In Xenopus, as in all amphibians and possibly in vertebrate embryos in general, mesoderm formation and the establishment of the dorsoventral axis depend on inductive cell interactions. Molecules involved in mesoderm induction include FGF which acts predominantly as a ventrolateral inducer, the TGF‐β homolog activin which can induce all types of mesoderm, and members of the Wnt family which have powerful dorsalizing effects. Early effects of inducer action include the activation of regulatory genes. Among such genes, particular interest is focused (...) on three genes encoding putative transcription factors that are expressed specifically in the Spemann organizer region of the gastrula. Expression of one of these genes, goosecoid, has been shown to be sufficient to elicit the formation of a dorsal axis including head and notochord in the embryo. (shrink)

Scientific theories are hard to find, and once scientists have found a theory, H, they often believe that there are not many distinct alternatives to H. But is this belief justified? What should scientists believe about the number of alternatives to H, and how should they change these beliefs in the light of new evidence? These are some of the questions that we will address in this article. We also ask under which conditions failure to find an alternative to H (...) confirms the theory in question. This kind of reasoning is frequently used in science and therefore deserves a careful philosophical analysis. 1 Introduction2 The Conceptual Framework3 The No Alternatives Argument4 Discussion I: A Quantitative Analysis of the No Alternatives Argument5 Discussion II: The Number of Alternatives and the Problem of Underdetermination6 ConclusionsAppendix AAppendix B. (shrink)

String dualities establish empirical equivalence between theories that often look entirely different with respect to their basic ontology and physical structure. Therefore, they represent a particularly interesting example of empirical equivalence in physics. However, the status of duality relations in string physics differs substantially from the traditional understanding of the role played by empirical equivalence. The paper specifies three important differences and argues that they are related to a substantially altered view on the underdetermination of theory building.

The subjective Everettian approach to quantum mechanics presented by Deutsch and Wallace fails to constitute an empirically viable theory of quantum phenomena. The decision theoretic implementation of the Born rule realized in this approach provides no basis for rejecting Everettian quantum mechanics in the face of empirical data that contradicts the Born rule. The approach of Greaves and Myrvold, which provides a subjective implementation of the Born rule as well but derives it from empirical data rather than decision theoretic arguments, (...) avoids the problem faced by Deutsch and Wallace and is empirically viable. However, there is good reason to cast doubts on its scientific value. (shrink)

Dawid's account of non-empirical theory assessment is meant to complement traditional theory assessments. I contend that his arguments don't provide support for this account. His three arguments, the no alternatives argument, the unexpected explanatory connections argument, and the meta-inductive argument from prior theories' success, are all problematic, particularly for an assessment of string theory. In particular, I argue that the meta-inductive argument is idle, because it's role in underwriting the future predictive success of a theory is subsumed by the (...) normal accounting of its predecessor's predictions in theory growth and testing. Dawid's arguments are interdependent, so showing that one fails is sufficient to cast doubt on his entire account. (shrink)

