bluuebunny/crossref_metadata_2025 huggingface dataset:
Folk Psychology and Cognitive Architecture
Authors: Egan Frances
Published: December 2007

It has recently been argued that the success of the connectionist program in cognitive science would threaten folk psychology. I articulate and defend a “minimalist” construal of folk psychology that comports well with empirical evidence on the folk understanding of belief and is compatible with even the most radical developments in cognitive science.
The Impossibility of Accurate State Self-Measurements
Authors: Breuer Thomas
Published: December 2007

It is shown that it is impossible for an observer to distinguish all present states of a system in which he or she is contained, irrespective of whether this system is a classical or a quantum mechanical one and irrespective of whether the time evolution is deterministic or stochastic. As a corollary, this implies that it is impossible for an observer to measure the EPR-correlations between himself or herself and an outside system. Implications of the main result are discussed for how we have to conceive of universally valid theories.
Truthlikeness, Translation, and Approximate Causal Explanation
Authors: Barnes Eric
Published: December 2007

D. Miller's demonstrations of the language dependence of truthlikeness raise a profound problem for the claim that scientific progress is objective. In two recent papers (Barnes 1990, 1991) I argue that the objectivity of progress may be grounded on the claim that the aim of science is not merely truth but knowledge; progress thus construed is objective in an epistemic sense. In this paper I construct a new solution to Miller's problem grounded on the notion of “approximate causal explanation” which allows for linguistically invariant progress outside an epistemic context. I suggest that the notion of “approximate causal explanation” provides the resources for a more robust theory of progress than that provided by the notion of “approximate truth.”
Is Mathematical Competence Innate?
Authors: Schwartz Robert
Published: December 2007

Despite a vast philosophical literature on the epistemology of mathematics and much speculation about how, in principle, knowledge of this domain is possible, little attention has been paid to the psychological findings and theories concerning the acquisition, comprehension and use of mathematical knowledge. This contrasts sharply with recent philosophical work on language where comparable issues and problems arise. One topic that is the center of debate in the study of mathematical cognition is the question of innateness. This paper critically examines the controversy.
Toward A Defensible Bootstrapping
Authors: Mitchell Sam
Published: December 2007

An amended bootstrapping can avoid Christensen's counterexamples. Earman and Edidin argue that Christensen's examples to bootstrapping rely on his failure to analyze background knowledge. I add an additional condition to bootstrapping that is motivated by Glymour's remarks on variety of evidence. I argue that it avoids the problems that the examples raise. I defend the modification against the charge that it is holistic, and that it collapses into Bayesianism.
Explanation and Evaluation in Cognitive Science
Authors: Montgomery Richard
Published: December 2007

With some regularity, cognitive scientists seem to introduce cognitivevaluesinto their explanations. After identifying examples of this practice, I sketch an account of psychological explanation that, under certain conditions, legitimizes value-laden cognitive explanations in which evaluative claims appear in the explanandum. I then present and discuss two applications of the proposed account in order to show its viability and explore its consequences.
Discussion: Salmon on Explanatory Relevance
Authors: Hitchcock Christopher Read
Published: December 2007

One of the motivations for Salmon's (1984) causal theory of explanation was the explanatory irrelevance exhibited by many arguments conforming to Hempel's covering-law models of explanation. However, the nexus of causal processes and interactions characterized by Salmon is not rich enough to supply the necessary conception of explanatory relevance. Salmon's (1994) revised theory, which is briefly criticized on independent grounds, fares no better. There is some possibility that the two-tiered structure of explanation described by Salmon (1984) may be pressed into service, but more work would have to be done. Ironically, Salmon's difficulties are similar to those suffered by his seventeenth-century predecessors.
Wisdom Updated
Authors: Falk Arthur
Published: December 2007

Given the personalist's latitudinarian conception of rationality, what is progress toward wisdom? An answer is in C. I. Lewis's concept of the “congruence” of propositions, propositions so related that the antecedent probability of any one of them will be increased if the remainder can be assumed. This effect can be modelled in the probability calculus with due attention to the temporal sequencing of our learning of contingent propositions without ever becoming certain of them, as Jeffrey proposes. A diachronic bootstrapping effect is obtained for Ockham's razor and premises of arguments about a god's existence. As a theory's probability rises with increased evidence, the probability of our earlier evidence rises too.
Holes and Determinism: Another Look
Authors: Leeds Stephen
Published: December 2007

I argue that Earman and Norton's familiar “hole argument” raises questions as to whether GTR is a deterministic theory only given a certain assumption about determinism: namely, that to ask whether a theory is deterministic is to ask about the physical situations described by the theory. I think this is a mistake: whether a theory is deterministic is a question about what sentences can be proved within the theory. I show what these sentences look like: for interesting theories, a harmless bit of infinitary logic puts in an appearance.
Objectivity in Experimental Inquiry: Breaking Data-Technique Circles
Authors: Culp Sylvia
Published: December 2007

