bluuebunny/crossref_metadata_2025 huggingface dataset:
The Background to the Forefront: A Response to Levi and Shapere
Authors: Worrall Joh
Published: January 2016

The papers by Isaac Levi and by Dudley Shapere, despite their many differences, share a common theme. This is the idea that science in a certain sense builds upon itself, that some of its assertions, having become firmly established, play important roles in the further development of science. Established science not only guides practical action, it also constrains possible conjectures, guides the construction of more extended and related theories, and even guides the construction of their eventual successors (though this last needs very careful handling). This basic idea is surely correct; but I have many disagreements with the particular (and different) ways that the basic idea is developed by Isaac Levi and Dudley Shapere. I shall therefore first, outline very roughly the sort of development of this basic idea that I would advocate.
Subjective Qualia from a Materialist Point of View
Authors: Churchland Paul M
Published: January 2016

It is frequently argued that the phenomenological or qualitative features of our sensations will never be satisfactorily reduced by a purely materialistic neuroscience. They constitute, it is often said, a permanent barrier to the reductive aspirations of physlcalism. In what follows I provide a critical examination of several of the most popular of these arguments. I also explore the transformation and expansion of human subjective consciousness that a successful psycho-physical reduction could sustain. The conclusion is that, far from being Immune to neurophysiological explanation and reduction, the subjective qualities of our inner lives will enjoy a dramatic unfolding as the representational and computational strategies of the brain are revealed.
Symmetry Arguments in Probability Kinematics
Authors: Hughes R.I.G , van Fraassen Bas C
Published: January 2016

Probability kinematics is the theory of how subjective probabilities change with time, in response to certain constraints (accepted by the subject in response to his experience or incoming information). Transformations — rules for updating one's probabilities — which have been described and to some extent accepted in the literature, include (in increasing order of generality): conditionalization, Jeffrey conditionalization, and INFOMIN (relative information minimizing). The present paper investigates the general problem. By an argument purely based on symmetry considerations it is demonstrated that conditionalization and Jeffrey conditionalization are the unique admissible rules for the cases to which they apply. The general problem is thereby reduced to a sequence of two operations, the second a Jeffrey conditionalization and the first a determination of posterior odds on some partition. In Section 2 we give a new deduction of INFOMIN from a simple postulate; in Section 3 a rival rule (MTP) derived from an analogy to quantum mechanics. The Appendix presents some preliminary comparisons.
Sober’s Use of Unanimity in the Units of Selection Problem
Authors: Gifford Fred
Published: January 2016

The units of selection problem is an issue within evolutionary theory (or the philosophy thereof) and concerns the question of what units or objects are acted upon by natural selection -- for example, whether these are genes, organisms or groups of organisms. One of the central theses of Elliot Sober’s recent book,The Nature of Selection, is that the philosophical problem of what it means for something to be a unit of selection is to be understood by applying the correct account of what it isin generalfor a factor to be a cause in a population.

The account of population-causation that Sober utilizes for this purpose comes from the recent literature on probabilistic causality. This account requires that for C to cause E in a population, aunanimitycondition must be satisfied: C must raise the probability of E in each causal context.
Taking Analogical Inference Seriously: Darwin's Argument From Artificial Selection
Authors: Waters C. Kenneth
Published: January 2016

“The question for us,” as Ronald Giere writes in Understanding Scientific Reasoning, “is whether analogies play any role in the JUSTIFICATION of [a] new theory.” Giere’s answer is an emphatic “No.” (Giere 1984, pp. 79-80). Although most philosophers of science would probably qualify Giere’s unmitigated rejection of analogical justification, few attribute much significance to analogical arguments in science. And when philosophers do grudgingly acknowledge an analogical argument, they are hesitant to analyze it.

Take, for example, Charles Darwin’s argument for natural selection. It is difficult to deny that the analogy between artificial and natural selection played an important justificatory role. After all, artificial selectibn was the topic of the first chapter of Darwin’s Origin of Species and was referred to in countless arguments throughout the text.2
What's Really Wrong with Quantitative Risk Assessment?
Authors: Longino Helen E.
Published: January 2016

Risk assessment is one part of the multistage process of determining the acceptability of risks. Risk assessment, as I understand it, and as I think Dale Hattis is talking about it (Hattis, 1986), is the estimation of the hazards likely to be incurred by proceeding with a given course of action—adopting a new pesticide, using a sugar substitute in processing foods, employing some method of generating energy, installing a toxic or radioactive waste disposal system in a particular location. The hazards in question are generally health hazards as distinct from economic costs, although many critics of current technology assessment (or non-assessment) programs might well argue that this is too limited a conception of hazard—that there may be social and political effects of a technology's adoption that are not encompassed in calculations of biological risk or economic cost. Risk evaluation generally refers to the procedures for deciding whether to employ a particular technology, chemical, etc. i.e. whether to accept the risks involved or not.
On the Logic of Interrogative Inquiry
Authors: Hintikka Jaakko , Harris Stephen
Published: January 2016