THE ART OF CAUSAL CONJECTURE Glenn Shafer Table of Contents Chapter 1. Introduction........................................................................................ ...........1 1.1. Probability Trees..........................................................................................3 1.2. Many Observers, Many Stances, Many Natures..........................................8 1.3. Causal Relations as Relations in Nature’s Tree...........................................9 1.4. Evidence............................................................................................ ...........13 1.5. Measuring the Average Effect of a Cause....................................................17 1.6. Causal Diagrams..........................................................................................20 1.7. Humean Events............................................................................................23 1.8. Three Levels of Causal Language................................................................27 1.9. An Outline of the Book................................................................................27 Chapter 2. Event Trees............................................................................................... .....31 2.1. Situations and Events...................................................................................32 2.2. The Ordering of Situations and Moivrean Events.......................................35 2.3. Cuts................................................................................................ ..............39 2.4. Humean Events............................................................................................43 2.5. (...) Moivrean Variables......................................................................................49 2.6. Humean Variables........................................................................................53 2.7. Event Trees for Stochastic Processes...........................................................54 2.8. Timing in Event Trees.................................................................................56 2.9. Intersecting Event Trees...............................................................................60 2.10. Notes on the Literature...............................................................................61 Chapter 3. Probability Trees...........................................................................................63 3.1. Some Types of Probability Trees.................................................................64 ii 3.2. Axioms for the Probabilities of Moivrean Events.......................................68 3.3. Zero Probabilities....................................................................................... ..70 3.4. A Sample-Space Analysis of the Event-Tree Axioms.................................72 3.5. Probabilities and Expected Values for Variables.........................................74 3.6. Martingales......................................................................................... .........79 3.7. The Expectation of a Variable in a Cut........................................................83 3.8. Conditional Expected Value and Conditional Expectation.........................87 Chapter 4. The Meaning of Probability...........................................................................91 4.1. The Interpretation of Expected Value..........................................................92 4.2. The Interpretation of Expectation................................................................95 4.3. The Long Run..............................................................................................98 4.4. Changes in Belief.........................................................................................101 4.5. The Empirical Validation of Probability......................................................106 4.6. The Diversity of Uses of Probability...........................................................108 4.7. Notes on the Literature.................................................................................110 Chapter 5. Independent Events.......................................................................................113 5.1. Independence........................................................................................ .......114 5.2. Weak Independence.....................................................................................118 5.3. The Principle of the Common Cause...........................................................121 5.4. Conditional Independence............................................................................128 5.5. Notes on the Literature.................................................................................133 Chapter 6. Events Tracking Events.................................................................................135 6.1. Tracking............................................................................................ ...........137 6.2. Tracking and Conditional Independence.....................................................142 6.3. Stochastic Subsequence...............................................................................143 6.4. Singular Diagrams for Stochastic Subsequence...........................................147 6.5. Conjunctive and Interactive Forks...............................................................149 Chapter 7. Events as Signs of Events..............................................................................153 iii 7.1. Sign................................................................................................ ..............154 7.2. Weak Sign................................................................................................ ....159 7.3. The Ethics of Causal Talk............................................................................160 7.4. Screening Off...............................................................................................16 2 Chapter 8. Independent Variables...................................................................................167 8.1. Unconditional Independence........................................................................170 8.2. Conditional Independence............................................................................175 8.3. Independence for Partitions.........................................................................177 8.4. Independence for Families of Variables......................................................182 8.5. Individual Properties of the Independence Relations...................................186 Chapter 9. Variables Tracking Variables........................................................................189 9.1. Tracking and Conditional Independence: A Summary...............................190 9.2. Strong Tracking............................................................................................ 192 9.3. Strong Tracking and Conditional Independence..........................................198 9.4. Stochastic Subsequence...............................................................................201 9.5. Functional Dependence................................................................................203 9.6. Tracking in Mean.........................................................................................204 9.7. Linear Tracking............................................................................................ 207 9.8. Tracking by Partitions..................................................................................210 9.9. Tracking by Families of Variables...............................................................212 Chapter 10. Variables as Signs of Variables...................................................................215 10.1. Sign................................................................................................ ............219 10.2. Linear Sign................................................................................................ .222 10.3. Scored Sign................................................................................................ 225 10.4. Families of Variables.................................................................................227 Chapter 11. AnTheory of Event Trees.............................................................229 11.1. Event Trees as Sets of Sets........................................................................230 11.2. Event Trees as Partially Ordered Sets........................................................232 iv 11.3. Regular Event Trees...................................................................................240 11.4. The Resolution of Moivrean Variables......................................................244 11.5. Humean Events and Variables...................................................................246 Chapter 12. Martingale Trees..........................................................................................247 12.1. Examples of Decision Trees......................................................................249 12.2. The Meaning of Probability in a Decision Tree.........................................253 12.3. Martingales......................................................................................... .......257 12.4. The Structure of Martingale Trees.............................................................261 12.5. Probability and Causality...........................................................................265 12.6. Lower and Upper Probability.....................................................................269 12.7. The Law of Large Numbers.......................................................................272 12.8. Notes on the Literature...............................................................................274 Chapter 13. Refining............................................................................................ ...........275 13.1. Examples of Refinement............................................................................277 13.2. A Constructive Definition of Finite Refinement.......................................281 13.3. Axioms for Refinement..............................................................................282 13.4. Lifting Moivrean Events and Variables.....................................................288 13.5. Refining Martingale Trees.........................................................................288 13.6. Grounding........................................................................................... .......294 Chapter 14. Principles of Causal Conjecture..................................................................299 14.1. The Diversity of Causal Explanation.........................................................302 14.2. The Mean Effect of the Happening of a Moivrean Event..........................305 14.3. The Effect of a Humean Variable..............................................................311 14.4. Attribution and Generality.........................................................................316 14.5. The Statistical Measurement of the Effect of a Cause...............................319 14.6. Measurement by Experiment.....................................................................320 14.7. Using Our Knowledge of How Things Work............................................322 v 14.8. Sampling Error...........................................................................................329 14.9. The Sampling Frame..................................................................................329 14.10. Notes on the Literature.............................................................................330 Chapter 15. Causal Models.............................................................................................3 31 15.1. The Causal Interpretation of Statistical Prediction....................................333 15.2. Generalizing to a Family of Exogenous Variables....................................337 15.3 Some Joint Causal Diagrams......................................................................339 15.4. Causal Path Diagrams................................................................................342 15.5. Causal Relevance Diagrams.......................................................................346 15.6. The Meaning of Latent Variables..............................................................352 15.7. Notes on the Literature...............................................................................357 Chapter 16. Representing Probability Trees...................................................................359 16.1. Three Graphical Representations...............................................................361 16.2. Skeletal Simplifications.............................................................................368 16.3. Martingale Trees in Type Theory...............................................................371 Appendix A. Huygens’s Probability Trees.....................................................................379 Huygens’s Manuscript in Translation..................................................................380 Appendix B. Some Elements of Graph Theory..............................................................385 B1. Undirected Graphs........................................................................................385 B2. Directed Graphs............................................................................................38 6 Appendix C. Some Elements of Order Theory...............................................................393 C1. Partial and Quasi Orderings.........................................................................393 C2. Singular and Joint Diagrams for Binary Relations.......................................394 C3. Lattices............................................................................................ .............395 C4. The Lattice of Partitions of a Set..................................................................396 Appendix D. The Sample-Space Framework for Probability.........................................399 D1. Probability Measures....................................................................................399 D2. Variables........................................................................................... ...........400 vi D3. Families of Variables...................................................................................401 D4. Expected Value............................................................................................402 D5. The Law of Large Numbers.........................................................................405 D6. Conditional Probability................................................................................406 D7. Conditional Expected Value........................................................................407 Appendix E. Prediction in Probability Spaces................................................................409 E1. Conditional Distribution...............................................................................411 E2. Regression on a Single Variable...................................................................412 E3. Regression on a Partition or a Family of Variables......................................415 E4. Linear Regression on a Single Variable.......................................................418 E5. Linear Regression on a Family of Variables................................................422 Appendix F. Sample-Space Concepts of Independence.................................................425 F1. Overview............................................................................................ ...........426 F2. Independence Proper.....................................................................................432 F3. Unpredictability in Mean..............................................................................434 F4. Simple Uncorrelatedness..............................................................................437 F5. Mixed Uncorrelatedness...............................................................................438 F6. Partial Uncorrelatedness...............................................................................440 F7. Independence for Partitions..........................................................................442 F8. Independence for Families of Variables.......................................................445 F9. The Basic Role of Uncorrelatedness.............................................................448 F10. Dawid’s Axioms.........................................................................................449 Appendix G. Prediction Diagrams..................................................................................453 G1. Path Diagrams............................................................................................ ..454 G2. Generalized Path Diagrams..........................................................................462 G3. Relevance Diagrams.....................................................................................466 G4. Bubbled Relevance Diagrams......................................................................475 Appendix H. Abstract Stochastic Processes...................................................................479 vii H1. Probability Conditionals and Probability Distributions...............................477 H2. Abstract Stochastic Processes......................................................................479 H3. Embedding Variables and Processes in a Sample Space.............................480 References.......................................................................................... ..............................491. (shrink)

