Evidence-based medicine (EBM) makes use of explicit procedures for grading evidence for causal claims. Normally, these procedures categorise evidence of correlation produced by statistical trials as better evidence for a causal claim than evidence of mechanisms produced by other methods. We argue, in contrast, that evidence of mechanisms needs to be viewed as complementary to, rather than inferior to, evidence of correlation. In this paper we first set out the case for treating evidence of mechanisms alongside evidence of correlation in (...) explicit protocols for evaluating evidence. Next we provide case studies which exemplify the ways in which evidence of mechanisms complements evidence of correlation in practice. Finally, we put forward some general considerations as to how the two sorts of evidence can be more closely integrated by EBM. (shrink)

We currently have on offer a variety of different theories of causation. Many are strikingly good, providing detailed and plausible treatments of exemplary cases; and all suffer from clear counterexamples. I argue that, contra Hume and Kant, this is because causation is not a single, monolithic concept. There are different kinds of causal relations imbedded in different kinds of systems, readily described using thick causal concepts. Our causal theories pick out important and useful structures that fit some familiar cases—cases we (...) discover and ones we devise to fit. (shrink)

This article argues that the basic account of mechanism and mechanistic explanation, involving sequential execution of qualitatively characterized operations, is itself insufficient to explain biological phenomena such as the capacity of living organisms to maintain themselves as systems distinct from their environment. This capacity depends on cyclic organization, including positive and negative feedback loops, which can generate complex dynamics. Understanding cyclically organized mechanisms with complex dynamics requires coordinating research directed at decomposing mechanisms into parts and operations with research using computational (...) models to recompose mechanisms and determine their dynamic behavior. This coordinated endeavor yields dynamic mechanistic explanations. (shrink)

Systems biology provides alternatives to the strategies to developing mechanistic explanations traditionally pursued in cell and molecular biology and much discussed in accounts of mechanistic explanation. Rather than starting by identifying a mechanism for a given phenomenon and decomposing it, systems biologists often start by developing cell-wide networks of detected connections between proteins or genes and construe clusters of highly interactive components as potential mechanisms. Using inference strategies such as ‘guilt-by-association’, researchers advance hypotheses about functions performed of these mechanisms. I (...) examine several examples of research on budding yeast, first on what are taken to be enduring networks and subsequently on networks that change as cells perform different activities or respond to different external conditions. (shrink)

Perhaps the most readable and accessible of the great works of scientific imagination, The Origin of Species sold out on the day it was published in 1859. Theologians quickly labeled Charles Darwin the most dangerous man in England, and, as the Saturday Review noted, the uproar over the book quickly "passed beyond the bounds of the study and lecture-room into the drawing-room and the public street." Yet, after reading it, Darwin's friend and colleague T. H. Huxley had a different reaction: (...) "How extremely stupid not to have thought of that." Based largely on Darwin's experience as a naturalist while on a five-year voyage aboard H.M.S. Beagle, The Origin of Species set forth a theory of evolution and natural selection that challenged contemporary beliefs about divine providence and the immutability of species. A landmark contribution to philosophical and scientific thought, this edition also includes an introductory historical sketch and a glossary Darwin later added to the original text. Charles Darwin grew up considered, by his own account, "a very ordinary boy, rather below the common standard of intellect." A quirk of fate kept him from the career his father had deemed appropriate--that of a country parson--when a botanist recommended Darwin for an appointment as a naturalist aboard H.M.S. Beagle from 1831 to 1836. Darwin is also the author of the five-volume work Zoology of the Voyage of the Beagle (1839) and The Descent of Man (1871). (shrink)

Generelle Morphologie der Organismen - Allgemeine Grundzuge der organischen Formen-Wissenschaft mechanisch begrundet durch die von Charles Darwin reformierte Deskendenz-Theorie ist ein unveranderter, hochwertiger Nachdruck der Originalausgabe aus dem Jahr 1866. Hansebooks ist Herausgeber von Literatur zu unterschiedlichen Themengebieten wie Forschung und Wissenschaft, Reisen und Expeditionen, Kochen und Ernahrung, Medizin und weiteren Genres.Der Schwerpunkt des Verlages liegt auf dem Erhalt historischer Literatur.Viele Werke historischer Schriftsteller und Wissenschaftler sind heute nur noch als Antiquitaten erhaltlich. Hansebooks verlegt diese Bucher neu und tragt damit (...) zum Erhalt selten gewordener Literatur und historischem Wissen auch fur die Zukunft bei. (shrink)

The mathematical theory of communication.

