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.     

Cell size and cell division of the anterior pituitary: time course in the growing rat

Pituitary cells increase their numbers more than 3-fold during the 1st 10 days of life while maintaining the same cell size ratios. In the 25-day-old animal, the rate of cell division slows and there is a slight increase in the number of large cells. An increase in adult weight is attributed to hyperplasia and a shift to a population of larger cells.     

Cell size and cell division of the anterior pituitary: Time course in the growing rat

Summary Pituitary cells increase their numbers more than 3-fold during the 1st 10 days of life while maintaining the same cell size ratios. In the 25-day-old animal, the rate of cell division slows and there is a slight increase in the number of larger cells. An increase in adult weight is attributed to hyperplasia and a shift to a population of larger cells.Supported by NIH grant HD08844.     

Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite

From the standpoints of both basic research and biotechnology, there is considerable interest in reaching a clearer understanding of the diversity of biological mechanisms employed during lignocellulose degradation. Globally, termites are an extremely successful group of wood-degrading organisms and are therefore important both for their roles in carbon turnover in the environment and as potential sources of biochemical catalysts for efforts aimed at converting wood into biofuels. Only recently have data supported any direct role for the symbiotic bacteria in the gut of the termite in cellulose and xylan hydrolysis. Here we use a metagenomic analysis of the bacterial community resident in the hindgut paunch of a wood-feeding 'higher' Nasutitermes species (which do not contain cellulose-fermenting protozoa) to show the presence of a large, diverse set of bacterial genes for cellulose and xylan hydrolysis. Many of these genes were expressed in vivo or had cellulase activity in vitro, and further analyses implicate spirochete and fibrobacter species in gut lignocellulose degradation. New insights into other important symbiotic functions including H2 metabolism, CO2-reductive acetogenesis and N2 fixation are also provided by this first system-wide gene analysis of a microbial community specialized towards plant lignocellulose degradation. Our results underscore how complex even a 1-microl environment can be.     

Analysis of the DNA sequence and duplication history of human chromosome 15

Here we present a finished sequence of human chromosome 15, together with a high-quality gene catalogue. As chromosome 15 is one of seven human chromosomes with a high rate of segmental duplication, we have carried out a detailed analysis of the duplication structure of the chromosome. Segmental duplications in chromosome 15 are largely clustered in two regions, on proximal and distal 15q; the proximal region is notable because recombination among the segmental duplications can result in deletions causing Prader-Willi and Angelman syndromes. Sequence analysis shows that the proximal and distal regions of 15q share extensive ancient similarity. Using a simple approach, we have been able to reconstruct many of the events by which the current duplication structure arose. We find that most of the intrachromosomal duplications seem to share a common ancestry. Finally, we demonstrate that some remaining gaps in the genome sequence are probably due to structural polymorphisms between haplotypes; this may explain a significant fraction of the gaps remaining in the human genome.     

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.