I respond to H. M. Collins's claim (1985, 1990, 1993) that experimental inquiry cannot be objective because the only criterium experimentalists have for determining whether a technique is “working” is the production of “correct” (i.e., the expected) data. Collins claims that the “experimenters' regress,” the name he gives to this data-technique circle, cannot be broken using the resources of experiment alone. I argue that the data-technique circle, can be broken even though any interpretation of the raw data produced by techniques is theory-dependent. However, it is possible to break this circle by eliminating dependence on even those theoretical presuppositions that are shared by an entire scientific community through the use of multiple independently theory-dependent techniques to produce robust bodies of data. Moreover, I argue, that it is the production of robust bodies of data that convinces experimentalists of the objectivity of their data interpretations.
Discussion: Why Bohm's Theory Solves the Measurement Problem
Authors: Maudlin Tim
Published: December 2007

Abraham Stone recently has published an argument purporting to show that David Bohm's interpretation of quantum mechanics fails to solve the measurement problem. Stone's analysis is not correct, as he has failed to take account of the conditions under which the theorems he cites are proven. An explicit presentation of a Bohmian measurement illustrates the flaw in his reasoning.
The Force of Newtonian Cosmology: Acceleration is Relative
Authors: Norton John D.
Published: December 2007

1. Introduction. David Malament (1995) has described a natural and satisfying resolution of the traditional problems of Newtonian cosmology—natural in the sense that it effects the escape by altering Newtonian gravitation theory in a way that leaves its observational predictions completely unaffected. I am in full agreement with his approach. There is one part of his account, however, over which Malament has been excessively modest. The resolution requires a modification to Newtonian gravitation theory. Malament presents the modification as so straightforward as to be automatic. This trivializes the crucial postulate, which I shall call the “relativity of acceleration.” It is a significant physical statement in its own right and requires careful justification. Moreover the postulate proved easy to overlook for decades of discussion of the paradox. It really only becomes natural from the perspective of the newer geometric methods Malament exploits. There the postulate has become a commonplace. My purpose here is to develop the following:

While Newtonian cosmology can be repaired satisfactorily, in its traditional form it remains deeply troubled. These troubles can be expressed most vividly as the paradoxical contradictions indicated below. They persist in both the integral and differential formulations of Newtonian gravitation theory. (Section 2)

Malament's careful geometric treatment is necessarily dense. By taking some liberties with precision, his core result can be expressed in a far simpler form. (Section 4)

Attempts to avoid the resolution Malament describes do lead to disaster. Therefore this episode can be inverted and used as the strongest extant argument for the relativity of acceleration in Newtonian gravitation theory. (Section 5)
Units of Behavior
Authors: Enç Berent
Published: December 2007

1. Introduction. One major concern in cognitive psychology is explaining cognitively motivated behavior. However, attempts to specify the nature of the behavior that psychology is to explain have proved to be somewhat controversial. The aim of this paper is to conduct a preliminary investigation into the kinds of behavior psychology is (or should be) concerned with.
On the Empirical Foundations of the Quantum No-Signalling Proofs
Authors: Kennedy J. B.
Published: December 2007

I analyze a number of the quantum no-signalling proofs (Ghirardi et al. 1980, Bussey 1982, Jordan 1983, Shimony 1985, Redhead 1987, Eberhard and Ross 1989, Sherer and Busch 1993). These purport to show that the EPR correlations cannot be exploited for transmitting signals, i.e., are not causal. First, I show that these proofs can be mathematically unified; they are disguised versions of a single theorem. Second, I argue that these proofs are circular. The essential theorem relies upon the tensor product representation for combined systems, which has no physical basis in the von Neumann axioms. Historically, the construction of this representation scheme by von Neumann and Weyl built no-signalling assumptions into the quantum theory. Signalling between the wings of the EPR-Bell experiments is unlikely but is not ruled out empirically by the class of proofs considered.
Beyond Bootstrapping: A New Account of Evidential Relevance
Authors: Culler Madison
Published: December 2007

This paper investigates the adequacy of evidential relevance relations proposed by Glymour and others. These accounts incorporate, as a necessary condition, what I call the Positive Instance Condition (PIC): the evidence statement and auxiliary assumptions entail a “positive instance” of the hypothesis. I argue that any account which incorporates PIC as a necessary condition while allowing “bootstrap testing” is doomed to fail. A nonbootstrapping evidential relevance relation of similar form is proposed, and it is argued that, in addition to avoiding published counter examples, this new relation meets two general requirements which, if not met, would undermine the ability of any account that incorporates PIC to accord with our intuitions of evidential relevance.
Biological Function, Adaptation, and Natural Design
Authors: Allen Colin , Bekoff Marc
Published: December 2007

Recently something close to a consensus about the best way to naturalize the notion of biological function appears to be emerging. Nonetheless, teleological notions in biology remain controversial. In this paper we provide a naturalistic analysis for the notion of natural design. Many authors assume that natural design should be assimilated directly to function. Others find the notion problematic because it suggests that evolution is a directed process. We argue that both of these views are mistaken. Our naturalistic account does not simply equate design with function. We argue that the distinction between function and design is important for understanding the evolution of the physical and behavioral traits of organisms.
Theory-Dependent Terms
Authors: Papineau David
Published: December 2007