In earlier publications Jaakko Hintikka has introduced the interrogative model of inquiry and studied some of its applications.1 At its simplest, the interrogative model takes the form of a game between a player known as the Inquirer and a source of information we call Nature. The inquirer is trying to derive a conclusion C from a given set of premises T by standard deductive means augmented by additional information gained from Nature. (We can think of C as a set of formulas related disjunctively to each other.) The inquirer may obtain this additional information by means of questions put to Nature. The answers to these questions, when available, are then added to the premise set T. When a question is answerable but no true answer is available, Nature may respond with a false answer.

The deductive steps employed are subject to certain limitations. For instance, if the derivation is being carried out in a Beth-style tableau system, we require that the deductive steps obey the subformula principle.2
Non-Formal Properties of Real Mathematical Proofs
Authors: Van Bendegem Jean Paul
Published: January 2016

Suppose you attend a seminar where a mathematician presents a proof to some of his colleagues. Suppose further that what he is proving is an important mathematical statement Now the following happens: as the mathematician proceeds, his audience is amazed at first, then becomes angry and finally ends up disturbing the lecture (some walk out, some laugh, …). If in addition, you see that the proof he is presenting is formally speaking (nearly) correct, would you say you are witnessing an extraordinary event in urgent need of explanation? Surely, your answer would be yes. But do events of this type actually occur? The matter of the fact is, yes, they do. This paper presents the details of such an event, suggests a possible explanation and examines its implications for our understanding of mathematical practice.
Albert Einstein Meets David Lewis
Authors: Butterfield Jeremy
Published: January 2016

With help from Einstein, John Norton and John Earman (1987; this volume) have invented a fascinating argument against spacetime substantivalism. It gives the philosophy of space and time a refreshing stimulus: all credit to them. The idea of the argument is that substantivalism rules out determinism, even of very weak kinds. Norton and Earman have no special brief to defend determinism. But they believe that if it fails, it should fail for reasons of physics that vary from case to case—it should not fail at a stroke for the sake of a philosophical doctrine such as substantivalism. They conclude that in the conflict between substantivalism and determinism, it is substantivalism that must go.

The conflict arises from ‘hole diffeomorphisms’. These enable us, once we are given a model for a spacetime theory, to produce another model.
Lorentz Invariant State Reduction, and Localization
Authors: Fleming Gordon N.
Published: January 2016

In this paper I will present conceptions of state reduction and particle and/or system localization which render these subjects fully compatible with the general requirements of a relativistic, i.e. Lorentz invariant, quantum theory. In the case of state reduction, the concept presented has, in it's main features, been advanced by several investigators in recent years, (Giovannini 1983), (Aharonov and Albert 1984), (Malin 1984), (Dieks 1985). My own contribution to this topic has been to elaborate the concept in question and examine, in some detail, the often counterintuitive but never causally anomalous or internally inconsistent consequences that emerge from taking the concept seriously (Fleming 1985,1986). In the case of particle and system localization, the concepts are more nearly my own and have been pursued by me for some time (Fleming 1964, 1965, 1966) as a way of freeing the subject of localization in relativistic quantum systems from the conceptual problems pointed out by Newton and Wigner (1949) myself (Fleming 1965) and extensively studied by Hegerfeldt et. al. (1974, 1980) and Ruijsenaars (1981).
From Logical Formalism to Control Structure: The Evolution of Methodological Understanding
Authors: Hooker C. A.
Published: January 2016

Over the past two centuries the character of science has changed markedly and crucially. When humans had relatively small amounts of information and energy available they perforce had no option but to attempt to describe objectively a world which behaved independently of them. The basic practical problem was to discover what the pattern of the world was so as to adapt themselves as best they may to it, a little in anticipation of events, but mostly in reaction to them. It is these circumstances which give most sense to the empiricist paradigm of objective knowledge.

