Showing papers on "Philosophy of biology published in 2005"

Discovering Cell Mechanisms: The Creation of Modern Cell Biology

Abstract: Between 1940 and 1970 pioneers in the new field of cell biology discovered the operative parts of cells and their contributions to cell life. They offered mechanistic accounts that explained cellular phenomena by identifying the relevant parts of cells, the biochemical operations they performed, and the way in which these parts and operations were organised to accomplish important functions. Cell biology was a revolutionary science but in this book it also provides fuel for yet another revolution, one that focuses on the very conception of science itself. Laws have traditionally been regarded as the primary vehicle of explanation, but in the emerging philosophy of science it is mechanisms that do the explanatory work. Bechtel emphasises how mechanisms were discovered, focusing especially on the way in which new instruments made these inquiries possible. He also describes how new journals and societies provided institutional structure to this new enterprise.

Fundamental issues in systems biology.

Abstract: Summary In the context of scientists’ reflections on genomics, we examine some fundamental issues in the emerging postgenomic discipline of systems biology. Systems biology is best understood as consisting of two streams. One, which we shall call ‘pragmatic systems biology’, emphasises large-scale molecular interactions; the other, which we shall refer to as ‘systems-theoretic biology’, emphasises system principles. Both are committed to mathematical modelling, and both lack a clear account of what biological systems are. We discuss the underlying issues in identifying systems and how causality operates at different levels of organisation. We suggest that resolving such basic problems is a key task for successful systems biology, and that philosophers could contribute to its realisation. We conclude with an argument for more sociologically informed collaboration between scientists and philosophers. BioEssays 27: 1270–1276, 2005. 2005 Wiley Periodicals, Inc.

Eco-efficiency: Philosophy, Theory, and Tools

Abstract: It is ironic that I am writing this column on the philosophy, theory, and tools of eco-efficiency, because I expressed my skepticism concerning the subject at the meeting that is the source of this special issue. The concept of eco-efficiency was first described by Schaltegger and Sturm (1989) and then widely publicized in 1992 in Changing Course (Schmidheiny 1992), a publication of the World Business Council for Sustainable Development (WBCSD). Since then it has been accepted

The function debate in philosophy.

Abstract: This paper reviews the debate on the notion of biological function and on functional explanation as this takes place in philosophy. It describes the different perspectives, issues, intuitions, theories and arguments that have emerged. The author shows that the debate has been too heavily influenced by the concerns of a naturalistic philosophy of mind and argues that in order to improve our understanding of biology the attention should be shifted from the study of intuitions to the study of the actual practice of biological inquiry.

Discussion: Three ways to misunderstand developmental systems theory

Abstract: Developmental systems theory (DST) is a general theoretical perspective on development, heredity and evolution. It is intended to facilitate the study of interactions between the many factors that influence development without reviving `dichotomous' debates over nature or nurture, gene or environment, biology or culture. Several recent papers have addressed the relationship between DST and the thriving new discipline of evolutionary developmental biology (EDB). The contributions to this literature by evolutionary developmental biologists contain three important misunderstandings of DST.