The main puzzle about theoretical definitions is that nothing seems to decide which assumptions contribute to such definitions and which do not. I argue that theoretical definitions are indeed imprecise, but that this does not normally matter, since the definitional imprecision does not normally produce indeterminacy of referential value. Sometimes, however, the definitional imprecision is less benign, and does generate referential indeterminacy. In these special cases, but not otherwise, it is necessary to refine the term's definition.
Darwinian Algorithms and Indexical Representation
Authors: Clarke Murray
Published: December 2007

In this paper, I argue that accurate indexical representations have been crucial for the survival and reproduction of homo sapiens sapiens. Specifically, I want to suggest that reliable processes have beenselected forbecause of their indirect, but close, connection to true belief during the Pleistocene hunter-gatherer period of our ancestral history. True beliefs are not heritable, reliable processes are heritable. Those reliable processes connected with reasoning take the form of Darwinian Algorithms: a plethora of specialized, domain-specific inference rules designed to solve specific, recurrent, adaptive problems in social exchange contexts. Humans do not reason logically, but adaptively.
Empirical Adequacy and the Availability of Reliable Records in Quantum Mechanics
Authors: Barrett Jeffrey A.
Published: December 2007

In order to judge whether a theory is empirically adequate one must have epistemic access to reliable records of past measurement results that can be compared against the predictions of the theory. Some formulations of quantum mechanics fail to satisfy this condition. The standard theory without the collapse postulate is an example. Bell's reading of Everett's relative-state formulation is another. Furthermore, there are formulations of quantum mechanics that only satisfy this condition for a special class of observers, formulations whose empirical adequacy could only be judged by an observer who records her measurement results in a special way. Bohm's theory is an example. It is possible to formulate hidden-variable theories that do not suffer from such a restriction, but these encounter other problems.
Inference to the Best Explanation: Is it Really Different from Mill's Methods?
Authors: Rappaport Steven
Published: December 2007

Peter Lipton has attempted to flesh out a model of Inference to the Best Explanation (IBE) by clarifying explanation in terms of a causal model. But Lipton's account of explanation makes an adequate explanation depend on a principle which is virtually identical to Mill's Method of Difference. This has the result of collapsing IBE on Lipton's account of it into causal inference as conceived by the Causal-Inference model of induction. According to this model, many of our inductions are inferences from effects to their probable causes, and Mill's Methods are canons to guide such inferences. Thus, Lipton's account of IBE fails to represent an advance over the already familiar Causal-Inference Model of induction.
A Note on Van Fraassen's Modal Interpretation of Quantum Mechanics
Authors: Leeds Stephen , Healey Richard
Published: December 2007

Although there has been some discussion in the literature of Bas van Fraassen's modal interpretation of Quantum Mechanics, it has for the most part been concentrated on difficulties that van Fraassen's viewpoint shares with those of some other authors, including Kochen, Dieks, and Healey. van Fraassen's approach has, however, some problems of its own; in this note we want to focus on what seems to us to be one of the most serious of these. The difficulty concerns immediately repeated non-disturbing measurements of the same observable on a single system. As is well known, von Neumann's Projection Postulate guarantees that such measurements will always give the same outcome; likewise, in the approaches of the “modalists” mentioned above, such ‘consilience of repeated measurements’ is in one way or another built into the formalism. By contrast, we shall argue, van Fraassen's modal interpretation neither guarantees this result nor adequately explains why it is unnecessary to do so.
Discussion: Screening-Off and Natural Selection
Authors: van der Steen Wim J.
Published: December 2007

Sober (1992) and Brandon et al. (1994) disagree about the role of screening-off in the appraisal of theories of natural selection. Some problems disregarded by them are unearthed in this discussion note.
Subjective and Objective Confirmation
Authors: Maher Patrick
Published: December 2007

Confirmation is commonly identified with positive relevance, E being said to confirm H if and only if E increases the probability of H. Today, analyses of this general kind are usually Bayesian ones that take the relevant probabilities to be subjective. I argue that these subjective Bayesian analyses are irremediably flawed. In their place I propose a relevance analysis that makes confirmation objective and which, I show, avoids the flaws of the subjective analyses. What I am proposing is in some ways a return to Carnap's conception of confirmation, though there are also important differences between my analysis and his. My analysis includes new accounts of what evidence is and of the indexicality of confirmation claims. Finally, I defend my analysis against Achinstein's criticisms of the relevance concept of confirmation.
Macroscopic Objects: An Exercise in Duhemian Ontology
Authors: Needham Paul
Published: December 2007

Aristotelian ideas are presented in a favorable light in Duhem's historical works surveying the history of the notion of chemical combination (1902) and the development of mechanics (1903). The importance Duhem was later to ascribe to Aristotelian ideas as reflected in the weight he attached to medieval science is well known. But the Aristotelian influence on his own mature philosophical perspective, and more particularly on his concern for logical coherence and the development of his ontological views, is not generally acknowledged. There are, however, clear pointers in this direction in these two earlier books on the history of science, which are unashamedly written in such a way as to project the author's own view of what is important in the relevant areas. Thermodynamics was the pinnacle of Duhemian science, and its interpretation requires the reinstatement, in Duhem's view, of Aristotelian conceptions which have been unfashionable since the rise of certain ideas with the scientific revolution of the seventeenth century.