But the more information and energy is available to us, the more we are able to ascend from merely correct description of what is to a grasp of what is possible. Newton's laws don't merely describe the paths of the actual projectiles that have fallen and will fall, they describe the paths of all possible projectiles.
Descartes and Method in 1637
Authors: Garber Daniel
Published: January 2016

The Discours de la Méthode and the three essays that were published with it, the Dioptrique, the Météores, and the Géometrie make up a very curious book. The very title page emphasizes the preliminary discourse, and that discourse, the Discours de la Méthode, emphasizes method, the importance that method had for Descartes in making the discoveries he made, the importance that the method Descartes claims to have found will have for the progress of the sciences and for the benefit of humankind as whole. Descartes is not, of course, telling us that we are obligated to follow his method; the Discours is, after all, proposed “as a story, or, if you prefer, as a fable.” (AT VI 4). But Descartes expects that we will all see the light, the light of reason, of course, and follow his example.
Common Knowledge and Games with Perfect Information
Authors: Reny Philip J.
Published: January 2016

It is by now rather well understood that the notion of common knowledge (first introduced by Lewis (1969) and later formalized by Aumann (1976)) plays a central role in the theory of games. (An event E is common knowledge between two individuals, if each knows E, each knows the other knows E, etc…). Indeed, most justifications of Nash's (1951) equilibrium concept usually include (perhaps only implicitly) the assumption that it is common knowledge among the players that both the Nash equilibrium in question will be played by all and that all players are expected utility maximizers. (We shall henceforth call expected utility maximizers, “rational”.) We hope to illustrate in an informal manner that there is in fact a large class of extensive form games, in which each of which it is not possible for rationality to be common knowledge throughout the game.
Local Incommensurability and Communicablity
Authors: Chen Xiang
Published: January 2016

One of the most controversial ideas in recent philosophy of science is the incommensurability of scientific theories. For Kuhn, the claim that two theories are incommensurable is the claim that there is no common language within which both theories could be fully expressed (Kuhn 1977, p. 301). In others words, two theories are incommensurable if and only if they are articulated in languages that are not mutually translatable or communicable without loss. This type of incommensurability, according to Kuhn, is the result of changes in worldview. The proponents of different paradigms practice their researches in different worlds (Kuhn 1970, p. 150). They may have different classifications of objects in the world due to their different cultures. For example, the astronomers who belonged to Ptolemy’s paradigm grouped the sun, moon, and Mars into the same set, while the astronomers who belonged to Copernicus’s paradigm classified them into three different categories.
The Chromosome Theory of Mendelian Inheritance: Explanation and Realism in Theory Construction
Authors: Vicedo Marga
Published: January 2016

Cytogenetics was born of the confluence of two so-far independent fields: cytological studies and breeding studies, which merged through the identification of genes with chromosomes. In this paper I argue that genes were introduced as functional entities. Functional explanations are presented here as a subclass of inferences to the best explanation and I argue that abductive arguments do not offer conclusive proof for the existence of the entities postulated through them. However, functional explanations usually follow a scheme laid out by Fodor (1968): there is a first phase where hypothetical entities are postulated and individuated through their effects; there is a second phase where the physical structures responsible for these effects are sought. I analyze the development of both phases in the construction of the chromosome theory of Mendelian inheritance. I will argue that first-phase theories are important to set conditions of identification for the functions played by a certain structure in a given containing system.
Assessing Functional Explanations in the Social Sciences
Authors: Kincaid Harold
Published: January 2016

Despite decades of controversy, functionalism continues to be a lively research tradition in the social sciences. Furthermore, social scientists who reject Parsonian functionalism and its variants frequently make liberal use of functional explanations. Yet, neither social scientists nor philosophers have reached any consensus on when and where functional accounts are legitimate. Critics doubt that functionalism is really explanatory or testable; advocates are unfortunately vague on their claims and the evidence for them. In what follows I try to clarify what functionalism entails, discuss some ways in which functional hypotheses can be confirmed, and evaluate criticisms. While I think much functionalism is bad science, I hope to show that the problem is not one of principle but of practice.

Social scientists use the term “functionalism” in diverse ways. At times the term refers to a specific theoretical movement in sociology and anthropology—the movement identified with Malinowski and Parsons.
Reinventing Certainty: The Significance of Ian Hacking’s Realism
Authors: Gross Alan G.
Published: January 2016

In a recent paper (1989), Ian Hacking has extended his discussion of entity realism, a discussion begun six years ago in the final chapter of Representing and Intervening (1983). This extension allows us to examine for the first time the whole of one impressive attempt to rescue scientific realism from the ever more subtle skepticism of post-positivist thinking (Laudan 1984; Fine 1986). Hacking’s approach complements that of Nancy Cartwright. Like Cartwright, he implies that a full-blown realism about scientific theories and entities can survive neither the facts of history nor the arguments of opponents. Hacking is a realist only about some unobservable entities, those he thinks durable enough to survive most alterations in theory. This is the science that Kuhn said survived even paradigm change.