This is a first-hand account of the discussions going on between biologists of different persuasions. On the one hand are the ultradarwinians, who emphasize the supremacy of the gene and natural selection, and on the other, the naturalists, who focus on whole creatures, rather than on genes.

Reductionism is a widely endorsed methodology among biologists, a metaphysical theory advanced to vindicate the biologist's methodology, and an epistemic thesis those opposed to reductionism have been eager to refute. While the methodology has gone from strength to strength in its history of achievements, the metaphysical thesis grounding it remained controversial despite its significant changes over the last 75 years of the philosophy of science. Meanwhile, antireductionism about biology, and especially Darwinian natural selection, became orthodoxy in philosophy of mind, philosophy (...) of science, and philosophy of biology. This Element expounds the debate about reductionism in biology, from the work of the post-positivists to the end of the century debates about supervenience, multiple realizability, and explanatory exclusion. It shows how the more widely accepted 21st century doctrine of 'mechanism' - reductionism with a human face - inherits both the strengths and the challenges of the view it has largely supplanted. (shrink)

Explores the possiblity and process of evolution beyond the standard and established scientific principles.

This volume argues for a new image of science that understands both natural and social phenomena to be the product of mechanisms, casting the work of science as an effort to understand those mechanisms. Glennan offers an account of the nature of mechanisms and of the models used to represent them in physical, life, and social sciences.

A number of recent biologists have used multi-level selection theory to help explain the major transitions in evolution. I argue that in doing so, they have shifted from a ‘synchronic’ to a ‘diachronic’ formulation of the levels of selection question. The implications of this shift in perspective are explored, in relation to an ambiguity in the meaning of multi-level selection. Though the ambiguity is well-known, it has never before been discussed in the context of the major transitions.

Recently, a number of philosophers of science have claimed that much explanation in the sciences, especially in the biomedical and social sciences, is mechanistic explanation. I argue the account of mechanistic explanation provided in this tradition has not been entirely satisfactory, as it has neglected to describe in complete detail the crucial causal structure of mechanistic explanation. I show how the interventionist approach to causation, especially within a structural equations framework, provides a simple and elegant account of the causal structure (...) of mechanisms. This account explains the many useful insights of traditional accounts of mechanism, such as Carl Craver's account in his book Explaining the Brain , but also helps to correct the omissions of such accounts. One of these omissions is the failure to provide an explicit formulation of a modularity constraint that plays a significant role in mechanistic explanation. One virtue of the interventionist/structural equations framework is that it allows for a simple formulation of a modularity constraint on mechanistic explanation. I illustrate the role of this constraint in the last section of the paper, which describes the form that mechanistic explanation takes in the computational, information-processing paradigm of cognitive psychology. (shrink)

The concept of mechanism is analyzed in terms of entities and activities, organized such that they are productive of regular changes. Examples show how mechanisms work in neurobiology and molecular biology. Thinking in terms of mechanisms provides a new framework for addressing many traditional philosophical issues: causality, laws, explanation, reduction, and scientific change.

After a decade of intense debate about mechanisms, there is still no consensus characterization. In this paper we argue for a characterization that applies widely to mechanisms across the sciences. We examine and defend our disagreements with the major current contenders for characterizations of mechanisms. Ultimately, we indicate that the major contenders can all sign up to our characterization.