The present paper is not primarily an exposition of these Aristotelian views of Duhem's, but an attempt to pursue the interpretation of a macroscopic, thermodynamical perspective on chemical substances from an elementary viewpoint in the spirit of Duhem (1902), sometimes being more definite than Duhem seems to be, and occasionally taking issue with him on certain points. Some of his leading ideas will determine the general approach, but views and problems will also be taken from modern textbooks in an attempt to lay down the general lines along which an explicit ontology—in Quine's sense—of macroscopic theory might be developed.
Emergence and Strange Attractors
Authors: Newman David V.
Published: December 2007

Recent work in the Philosophy of Mind has suggested that alternatives to reduction are required in order to explain the relationship between psychology and biology or physics. Emergence has been proposed as one such alternative. In this paper, I propose a precise definition of emergence, and I argue that chaotic systems provide concrete examples of properties that meet this definition. In particular, I suggest that being in the basin of attraction of a strange attractor is an emergent property of any chaotic nonlinear dynamical system. This shows that non-reductive accounts of inter-theoretic relations are necessary, and that non-reductive accounts of the mental are possible. Moreover, this work provides a foundation for future work investigating the nature of explanation, prediction, and scientific understanding of non-reductive phenomena.
Critical Review: Paul Teller'sInterpretive Introduction to Quantum Field Theory
Authors: Huggett Nick , Weingard Robert
Published: December 2007

Paul Teller's (1995) new book, “An Interpretive Introduction to Quantum Field Theory”, is a pioneering work. To the best of our knowledge it is the first book by a philosopher devoted not only to explaining what quantum field theory (QFT) is, but to clarifying the conceptual issues and puzzles to which the theory gives rise (though Auyung 1995 treats some different issues in QFT). As such it is an important book, which we hope will greatly stimulate work in the area as other philosophers and physicists react to it.
The Indeterministic Character of Evolutionary Theory: No “No Hidden Variables Proof” But no Room For Determinism Either
Authors: Brandon Robert N. , Carson Scott
Published: December 2007

In this paper we first briefly review Bell's (1964, 1966) Theorem to see how it invalidates any deterministic “hidden variable” account of the apparent indeterminacy of quantum mechanics (QM). Then we show that quantum uncertainty, at the level of DNA mutations, can “percolate” up to have major populational effects. Interesting as this point may be it does not show any autonomous indeterminism of the evolutionary process. In the next two sections we investigate drift and natural selection as the locus of autonomous biological indeterminacy. Here we conclude that the population-level indeterminacy of natural selection and drift are ultimately based on the assumption of a fundamental indeterminacy at the level of the lives and deaths of individual organisms. The following section examines this assumption and defends it from the determinists' attack. Then we show that, even if one rejects the assumption, there is still an important reason why one might think evolutionary theory (ET) is autonomously indeterministic. In the concluding section we contrast the arguments we have mounted against a deterministic hidden variable account of ET with the proof of the impossibility of such an account of QM.
On the Brussels School's Arrow of Time in Quantum Theory
Authors: Karakostas Vassilios
Published: December 2007

This paper examines the problem of founding irreversibility on reversible equations of motion from the point of view of the Brussels school's recent developments in the foundations of quantum statistical mechanics. A detailed critique of both their ‘subdynamics’ and ‘transformation’ theory is given. It is argued that the subdynamics approach involves a generalized form of ‘coarse-graining’ description, whereas, transformation theory cannot lead to truly irreversible processes pointing to a preferred direction of time. It is concluded that the Brussels school's conception of microscopic temporal irreversibility, as such, is tacitly assumed at the macroscopic level. Finally a logical argument is provided which shows, independently of the mathematical formalism of the theory concerned, that statistical reasoning alone is not sufficient to explain the arrow of time.
Plantinga's Case Against Naturalistic Epistemology
Authors: Fales Evan
Published: December 2007

InWarrant and Proper Function, Alvin Plantinga claims that metaphysical naturalism, when joined to a naturalized epistemology, is self-undermining. Plantinga argues that naturalists are committed to a neoDarwinian account of our origins, and that the reliability of our cognitive faculties is improbable or unknown relative to that theory. If the theory is true, then we are in no position to know that, whereas theism, if true, underwrites cognitive reliability. I seek to turn the tables on Plantinga, showing that neoDarwinism provides strong reasons for expecting general cognitive reliability, whereas the likelihood of that relative to theism is unknowable.
Some Comments on Rosenberg's Review
Authors: Sober Elliott
Published: December 2007