Electrons are Hacking’s example of a real unobservable entity. Their behavior is so consistent and so well-known that they are used as tools: they are manipulated in the engineering of scientific experiments designed to extend the bounds of the known.
The Road Since Structure
Authors: Kuhn Thomas S.
Published: January 2016

On this occasion, and in this place, I feel that I ought, and am probably expected, to look back at the things which have happened to the philosophy of science since I first began to take an interest in it over half a century ago. But I am both too much an outsider and too much a protagonist to undertake that assignment. Rather than attempt to situate the present state of philosophy of science with respect to its past — a subject on which I’ve little authority — I shall try to situate my present state in philosophy of science with respect to its own past — a subject on which, however imperfect, I’m probably the best authority there is.

As a number of you know, I’m at work on a book, and what I mean to attempt here is an exceedingly brief and dogmatic sketch of its main themes. I think of my project as a return, now underway for a decade, to the philosophical problems left over from the Structure of Scientific Revolutions.
Are Pictures Really Necessary? The Case of Sewell Wright’s “Adaptive Landscapes”
Authors: Ruse Michael
Published: January 2016

Biologists are remarkably visual people. Yet, the classics of logical empiricism never raised the general question of scientific illustration. Moreover, one suspects that the silence was, if anything, actively hostile. People did not talk about biological illustration, because they did not judge it to be part of “real science”. This enterprise produces statements or propositions, ideally embedded in a formal system. It may beaboutthe real world, but it is not in any senseofthe real world, in being a copy or mirror image. Philosophers recognized that regretfully human weakness demanded the visual. But it was judged at best a prop. (See, for instance, Braithwaite 1953, Hempel 1965, and Bunge 1967; although see also Achinstein 1968. The best discussion of scientific illustration that I know is Rudwick 1976.)
Conventionalism and the Origins of the Inertial Frame Concept
Authors: DiSalle Robert
Published: January 2016

The obvious metaphysical differences between Newton and Leibniz concerning space, time, and motion reflect less obvious differences concerning the relation between geometry and physics, expressed in the questions: what are the invariant quantities of classical mechanics, and what sort of geometrical frame of reference is required to represent those quantities? Leibniz thought that the fundamental physical quantity was “living force” (mv2), of which every body was supposed to have a definite amount; this notion violates the classical principle of relativity, since it makes a physical distinction between uniform velocity and absolute rest. But Leibniz did not try to represent this physical quantity in a spatio-temporal reference frame, assuming, instead, that all such frames are equivalent so long as they agree on the relative motions (changes in the mutual Euclidean distances) among bodies.
Philosophical Interpretations of Relativity Theory: 1910-1930
Authors: Hentschel Klaus
Published: January 2016

This paper is a summary of my doctoral dissertation on philosophical interpretations of Einstein’s special and general theories of relativity, submitted to the Dept. for History of Science, Univ. of Hamburg, in 1989, which was recently published in the Series Science Networks at Birkäuser.2 After a brief overview of its content I will focus on a discussion of the method employed to analyse philosophical interpretations of a physical theory.

My analysis is based

- firstly on about 2500 contemporary published texts about the theories of relativity written both by scientists and philosophers. These texts have not been of particular interest to historians or philosophers of science up to now; this is understandable from the fact that many of diem contain gross oversimplifications, misinterpretations and incorrect statements about the theories of relativity.
Self Organization and Adaptation in Insect Societies
Authors: Page Robert E. , Mitchell Sandra D.
Published: January 2016

The social organization of insect colonies has fascinated biologists and natural historians for centuries. Aristotle wrote in History of Animals about a division of labor among workers within the hive that is based on age. He observed that the field bees foraging for nectar and pollen have less “hair” on their bodies than the hive bees that care for young larvae and tend the nest. He concluded that the more pubescent hive bees must be older. We now know that, in fact, the field bees are older and have less hair because the hairs break off as the bees age. The phenomenon of age related changes in behavior, age-polyethism, is now well documented for many social insects (Oster and Wilson 1978).

Evidence of the ecological success of social insects is inescapable. Virtually everywhere you look you see them or the results of their activities.
Computer Simulation in the Physical Sciences
Authors: Rohrlich Fritz
Published: January 2016

The central claim of this paper is that computer simulation provides (though not exclusively) a qualitatively new and different methodology for the physical sciences, and that this methodology lies somewhere intermediate between traditional theoretical physical science and its empirical methods of experimentation and observation. In many cases it involves a new syntax which gradually replaces the old, and it involves theoretical model experimentation in a qualitatively new and interesting way. Scientific activity has thus reached a new milestone somewhat comparable to the milestones that started the empirical approach (Galileo) and the deterministic mathematical approach to dynamics (the old syntax of Newton and Laplace). Computer simulation is consequently of considerable philosophical interest. In view of further technical developments in the near future, computer experts suggest that we are at present only at the very beginning of this new era.
How Free are Initial Conditions?
Authors: Sklar Lawrence
Published: January 2016

