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In complex spatial models, as used to predict the climate response to greenhouse gas emissions, parameter variation within plausible bounds has major effects on model behavior of interest. Here, we present an unprecedentedly large ensemble of >57,000 climate model runs in which 10 parameters, initial conditions, hardware, and software used to run the model all have been varied. We relate information about the model runs to large-scale model behavior (equilibrium sensitivity of global mean temperature to a doubling of carbon dioxide). We demonstrate that effects of parameter, hardware, and software variation are detectable, complex, and interacting. However, we find most of the effects of parameter variation are caused by a small subset of parameters. Notably, the entrainment coefficient in clouds is associated with 30% of the variation seen in climate sensitivity, although both low and high values can give high climate sensitivity. We demonstrate that the effect of hardware and software is small relative to the effect of parameter variation and, over the wide range of systems tested, may be treated as equivalent to that caused by changes in initial conditions. We discuss the significance of these results in relation to the design and interpretation of climate modeling experiments and large-scale modeling more generally. classification and regression trees | climate change | distributed computing | general circulation models | sensitivity analysis

The physical characteristics of proteins are fundamentally important in organismal function. We used the complete predicted proteomes of > 100 organisms spanning the three domains of life to investigate the comparative biology and evolution of proteomes. Theoretical 2D gels were constructed with axes of protein mass and charge (pI) and converted to density estimates comparable across all types and sizes of proteome. We asked whether we could detect general patterns of proteome conservation and variation. The overall pattern of theoretical 2D gels was strongly conserved across all life forms. Nevertheless, coevolved replicons from the same organism (different chromosomes or plasmid and host chromosomes) encode proteomes more similar to each other than those from different organisms. Furthermore, there was disparity between the membrane and nonmembrane subproteomes within organisms (proteins of membrane proteomes are on the average more basic and heavier) and their variation across organisms, suggesting that membrane proteomes evolve most rapidly. Experimentally, a significant positive relationship independent of phylogeny was found between the predicted proteome and Biolog profile, a measure associated with the ecological niche. Finally, we show that, for the smallest and most alkaline proteomes, there is a negative relationship between proteome size and basicity. This relationship is not adequately explained by AT bias at the DNA sequence level. Together, these data provide evidence of functional adaptation in the properties of complete proteomes.

We show that a signal from the germ line represses growth in the nematode Caenorhabditis elegans. Laser-microbeam ablation of cells that give rise to the germ line causes adults to become giant. Ablation of these cells in self-sterile mutant worms also causes gigantism, suggesting that the germ line represses growth because it is the source of a growth-antagonizing signal rather than because of a sink of resources required for reproduction. The C. elegans germ line also emits a signal that represses longevity. This longevity-repressing signal requires the activity of DAF-16, a forkhead/winged-helix transcription factor, but we find that that the growth-repressing signal does not. The growth-repressing signal also does not require the activity of DBL-1, a transforming growth factor [beta]-related protein that promotes growth in worms. By ablating the germ-line precursors of other species of free-living nematodes, we also found that both the growth-repressing and longevity-repressing signals are evolutionarily variable. Some species have both signals; others have just one or the other. We suggest that variation in germ-line signaling contributes to body size and life-history diversity in the nematodes.