Intervening on time derivatives

Interventionism analyses causal influence in terms of correlations of changes under a distribution of interventions. But the correspondence between correlated changes and causal influence is not obvious. I probe its plausibility with a problem-case involving variables related as time derivative (velocity) to integral (position), such that the latter variable must change given an intervention on the former unless dependencies are introduced among the testing and controlling interventions. Under the orthodox criteria such interventions will fail to be appropriate for causal analysis. I consider various alternatives, including permitting control interventions to be chancy, restricting the available models and mitigating variation of off-path variables. None of these work. I then present a fourth suggestion which modifies the interventionist criteria in order to permit interventions which can influence other variables than just their own targets. The correspondence between correlated changes and causal influence can thereby saved when dependencies are introduced among such interventions. This modification and the required dependencies, I argue, are perfectly in line with practice and may also assist in a wider class of cases.     

Eocene/Oligocene ocean de-acidification linked to Antarctic glaciation by sea-level fall

One of the most dramatic perturbations to the Earth system during the past 100 million years was the rapid onset of Antarctic glaciation near the Eocene/Oligocene epoch boundary (approximately 34 million years ago). This climate transition was accompanied by a deepening of the calcite compensation depth--the ocean depth at which the rate of calcium carbonate input from surface waters equals the rate of dissolution. Changes in the global carbon cycle, rather than changes in continental configuration, have recently been proposed as the most likely root cause of Antarctic glaciation, but the mechanism linking glaciation to the deepening of calcite compensation depth remains unclear. Here we use a global biogeochemical box model to test competing hypotheses put forward to explain the Eocene/Oligocene transition. We find that, of the candidate hypotheses, only shelf to deep sea carbonate partitioning is capable of explaining the observed changes in both carbon isotope composition and calcium carbonate accumulation at the sea floor. In our simulations, glacioeustatic sea-level fall associated with the growth of Antarctic ice sheets permanently reduces global calcium carbonate accumulation on the continental shelves, leading to an increase in pelagic burial via permanent deepening of the calcite compensation depth. At the same time, fresh limestones are exposed to erosion, thus temporarily increasing global river inputs of dissolved carbonate and increasing seawater delta13C. Our work sheds new light on the mechanisms linking glaciation and ocean acidity change across arguably the most important climate transition of the Cenozoic era.     

Spin-dependent exciton formation in pi-conjugated compounds.

The efficiency of light-emitting diodes (LEDs) made from organic semiconductors is determined by the fraction of injected electrons and holes that recombine to form emissive spin-singlet states rather than non-emissive spin-triplet states. If the process by which these states form is spin-independent, the maximum efficiency of organic LEDs will be limited to 25 per cent. But recent reports have indicated fractions of emissive singlet states ranging from 22 to 63 per cent, and the reason for this variation remains unclear. Here we determine the absolute fraction of singlet states generated in a platinum-containing conjugated polymer and its corresponding monomer. The spin-orbit coupling introduced by the platinum atom allows triplet-state emission, so optically and electrically generated luminescence from both singlet and triplet states can be compared directly. We find an average singlet generation fraction of 22 +/- 1 per cent for the monomer, but 57 +/- 4 per cent for the polymer. This suggests that recombination is spin-independent for the monomer, but that a spin-dependent process, favouring singlet formation, is effective in the polymer. We suggest that this process is a consequence of the exchange interaction, which will operate on overlapping electron and hole wavefunctions on the same polymer chain at their capture radius.     

DNA sequence and analysis of human chromosome 8

The International Human Genome Sequencing Consortium (IHGSC) recently completed a sequence of the human genome. As part of this project, we have focused on chromosome 8. Although some chromosomes exhibit extreme characteristics in terms of length, gene content, repeat content and fraction segmentally duplicated, chromosome 8 is distinctly typical in character, being very close to the genome median in each of these aspects. This work describes a finished sequence and gene catalogue for the chromosome, which represents just over 5% of the euchromatic human genome. A unique feature of the chromosome is a vast region of approximately 15 megabases on distal 8p that appears to have a strikingly high mutation rate, which has accelerated in the hominids relative to other sequenced mammals. This fast-evolving region contains a number of genes related to innate immunity and the nervous system, including loci that appear to be under positive selection--these include the major defensin (DEF) gene cluster and MCPH1, a gene that may have contributed to the evolution of expanded brain size in the great apes. The data from chromosome 8 should allow a better understanding of both normal and disease biology and genome evolution.     

Mitochondrial genetic variation within and between Holbrookia lacerata lacerata and Holbrookia lacerata subcaudalis,the spot-tailed earless lizards of Texas

ABSTRACT

We examined genetic relationships among individuals and populations of the species Holbrookia lacerata, the spot-tailed earless lizard, using whole mitochondrial genomes. Lizards were collected from south, central and west Texas. We found significant amounts of genetic structure among populations and evidence of two major reciprocally monophyletic groups of spot-tailed earless lizards in Texas. Holbrookia lacerata lacerata occurs on the Edwards Plateau and adjacent regions of West Texas north of the Balcones Escarpment, while Holbrookia lacerata subcaudalis occurs in South Texas and adjacent Mexico south of the Balcones Escarpment. These two recognised subspecies correspond to the two clades we discovered. Holbrookia l. lacerata occupies much of its historical range at sometimes high population densities, while populations of H. l. subcaudalis appear to be highly fragmented based on recent observations compared to their historical range.     

Depression by ethionine of phosphorylating oxidation in hepatic mitochondria

Induction of hepatic steatosis and suppression of hepatic ATP levels, protein synthesis and gluconeogenesis subsequent to administration of ethionine may be consequences of interference by this compound with mitochondrial phosphorylation of ADP. The mitochondrial dysfunction is not a direct action of ethionine on the organelle.     

Persistance of maternally derived3H-estradiol in fetal and neonatal rats

Summary Injection of³H-estradiol into pregnant rats resulted in fetal blood radioactivity 5 times higher than in maternal blood. Significant amounts of³H-estradiol were found in fetal blood 24 h later and in the offspring 5 days after birth.Supported by NIH Grant HD 08844.     

Initial sequencing and comparative analysis of the mouse genome

The sequence of the mouse genome is a key informational tool for understanding the contents of the human genome and a key experimental tool for biomedical research. Here, we report the results of an international collaboration to produce a high-quality draft sequence of the mouse genome. We also present an initial comparative analysis of the mouse and human genomes, describing some of the insights that can be gleaned from the two sequences. We discuss topics including the analysis of the evolutionary forces shaping the size, structure and sequence of the genomes; the conservation of large-scale synteny across most of the genomes; the much lower extent of sequence orthology covering less than half of the genomes; the proportions of the genomes under selection; the number of protein-coding genes; the expansion of gene families related to reproduction and immunity; the evolution of proteins; and the identification of intraspecies polymorphism.