Some of what is true about the world is thought, by some, to be true of necessity. Other truths about the world are merely contingently true, it is said. Next we get a familiar distinguishing of necessity into its various kinds. Anything whose contrary would contradict the laws of logic is logically necessary. Anything compatible with these laws is logically contingent. There are, of course, grave problems in finding a principled way of discriminating the logical truths from all the others. Some propositions are not logically necessary but are metaphysically necessary. For Kant, I suppose, the alleged facts that every event had a cause, and that in any change a substance remained unchanged would be such facts. So, I suppose, would be the necessary but synthetic truths of geometry and arithmetic. For more contemporary philosophers genuine identity statements, either singular or general, might have such a status.
Value-definiteness and Contextualism: Cut and Paste with Hilbert Space
Authors: Stairs Allen
Published: January 2016

My topics are two theses about quantum mechanics that are widely doubted but curiously tempting: value-definiteness and contextualism. Value-definiteness holds that every observable has a definite value; contextualism follows from value-definiteness, and claims that one Hermitian operator can represent many observables. In fact, contextualism is my deeper interest Although it is not a view with an army of defenders, it has a long history of discussion in the literature. (See, for example, Belinfante 1973, van Fraassen 1973, Shimony 1984, Redhead 1987). The bulk of this paper will be concerned with a puzzle about degenerate operators that arises out of the standard accounts of contextualism. But before we get to the details, let us begin with a lurid example.
The Importance of Models in Theorizing: A Deflationary Semantic View
Authors: Downes Stephen M.
Published: January 2016

It is commonly acknowledged in science that model construction is one of the most important components of theorizing. Philosophers of science are gradually coming to acknowledge this situation, spurred on by holders of the semantic view of theories. In this paper I wish to defend a very deflationary version of the semantic view of theories, which is more or less a re-statement of the above commonplace. I reject the view encapsulated in the identity statement “scientific theories are families of models,” although acknowledging the useful insights into science that holders of this strong position have given us. My position derives from a critique of various of the semantic views of theories, and further from a guiding presupposition that rather than providing necessary and sufficient conditions for what a theory is, philosophers should focus on the nature of scientific theorizing. Theorizing is carried out by practicing scientists, and we cannot say what scientific theories are unless we appreciate the myriad ways they are used and developed in all of the sciences.
Dutch Strategies for Diachronic Rules: When Believers See the Sure Loss Coming
Authors: Armendt Brad
Published: January 2016

Diachronic Dutch book arguments, or Dutch strategy arguments, have been used to recommend the rule of conditionalization (C) Jeffrey’s rule for fallible learning (J), and the principle of reflection (R). The arguments have been criticized in a variety of ways—more ways than can be discussed in this paper. Here we will look at two of the criticisms. As we proceed, it will become apparent how some criticisms not explicitly raised can be met; others will go unexamined. The criticisms are these: First, Dutch strategy arguments are said to fail as defenses of rules J and C, and principle R, because rational agents may violate each of those constraints, yet avoid vulnerability to a Dutch strategy; their knowledge of Dutch strategy arguments enables them to do this. Second, it is said to be no wonder that the arguments fail, because there are counter-examples to each of these purportedly general constraints on rational belief.
A Kernel of Truth? On the Reality of the Genetic Program
Authors: Moss Lenny
Published: January 2016

The full understanding of the nature of the genetic program was achieved by molecular biology only in the 1950's after the elucidation of the structure of DNA. Yet, it was already felt by the ancients that there had to be something that ordered the raw material into the patterned system of living beings….What is particularly important is that the genetic program itself remains unchanged while it sends out its instructions to the body.

One of the properties of the genetic program is that it can supervise its own precise replication and that of other living systems such as organelles, cells, and whole organisms.

Ernst Mayr (1982)

The notion of a genetic program, as described by Mayr, is ripe for an analysis inspired, at least in part, by recent debates in the philosophy of science taken under the heading of realism versus anti-realism.
Convergent Realism and Approximate Truth
Authors: Resnik David B.
Published: January 2016

Convergent realists typically maintain the following theses:

Tl:

Some scientific theories, literally interpreted, are at least approximately true.

T2:

Some scientific theories, literally interpreted, genuinely refer.

T3:

The history of mature sciences is a progressive approximation to the truth.

T4:

The world (reality) described by scientific theories is independent of our thoughts or theoretical commitments.

