Protein Import Into Chloroplasts: An Ever-Evolving Story

Chloroplasts are but one type of a diverse group of essential organelles that distinguish plant cells and house many critical biochemical pathways, including photosynthesis. The biogenesis of plastids is essential to plant growth and development and relies on the targeting and import of thousands of nuclear-encoded proteins from the cytoplasm. The import of the vast majority of these proteins is dependent on translocons located in the outer and inner envelope membranes of the chloroplast, termed the Toc and Tic complexes, respectively. The core components of the Toc and Tic complexes have been identified within the last 12 years; however, the precise functions of many components are still being elucidated, and new components are still being identified. In Arabidopsis thaliana (and other species), many of the components are encoded by more than one gene, and it apperas that the isoforms differentially associate with structurally distinct import complexes. Furthermore, it appears that these complexes represent functionally distinct targeting pathways, and the regulation of import by these separate pathways may play a role in the differentiation and specific functions of distinct plastid types during plant growth and development. This review summarizes these recent discoveries and emphasizes the mechanisms of differential Toc complex assembly and substrate recognition

Book Review: Fairness vs. Welfare

Reviewing Louis Kaplow & Steven Shavell, Fairness versus Welfare (2002

Constitutional Fidelity, The Rule of Recognition, and the Communitarian Turn in Contemporary Positivism

Contemporary positivism has taken a communitarian turn. Hart, in the Postscript to the Concept of Law, clarifies that the rule of recognition is a special sort of social practice: a convention. It is not clear whether Hart, here, means “convention” in the strict sense elaborated by David Lewis, or in some weaker sense. A number of contemporary positivists, including Jules Coleman (at one point), Andrei Marmor, and Gerald Postema, have argued that the rule of recognition is something like a Lewis-convention. Others have suggested that the rule of recognition is conventional in a weaker sense -- specifically, by figuring in a “shared cooperative activity” (SCA) among officials. Chris Kutz, Scott Shapiro, and Jules Coleman (more recently) have adopted this model. This Article criticizes the Lewis-convention and SCA models of the rule of recognition, drawing on U.S. constitutional theory. Imagine a society of U.S. officials who are committed to the text of the 1787 Constitution in a strong form: each official would continue to accept the text as supreme law even if every other official defected to an alternative text, and no official is prepared to bargain or negotiate with the others about the supremacy of the text. The social practice among these officials is neither a Lewis-convention (since there is no alternative text to which every official would shift if every other official did), nor an SCA (since the officials have no general intention to “mesh” their conceptions of legal validity with each other, and in particular have no intention to compromise with officials who deny the supremacy of the 1787 text). Therefore, under the Lewis-convention and SCA models, a hypothetical society of U.S. officials who are committed, first and foremost, to the 1787 text rather than to the community of officials, is not a full-fledged legal system. But this is deeply counterintuitive. The hypothetical society simply embodies, in a particularly pure form, an attitude of fidelity to the 1787 text that many officials and citizens currently profess. The tension between the Lewis-convention and SCA models of the rule of recognition, and constitutional fidelity, points the way to a different model of the rule of recognition: namely, that the rule of recognition is a social norm

Translated Chemical Reaction Networks

Many biochemical and industrial applications involve complicated networks of simultaneously occurring chemical reactions. Under the assumption of mass action kinetics, the dynamics of these chemical reaction networks are governed by systems of polynomial ordinary differential equations. The steady states of these mass action systems have been analysed via a variety of techniques, including elementary flux mode analysis, algebraic techniques (e.g. Groebner bases), and deficiency theory. In this paper, we present a novel method for characterizing the steady states of mass action systems. Our method explicitly links a network's capacity to permit a particular class of steady states, called toric steady states, to topological properties of a related network called a translated chemical reaction network. These networks share their reaction stoichiometries with their source network but are permitted to have different complex stoichiometries and different network topologies. We apply the results to examples drawn from the biochemical literature

ADADELTA: An Adaptive Learning Rate Method

We present a novel per-dimension learning rate method for gradient descent called ADADELTA. The method dynamically adapts over time using only first order information and has minimal computational overhead beyond vanilla stochastic gradient descent. The method requires no manual tuning of a learning rate and appears robust to noisy gradient information, different model architecture choices, various data modalities and selection of hyperparameters. We show promising results compared to other methods on the MNIST digit classification task using a single machine and on a large scale voice dataset in a distributed cluster environment.Comment: 6 page