Using structural information to change the phosphotransfer specificity of a two-component chemotaxis signalling complex.

addresses: Oxford Centre for Integrative Systems Biology, Department of Biochemistry, University of Oxford, Oxford, United Kingdom.notes: PMCID: PMC2817712types: Journal Article; Research Support, Non-U.S. Gov'tCopyright: © 2010 Bell et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Two-component signal transduction pathways comprising histidine protein kinases (HPKs) and their response regulators (RRs) are widely used to control bacterial responses to environmental challenges. Some bacteria have over 150 different two-component pathways, and the specificity of the phosphotransfer reactions within these systems is tightly controlled to prevent unwanted crosstalk. One of the best understood two-component signalling pathways is the chemotaxis pathway. Here, we present the 1.40 A crystal structure of the histidine-containing phosphotransfer domain of the chemotaxis HPK, CheA(3), in complex with its cognate RR, CheY(6). A methionine finger on CheY(6) that nestles in a hydrophobic pocket in CheA(3) was shown to be important for the interaction and was found to only occur in the cognate RRs of CheA(3), CheY(6), and CheB(2). Site-directed mutagenesis of this methionine in combination with two adjacent residues abolished binding, as shown by surface plasmon resonance studies, and phosphotransfer from CheA(3)-P to CheY(6). Introduction of this methionine and an adjacent alanine residue into a range of noncognate CheYs, dramatically changed their specificity, allowing protein interaction and rapid phosphotransfer from CheA(3)-P. The structure presented here has allowed us to identify specificity determinants for the CheA-CheY interaction and subsequently to successfully reengineer phosphotransfer signalling. In summary, our results provide valuable insight into how cells mediate specificity in one of the most abundant signalling pathways in biology, two-component signal transduction

Ambiguous figures and the content of experience

Representationalism is the position that the phenomenal character of an experience is either identical with, or supervenes on, the content of that experience. Many representationalists hold that the relevant content of experience is nonconceptual. I propose a counterexample to this form of representationalism that arises from the phenomenon of Gestalt switching, which occurs when viewing ambiguous figures. First, I argue that one does not need to appeal to the conceptual content of experience or to judgements to account for Gestalt switching. I then argue that experiences of certain ambiguous figures are problematic because they have different phenomenal characters but that no difference in the nonconceptual content of these experiences can be identified. I consider three solutions to this problem that have been proposed by both philosophers and psychologists and conclude that none can account for all the ambiguous figures that pose the problem. I conclude that the onus is on representationalists to specify the relevant difference in content or to abandon their position

The Facts and Practices of Moral Responsibility

Strawsonians about moral responsibility often claim that our practices of holding morally responsible fix the facts of moral responsibility, rather than the other way round. Many have argued that such ‘reversal’ claims have an unwelcome consequence: If our practices of holding morally responsible fix the facts of moral responsibility, does this not imply, absurdly, that if we held severely mentally ill people responsible, they would be responsible? We provide a new Strawsonian answer to this question, and we explore the relation between reversal claims and (in)compatibilism.status: publishe

Stylasterid corals: a new paleotemperature archive

Stylasterids are a ubiquitous deep-sea coral taxon that build their skeletons from either calcite, aragonite, or both. Yet, robust geochemical proxy data from these corals are limited. In this study, 95 modern stylasterids, spanning a wide range of depths (63 to 2894 m) and ambient seawater temperatures (0 to 17 °C), were tested for their potential use as paleoceanographic archives. Stable oxygen and carbon isotopic composition (O and C) were measured from the main trunk of all specimens and five specimens were further sub-sampled to assess internal chemical variability. The isotope data show non-equilibrium precipitation from seawater for both O and C, with the growing tips of colonies yielding the isotopically lowest values. Overall, the calcitic corals showed lower isotope values for O and C than aragonitic specimens. Within the aragonite corals, we present a O:temperature calibration that exhibits a significant linear relationship with the equation Ocoral-seawater = −0.22(°C) + 3.33(±0.06) across a temperature range of 0 to 30 °C, using samples from this study and published data. This work highlights the potential application of stylasterid coral O data to reconstruct paleo seawater temperature

Normative Alethic Pluralism

Some philosophers have argued that truth is a norm of judgement and have provided a variety of formulations of this general thesis. In this paper, I shall side with these philosophers and assume that truth is a norm of judgement. What I am primarily interested in here are two core questions concerning the judgement-truth norm: (i) what are the normative relationships between truth and judgement? And (ii) do these relationships vary or are they constant? I argue for a pluralist picture—what I call Normative Alethic Pluralism (NAP)—according to which (i) there is more than one correct judgement-truth norm and (ii) the normative relationships between truth and judgement vary in relation to the subject matter of the judgement. By means of a comparative analysis of disagreement in three areas of the evaluative domain—refined aesthetics, basic taste and morality—I show that there is an important variability in the normative significance of disagreement—I call this the variability conjecture. By presenting a variation of Lynch’s scope problem for alethic monism, I argue that a monistic approach to the normative function of truth is unable to vindicate the conjecture. I then argue that normative alethic pluralism provides us with a promising model to account for it

I Me Mine: on a Confusion Concerning the Subjective Character of Experience

In recent debates on phenomenal consciousness, a distinction is sometimes made, after Levine (2001) and Kriegel (2009), between the “qualitative character” of an experience, i.e. the specific way it feels to the subject (e.g. blueish or sweetish or pleasant), and its “subjective character”, i.e. the fact that there is anything at all that it feels like to her. I argue that much discussion of subjective character is affected by a conflation between three different notions. I start by disentangling the three notions in question, under the labels of “for-me-ness”, “me-ness” and “mineness”. Next, I argue that these notions are not equivalent; in particular, there is no conceptual implication from for-me-ness to me-ness or mineness. Empirical considerations based on clinical cases additionally suggest that the three notions may also correspond to different properties (although the claim of conceptual non-equivalence does not depend on this further point). The aim is clarificatory, cautionary but also critical: I examine four existing arguments from subjective character that are fuelled by an undifferentiated use of the three notions, and find them to be flawed for this reason

How to return to subjectivity? Natorp, Husserl, and Lacan on the limits of reflection

This article discusses the recent call within contemporary phenomenology to return to subjectivity in response to certain limitations of naturalistic explanations of the mind. The meaning and feasibility of this call is elaborated by connecting it to a classical issue within the phenomenological tradition concerning the possibility of investigating the first-person perspective through reflection. We will discuss how this methodological question is respectively treated and reconfigured in the works of Natorp, Husserl, and Lacan. Finally, we will lay out some possible consequences of such a cross-reading for the conception of subjectivity and the concomitant effort to account for this dimension of first-person experience in response and in addition to its omission within the standard third-person perspective of psychological research

Free Will in a Quantum World?

In this paper, I argue that Conway and Kochen’s Free Will Theorem (1,2) to the conclusion that quantum mechanics and relativity entail freedom for the particles, does not change the situation in favor of a libertarian position as they would like. In fact, the theorem more or less implicitly assumes that people are free, and thus it begs the question. Moreover, it does not prove neither that if people are free, so are particles, nor that the property people possess when they are said to be free is the same as the one particles possess when they are claimed to be free. I then analyze the Free State Theorem (2), which generalizes the Free Will Theorem without the assumption that people are free, and I show that it does not prove anything about free will, since the notion of freedom for particles is either inconsistent, or it does not concern our common understanding of freedom. In both cases, the Free Will Theorem and the Free State Theorem do not provide any enlightenment on the constraints physics can pose on free will