Convergent realists usually offer the infamous “success of science” argument as the strongest defense of their view. Scientific realism, according to convergent realists, is the only view that does not portray the success of science as miraculous (i.e., unexplainable). Various versions of convergent realism have been defended by writers such as Richard Boyd (1973,1980,1984), W.H. Newton-Smith (1978), Hilary Putnam (1975,1978), JJ.C. Smart (1963,1985,1989), and Russell Hardin and Jay Rosenberg (1982). Critics of convergent realism include Larry Laudan (1981), Arthur Fine (1984), and Bas van Fraassen (1980).
On the Nature of Bayesian Convergence
Authors: Hawthorne James
Published: January 2016

Bayesians assess the inductive support for theoretical hypotheses on the
basis of two sorts of factors, one fairly objective, the other highly
subjective. The objective factor consists of the
likelihoods or direct inference
probabilities that theoretical hypotheses specify for
evidential events. This is the means by which evidence affects inductive
support. The subjective factor consists of the prior
probabilities assigned to the various competing
hypotheses. For a Bayesian agent the prior
probability of a hypothesis represents how plausible the agent considers the
hypothesis to be before the impact of evidence is
considered, and Bayesian agents may radically differ in their initial
plausibility assessments. Bayes’ formula combines likelihoods with an
agent's prior probabilities to produce the agent's posterior
probability for each hypothesis.
Posterior probabilities represent how
plausible an agent considers the hypothesis to be
after the evidence is taken into
account.
Of Nulls and Norms
Authors: Godfrey-Smith Peter
Published: January 2016

When the Neyman-Pearson approach to the testing of statistical
hypotheses was introduced in the 1930's and 1940's it was presented with an
accompanying philosophy of science. Jerzy Neyman held a strong form of
pragmatism. He sought not just to model scientific decision on practical
decision, but in a sense to reduce it to
practical decision. Neyman-Pearson techniques are used to compare hypotheses
in the light of experimental data, and they contain an asymmetry, in that
one hypothesis—the “null”—typically gets the benefit of the doubt. For
Neyman, the choice of which hypothesis gets this benefit is governed by
behavioral considerations. When presented as an account of testing in
science this claim was met with vigorous resistance.

Though the philosophy was controversial, the methods became standard.
Philosophers and statisticans have produced alternative interpretations of
many distinctive features of these tests. But they are not the only ones who
have had to give a new rationale for Neyman-Pearson methods.
Sherlock Holmes, Galileo, and the Missing History of Science
Authors: Thomason Neil
Published: January 2016

Much of the history of science is missing much of the time. The missing
history I have in mind is not missing because of lost documents or state
secrecy. Nor is it missing because it is obscure. I am talking about central
episodes in the history of science and absolutely central issues in the
logical structure and evidential support of those episodes. In fact, the
episodes are so central and well known, and the missing history (once seen)
so obvious, that one feels compelled to hold that there must be a widespread
systematic bias among historians and philosophers against seeing certain
explanatory patterns.

My explanation for this missing history of science is that there is a
strong tendency among historians and philosophers of science toward what I
will call “Psychological Predictivism” to distinguish it from “Logical
Predictivism.” Logical Predictivism is the position that, if an observed
phenomenon provides good evidence for a hypothesis, then that hypothesis
(plus unproblematic auxiliary hypotheses), predicts the phenomenon.
The ‘Decoherence’ Approach to the Measurement Problem in Quantum
Mechanics
Authors: Elby Andrew
Published: January 2016

The decoherence approach to the measurement problem invokes dissipative
interactions between a measuring apparatus and its environment to explain,
within the context of ‘pure’ quantum mechanics (QM), why such devices appear
to possess definite pointer readings. By ‘pure’ QM, I mean Schrödinger
evolution with no wavefunction collapse. Several classes of interpretations
of pure QM can rely on decoherence. One class is the ‘modal’ interpretations
of van Fraassen (1979), Dieks (1989), Healey (1989), and others. Another
class is the relative-state and many-world interpretations.

I will argue that decoherence cannot help these interpretations address
the general metaphysical challenges raised against them. But decoherence can
help pick out a ‘special’ basis that determines which observables receive
definite values. I'll explore to what extent decoherence rescues the modal
(biorthogonal) basis-selection rule, and Zurek's (environmental interaction)
basis-selection rule, from the basis degeneracy problem and the imperfect
measurement problem.
The Epistemic Authority of Expertise
Authors: Pierson Robert
Published: January 2016

All of us defer to the authority of experts. Living in a world of
increasing specialization we find that deferral to experts is integral to
even the most mundane habits of our ordinary life. I regularly complain
about mistakes in meteorologist's forecasts, yet I still carry an umbrella
when rain is predicted, even when a glance outside reveals that there is not
a cloud in the sky. If I develop a rash on my arm and the doctor says that
it is nothing more than an allergic reaction, I do not ask her to list all
the evidence and reasoning that led her to that conclusion, but trust her
judgment and get on with my day. Now, while we defer to experts as a matter
of course, we often do so with a measure of resentment and fear.

