Online research in philosophy

This paper, which is based on recent empirical research at the University of Leeds, the University of Edinburgh, and the University of Bristol, presents two difficulties which arise when condensed matter physicists interact with molecular biologists: (1) the former use models which appear to be too coarse-grained, approximate and/or idealized to serve a useful scientific purpose to the latter; and (2) the latter have a rather narrower view of what counts as an experiment, particularly when it comes to computer simulations, (...) than the former. It argues that these findings are related; that computer simulations are considered to be undeserving of experimental status, by molecular biologists, precisely because of the idealizations and approximations that they involve. The complexity of biological systems is a key factor. The paper concludes by critically examining whether the new research programme of ‘systems biology’ offers a genuine alternative to the modelling strategies used by physicists. It argues that it does not. (shrink)

I defend the view that single experiments can provide a sufficient reason for preferring one among a group of hypotheses against the widely held belief that “crucial experiments” are impossible. My argument is based on the examination of a historical case from molecular biology, namely the Meselson-Stahl experiment. “The most beautiful experiment in biology”, as it is known, provided the first experimental evidence for the operation of a semi-conservative mechanism of DNA replication, as predicted by Watson (...) and Crick in 1953. I use a mechanistic account of explanation to show that this case is best construed as an inference to the best explanation (IBE). Furthermore, I show how such an account can deal with Duhem's well-known arguments against crucial experiments as well as Van Fraassen's “bad lot” argument against IBE. (shrink)

Stem cell biology is driven by experiment. Its major achievements are striking experimental productions: "immortal" human cell lines from spare embryos (Thomson et al. 1998); embryo-like cells from "reprogrammed" adult skin cells (Takahashi and Yamanaka 2006); muscle, blood and nerve tissue generated from stem cells in culture (Lanza et al. 2009, and references therein). Well-confirmed theories are not so prominent, though stem cell biologists do propose and test hypotheses at a profligate rate. 1 This paper aims to characterize the (...) role of experiment in stem cell biology, so as to answer the following question: how do experiments contribute to our knowledge of stem cells and related phenomena? The .. (shrink)

Eric Olson argues in The Human Animal that thought-experiments involving body-swapping do not in the end offer any support to psychological continuity theories, nor do they pose any threat to his Biological View. I argue that he is mistaken in at least the second claim.

This paper provides an account of the experimental conditions required for establishing whether correlating or causally relevant factors are constitutive components of a mechanism connecting input (start) and output (finish) conditions. I argue that two-variable experiments, where both the initial conditions and a component postulated by the mechanism are simultaneously manipulated on an independent basis, are usually required in order to differentiate between correlating or causally relevant factors and constitutively relevant ones. Based on a typical research project molecular (...) class='Hi'>biology, a flowchart model detailing typical stages in the formulation and testing of hypotheses about mechanistic components is also developed. (shrink)

Mechanistic models in molecular systems biology are generally mathematical models of the action of networks of biochemical reactions, involving metabolism, signal transduction, and/or gene expression. They can be either simulated numerically or analyzed analytically. Systems biology integrates quantitative molecular data acquisition with mathematical models to design new experiments, discriminate between alternative mechanisms and explain the molecular basis of cellular properties. At the heart of this approach are mechanistic models of molecular networks. We focus on the articulation and (...) development of mechanistic models, identifying five constraints which guide the articulation of models in molecular systems biology. These constraints are not independent of one another, with the result that modeling becomes an iterative process. We illustrate the use of these constraints in the modeling of the mechanism for bistability in the lac operon. (shrink)

What is artificial life? Much has been said about this interesting collection of efforts to artificially simulate and synthesize lifelike behavior and processes, yet we are far from having a robust philosophical understanding of just what Alifers are doing and why it ought to interest philosophers of science, and philosophers of biology in particular. In this paper, I first provide three introductory examples from the particular subset of artificial life I focus on, known as ‘soft Alife’ (s-Alife), and follow (...) up with a more in-depth review of the Avida program, which serves as my case study of s-Alife. Next, I review three well-known accounts of thought experiments, and then offer my own synthesized account, to make the argument that s-Alife functions as thought experimentation in biology. I draw a comparison between the methodology of the thought-experimental world that yields real-world results, and the s-Alife research that informs our understanding of natural life. I conclude that the insights provided by s-Alife research have the potential to fundamentally alter our understanding of the nature of organic life and thus deserve the attention of both philosophers and natural scientists. (shrink)

H. B. D. Kettlewell's field experiments on industrial melanism in the peppered moth, Biston betularia, have become the best known demonstration of natural selection in <span class='Hi'>action</span>. I argue that textbook accounts routinely portray this research as an example of controlled experimentation, even though this is historically misleading. I examine how idealized accounts of Kettlewell's research have been used by professional biologists and biology teachers. I also respond to some criticisms of David Rudge to my earlier discussions of (...) this case study, and I question Rudge's claims about the importance of purely observational studies for the eventual acceptance and popularization of Kettlewell's explanation for the evolution of industrial melanism. (shrink)

