Chuang Liu

Posttranslational modification of proteins and peptides is important for diverse biological processes in plants and animals. The paucity of heterologous expression systems for PTMs and the technical challenges associated with chemical synthesis of these modified proteins has limited detailed molecular characterization and therapeutic applications. Here we describe an optimized system for expression of tyrosine-sulfated proteins in Escherichia coli and its application in a bio-based crop protection strategy in rice.

In this essay I argue against the idea that modeling in science is analogous to fiction making in literary works by pointing out that a typical move in the former, which is widely acknowledged in philosophy literature as a signal for fictionalization, is never present in works of fiction. I further argue that the reason for such a disparity is profound and profoundly against conceiving modeling as fictionalization. I then explain the difference between the hypothetical and the fictional, and argue that modeling in science belongs to the former.

En este artículo, exploro una metáfora engeometría que nos ayuda a entender mejorel debate sobre la unidad y la desunidad dela ciencia, a saber, la posibilidad de poner unsistema global de coordenadascartesianas sobreuna variedad .Explicaré las razones por las que ésta es unabuena metáfora capaz de mostrar lo quesignifica launificación para la ciencia. Posteriormente,examinaré una parte de la literatura sobre eldebate unidad/desunidad y mostraré cómoesta metáfora puede iluminar algunos de losargumentos y puntos de vista.n this essay, I explore a metaphor in geometryfor the debate between the unity and thedisunity of science, namely, the possibility ofputting a global coordinate system on a manifold. I explain why the former is agood metaphor that shows what it means for science to beunified. I then go through some of the existingliterature on the unity/disunity debate andshow how the metaphor sheds light on someof the views and arguments

The paper discusses the recent literature on abstraction/idealization in connection with the “paradox of infinite idealization.” We use the case of taking thermodynamics limit in dealing with the phenomena of phase transition and critical phenomena to broach the subject. We then argue that the method of infinite idealization is widely used in the practice of science, and not all uses of the method are the same. We then confront the compatibility problem of infinite idealization with scientific realism. We propose and defend a contextualist position for realism and argue that the cases for infinite idealization appear to be fully compatible with contextual realism.

The paper discusses the recent literature on abstraction/idealization in connection with the “paradox of infinite idealization.” We use the case of taking thermodynamics limit in dealing with the phenomena of phase transition and critical phenomena to broach the subject. We then argue that the method of infinite idealization is widely used in the practice of science, and not all uses of the method are the same. We then confront the compatibility problem of infinite idealization with scientific realism. We propose and defend a contextualist position for realism and argue that the cases for infinite idealization appear to be fully compatible with contextual realism.

Kripke has taken the Gödel case as a counterexample for reference descriptivism. Machery et al. question the validity of Kripke’s case and had conducted empirical studies to show its inadequacy. Experimental data suggest intuitions on this matter vary both across and within cultures. However, there is a descriptive ambiguity, we argue, in Kripke’s Gödel case, for people associate different types of descriptions with proper names, such as the description of brute facts and the description of social facts. We argue in this paper with experimental data that the descriptive ambiguity exists and affects the actual ratio of Kripkeans in reference. This result flaws Machery et al.’s interpretation on empirical research, but does not challenge their claim on cross-cultural divergence. In fact, there are more East Asian descriptivists than Machery et al. expected.

This volume contains the contributed papers of invitees to SEMS 2012 who have also given talks at the conference. The invitees are experts in philosophy of science and technology from Asia (besides China), Australia, Europe, Latin America, North America, as well as from within China. The papers in this volume represent the latest work of each researcher in his or her expertise; and as a result, they give a good representation of the cutting-edge researches in diverse areas in different parts of the world.