I am grateful to Philip Kitcher for inviting me to comment on Alexander Rosenberg's (1996) review of Philosophy of Biology (Sober 1993) and to Rosenberg for his kind words about my book at the very beginning and the very end of his review. However, I cannot help feeling that most of the material in Rosenberg's review describes a different book from the one I wrote. Of the four philosophical claims that he ascribes to me, only one of them is asserted or implied in Philosophy of Biology. Rosenberg is right that I have argued that many evolutionary laws turn out, when stated carefully, to be a priori mathematical truths. However, he is mistaken in thinking that I am a “historicist” who holds that “fundamental theory in biology is narrative.” Rosenberg also misconstrues my views on the meaning of probability statements in evolutionary theory.
Time, Bohm's Theory, and Quantum Cosmology
Authors: Callender Craig , Weingard Robert
Published: December 2007

One of the problems of quantum cosmology follows from the fact that the Hamiltonian H of classical general relativity equals zero. Quantizing canonically in the Schrodinger picture, the Schrodinger equation for the wave function Ψ of the universe is therefore the so-called Wheeler-DeWitt equation

(where Ĥ is the operator version of H) and we have no quantum dynamics. In particular, it follows directly that, if Ȓ is the operator representing the radius of the universe,

where <Ȓ>ψ = Ψ<|Ȓ|>Ψ, for every Ψ. The universe described by (1) does not expand. But worse still is the fact that there is no time development, contrary to our experience. Like a particle in an eigenstate of zero energy, the state of the universe does not change. The still universe resulting from (1) is a manifestation of the more general “problem of time” afflicting canonical quantum gravity. Despite rare claims to the contrary, most consider it to be a serious difficulty for quantum cosmology.
The Scientist as Adult
Authors: Giere Ronald N.
Published: December 2007

My concern is with the possible implications of research in developmental psychology for understanding the workings of modern science. I agree both with Gopnik's general naturalistic orientation and with her more specific claims about scientists as cognitive agents. Neither the formal structure of propositions nor the social structure of scientific communities provides sufficient resources for the understanding we seek. So I agree that the empirical study of human cognition is not only relevant, but necessary, for understanding how science works (Giere 1988, 1989).
Freud's ‘Tally’ Argument, Placebo Control Treatments, and the Evaluation of Psychotherapy
Authors: Greenwood John D.
Published: December 2007

In this paper it is suggested that Freud's ‘tally argument’ (Grünbaum 1984) is not best interpreted as a risky claim concerning the efficacy of psychoanalytic therapy, but as a risky claim concerning the implications of theoretical psychoanalytic explanations of the efficacy of psychoanalytic therapy. Despite the fact that Freud never empirically established that these implications hold, the ‘tally argument’ does draw attention to a critical distinction that is too often neglected in contemporary empirical studies of psychoanalysis and other forms of psychotherapy: between empirical evaluations of the efficacy of psychotherapy and empirical evaluations of theoretical explanations of the efficacy of psychotherapy, and the different forms of comparative enquiry relevant to each. It is argued that the contemporary neglect of this critical distinction, in conjunction with the common negative conception of placebo control treatments in psychotherapy research, has led to the epistemic impoverishment of experimental studies of the various professional psychotherapies. In consequence, although there is good empirical evidence for the efficacy of psychoanalysis and other forms of professional psychotherapy, there is no good empirical evidence for theoretical psychoanalytic explanations of the efficacy of psychoanalysis, or for traditional theoretical explanations of the efficacy of other forms of professional psychotherapy.
Bayesianism and Diverse Evidence: A Reply to Andrew Wayne
Authors: Myrvold Wayne C.
Published: December 2007

Andrew Wayne (1995) discusses some recent attempts to account, within a Bayesian framework, for the “common methodological adage” that “diverse evidence better confirms a hypothesis than does the same amount of similar evidence” (112). One of the approaches considered by Wayne is that suggested by Howson and Urbach (1989/1993) and dubbed the “correlation approach” by Wayne. This approach is, indeed, incomplete, in that it neglects the role of the hypothesis under consideration in determining what diversity in a body of evidence is relevant diversity. In this paper, it is shown how this gap can be filled, resulting in a more satisfactory account of the evidential role of diversity of evidence. In addition, it is argued that Wayne's criticism of the correlation approach does not indicate a serious flaw in the approach.
Bayesianism and the Value of Diverse Evidence
Authors: Steel Daniel
Published: December 2007

In a recent essay (1995), Andrew Wayne charges that Bayesian attempts to account for the rule that, ceteris paribus, diverse evidence confirms better than narrow evidence are inadequate. I reply to these criticisms and argue that, on the contrary, one of the Bayesian approaches considered by Wayne does an excellent job of explaining why, and under what circumstances, diverse evidence is valuable.
Biphasic Incorporation of Centromeric Histone CENP-A in Fission Yeast
Authors: Takayama Yuko , Sato Hiroshi , Saitoh Shigeaki , Ogiyama Yuki , Masuda Fumie , Takahashi Kohta
Published: December 2007