Stem cell biology and systems biology are two prominent new approaches to studying cell development. In stem cell biology, the predominant method is experimental manipulation of concrete cells and tissues. Systems biology, in contrast, emphasizes mathematical modeling of cellular systems. For scientists and philosophers interested in development, an important question arises: how should the two approaches relate? This essay proposes an answer, using the model of Waddington’s landscape to triangulate between stem cell and systems approaches. This (...) simple abstract model represents development as an undulating surface of hills and valleys. Originally constructed by C. H. Waddington to visually explicate an integrated theory of genetics, development and evolution, the landscape model can play an updated unificatory role. I examine this model’s structure, representational assumptions, and uses in all three contexts, and argue that explanations of cell development require both mathematical models and concrete experiments. On this view, the two approaches are interdependent, with mathematical models playing a crucial but circumscribed role in explanations of cell development. (shrink)

Robots are being extensively used for the purpose of discovering and testing empirical hypotheses about biological sensorimotor mechanisms. We examine here methodological problems that have to be addressed in order to design and perform “good” experiments with these machine models. These problems notably concern the mapping of biological mechanism descriptions into robotic mechanism descriptions; the distinction between theoretically unconstrained “implementation details” and robotic features that carry a modeling weight; the role of preliminary calibration experiments; the monitoring of experimental (...) environments for disturbing factors that affect both modeling features and theoretically unconstrained implementation details of robots. Various assumptions that are gradually introduced in the process of setting up and performing these robotic experiments become integral parts of the background hypotheses that are needed to bring experimental observations to bear on biological mechanism descriptions. (shrink)

Philosophers have committed sins while studying science, it is said – philosophy of science focused on physics to the detriment of biology, reconstructed idealizations of scientific episodes rather than attending to historical details, and focused on theories and concepts to the detriment of experiments. Recent generations of philosophers of science have tried to atone for these sins, and by the 1980s the exculpation was in full swing. Marcel Weber’s Philosophy of Experimental Biology is a zenith mea culpa (...) for philosophy of science: it carefully describes several historical examples from twentieth century biology to address both ‘old’ philosophical topics, like reductionism, inference, and realism, and ‘new’ topics, like discovery, models, and norms. Biology, experiments, history – at last, philosophy of science, free of sin. (shrink)

Although humans are endowed with domain-specific constraints for acquiring informal biology, its construction requires considerable experience with living things and their cultural representations. Less experienced adults may not know what constitutes generic species, and young children may rely on personification rather than category-based inference. Atran's postulate of the living-kind module that promptly produces universal folk taxonomy does not seem tenable.

Thought experiments have a mysterious way of informing us about the world, apparently without examining it, yet with a great degree of certainty. It is tempting to try to explain this capacity by making use of the idea that in thought experiments, the mind somehow simulates the processes about which it reaches conclusions. Here, I test this idea. I argue that when they predict the outcomes of hypothetical physical situations, thought experiments cannot simulate physical processes. They use (...) mental models, which should not be confused with process-driven simulations. A convincing case can be made that thought experiments about hypothetical mental processes are mental simulations. Concerning moral thought experiments, I argue that construing them as simulations of mental processes favours certain moral theories over others. The scope of mental simulation in thought experiments is primarily limited by the constraint of relevant similarity on source and target processes: on one hand, this constraint disqualifies thought from simulating external natural processes; on the other hand, it is a source of epistemic bias in moral thought experiments. In view of these results, I conclude that thought experiments and mental simulations cannot be assimilated as means of acquiring knowledge. (shrink)

Going back at least to Duhem, there is a tradition of thinking that crucial experiments are impossible in science. I analyse Duhem's arguments and show that they are based on the excessively strong assumption that only deductive reasoning is permissible in experimental science. This opens the possibility that some principle of inductive inference could provide a sufficient reason for preferring one among a group of hypotheses on the basis of an appropriately controlled experiment. To be sure, there are analogues (...) to Duhem's problems that pertain to inductive inference. Using a famous experiment from the history of molecular biology as an example, I show that an experimentalist version of inference to the best explanation (IBE) does a better job in handling these problems than other accounts of scientific inference. Furthermore, I introduce a concept of experimental mechanism and show that it can guide inferences from data within an IBE-based framework for induction. Introduction Duhem on the Logic of Crucial Experiments ‘The Most Beautiful Experiment in Biology’ Why Not Simple Elimination? Severe Testing An Experimentalist Version of IBE 6.1 Physiological and experimental mechanisms 6.2 Explaining the data 6.3 IBE and the problem of untested auxiliaries 6.4 IBE-turtles all the way down Van Fraassen's ‘Bad Lot’ Argument IBE and Bayesianism Conclusions CiteULike Connotea Del.icio.us What's this? (shrink)

