Catastrophic wildfire and number of populations as factors influencing risk of extinction for Gila trout ( Oncorhynchus gilae )

We used the computer program RAMAS to explore the sensitivity of an extinction-risk model for the Gila trout ( Oncorhynchus gilae ) to management of wildfires and number of populations of the species. The Gila trout is an endangered salmonid presently restricted to very few headwaters of the Gila and San Francisco river tributaries in southwestern New Mexico. Life history data for 10 extant populations were used to examine sensitivity of the species viability to changes in a variety of factors including population size, fecundity, life stage structure, number of populations, severity and probability of forest fires, and a regulated fishery. The probability and severity of forest fires and number of populations had the greatest effect on viability. Results indicate that successful conservation of Gila trout requires establishment of additional populations and reduction of the severity of forest fires through a program incorporating more frequent, but less severe, fires.     

Black-tailed prairie dog populations one year after treatment with rodenticides

Three rodenticide treatments, zinc phosphide with prebait, strychnine with prebait, and strychnine without prebait, were applied to black-tailed prairie dog Cynomys ludovicianus colonies in west central South Dakota. Results were compared immediately posttreatment and for one year after application. Zinc phosphide was the most effective for reducing prairie dog numbers immediately. When burrow activity levels of prairie dogs were initially reduced by 45% with strychnine only, they returned to untreated levels within ten months. When initial reductions were 95% with zinc phosphide, however, the number of active burrows was still reduced 77% in September the following year. Strychnine with prebait treatment showed initial reductions of 83% in burrow activity. Bait consumption by prairie dogs was highest for zinc phosphide.     

Confirmational holism and its mathematical (w)holes

I critically examine confirmational holism as it pertains to the indispensability arguments for mathematical Platonism. I employ a distinction between pure and applied mathematics that grows out of the often overlooked symbiotic relationship between mathematics and science. I argue that this distinction undercuts the notion that (pure) mathematical theories fall under the holistic scope of the confirmation of our scientific theories.     

On the verge of <Emphasis Type="Italic">Umdeutung</Emphasis> in Minnesota: Van Vleck and the correspondence principle. Part one

In October 1924, The Physical Review, a relatively minor journal at the time, published a remarkable two-part paper by John H. Van Vleck, working in virtual isolation at the University of Minnesota. Using Bohr’s correspondence principle and Einstein’s quantum theory of radiation along with advanced techniques from classical mechanics, Van Vleck showed that quantum formulae for emission, absorption, and dispersion of radiation merge with their classical counterparts in the limit of high quantum numbers. For modern readers Van Vleck’s paper is much easier to follow than the famous paper by Kramers and Heisenberg on dispersion theory, which covers similar terrain and is widely credited to have led directly to Heisenberg’s Umdeutung paper. This makes Van Vleck’s paper extremely valuable for the reconstruction of the genesis of matrix mechanics. It also makes it tempting to ask why Van Vleck did not take the next step and develop matrix mechanics himself. This paper was written as part of a joint project in the history of quantum physics of the Max Planck Institut für Wissenschaftsgeschichte and the Fritz-Haber-Institut in Berlin.     

Loss of ACTN3 gene function alters mouse muscle metabolism and shows evidence of positive selection in humans

More than a billion humans worldwide are predicted to be completely deficient in the fast skeletal muscle fiber protein alpha-actinin-3 owing to homozygosity for a premature stop codon polymorphism, R577X, in the ACTN3 gene. The R577X polymorphism is associated with elite athlete status and human muscle performance, suggesting that alpha-actinin-3 deficiency influences the function of fast muscle fibers. Here we show that loss of alpha-actinin-3 expression in a knockout mouse model results in a shift in muscle metabolism toward the more efficient aerobic pathway and an increase in intrinsic endurance performance. In addition, we demonstrate that the genomic region surrounding the 577X null allele shows low levels of genetic variation and recombination in individuals of European and East Asian descent, consistent with strong, recent positive selection. We propose that the 577X allele has been positively selected in some human populations owing to its effect on skeletal muscle metabolism.     

Group formation stabilizes predator-prey dynamics

Theoretical ecology is largely founded on the principle of mass action, in which uncoordinated populations of predators and prey move in a random and well-mixed fashion across a featureless landscape. The conceptual core of this body of theory is the functional response, predicting the rate of prey consumption by individual predators as a function of predator and/or prey densities. This assumption is seriously violated in many ecosystems in which predators and/or prey form social groups. Here we develop a new set of group-dependent functional responses to consider the ecological implications of sociality and apply the model to the Serengeti ecosystem. All of the prey species typically captured by Serengeti lions (Panthera leo) are gregarious, exhibiting nonlinear relationships between prey-group density and population density. The observed patterns of group formation profoundly reduce food intake rates below the levels expected under random mixing, having as strong an impact on intake rates as the seasonal migratory behaviour of the herbivores. A dynamical system model parameterized for the Serengeti ecosystem (using wildebeest (Connochaetes taurinus) as a well-studied example) shows that grouping strongly stabilizes interactions between lions and wildebeest. Our results suggest that social groups rather than individuals are the basic building blocks around which predator-prey interactions should be modelled and that group formation may provide the underlying stability of many ecosystems.     

Expanding the diversity of chemical protein modification allows post-translational mimicry

One of the most important current scientific paradoxes is the economy with which nature uses genes. In all higher animals studied, we have found many fewer genes than we would have previously expected. The functional outputs of the eventual products of genes seem to be far more complex than the more restricted blueprint. In higher organisms, the functions of many proteins are modulated by post-translational modifications (PTMs). These alterations of amino-acid side chains lead to higher structural and functional protein diversity and are, therefore, a leading contender for an explanation for this seeming incongruity. Natural protein production methods typically produce PTM mixtures within which function is difficult to dissect or control. Until now it has not been possible to access pure mimics of complex PTMs. Here we report a chemical tagging approach that enables the attachment of multiple modifications to bacterially expressed (bare) protein scaffolds: this approach allows reconstitution of functionally effective mimics of higher organism PTMs. By attaching appropriate modifications at suitable distances in the widely-used LacZ reporter enzyme scaffold, we created protein probes that included sensitive systems for detection of mammalian brain inflammation and disease. Through target synthesis of the desired modification, chemistry provides a structural precision and an ability to retool with a chosen PTM in a manner not available to other approaches. In this way, combining chemical control of PTM with readily available protein scaffolds provides a systematic platform for creating probes of protein-PTM interactions. We therefore anticipate that this ability to build model systems will allow some of this gene product complexity to be dissected, with the aim of eventually being able to completely duplicate the patterns of a particular protein's PTMs from an in vivo assay into an in vitro system.