The philosophy of chemistry : From infancy toward maturity

Abstract: s) has, besides physics, also “electrical engineering, electronics, communications, control engineering, computers and computing, and information technology” and a “significant coverage in areas such as materials science, oceanography, nuclear engineering, geophysics, biomedical engineering, and biophysics.”4 Yet, despite the rapid growth of computer sciences and information technology, all that now comes to less than 40% of the coverage of Chemical Abstracts. In addition, Biological Abstracts could greatly flourish in the past decade by covering, besides biology, also “biochemistry, biotechnology, pre-clinical and experimental medicine, pharmacology, agriculture, and veterinary science.”5 Despite the boom of the biomedical sciences and the overlap with chemistry, it is still only 40% of Chemical Abstracts. The earth sciences, less than a 10th of the size of chemistry, are even smaller than the social sciences and psychology. The quantitative dominance of chemistry is no new phenomenon. To the contrary, many of the other abstract journals have grown more rapidly than Chemical Abstracts during the past three to four decades for various reasons. They could benefit from booming trends, as Psychological Abstracts from cognitive psychology; they absorbed new fields, as Science Abstracts did with computer science and information technology to become INSPEC; or they increased the overlap with chemistry, as Biological Abstracts did with biochemistry. By 1979, when no philosopher of science THE PHILOSOPHY OF CHEMISTRY 21 could even imagine the existence of philosophy of chemistry, Chemical Abstracts was more than four times as big as Science Abstracts (physics) and about three times as big as Biological Abstracts. Had those philosophers without prejudice gone into the laboratories, then they would have stumbled on chemistry almost everywhere. Nowadays, philosophers overall write as many publications per year as chemists do in four days. Ironically, the figure suggests a rule of thumb about the philosophers’ interest in the sciences: the smaller the discipline, the more do philosophers write about it, with the exception of the earth sciences. In the approximate order, philosophers write: (1) about philosophy, as history of philosophy or, to be more correct, about what philosophical classics have published or left unpublished; (2) about mathematics, as mathematical logic and philosophy of mathematical physics (“philosophy of science”); (3) about psychology, as philosophy of mind or naturalized epistemology; (4) about the social sciences, as social and political philosophy and philosophy of social sciences; (5) about experimental physics, as “philosophy of science”; (6) about biology as philosophy of biology; and (7) to the smallest degree, about chemistry. Thus, if philosophers produce general ideas about “science,” there are good reasons to be mistrustful. On the other hand, if one really wants to understand the natural sciences, there are good reasons to start with chemistry. A history of philosophy explanation Many explanations have been advanced for the fact that philosophers have so stubbornly neglected chemistry as if it were virtually non-existent. Is it the lack of “big questions” in chemistry, its close relationship to technology, or the historically rooted pragmatism of chemists and their lack of interest in metaphysical issues? Or, is the alleged reduction of chemistry to physics (quantum mechanics) the main obstacle, so that, if chemistry were only an applied branch of physics, there would be no genuine philosophical issue of chemistry? What all these approaches have in common is that they try to explain the neglect of philosophers by reference to chemistry, as if there were something wrong with chemistry. If there is only a bit of truth in our rule of thumb, however, it is the strange order of interest of philosophers that calls for explanation. In such an explanation, the neglect of chemistry would turn out to be only a special case, albeit an extreme one. I do not intend to provide a full explanation, but some hints from the disciplinary history of philosophy. Although we can, in retrospect, build a history of texts that we nowadays call philosophy, there is anything else than a continuous history of a discipline called philosophy, i.e., a history of a profession. The topical preferences of today’s philosophers reflect the surprisingly young and awkward history of their discipline. The relationship to mathematics goes back to a time, still at the turn to the 19th century, when “philosophy” was just the generic term for all the arts and sciences

Matthen and Ariew’s Obituary for Fitness: Reports of its Death have been Greatly Exaggerated

Abstract: Philosophers of biology have been absorbed by the problem of defining evolutionary fitness since Darwin made it central to biological explanation. The apparent problem is obvious. Define fitness as some biologists implicitly do, in terms of actual survival and reproduction, and the principle of natural selection turns into an empty tautology: those organisms which survive and reproduce in larger numbers, survive and reproduce in larger numbers. Accordingly, many writers have sought to provide a definition for 'fitness' which avoid this outcome. In particular the definition of fitness as a probabilistic propensity has been widely favored. 1 Others, recognizing that no definition both correct and complete can actually be provided, have accepted the consequence that the leading principle of the theory is a definitional truth and attempted to mitigate the impact of this outcome for the empirical character of the theory. 2 Still others have argued that 'fitness' is properly viewed as a term undefined in the theory of natural selection (on the model of mass—a term undefined in Newtonian mechanics). 3 But few have contemplated the solution to this problem proposed by Mohan Matthen and André Ariew (hereafter, MA), in 1 See for instance R. Brandon, \" Adaptation and evolutionary theory, \" Studies in the History and

Revisiting the eclipse of Darwinism.