I discuss two types of evidential problems with the most widely touted experiments in evolutionary psychology, those performed by Leda Cosmides and interpreted by Cosmides and John Tooby. First, and despite Cosmides and Tooby's claims to the contrary, these experiments don't fulfil the standards of evidence of evolutionary biology. Second Cosmides and Tooby claim to have performed a crucial experiment, and to have eliminated rival approaches. Though they claim that their results are consistent with their theory but (...) contradictory to the leading non-evolutionary alternative, Pragmatic Reasoning Schemas theory, I argue that this claim is unsupported. In addition, some of Cosmides and Tooby's interpretations arise from misguided and simplistic understandings of evolutionary biology. While I endorse the incorporation of evolutionary approaches into psychology, I reject the claims of Cosmides and Tooby that a modular approach is the only one supported by evolutionary biology. Lewontin's critical examinations of the applications of adaptationist thinking provide a background of evidentiary standards against which to view the currently fashionable claims of evolutionary psychology. (shrink)

Philosophers of experiment have acknowledged that experiments are often more than mere hypothesis-tests, once thought to be an experiment's exclusive calling. Drawing on examples from contemporary biology, I make an additional amendment to our understanding of experiment by examining the way that `wide' instrumentation can, for reasons of efficiency, lead scientists away from traditional hypothesis-directed methods of experimentation and towards exploratory methods.

Following Mayr (1961) evolutionary biologists often maintain that the hallmark of biology is its evolutionary perspective. In this view, biologists distinguish themselves from other natural scientists by their emphasis on why-questions. Why-questions are legitimate in biology but not in other natural sciences because of the selective character of the process by means of which living objects acquire their characteristics. For that reason, why-questions should be answered in terms of natural selection. Functional biology is seen as a reductionist (...) science that applies physics and chemistry to answer how-questions but lacks a biological point of view of its own. In this paper I dispute this image of functional biology. A close look at the kinds of issues studied in biology and at the way in which these issues are studied shows that functional biology employs a distinctive biological perspective that is not rooted in selection. This functional perspective is characterized by its concern with the requirements of the life-state and the way in which these are met. (shrink)

What makes a biological entity an individual? Jack Wilson shows that past philosophers have failed to explicate the conditions an entity must satisfy to be a living individual. He explores the reason for this failure and explains why we should limit ourselves to examples involving real organisms rather than thought experiments. This book explores and resolves paradoxes that arise when one applies past notions of individuality to biological examples beyond the conventional range, and presents a new analysis of identity (...) and persistence. The book's main purpose is to bring together two lines of research, theoretical biology and metaphysics, which have dealt with the same subject in isolation from one another. Wilson explains a new theory about biological individuality which solves problems which cannot be addressed by either field alone. He presents a more fine-grained vocabulary of individuation based on diverse kinds of living things, allowing him to clarify previously muddled disputes about individuality in biology. (shrink)

How does evolutionary biology fit with Thomas Kuhn's famous distinction between puzzle solving and paradigm shifts in science?

This paper aims to bring the epistemic dimensions of stem cell experiments out of the background, and show that they can be critically evaluated. After introducing some basic concepts of stem cell biology, I set out the current “gold standard” for experimental success in that field (§2). I then trace the origin of this standard to a 1988 controversy over blood stem cells (§3). Understanding the outcome of this controversy requires attention to the details of experimental techniques, the (...) organization of epistemic communities, and relations between the two (§4). With its resolution, a standard for experimental success was established for HSC research, which in turn serves as an exemplar for studies of other stem cells. This historical case study reveals a robust standard for experimental success in stem cell biology: to trace processes of development at the single-cell level, in the form of cell lineage hierarchies. Experiments conforming to this standard can be further critically assessed as means to the therapeutic end of stem cell research: use of stem cells to repair human organs and tissues. (shrink)

An explorative contribution to the ongoing discussion of thought experiments. While endorsing the majority view that skepticism about thought experiments is not well justified, in what follows we attempt to show that there is a kind of “bodiliness” missing from current accounts of thought experiments. That is, we suggest a phenomenological addition to the literature. First, we contextualize our claim that the importance of the body in thought experiments has been widely underestimated. Then we discuss David (...) Gooding's work, which contains the only explicit recognition of the importance of the body to understanding thought experiments. Finally, we introduce a phenomenological perspective of the body, which will give us the opportunity to sketch the power and promise of a phenomenological approach to thought experiments. (shrink)