If it were possible, I suspect that most of us would rather govern what
we do according to our own good reasons rather than expert
authority.
Circular Justifications
Authors: Brown Harold I.
Published: January 2016

It is common practice to reject a justification out-of-hand if the
argument that yields the justification is circular. Here are two recent
examples. Siegel, criticizing Giere's (1988) proposal for a naturalistic
philosophy of science, lists a number of questions about the justification
relation between evidence and theory. Siegel then maintains that any attempt
to provide a scientific account of this relation
must fail:

any answer to the question of the relationship between evidence
and a justified theory, if arrived at scientifically, would depend
upon exactly the same relationship between it and the evidence for
it as it recommends for the relationship between any justified
theory and the evidence for it. Because these general questions
about the epistemology of science cannot be answered
naturalistically without begging the question, they cannot be so
pursued. (1989, 369.)
Methodological Norms in Traditional and Feminist Philosophy of Science
Authors: Potter Elizabeth
Published: January 2016

This essay explores one of the fundamental ways in which feminist methodology in philosophy of science differs from most standard philosophy of science. Methodology in general arises from goals which the methods are designed to reach. Feminist goals in philosophy have been scandalous precisely because they are avowed political interventions into what has been considered a cool, apolitical academic activity. Another way to put this point is that feminism self-consciously inserts certain moral and political values into an activity considered to be neutral among moral and political values; it advocates a moral and political point of view in an area presumed to be objective in the sense that it is without any point of view. And precisely because the goals of feminist efforts in philosophy of science are moral and political ones, they appear inimical to the central goals of philosophy of science itself—the morally neutral and apolitical production of theories about how science works.
Feminist Values and Cognitive Virtues
Authors: Nelson Lynn Hankinson , Nelson Jack
Published: January 2016

Commonly-cited criteria for the assessment of hypotheses, research projects, and theories include empirical adequacy, simplicity, conservatism, explanatory power, generality of scope, fecundity, reproducibility, and interconnectedness with other going theories. The list of criteria for good scientific practice typically includes objectivity (though what objectivity comes to is much disputed), respect for evidence, open mindedness, and tentativeness. Feminist scientists and science scholars have of late proposed additional and, in some cases, alternative criteria (e.g., Biology and Gender Study Group 1989, Bleier 1984, Fausto-Sterling 1985, Haraway 1978, Keller 1983 and 1985, Longino 1994, and Nelson 1990). We here consider the nature and rationale of some of these proposed criteria, focusing on several articulated by Helen Longino. A research program in neuroendocrinology investigating a hormonal basis for alleged sex-differentiated lateralization and feminist critiques of this research serve as our case study.
Empirical and Rational Components in Scientific Confirmation
Authors: Shimony Abner
Published: January 2016

A common device in popular presentations of science is a sequence of views from cosmic to terrestrial to local to microscopic, thereby placing the subject to which the program is devoted in a proper perspective. I wish to use an adaptation of this device to place the announced topic of our panel — “Do Explanations or Predictions Provide More Evidential Support for Scientific Theories?” — in perspective. My four steps, from the largest to the smallest scale, are the following:

1.

A brief summary of the world view suggested by the discoveries of the natural sciences and by philosophical reflections on them;

2.

a consideration of the methodology for scientific investigation, upon assumption that this world view is approximately correct;

3.

the formulation of a version of Bayesian scientific inference satisfying the desiderata of step 2;

4.

the topic of our panel — explanation vs. prediction.
Explanation v. Prediction: Which Carries More Weight?
Authors: Achinstein Peter
Published: January 2016

According to a standard view, predictions of new phenomena provide stronger evidence for a theory than explanations of old ones. More guardedly, a theory that predicts phenomena that did not prompt the initial formulation of that theory is better supported by those phenomena than is a theory by known phenomena that generated the theory in the first place. So say various philosophers of science, including William Whewell (1847) in the 19th century and Karl Popper (1959) in the 20th, to mention just two.