Philosophers have cataloged a range of genealogical methods by which different sorts of normative conclusions can be established. Although such methods provide diverging ways of pursuing genealogical inquiry, they typically converge in eschewing historiographic methodology, in favor of a uniquely philosophical approach. In contrast, one genealogist who drew on historiographic methodology is Michel Foucault. This article presents the motivations and advantages of Foucault's genealogical use of such a methodology. It advances two mains claims. First, that Foucault's early 1970s work employs (...) a distinct genealogical method, which borrows from contemporary historiographic models of explanation to expand the range of objects that are proper to genealogical accounts of historical change. I demonstrate how Foucault modifies two central commitments of Nietzsche by broadening the dimensions of genealogical inquiry and explanation. Second, that historical method has normative relevance for genealogy, insofar as different historiographic choices can lead to different normative conclusions. I motivate this second claim by explaining how Foucault's multidimensional genealogical method expands both (a) the range of objects that are subject to evaluative assessment, and (b) the set of possible prescriptive recommendations that follow from such assessment. (shrink)

Bridging the gap between the world of science and the realm of the spiritual, B. Alan Wallace introduces a natural theory of human consciousness that has its roots in contemporary physics and Buddhism. Wallace's "special theory of ontological relativity" suggests that mental phenomena are _conditioned_ by the brain, but do not _emerge_ from it. Rather, the entire natural world of mind and matter, subjects and objects, arises from a unitary dimension of reality that is more fundamental than these dualities, as (...) proposed by Wolfgang Pauli and Carl Jung. To test his hypothesis, Wallace employs the Buddhist meditative practice of _samatha_, refining one's attention and metacognition, to create a kind of telescope to examine the space of the mind. Drawing on the work of the physicist John Wheeler, he then proposes a more general theory in which the participatory nature of reality is envisioned as a self-excited circuit. In comparing these ideas to the Buddhist theory known as the Middle Way philosophy, Wallace explores further aspects of his "general theory of ontological relativity," which can be investigated by means of _vipasyana_, or insight, meditation. Wallace then focuses on the theme of symmetry in reference to quantum cosmology and the "problem of frozen time," relating these issues to the theory and practices of the Great Perfection school of Tibetan Buddhism. He concludes with a discussion of the general theme of complementarity as it relates to science and religion. The theories of relativity and quantum mechanics were major achievements in the physical sciences, and the theory of evolution has had an equally deep impact on the life sciences. However, rigorous scientific methods do not yet exist to observe mental phenomena, and naturalism has its limits for shedding light on the workings of the mind. A pioneer of modern consciousness research, Wallace offers a practical and revolutionary method for exploring the mind that combines the keenest insights of contemporary physicists and philosophers with the time-honored meditative traditions of Buddhism. (shrink)

Journal of the History of Biology provides a fifty-year long record for examining the evolution of the history of biology as a scholarly discipline. In this paper, we present a new dataset and preliminary quantitative analysis of the thematic content of JHB from the perspectives of geography, organisms, and thematic fields. The geographic diversity of authors whose work appears in JHB has increased steadily since 1968, but the geographic coverage of the content of JHB articles remains strongly lopsided toward the (...) United States, United Kingdom, and western Europe and has diversified much less dramatically over time. The taxonomic diversity of organisms discussed in JHB increased steadily between 1968 and the late 1990s but declined in later years, mirroring broader patterns of diversification previously reported in the biomedical research literature. Finally, we used a combination of topic modeling and nonlinear dimensionality reduction techniques to develop a model of multi-article fields within JHB. We found evidence for directional changes in the representation of fields on multiple scales. The diversity of JHB with regard to the representation of thematic fields has increased overall, with most of that diversification occurring in recent years. Drawing on the dataset generated in the course of this analysis, as well as web services in the emerging digital history and philosophy of science ecosystem, we have developed an interactive web platform for exploring the content of JHB, and we provide a brief overview of the platform in this article. As a whole, the data and analyses presented here provide a starting-place for further critical reflection on the evolution of the history of biology over the past half-century. (shrink)

