bluuebunny/crossref_metadata_2025_split huggingface dataset:
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
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
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.
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.
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.
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.
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).
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.
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.
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.
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

Abstract
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.