Fictional models in science -- The hypothetical versus the fictional -- What is wrong with the new fictionalism of scientific models? -- Re-inflating the conception of scientific representation -- Idealization, confirmation, and scientific realism -- Laws and models in a theory of idealization -- Approximation and its measures -- Approximation, idealization, and the laws of nature -- Coordination of space and unity of science -- Gauge gravity and the unification of natural forces -- Models and theories II: issues and applications -- Models and theories I: the semantic view revisited -- Explaining quantum spontaneous symmetry breaking -- Review: symmetries in physics: philosophical reflections -- Classical spontaneous symmetry breaking -- Spontaneous symmetry breaking and chance in a classical world -- Approximations, idealizations, and models in statistical mechanics -- Infinite systems in SM explanations: thermodynamic limit, renormalization (semi-) groups, and irreversibility -- Explaining the emergence of cooperative phenomena -- A possible unified understanding of probabilistic objects -- Particularism and holism revisited -- Potential, propensity and categorical realism -- The Aharonov-Bohm effect and the reality of wave packets -- Realism and spacetime: of arguments against metaphysical realism and manifold realism -- Gauge invariance, Cauchy problem, indeterminism, and symmetry breaking -- Is there a relativistic thermodynamics? a case study of the meaning of special relativity.

In this paper, we argue that symbols are conventional vehicles whose chief function is denotation, while models are epistemic vehicles, and their chief function is to show what their targets are like in the relevant aspects. And we explain why this is incompatible with the deflationary view on scientific modeling. Although the same object may serve both functions, the two vehicles are conceptually distinct and most models employ both elements. With the clarification of this point we offer an alternative account to the deflationary view – the Hybrid Account; and we defend our account in contrast with deflationism

This essay explores the nature of spontaneous symmetry breaking (SSB) in connection with a cluster of interrelated concepts such as Curie's symmetry principle, ergodicity, and chance and stability in classical systems. First, a clarification of the two existing senses of SSB is provided and an argument developed for a proposal for SSB, in which not only the possibilities but also the actual breakings are referred to. Second, a detailed analysis is given of classical SSB that answers the questions: (i) how we are justified in regarding it as a matter of chance, and (ii) why the breakings in it are equally probable. The answer provides some support to the applicability of ergodicity in special systems (such as ours).

This paper aims at answering the simple question `what is spontaneous symmetry breaking (SSB)?` by analyzing from a philosophical perspective a simple classical model which exhibits all the requisite properties of SSB. Related questions include: what does it mean to say that a symmetry is spontaneously broken? Is it broken without any cause, or is the symmetry not broken but merely hidden? Is the meta-principle, `no asymmetry in, no asymmetry out,` violated by SSB? And what is the role in this of random perturbations (or fluctuations)?

I argue that categorical realism, contrary to what most believe today, holds for quantum (and indeed for all) objects and substances. The main argument consists of two steps: (i) the recent experimental verification of the AB effect gives strong empirical evidence for taking quantum potentials as physically real (or substantival), which suggests a change of the data upon which any viable interpretation of quantum theory must rely, and (ii) quantum potentials may be consistently taken as the categorical properties of quantum objects so that categorical realism can be restored.

This paper examines the justifications for using infinite systems to 'recover' thermodynamic properties, such as phase transitions (PT), critical phenomena (CP), and irreversibility, from the micro-structure of matter in bulk. Section 2 is a summary of such rigorous methods as in taking the thermodynamic limit (TL) to recover PT and in using renormalization (semi-) group approach (RG) to explain the universality of critical exponents. Section 3 examines various possible justifications for taking TL on physically finite systems. Section 4 discusses the legitimacy of applying TL to the problem of irreversibility and assesses the repercussions for its legitimacy on its home turf

The present essay aims at broadening the recent discussion on the issue of holism vs. particularism in quantum physics. I begin with a clarification of the relation between the holism/particularism debate and the discussion of supervenience relation. I then defend particularism in physics (including quantum physics) by considering a new classification of properties of physical systems. With such a classification, the results in the Bell theorem are shown to violate spatial separability but not physical particularism

Physics seems to tell us that there are four fundamental force-fields in nature: the gravitational, the electromagnetic, the weak, and the strong (or interactions). But it also seems to tell us that gravity cannot possibly be a force-field, in the same sense as the other three are. And yet the search for a grand unification of all four force-fields is today one of the hottest pursuits. Is this the result of a simple confusion? This article aims at clarifying this situation by (i) reviewing the gauge-field programme and its conception of unification of force-fields, (ii) examining the various attempts at a gauge theory of gravity, and (iii) articulating the nature of "gauging" and using it to explain the difference between gravity and the other force-fields.