This paper traces the background to R. A. Fisher's multi-factorial theory of inheritance. It is argued that the traditional account is incomplete, and that Karl Pearson's well-known pre-Fisherian objections to the theory were in fact overcome by Pearson himself. It is further argued that Pearson's stated reasons for not accepting his own achievement has to be seen as a rationalization, standing in for deeper-seated metaphysical objections to the Mendelian paradigm of a type not readily discussed in a formal scientific paper. (...) The apparent, post-Fisherian, continued acceptance of Pearson's objections is presented as an interesting problem for the historian and sociologist. (shrink)

It is common to account for our senses on the basis of our sensory organs. One way of glossing why Aristotle famously counted five senses—and why his count became common sense in the West and elsewhere—is because there are five rather obvious organs of sense. In more modern accounts, this organ criterion of the senses has transformed into a neurobiological criterion; that is to say, part of what it means to be a sense is to have an associated organ with (...) appropriate physiological properties. For example, part of the claim that humans have a sense of vision is that we have a non-vestigial organ (the eye) that has cells (photoreceptors) especially sensitive to the properties of electromagnetic radiation. However, the nature of this “organ criterion” is a point of some contention. Is it a sufficient criterion? Necessary? To be called “vision” need the organ mediating it give rise to “visual experiences”? This chapter will consider the neurobiological criterion as it was originally presented in Aristotle and later reconceptualized in 19th-century neurophysiologist Johannes Müller’s “Law of Specific Nerve Energies.” By understanding the role of neurobiology in these accounts, we will be able to explore the deficiencies of contemporary accounts that downplay neurobiology in differentiating the senses. We will consider one of these accounts in detail: Alva Noë’s recent arguments in favor of an enactive approach to perceptual psychology. (shrink)

In 2004 Orlando Florida was hit with an almost unprecedented series of storms and hurricanes. Within two months, Hurricanes Charley, Frances, and Jeanne hit, and Hurricane Ivan made a near miss. Billions of dollars of damage resulted from these disasters, and several dozen lives were lost. It is tempting, in the case of extreme events, to either regard them as having no need of interpretation (that is, as simply given, material events shared by everyone), or as a kind of rare (...) window on the workings of a community.1 In this paper I want to examine the public construction of the meaning of the hurricane in Orlando, particularly as represented in reports at the time in the major newspaper, the Orlando Sentinel. I am especially interested in placemaking, that is, the ways in which places gain or fail to gain meaning in times of stress. I will suggest that opportunities for place-making were lost in Orlando because of the frame the events around Hurricane Charley were given. Hurricane Frances, though, was treated differently in the Orlando press, and the discourse around the hurricanes of 2004 provides a contrast to the kind of rhetorical response that circulated during the disastrous hurricane season of 2005. In the case of some disasters, community is reinforced, and the skills of place-making are exercised. The reaction to Hurricane Charley in Orlando, on the other hand, tended not to reinforce community, and tended not to contribute to place-making. While it is extremely difficult to measure sense of place or sense of community quantitatively, it is possible to make sense out of the interpretive tools people have at their disposal in a disaster. What comes out of all this, I think, is something I want to call “place-making imagination”. This is analogous to the 1 concept of “moral imagination” in ethics (Johnson). Our moral options extend as far as our imagination will allow. A person might boil the moral universe down to polarized options – fight or flight, kill or be killed, choose A or B – when in fact a more cultivated and aware imagination may have afforded other options, perhaps better ones than either polarized one.. (shrink)

Neuronal aggregates involved in conscious awareness are not evenly distributed throughout the CNS but comprise key components referred to as the neural network correlates of consciousness (NNCC). A critical node in this network is the posterior cingulate, precuneal, and retrosplenial cortices. The cytological and neurochemical composition of this region is reviewed in relation to the Brodmann map. This region has the highest level of cortical glucose metabolism and cytochrome c oxidase activity. Monkey studies suggest that the anterior thalamic projection likely (...) drives retrosplenial and posterior cingulate cortex metabolism and that the midbrain projection to the anteroventral thalamic nucleus is a key coupling site between the brainstem system for arousal and cortical systems for cognitive processing and awareness. The pivotal role of the posterior cingulate, precuneal, and retrosplenial cortices in consciousness is demonstrated with posterior cingulate epilepsy cases, midcingulate lesions that de-afferent this region and are associated with unilateral sensory neglect, observations from stroke and vegetative state patients, alterations in blood flow during sleep, and the actions of general anesthetics. Since this region is critically involved in self reflection, it is not surprising that it is similarly a site for the NNCC. Interestingly, information processing during complex cognitive tasks and during aversive sensations such as pain induces efforts to terminate self reflection and result in decreased processing in posterior cingulate and precuneal cortices. (shrink)