Stephen Brush takes issue with this on historical grounds. In a series of fascinating papers he argues that generally speaking scientists do not regard the fact that a theory predicts new phenomena, even ones of a kind totally different from those that prompted the theory in the first place, as providing better evidential support for that theory than is provided by already known facts explained by the theory.
Psychological, Social, and Epistemic Factors in the Theory of Science
Authors: Goldman Alvin I.
Published: January 2016

Traditional philosophy of science concentrated on logic and methodology, dismissing psychology and sociology as irrelevant (except for the context of discovery). Recent movements to ‘naturalize’ philosophy of science have reinstated psychological and social factors repudiated by the tradition, but these two types of factors have mostly been addressed independently and by different authors. Most cognitive approaches (e.g., Thagard 1989a, 1992; Churchland 1989) pursue the microcognition of science in abstraction from the social, and most sociologists of science ignore, post pone, or reject cognitive explanations of science (Latour and Woolgar 1986, 280). More recently, however, several philosophers of science have urged a blending of the cognitive and the social (Thagard 1993, in press, Solomon 1992, 1994a, 1994b, Kitcher 1993, Giere 1988), and this paper has a similar thrust. I shall not endorse a reduction of the social to the psychological, but a substantial overlap or intermingling of the two.
Subversive Reflections on the Human Genome Project
Authors: Rosenberg Alex
Published: January 2016

In the Museum of Science and Technology in San Jose, California, there is a display dedicated to advances in biotechnology. Most prominent in the display is a double helix of telephone books stacked in two staggered spirals from the floor to the ceiling twenty five feet above. The books are said to present the current state of our knowledge or the eurcaryotic genome: the primary sequences of DNA polynucleotides for the gene products which have been discovered so far in the twenty years since cloning and sequencing the genome became possible.

In order to grasp what is problematical about the human genome project (HGP), I want you to hold on to this image of a stack of phone books, or rather two stacks, helictical in shape. Imagine that each of the phone books about the size of the Manhattan white pages, and that the two stacks of phone books reach up a mile and a half into the sky.
Contextualizing Science: From Science Studies to Cultural Studies
Authors: Smocovitis Vassiliki Betty
Published: January 2016

For once I find myself in the unusual position of disagreeing with Joe Rouse for I do not think that science studies can or should be simply “modeled’ after cultural studies as he has suggested. Instead I will argue for a stronger relationship between science studies and cultural studies that follows historically, if not logically from the progression from HPS to science studies and thence to the cultural study of scientific knowledge. The endpoint of the cultural study of scientific knowledge, at least as I will locate it in this paper and elsewhere, for it depends on how one locates the meaning of culture and its study, is a return to the perspective of the scientist having made roughly a 359 degree angle of departure; that one degree more or less gives the critical distance to “defamiliarize the familiar” perspective of the scientist and to “contextualize” scientific practice.
German Scholarship On The Renaissance and Reformation
Authors: Bainton Roland H.
Published: January 2016

During the summer of 1948 I was privileged, while travelling in Germany for the American Friends Service Committee, to pick up a sheaf of gleanings with regard to studies in the field of Renaissance and Reformation. First a word with regard to works which appeared during or directly after the war. Every college library in this country should seek to obtain Die neue Propylaenweltgeschichte, hrsg. Willy Andreas, vol. III, Das Zeitalter der Entdeckungen, der Renaissance und der Glaubenskämpfe (Berlin, 1941).
SV-Bay: structural variant detection in cancer genomes using a Bayesian approach with correction for GC-content and read mappability
Authors: Iakovishina Daria , Janoueix-Lerosey Isabelle , Barillot Emmanuel , Regnier Mireille , Boeva Valentina
Published: January 2016

Motivation: Whole genome sequencing of paired-end reads can be applied to characterize the landscape of large somatic rearrangements of cancer genomes. Several methods for detecting structural variants with whole genome sequencing data have been developed. So far, none of these methods has combined information about abnormally mapped read pairs connecting rearranged regions and associated global copy number changes automatically inferred from the same sequencing data file. Our aim was to create a computational method that could use both types of information, i.e. normal and abnormal reads, and demonstrate that by doing so we can highly improve both sensitivity and specificity rates of structural variant prediction.

Results: We developed a computational method, SV-Bay, to detect structural variants from whole genome sequencing mate-pair or paired-end data using a probabilistic Bayesian approach. This approach takes into account depth of coverage by normal reads and abnormalities in read pair mappings. To estimate the model likelihood, SV-Bay considers GC-content and read mappability of the genome, thus making important corrections to the expected read count. For the detection of somatic variants, SV-Bay makes use of a matched normal sample when it is available. We validated SV-Bay on simulated datasets and an experimental mate-pair dataset for the CLB-GA neuroblastoma cell line. The comparison of SV-Bay with several other methods for structural variant detection demonstrated that SV-Bay has better prediction accuracy both in terms of sensitivity and false-positive detection rate.

Availability and implementation:  https://github.com/InstitutCurie/SV-Bay

Contact:  valentina.boeva@inserm.fr

Supplementary information:  Supplementary data are available at Bioinformatics online.