In this paper, a criticism of the traditional theories of approximation and idealization is given as a summary of previous works. After identifying the real purpose and measure of idealization in the practice of science, it is argued that the best way to characterize idealization is not to formulate a logical model – something analogous to Hempel's D-N model for explanation – but to study its different guises in the praxis of science. A case study of it is then made in thermostatistical physics. After a brief sketch of the theories for phase transitions and critical phenomena, I examine the various idealizations that go into the making of models at three difference levels. The intended result is to induce a deeper appreciation of the complexity and fruitfulness of idealization in the praxis of model-building, not to give an abstract theory of it.

Purpose To investigate the reliability and accuracy of two pseudo-continuous arterial spin labeling sequences, using two-dimensional gradient-echo echo planar imaging and 3D gradient and spin echo as the readout, respectively. Materials and Methods Each sequence was performed twice 4 weeks apart on six normal control subjects, six elderly subjects with mild cognitive impairment, and one participant with Alzheimer's disease. Eight of these subjects also underwent H 215O positron emission tomography scans on the same day or proximal to their second MRI scan. The longitudinal repeatability of EPI and GRASE pCASL were evaluated with the intraclass correlation coefficient and within-subject coefficient of variation. Results The ICCs of global perfusion measurements were 0.697 and 0.413 for GRASE and EPI based pCASL respectively. GRASE pCASL also demonstrated a higher longitudinal repeatability for regional perfusion measurements across 24 regions-of-interests compared with EPI pCASL. When compared with PET, EPI pCASL showed a higher degree of spatial correlation with PET than GRASE pCASL, although the difference was not statistically significant. Conclusion The 3D GRASE pCASL offers better repeatability than 2D EPI pCASL, thereby may provide a reliable imaging marker for the evaluation of disease progression and treatment effects in MCI and early AD subjects. © 2013 Wiley Periodicals, Inc.

The use of models to scientifically represent and study reality is widely recognized with good reasons as indispensable for the practice of science. Because models, unlikely pure verbal representation, are justifiably regarded as vehicles of representation that are not truth-apt, philosophical questions are natural raised concerning the nature of such vehicles and how they represent. A sizeable literature generated in recent years explores the possibility that ''scientific models are works of fiction''. Idealization and other similar strategies are often taken to be the means by which models are made. Arguing against this last claim, the thesis of this article is that most models in science are not fictional. The author argues against the idea that idealization is the means by which models of typically unobservable systems or mechanisms are made.

The concepts in the title refer to properties of physical theories and this paper investigates their nature and relations. The first three concepts, especially gauge invariance and indeterminism, have been widely discussed in connection to spacetime theories and the hole argument. Since the gauge invariance principle is at the crux of the issue, this paper aims at clarifying the nature of gauge invariance. I first explore the following chain of relations: gauge invariance $\Rightarrow $ the conservation laws $\Rightarrow $ the Cauchy problem $\Rightarrow $ indeterminism. Then I discuss gauge invariance in light of our understanding of the above relations and the possibility of spontaneous symmetry breaking

In this paper I argue against a deflationist view that as representational vehicles symbols and models do their jobs in essentially the same way. I argue that symbols are conventional vehicles whose chief function is denotation while models are epistemic vehicles whose chief function is showing what their targets are like in the relevant aspects. It is further pointed out that models usually do not rely on similarity or some such relations to relate to their targets. For that referential relation they reply instead on symbols (names and labels) given to them and their parts. And a Goodmanian view on pictures of fictional characters reveals the distinction between symbolic and model representations.

This paper contains four variations on Duhem's theme about the contrast between the abstract French mind and the concrete British mind. The first variation brings out the real contrast between two types of methods and their results: the A method or models and the C method or models. The second variation gives a critical discussion of the Callender-Cohen deflationary contruel of scientific representation. The third variation discusses Russell's structuralism in connection to the theme. And the fourth variation critically discusses the relationship between models and fiction in connection to the distinction between the A-models and the C-models. A coda maps out without sufficiently detailed arguments the author's view on the nature of the C-models and why they, and only they, can be viewed as fully fictional.