Developmental systems theory (DST) expands the unit of replication from genes to whole systems of developmental resources, which DST interprets in terms of cycling developmental processes. Expansion seems required by DST's argument against privileging genes in evolutionary and developmental explanations of organic traits. DST and the expanded replicator brook no distinction between biological and cultural evolution. However, by endorsing a single expanded unit of inheritance and leaving the classical molecular notion of gene intact, DST achieves only a nominal reunification of (...) heredity and development. I argue that an alternative conceptualization of inheritance denies the classical opposition of genetics and development while avoiding the singularity inherent in the replicator concept. It also yields a new unit--the reproducer--which genuinely integrates genetic and developmental perspectives. The reproducer concept articulates the non-separability of "genetic" and "developmental" roles in units of heredity, development, and evolution. DST reformulated in terms of reproducers rather than replicators preserves an empirically interesting distinction between cultural and biological evolution. (shrink)

Universal Darwinism provides a methodology to study the evolution of anatomical form and sociocultural behavior that centers on defining the units and levels of selection, and it identifies the conditions whereby natural selection operates. In previous work, I have examined how this selection-focused evolutionary epistemology may be universalized to include theories that associate with an extended synthesis. Applied evolutionary epistemology is a metatheoretical framework that understands any and all kinds of evolution as phenomena where units evolve by mechanisms at levels (...) of an ontological hierarchy; and it provides three heuristics to search for these units, levels and mechanisms. The heuristics are applicable to language and sociocultural evolution, and here, we give an in-depth analysis of how the unit-heuristic can be implemented into language origin and evolution studies. The importance of developing hierarchy theories is also more fully explained. (shrink)

We examine how insights made in socio-anthropological and evolutionary schools of thought necessitate us to reevaluate the classic philosophical distinction between epistemology and ontology. We adopt an applied evolutionary epistemological stance and demonstrate that both epistemology and ontology evolve. Epistemology is broadened to include all knowledge and information that all life forms evolve, and ontology encompasses all biologically informed realities that life builds. Through processes such as symbiosis and niche construction, organisms acquire and extend information and knowledge into their offspring, (...) onto unrelated organisms, and onto their niches. Life builds biorealities that change over time. Consequently, knowledge and reality are mutable and truth is spatiotemporally bounded. We conclude that the classic distinction between epistemology and ontology has become superfluous and instead, we argue that the evolving knowledge that comes in the form of organisms and their extended niches equals ontological realities. (shrink)

info:eu-repo/semantics/publishedVersion.

The thesis of this paper is that our understanding of life, as reflected in the biological and medical sciences but also in our everyday transactions, has been hampered by an inappropriate metaphysics. The metaphysics that has dominated Western philosophy, and that currently shapes most understanding of life and the life sciences, sees the world as composed of things and their properties. While these things appear to undergo all kinds of changes, it has often been supposed that this amounts to no (...) more than a change in the spatial relations of their unchanging parts. From antiquity, however, there has been a rival to this view, the process ontology, associated in antiquity with the fragmentary surviving writings of Heraclitus. In the last century it has been especially associated with the work of the British metaphysician and logician, Alfred North Whitehead. For process ontology, what most fundamentally exists is change, or process. What we are tempted to think of as constant things are in reality merely temporary stabilities in this constant flux of change, eddies in the flux of process. My main claim in this paper will be that a metaphysics of this latter kind is the only kind adequate to making sense of the living world. After explaining in more detail, the differences between these ontological views, I shall illustrate the advantages of a process ontology with reference to the category of organism. Finally I shall explore some further implications of a process ontology for biology and for philosophy. (shrink)

Explores the development of the ideas of evolutionary biology, particularly as affected by the increasing understanding of genetics and of the chemical basis of inheritance.