CENP-A is a centromere-specific histone H3 variant that is essential for kinetochore formation. Here, we report that the fission yeast Schizosaccharomyces pombe has at least two distinct CENP-A deposition phases across the cell cycle: S and G2. The S phase deposition requires Ams2 GATA factor, which promotes histone gene activation. In Δams2, CENP-A fails to retain during S, but it reaccumulates onto centromeres via the G2 deposition pathway, which is down-regulated by Hip1, a homologue of HIRA histone chaperon. Reducing the length of G2 in Δams2 results in failure of CENP-A accumulation, leading to chromosome missegregation. N-terminal green fluorescent protein-tagging reduces the centromeric association of CENP-A, causing cell death in Δams2 but not in wild-type cells, suggesting that the N-terminal tail of CENP-A may play a pivotal role in the formation of centromeric nucleosomes at G2. These observations imply that CENP-A is normally localized to centromeres in S phase in an Ams2-dependent manner and that the G2 pathway may salvage CENP-A assembly to promote genome stability. The flexibility of CENP-A incorporation during the cell cycle may account for the plasticity of kinetochore formation when the authentic centromere is damaged.
Uncertainty in homology inferences: Assessing and improving genomic sequence alignment
Authors: Lunter Gerton , Rocco Andrea , Mimouni Naila , Heger Andreas , Caldeira Alexandre , Hein Jotun
Published: December 2007

Sequence alignment underpins all of comparative genomics, yet it remains an incompletely solved problem. In particular, the statistical uncertainty within inferred alignments is often disregarded, while parametric or phylogenetic inferences are considered meaningless without confidence estimates. Here, we report on a theoretical and simulation study of pairwise alignments of genomic DNA at human–mouse divergence. We find that >15% of aligned bases are incorrect in existing whole-genome alignments, and we identify three types of alignment error, each leading to systematic biases in all algorithms considered. Careful modeling of the evolutionary process improves alignment quality; however, these improvements are modest compared with the remaining alignment errors, even with exact knowledge of the evolutionary model, emphasizing the need for statistical approaches to account for uncertainty. We develop a new algorithm, Marginalized Posterior Decoding (MPD), which explicitly accounts for uncertainties, is less biased and more accurate than other algorithms we consider, and reduces the proportion of misaligned bases by a third compared with the best existing algorithm. To our knowledge, this is the first nonheuristic algorithm for DNA sequence alignment to show robust improvements over the classic Needleman–Wunsch algorithm. Despite this, considerable uncertainty remains even in the improved alignments. We conclude that a probabilistic treatment is essential, both to improve alignment quality and to quantify the remaining uncertainty. This is becoming increasingly relevant with the growing appreciation of the importance of noncoding DNA, whose study relies heavily on alignments. Alignment errors are inevitable, and should be considered when drawing conclusions from alignments. Software and alignments to assist researchers in doing this are provided at http://genserv.anat.ox.ac.uk/grape/.
On the potential of a chemical Bonds: Possible effects of steroids on home run production in baseball
Authors: Tobin R. G.
Published: December 2007

In recent years several baseball players have hit a remarkable number of home runs, and there has been speculation that their achievements were enhanced by the use of anabolic steroids. Basic mechanics and physiology, combined with simple but reasonable models, show that steroid use by a player who is already highly skilled could produce such dramatic increases in home run production. Because home runs are relatively rare events on the tail of a batter’s range distribution, even modest changes in bat speed can increase the proportion of batted balls that result in home runs by 50–100%. The possible effect of steroid use by pitchers is briefly considered.
Calculation of determinants using contour integrals
Authors: Kirsten Klaus , Loya Paul
Published: December 2007

We show how the preexponential factor of the Feynman propagator for a large class of potentials can be calculated using contour integrals. This factor is relevant in the context of tunneling processes in quantum systems. The prerequisites for this analysis involve only introductory courses in ordinary differential equations and complex variables.
Observation of the Fresnel and Arago laws using the Mach-Zehnder interferometer
Authors: Kanseri Bhaskar , Bisht Nandan S. , Kandpal H. C. , Rath Shyama
Published: December 2007

An experimental study is conducted to determine the effect of polarization on the interference of light waves. By using the temporal coherence property of light in a Mach-Zehnder interferometer, we verified the four important Fresnel and Arago laws for linearly polarized and circularly polarized light. This experiment provides a simple method for undergraduates to study the phenomena of interference and polarization.
Simple spin models with non-concave entropies
Authors: Touchette Hugo
Published: December 2007

Two simple spin models are studied to show that the microcanonical entropy can be a non-concave function of the energy, and that the microcanonical and canonical ensembles can give non-equivalent descriptions of the same system in the thermodynamic limit. The two models are simple variations of the classical paramagnetic spin model of non-interacting spins and are solved as easily as the latter model.
The general relativistic infinite plane
Authors: Jones Preston , Muñoz Gerardo , Ragsdale Michael , Singleton Douglas
Published: December 2007

