isothermal (~ R^{-2}) and steepens on larger scales. These results can be used as a new test of the current cosmology when compared with upcoming observations of large-scale surveys.Comment: 33 pages, 15 figures, accepted to ApJ; minor content changes, some figures removed to shorten pape

Chemically gated electronic structure of a superconducting doped topological insulator system

Angle resolved photoemission spectroscopy is used to observe changes in the electronic structure of bulk-doped topological insulator Cu$_x$Bi$_2$Se$_3$ as additional copper atoms are deposited onto the cleaved crystal surface. Carrier density and surface-normal electrical field strength near the crystal surface are estimated to consider the effect of chemical surface gating on atypical superconducting properties associated with topological insulator order, such as the dynamics of theoretically predicted Majorana Fermion vortices

Quantitative genetics of disease traits

John James authored two key papers on the theory of risk to relatives for binary disease traits and the relationship between parameters on the observed binary scale and an unobserved scale of liability (James Annals of Human Genetics, 1971; 35: 47; Reich, James and Morris Annals of Human Genetics, 1972; 36: 163). These two papers are John James' most cited papers (198 and 328 citations, November 2014). They have been influential in human genetics and have recently gained renewed popularity because of their relevance to the estimation of quantitative genetics parameters for disease traits using SNP data. In this review, we summarize the two early papers and put them into context. We show recent extensions of the theory for ascertained case-control data and review recent applications in human genetics