Explanation in biology has long been characterized as being very different from explanation in other scientific disciplines, very much so from explanation in physics. One of the reasons was the existence in biology of explanation types that were unheard of in the physical sciences: teleological explanations (e.g. Hull 1974), evolutionary explanations (e.g. Mayr 1988), or even functional explanations (e.g. Neander 1991). More recently, and owing much to the rise of molecular biology, biological explanations have been depicted as mechanisms (e.g; Machamer, (...) Darden and Craver 2000). The aim of this volume is to shed some new light on the diversity of explanation types in biology. What are the different types of explanation that occur in biology? Are these types of explanation specific to particular sub-disciplines of biology, or to particular types of problems across biology? How do they relate to each another? Do they compete with one another for answering the same questions? Or do they complement each other, providing insights to different questions? What are the reasons for such diversity? Can this diversity be overcome by a broader unifying model of explanation or is it more profound and irreducible? Why? This volume aims at making sense of this diversity of types of explanations that are found in biology, of their relationship with one another. After all, explanation in biology may prove not only different from explanation in the physical sciences, but also much more diverse than originally anticipated. (shrink)

In the six decades since the publication of Julian Huxley's Evolution: The Modern Synthesis, spectacular empirical advances in the biological sciences have been accompanied by equally significant developments within the core theoretical framework of the discipline. As a result, evolutionary theory today includes concepts and even entire new fields that were not part of the foundational structure of the Modern Synthesis. In this volume, sixteen leading evolutionary biologists and philosophers of science survey the conceptual changes that have emerged since Huxley's (...) landmark publication, not only in such traditional domains of evolutionary biology as quantitative genetics and paleontology but also in such new fields of research as genomics and EvoDevo. Most of the contributors to Evolution—The Extended Synthesis accept many of the tenets of the classical framework but want to relax some of its assumptions and introduce significant conceptual augmentations of the basic Modern Synthesis structure—just as the architects of the Modern Synthesis themselves expanded and modulated previous versions of Darwinism. This continuing revision of a theoretical edifice the foundations of which were laid in the middle of the nineteenth century—the reexamination of old ideas, proposals of new ones, and the synthesis of the most suitable—shows us how science works, and how scientists have painstakingly built a solid set of explanations for what Darwin called the "grandeur" of life. (shrink)

One of our most brilliant evolutionary biologists, Richard Lewontin has also been a leading critic of those--scientists and non-scientists alike--who would misuse the science to which he has contributed so much. In The Triple Helix, Lewontin the scientist and Lewontin the critic come together to provide a concise, accessible account of what his work has taught him about biology and about its relevance to human affairs. In the process, he exposes some of the common and troubling misconceptions that misdirect and (...) stall our understanding of biology and evolution.The central message of this book is that we will never fully understand living things if we continue to think of genes, organisms, and environments as separate entities, each with its distinct role to play in the history and operation of organic processes. Here Lewontin shows that an organism is a unique consequence of both genes and environment, of both internal and external features. Rejecting the notion that genes determine the organism, which then adapts to the environment, he explains that organisms, influenced in their development by their circumstances, in turn create, modify, and choose the environment in which they live.The Triple Helix is vintage Lewontin: brilliant, eloquent, passionate, and deeply critical. But it is neither a manifesto for a radical new methodology nor a brief for a new theory. It is instead a primer on the complexity of biological processes, a reminder to all of us that living things are never as simple as they may seem. (shrink)

Traditionally, species have been treated as classes. In fact they may be considered individuals. The logical term “individual” has been confused with a biological synonym for “organism.” If species are individuals, then: 1) their names are proper, 2) there cannot be instances of them, 3) they do not have defining properties, 4) their constituent organisms are parts, not members. “ Species " may be defined as the most extensive units in the natural economy such that reproductive competition occurs among their (...) parts. Species are to evolutionary theory as firms are to economic theory: this analogy resolves many issues, such as the problems of “reality” and the ontological status of nomenclatorial types. (shrink)

neglected aspect: knowledge of error, or ‘‘negative’’ knowledge. The development of knowledge of what counts as error occurs via a kind of internal variation and selection, or quasi-evolutionary, process. Processes of reflection generate a hierarchy of principles of error.

In this paper Wimsatt's analysis of units of selection is taken as defining the units of selection question. A definition of levels of selection is offered and it is shown that the levels of selection question is quite different from the units of selection question. Some of the relations between units and levels are briefly explored. It is argued that the levels of selection question is the question relevant to explanatory concerns, and it is suggested that it is the question (...) relevant to ontological concerns. (shrink)