Uniform fields are one of the simplest and most pedagogically useful examples in introductory courses on electrostatics and Newtonian gravity. In general relativity there have been several proposals as to what constitutes a uniform field. We examine two metrics that can be considered the general relativistic version of the infinite plane with finite mass per unit area. One metric is the four-dimensional version of the five-dimensional “brane” world models of current interest. Another metric is the cosmological domain wall metric. We examine to what extent these metrics match or deviate from our Newtonian intuition about the gravitational field of an infinite plane. These solutions provide beginning students in general relativity both computational experience and conceptual insight into Einstein’s field equations and introduce them to material that is at the forefront of current research.
The geometrical nature and some properties of the capacitance coefficients based on Laplace’s equation
Authors: Herrera William J. , Diaz Rodolfo A.
Published: December 2007

The fact that the capacitance coefficients for a set of conductors are geometrical factors is derived in most electricity and magnetism textbooks. We present an alternative derivation based on Laplace’s equation that is accessible to students in an intermediate course on electricity and magnetism. The properties of Laplace’s equation permits us to determine many properties of the capacitance matrix. Some examples are given to illustrate the usefulness of these properties.
Resource Letter PSNAC-1: Physics and society: Nuclear arms control
Authors: Glaser Alexander , Mian Zia
Published: December 2007

This Resource Letter provides a guide to the literature on nuclear arms control for the nonspecialist. Journal articles and books are cited for the following topics: nuclear weapons, fissile materials, nonproliferation, missiles and missile defenses, verification, disarmament, and the role of scientists in arms control.
Physiological variation between tree-associated populations of Suillus granulatus as determined by in vitro mycorrhizal synthesis experiments
Authors: Jacobson Kathryn M. , Miller Jr. Orson K.
Published: December 2007

Mycorrhizal synthesis studies revealed that allopatric populations of Suillus granulatus differ in host specificity. Isolates of Suillus granulatus originated from Nepal (associated with Pinus wallichiana), Korea (Pinus densiflora), and the U.S.A. (Pinus strobus). Functional compatibility of the mycorrhizal association was used to measure host specificity. Useful characters for measuring mycorrhizal compatibility were defined as those which revealed statistical differences between the uninoculated controls and mycorrhizal treatments and which were stable within one population. Useful characters, as defined by these two tests, were shoot wet weight, total wet weight, percentage mycorrhizal short roots, shoot dry weight, total dry weight, and Hartig net penetration. Data for these characters were subsequently used in anova tests to determine whether allopatric populations of Suillus granulatus differ in functional compatibility. Isolates associated with Pinus strobus were most compatible with Pinus strobus and least compatible with the other trees, whereas isolates from Pinus wallichiana and Pinus densiflora showed variable compatibility with all three trees. Phenetic analyses used to determine how similarly the isolates responded with the hosts confirmed these results. We conclude that isolates associated with Pinus strobus are most specific for this host, whereas isolates from the other two trees are not host specific. The implications of these results are discussed in light of future investigations regarding the relatedness of these tree-associated isolates. Key words: Boletaceae, Suillus, Pinus, ectomycorrhizae.
A light and electron microscope study of the fungal endophytes in the sporophyte and gametophyte of Lycopodium cernuum with observations on the gametophyte–sporophyte junction
Authors: Duckett Jeffrey G. , Ligrone Roberto
Published: December 2007

The ventral epidermal cells of the photosynthetic, surface-living gametophytes of Lycopodium cernuum, collected from moist shaded banks in Peninsular Malaysia, contain an aseptate fungus. In some cells the hyphae are thick walled and form coils encapsulated by a thin layer of host wall material. In others the fungus is thin walled and shows limited differentiation into larger trunk hyphae and arbuscules. The adjacent host cytoplasm, separated from the fungus by a granular interfacial matrix, contains numerous chloroplasts, mitochondria, and microtubules. The hyphae contact the substratum via the ventral walls of the epidermal cells and the rhizoids are free from infection. In the protocorm and root nodules, aseptate hyphae initially colonize mucilage-filled schizogenous intercellular spaces. Subsequent invasion of the host cells is associated with the development of massive overgrowths of host wall material. The fungal associations in L. cernuum share a mixture of attributes otherwise found in different angiosperm mycorrhizae and in mycotrophic relationships in liverworts. Wall ingrowths are present in both the gametophyte and sporophyte cells in the placenta of L. cernuum. The very limited development of the placenta, compared with L. appressum, certain bryophytes and ferns, the diminutive size, and early senescence of the gametophytes of L. cernuum are all linked to the presence of the protocorm. This massive absorptive organ, homologous to a foot, in terms of its position in sporophyte ontogeny, but external to the parent gametophyte, derives its nutrition partly from photosynthesis and partly from its fungal endophyte. Key words: chloroplasts, Lycopodium, mycorrhiza, pteridophytes, root nodules, symbiosis, transfer cells.
Cytogeographic races of Arctagrostis latifolia (Poaceae) in Alaska
Authors: Mitchell W. W.
Published: December 2007

