Intrinsic limits to gene regulation by global crosstalk

Gene regulation relies on the specificity of transcription factor (TF) - DNA interactions. In equilibrium, limited specificity may lead to crosstalk: a regulatory state in which a gene is either incorrectly activated due to noncognate TF-DNA interactions or remains erroneously inactive. We present a tractable biophysical model of global crosstalk, where many genes are simultaneously regulated by many TFs. We show that in the simplest regulatory scenario, a lower bound on crosstalk severity can be analytically derived solely from the number of (co)regulated genes and a suitable parameter that describes binding site similarity. Estimates show that crosstalk could present a significant challenge for organisms with low-specificity TFs, such as metazoans, unless they use appropriate regulation schemes. Strong cooperativity substantially decreases crosstalk, while joint regulation by activators and repressors, surprisingly, does not; moreover, certain microscopic details about promoter architecture emerge as globally important determinants of crosstalk strength. Our results suggest that crosstalk imposes a new type of global constraint on the functioning and evolution of regulatory networks, which is qualitatively distinct from the known constraints acting at the level of individual gene regulatory elements

The s-Process in Rotating Asymptotic Giant Branch Stars

(abridged) We model the nucleosynthesis during the thermal pulse phase of a rotating, solar metallicity AGB star of 3M_sun. Rotationally induced mixing during the thermal pulses produces a layer (~2E-5M_sun) on top of the CO-core where large amounts of protons and C12 co-exist. We follow the abundance evolution in this layer, in particular that of the neutron source C13 and of the neutron poison N14. In our AGB model mixing persists during the entire interpulse phase due to the steep angular velocity gradient at the core-envelope interface. We follow the neutron production during the interpulse phase, and find a resulting maximum neutron exposure of tau_max =0.04 mbarn^-1, which is too small to produce any significant s-process. In parametric models, we then investigate the combined effects of diffusive overshooting from the convective envelope and rotationally induced mixing. Models with overshoot and weaker interpulse mixing - as perhaps expected from more slowly rotating stars - yield larger neutron exposures. We conclude that the incorporation of rotationally induce mixing processes has important consequences for the production of heavy elements in AGB stars. Through a distribution of initial rotation rates it may lead to a natural spread in the neutron exposures obtained in AGB stars of a given mass - as appears to be required by observations. Our results suggest that both processes, diffusive overshoot and rotational mixing, may be required to obtain a consistent description of the s-process in AGB stars which fulfils all observational constraints. Finally, we find that mixing due to rotation within our current framework does increase the production of N15 in the partial mixing zone, however still falling short of what seems required by observations.Comment: 50 pages, 13 figures, ApJ in press, tentatively scheduled for v593 n2 August 20, 200

Darwinism and environmentalism

What implications does Darwinism have for our attitude towards the environment? At first sight, it might look as though Darwinism is not friendly towards environmental concerns. Darwinism is often thought to paint a picture of ruthless competition between, as well as within, species. Moreover, Darwinism may be thought to encourage a view of the environment as something to be exploited for self-interested gain. The present paper proposes a more positive view. It will be argued that mutual benefit is just as central to evolution as is competition. This will be argued for partly drawing on the work of Lynn Margulis, who makes a case that many of the major transitions in evolution came about through the setting-up of symbiotic relationships, and that what we often think of as an ‘organism’ is in fact a collection of symbionts. Moreover, a proper understanding of evolution reveals the intimate connection between an organism and its environment. The organism is partially constituted by its environment, so that in radically altering the environment an organism is potentially damaging itself. Recent work in evolutionary developmental biology has revealed previously unsuspected deep structural similarities, as well as co-operation, across a wide spectrum of living things. Thus, it will be argued, there is an environment which has shaped, and been shaped by, terrestrial life as a whole. It will be concluded that, firstly, a view that sees our duties towards the environment as deriving from our duties towards other humans would lead to a strongly conservationist programme of action; and secondly, a view of the natural world as in a strong sense ‘ours’, where this means belonging to life as a whole, makes good sense in the light of evolutionary theory

Opinion diversity and community formation in adaptive networks

It is interesting and of significant importance to investigate how network structures co-evolve with opinions. The existing models of such co-evolution typically lead to the final states where network nodes either reach a global consensus or break into separated communities, each of which holding its own community consensus. Such results, however, can hardly explain the richness of real-life observations that opinions are always diversified with no global or even community consensus, and people seldom, if not never, totally cut off themselves from dissenters. In this article, we show that, a simple model integrating consensus formation, link rewiring and opinion change allows complex system dynamics to emerge, driving the system into a dynamic equilibrium with co-existence of diversified opinions. Specifically, similar opinion holders may form into communities yet with no strict community consensus; and rather than being separated into disconnected communities, different communities remain to be interconnected by non-trivial proportion of inter-community links. More importantly, we show that the complex dynamics may lead to different numbers of communities at steady state with a given tolerance between different opinion holders. We construct a framework for theoretically analyzing the co-evolution process. Theoretical analysis and extensive simulation results reveal some useful insights into the complex co-evolution process, including the formation of dynamic equilibrium, the phase transition between different steady states with different numbers of communities, and the dynamics between opinion distribution and network modularity, etc.Comment: 12 pages, 8 figures, Journa

On the robustness of H-deficient post-AGB tracks

We analyze the robustness of H--deficient post--AGB tracks regarding previous evolution of their progenitor stars and the constitutive physics of the remnants. Our motivation is a recent suggestion of Werner & Herwig (2006) that previous evolution should be important in shaping the final post--AGB track and the persisting discrepancy between asteroseismological and spectroscopical mass determinations. This work is thus complementary to our previous work (Miller Bertolami & Althaus 2006) and intends to shed some light on the uncertainty behind the evolutionary tracks presented there. We compute full evolutionary models for PG1159 stars taking into account different extramixing (overshooting) efficiencies and lifetimes on the TP-AGB during the progenitor evolution. We also assess the effect of possible differences in the opacities and equation of state by artificially changing them before the PG1159 stage. Also comparisons are made with the few H-deficient post--AGB tracks available in the literature. Contrary to our expectations, we found that previous evolution is not a main factor in shaping H--deficient post--AGB tracks. Interestingly enough, we find that only an increase of $\sim50$ in the intershell opacities at high effective temperatures may affect the tracks as to reconcile spectroscopic and asteroseismologic mass determinations. This forces us to conclude that our previous tracks (Miller Bertolami & Althaus 2006) are robust enough as to be used for spectroscopic mass determinations, unless opacities in the intershell region are substantially different. Our results, then, call for an analysis of possible systematics in the usually adopted asteroseismological mass determination methods.Comment: Accepted for publication in Astronomy and Astrophysc

Understanding evolutionary processes during past Quaternary climatic cycles: Can it be applied to the future?

Climate change affected ecological community make-up during the Quaternary which was probably both the cause of, and was caused by, evolutionary processes such as species evolution, adaptation and extinction of species and populations