In the paper I offer a brief sketch of one of the sources of utilitarianism. Our biological ancestry is a matter of fact that is not altered by the way we describe ourselves. With philosophical theories it is otherwise. Utilitarianism can be described in ways that make it look as if it is as old as moral philosophy – as J. S. Mill thought it was. For my historical purposes, it is more useful to have an account that brings out (...) what is specific about Benthamism and its descendants. Let us try to make do with the following. First, utilitarianism asserts that the fundamental requirement of morality is that we are to maximize good, for everyone and not just for the agent. This basic principle presupposes that it makes sense to think of aggregating goods to make a total, and of comparing amounts of good thus aggregated. Second, the good to be brought about is located in feelings of pleasure, and the evil to be avoided in feelings of pain. These feelings have inherent value or disvalue regardless of how they are caused to exist and regardless of their own consequences. Third, all moral principles can be derived from the requirement that good be maximized. The principles involved in evaluating agents as well as in giving moral direction to action are nothing but applications of the basic principle. (shrink)

String theory has played a highly influential role in theoretical physics for nearly three decades and has substantially altered our view of the elementary building principles of the Universe. However, the theory remains empirically unconfirmed, and is expected to remain so for the foreseeable future. So why do string theorists have such a strong belief in their theory? This book explores this question, offering a novel insight into the nature of theory assessment itself. Dawid approaches the topic from a (...) unique position, having extensive experience in both philosophy and high-energy physics. He argues that string theory is just the most conspicuous example of a number of theories in high-energy physics where non-empirical theory assessment has an important part to play. Aimed at physicists and philosophers of science, the book does not use mathematical formalism and explains most technical terms. (shrink)

It has been suggested that if the preservation and development of consciousness in the biological evolution is a result of natural selection, it is plausible that consciousness not only has been influenced by neural processes, but has had a survival value itself; and it could only have had this, if it had also been efficacious. This argument for mind-brain interaction is examined, both as the argument has been developed by William James and Karl Popper and as it has been discussed (...) by C.D. Broad. The problem of identifying mental phenomena with certain neural phenomena is also addressed. The main conclusion of the analysis is that an explanation of the evolution of consciousness in Darwinian terms of natural selection does not rule out that consciousness may have evolved as a mere causally inert effect of the evolution of the nervous system, or that mental phenomena are identical with certain neural phenomena. However, the interactionistic theory still seems, more plausible and more fruitful for other reasons brought up in the discussion. (shrink)

This essay reflects on 25 years since Christian Bioethics began publication and, in somewhat autobiographical fashion, engages two core concerns. First, although “non-ecumenism” may often appear a pretext for contention and division, I suggest that a respectful non-ecumenism may provide the opportunity for dialogue and the occasion for employing certain tools from religious studies. Second, although many are skeptical about the possibilities of identifying a “common morality,” a defense of that notion provides a plausible explanation for the development of limited (...) consensus on some issues in bioethics. (shrink)

B. Rundle; X—Transitivity and Indirect Speech, Proceedings of the Aristotelian Society, Volume 68, Issue 1, 1 June 1968, Pages 187–206, https://doi.org/10.1093/.

Speaking of Professor Geach's belief that pronouns in natural language function like the bound variables in quantification theory, Gareth Evans, in ‘Pronouns, Quantifiers, and Relative Clauses - I’ says :I want to try to show that there are pronouns with quantifier antecedents that function in a quite different way. Such pronouns typically stand in a different grammatical relation to their antecedents, and; in contrast with bound pronouns, must be assigned a reference, so that their most immediate sentential contexts can always (...) be assigned a truth value. The relevant grammatical relation appears to be Klima's relation of ‘in construction with’. When the pronoun is in construction with its antecedent, as in [‘Some man loves his mother’] and [‘No man is happy when he is in love’] the result is a bound pronoun. (shrink)