Chromosome counts were obtained on 117 plants of the circumpolar grass Arctagrostis latifolia (R. Br.) Griseb. collected across mainland Alaska. Three chromosome races were found in the state. A widespread distribution was indicated for the tetraploids (2n = 28) and octoploids (2n = 56) and a limited distribution for the hexaploids (2n = 42), heretofore unreported for North America. Both tetraploids and octoploids appeared to be well represented through the boreal interior and arctic, unglaciated refugia of Alaska. Only tetraploids were found on the heavily glaciated terrain of southcentral Alaska. Six hexaploid counts were obtained on plants collected from two locales at the ecotone of glaciated and unglaciated areas. Cytotype distribution was interpreted as indicating a greater mobility for the tetraploid race, better enabling it to occupy deglaciated terrain and other disturbances, and the possibility of survival of the tetraploid in local refugia within the extensively glaciated southcentral region. The data provided support for the inclusion of different chromosome races within a single taxon. Key words: refugia, cytotype, polyploidy, recolonization.
Nawawia nitida anam. sp.nov. (Hyphomycetes) and further records of Nawawia filiformis from Malaysia
Authors: Kuthubutheen A. J. , Liew G. M. , Nawawi A.
Published: December 2007

A new species of the anamorph genus Nawawia, isolated from submerged decaying twigs of an undetermined tree, is described and compared with the type species, Nawawia filiformis, and Bahusutrabeeja dwaya, a new record for Malaysia. Key words: Nawawia, Bahusutrabeeja, hyphomycetes, new species.
Cesium-137 monitoring using lichens and mosses from northern Greece
Authors: Sawidis Thomas , Heinrich George
Published: December 2007

Cesium-137 content in lichens and mosses from northern Greece was measured for regular periods of time during the 5 years following the Chernobyl reactor accident. A clear increase of the cesium interception was observed for about 2 years after the accident. Later a gradual decrease was detected that depended on the habitat and the collected species. A great variation in values was observed when comparing contamination in all the habitats investigated during the same collecting season. Key words: 137Cs, lichens, mosses, radionuclides, Chernobyl.
Cotyledon cell development in Arabidopsis thaliana during reserve deposition
Authors: Mansfield S. G. , Briarty L. G.
Published: December 2007

Cotyledon cell development in Arabidopsis thaliana L. during reserve deposition has been analyzed qualitatively and quantitatively. Development has been related to the previously defined time scale for Arabidopsis, hours after flowering. Between 144 and 216 h after flowering the major cell changes in the cotyledon are an increase in the cell volume, a decrease in the volume fraction of cytoplasm and plastids, and an increase in lipid and vacuole volume fractions. The endoplasmic reticulum and dictyosome volume fractions are high during early reserve formation (144 – 168 h after flowering) but decrease significantly thereafter. Evidence as to the origin of the storage lipid is inconclusive, although a dual involvement of plastids and rough endoplasmic reticulum is a likely theory. The 3-nm lipid body membrane, which allows the bodies to retain their individuality during accumulation, is probably a half-unit biological membrane, derived from closely associated rough endoplasmic reticulum cisternae. Much of the evidence obtained in this study indicates that both the endoplasmic reticulum and dictyosomes are involved in protein synthesis and transport to the vacuole. The accumulation of reserves occurs in a well-defined and relatively short period during late embryogenesis (144–216 h after flowering). Key words: Arabidopsis, cotyledons, embryogenesis, reserve deposition, stereology.
Leaf anatomy of tropical fern rheophytes, with its evolutionary and ecological implications
Authors: Kato Masahiro , Imaichi Ryoko
Published: December 2007

Rheophytes are restricted to stream beds that are regularly flooded by swift-running water after rains and are morphologically characterized by having narrow, (ob)lanceolate leaves – leaflets (stenophylls) and other features that are adapted to the unique habitat, decreasing resistance to the swift-running water. The present study characterized anatomically the leaves of fern rheophytes. Generally, the mesophyll cells of rheophytes are less expanded, and therefore their intercellular spaces are smaller than those of related dryland species. Furthermore, frequency of occurrence of stomata per unit leaf area is greater, the cuticular layer is thicker, and the epicuticular wax deposits on the leaf epidermis are denser in at least some rheophytes than in related dryland species. It can be assumed that the stenophylls of the rheophytes are produced by developmental events, including weaker cell expansion than in dryland species, and that a phylogenetic decrease in cell expansion in leaves was involved in the origin of stenophylls from broader leaves of ancestral dryland species. The leaf anatomical features are discussed in relation to the ecological specificity of the rheophytes. Key words: evolution, flood resistance, intercellular space, leaf anatomy, rheophytic ferns, stenophyll.