Abstract: The article sums up a number of points made by the author concerning the response to Darwinism in the late nineteenth and early twentieth centuries, and repeats the claim that a proper understanding of the theory's impact must take account of the extent to which what are now regarded as the key aspects of Darwin's thinking were evaded by his immediate followers Potential challenges to this position are described and responded to

The Emergence Principle in Biological Hierarchies

Abstract: Emergent properties have been described by Mill, Lewes, Broad, Morgan and others, as novel, nonadditive, nonpredictable and nondeducible within a hierarchical context. I have developed a more definitive concept of a hierarchy that can be used to inspect the phenomenon of emergence in a new and detailed manner. A hierarchy is held together by descending constraints and new features can arise when an upper level entity restrains its components in new combinations that are not expected when viewing these components alone. Examples of emergent features are (i) matching anticodons and amino acids by aminoacetyl-tRNA synthetase enzymes appearing early among the first forms of life, (ii) negative feedback in end-product inhibition first occurring in microbes, (iii) memory in animals and (iv) apical cells in plants. Until recently, life was considered only in terms of physics and chemistry, but now it is known to have a third aspect of information that along with the descendant constraints in its hierarchical organization makes emergentism possible within a reductionist’s framework.

How to Reconcile Physicalism and Antireductionism about Biology

Abstract: Physicalism and antireductionism are the ruling orthodoxy in the philosophy of biology. But these two theses are difficult to reconcile. Merely embracing an epistemic antireductionism will not suffice, as both reductionists and antireductionists accept that given our cognitive interests and limitations, non‐molecular explanations may not be improved, corrected or grounded in molecular ones. Moreover, antireductionists themselves view their claim as a metaphysical or ontological one about the existence of facts molecular biology cannot identify, express or explain. However, this is tantamount to a rejection of physicalism and so causes the antireductionist discomfort. In this paper we argue that vindicating physicalism requires a physicalistic account of the principle of natural selection, and we provide such an account. The most important payoff to the account is that it provides for the very sort of autonomy from the physical that antireductionists need without threatening their commitment to physicalism.

"It Ain't Over 'til it's Over": Rethinking the Darwinian Revolution.

Abstract: This paper attempts a critical examination of scholarly understanding of the historical event referred to as "the Darwinian Revolution." In particular, it concentrates on some of the major scholarly works that have appeared since the publication in 1979 of Michael Ruse's The Darwinian Revolution: Nature Red in Tooth and Claw. The paper closes by arguing that fruitful critical perspectives on what counts as this event can be gained by locating it in a range of historiographic and disciplinary contexts that include the emergence of the discipline of evolutionary biology (following the "evolutionary synthesis"), the 1959 Darwin centenary, and the maturation of the discipline of the history of science. Broader perspectives on something called the "Darwinian Revolution" are called for that include recognizing that it does not map a one-to-one correspondence with the history of evolution, broadly construed.

Deconstructing Darwin: Evolutionary theory in context

Abstract: The topic of this paper is external versus internal explanations, first, of the genesis of evolutionary theory and, second, its reception. Victorian England was highly competitive and individualistic. So was the view of society promulgated by Malthus and the theory of evolution set out by Charles Darwin and A.R. Wallace. The fact that Darwin and Wallace independently produced a theory of evolution that was just as competitive and individualistic as the society in which they lived is taken as evidence for the impact that society has on science. The same conclusion is reached with respect to the reception of evolutionary theory. Because Darwin’s contemporaries lived in such a competitive and individualistic society, they were prone to accept a theory that exhibited these same characteristics. The trouble is that Darwin and Wallace did not live in anything like the same society and did not formulate the same theory. Although the character of Victorian society may have influenced the acceptance of evolutionary theory, it was not the competitive, individualistic theory that Darwin and Wallace set out but a warmer, more comforting theory.

The Darwinian Revolution as Viewed by a Philosophical Biologist

Abstract: Darwin proclaimed his own work revolutionary. His revolution, however, is still in progress, and the changes that are going on are reflected in the contemporary historical and philosophical literature, including that written by scientists. The changes have taken place at different levels, and have tended to occur at the more superficial ones. The new ontology that arose as a consequence of the realization that species are individuals at once provides an analytical tool for explaining what has been happening and an example of the kind of changes that seem in order. It provides a clear distinction between the roles of history and of laws of nature. Pre-Darwinian “evolution” was superficial in the sense that it treated change as either as something pre-ordained or else due to timeless laws of nature, rather than historical contingency. Darwinism puts the ontological emphasis upon concrete, particular things (individuals) and therefore delegitimizes both essentialistic and teleological ways of thinking. However, traditional ways of thinking have persisted, if not explicitly, then often as assumptions and procedures that are merely implicit or even unconscious. As a result, anti-evolutionary attitudes continue to influence the practice of evolutionary biology as well as the study of its history and philosophy.

Again, what the philosophy of biology is not.

Abstract: There are many things that philosophy of biology might be. But, given the existence of a professional philosophy of biology that is arguably a progressive research program and, as such, unrivaled, it makes sense to define philosophy of biology more narrowly than the totality of intersecting concerns biologists and philosophers (let alone other scholars) might have. The reasons for the success of the “new” philosophy of biology remain poorly understood. I reflect on what Dutch and Flemish, and, more generally, European philosophers of biology could do to improve the situation of their discipline locally, regionally, and internationally, paying particular attention to the lessons to be learned from the “Science Wars.”

Innate Ideas as a Naturalistic Source of Metaphysical Knowledge

Abstract: This article starts from the assumption that there are various innate contributions to our view of the world and explores the epistemological implications that follow from this. Specifically, it explores the idea that if certain components of our worldview have an evolutionary origin, this implies that these aspects accurately depict the world. The simple version of the argument for this conclusion is that if an aspect of mind is innate, it must be useful, and the most parsimonious explanation for its usefulness is that it accurately depicts the world. There are a number of important criticisms of this argument. These include the idea that evolutionary justifications are circular, that evolved mental content and principles are not necessarily accurate, and that, if the argument is taken seriously, it has some highly dubious consequences. These criticisms necessitate various qualifications to the initial argument. Nonetheless, it is argued that, in some cases, important conclusions can be drawn about the world from an analysis of evolved contributions to our view of the world. An evolutionary approach cannot provide an ultimate justification for any belief; however, in certain circumstances, it supports the conclusion that a given belief is a reasonable first approximation. To the extent that innate content and principles pertain to topics in metaphysics, they can be viewed as a naturalistic source of metaphysical knowledge.

On the Explanatory Roles of Natural Selection

Abstract: Can selection explain why individuals have the traits they do? This question has generated significant controversy. I will argue that the debate encompasses two separable aspects, to detrimental effect: (1) the role of selection in explaining the origin and evolution of biological traits and (2) the implications this may have for explaining why individuals have the traits they do. (1) can be settled on the basis of evolutionary theory while (2) requires additional, extra-scientific assumptions. By making a distinction between traits affected by a single factor and traits affected by multiple factors I show that selection can, under certain conditions, help explain the origin of traits. Resolving the first aspect enables us to critically assess the various incompatible and independent philosophical commitments made within the second aspect of the debate.

Zooming in on Downward Causation

Abstract: An attempt is made to identify a concept of ‘downward causation’ that will fit the claims of some recent writers and apply to interesting cases in biology and cognitive theory, but not to trivial cases. After noting some difficulties in achieving this task, it is proposed that in interesting cases commonly used to illustrate ‘downward causation’, (a) regularities hold between multiply realizable properties and (b) the explanation of the parallel regularity at the level of the realizing properties is non-trivial. It is argued that the relation between a realizable property and the property that realizes its effect in a particular case is not usefully regarded as a species of causation and that use of the concept of downward causation deflects our attention from our central explanatory tasks.

Against "revolution" and "evolution".

Abstract: Those standard historiographic themes of “evolution” and “revolution” need replacing. They perpetuate mid-Victorian scientists’ history of science. Historians’ history of science does well to take in the long run from the Greek and Hebrew heritages on, and to work at avoiding misleading anachronism and teleology. As an alternative to the usual “evo-revo” themes, a historiography of origins and species, of cosmologies (including microcosmogonies and macrocosmogonies) and ontologies, is developed here. The advantages of such a historiography are illustrated by looking briefly at a number of transitions the transition from Greek and Hebrew doctrines to their integrations by medieval authors; the transition from the Platonist, Aristotelian, Christian Aquinas to the Newtonian Buffon and to the no less Newtonian Lamarck; the departures the early Darwin made away from Lamarck’s and from Lyell’s views. Issues concerning historical thinking about nature, concerning essentialism and concerning classification are addressed in an attempt to challenge customary stereotypes. Questions about originality and influence are raised, especially concerning Darwin’s “tree of life” scheme. The broader historiography of Darwinian science as a social ideology, and as a “worldview,” is examined and the scope for revisions emphasised. Throughout, graduate students are encouraged to see this topic area not as worked out, but as full of opportunities for fresh contributions.