Autoimmune diseases such as rheumatoid arthritis and gastrointestinal disorders such as stomach ulcers are often treated with drugs. NSAIDs, a common treatment in rheumatoid arthritis, may cause stomach ulcers which call for additional medications, notably antacids in the sense of drugs that suppress acid secretion by the stomach. Infection with Helicobacter pylori also plays a role in the ulcers. The infection is typically treated with antibiotics added to antacids. Considering NSAIDs and antacids, we suspect that overmedication is common to the (...) extent that particular diets are a better option. Current research and current treatments with these drugs are also problematic since circadian rhythms are mostly disregarded. All the processes involved in the disorders treated show marked variations in the course of the day. Hence experiments conforming to the guidelines of evidence-based medicine, and treatments in line with them, have outcomes strongly depending on the time factor. This calls for reforms in medicine with fresh inputs from biology. (shrink)

A recurrent theme in ethnomethodological research is that of instructed actions. Contrary to the classic traditions in the social and cognitive sciences, which attribute logical priority or causal primacy to instructions, rules, and structures of action, ethnomethodologists investigate the situated production of actions which enable such formulations to stand as adequate accounts. Consequently, a recitation of formal structures can not count as an adequate sociological description, when no account is given of the local production ofwhat those structures describe. The natural (...) sciences can be described as a domain of practical action in whichthe use of methods enables the intersubjective reproduction of naturalistic observations and experiments. As numerous sociological studies of laboratory practices have shown, the achievement of intersubjective order cannot be reduced to formal methods; instead, it arises from the work of custom-fitting relevant methods to the local circumstances of the research. In this paper we discuss a possible extension of this idea to cover two intertwined aspects of molecular biology: (1) the work of following instructions on how to perform routine laboratory procedures, and (2) the relationship between cellular orders and the encoded instructions contained in the DNA molecule. We suggest that a classic conception of scientific action is implied by the way formal instructions are treated as a primary basis, both for molecular biologists' actions and the cellular functions they study, and we envision an ethnomethodological alternative to those conceptions of social and biological order. (shrink)

This is a wide ranging and deeply learned examination of evolutionary developmental biology, and the foundations of life from the perspective of information theory. Hermeneutics was a method developed in the humanities to achieve understanding, in a given context, of texts, history, and artwork. In Readers of the Book of Life, the author shows that living beings are also hermeneutical interpreters of genetics texts saved in DNA; an interpretation based on the past experience of the cell (cell lineage, species), (...) confronted with and incorporating present environmental clues. This approach stresses the history, not only of the digital record saved in the DNA, but also of the flesh - the cellular organization which has a direct time-continuity with the very origins of life. This book is aimed at reconciling two opposite approaches to life. The first strictly sticking to a belief that all phenomena observed in the realm of the living can be explained from laws of physics. The opposite stressing the importance of features characteristic for a given level of description. To bring both views into a common understanding, the first part gives a comparison of the two problem solving strategies. The second part surveys the development of 20th century biology, bringing to light branches that never became part of the research mainstream. The third section of the book reviews a large body of recent evidence that can be interpreted in favor of the hermeneutic arguments. (shrink)

This article examines how a molecular "solution" to an important biological problem-how is antibody diversity generated? was obtained in the 1970s. After the primarily biological clonal selection theory (CST) was accepted by 1967, immunologists developed several different contrasting theories to complete the SCST. To choose among these theories, immunology had to turn to the new molecular biology, first to nucleic acid hybridization and then to recombinant DNA technology. The research programs of Tonegawa and Leder that led to the "solution" (...) are discussed, and some of their strategies and heuristics are broadly characterized: (1) to what extent does the new recombinant DNA technology provide what the scientists claim is "direct evidence," what does that term mean, and what are the implications of that claim for biological "realism," and (2) is this episode one of reduction, partial reduction, or explanatory extension, and what do these terms mean in the context of a successful molecular "solution" to a biological problem. (shrink)

In biology, man is an object of research; therefore the question might be asked whether inspirations can go from biological data to the reflections on the mind-matter relation in man. The social aspect of man, as treated by sociobiology, is left out of consideration. The knowledge that man is mind, or has a mind, is no result of biological research. It is a datum from philosophy. The biologist, however, is living in a culture which knows about the mental character (...) of man, and this is incorporated in his investigations. He knows that mental activities are connected with processes in the central nervous system and that, especially in the brain, localizations of mental activities are found. As a result of the split-brain experiments with patients and animals, some have arrived at the conclusion that there is a double consciousness.An approach from biology can lead to statements of a philosophical character, as, for example, statements about the unity, or even identity, of mind and matter. The theories of identity meet with great interest in scientific circles, and the truth value of identity statements is investigated. The system theory is taken into consideration. On a philosophical level a revaluation of the concept of matter can lead to a different sort of identity theory. (shrink)

The epistemology and ontology of experimentation are discussed in depth with special reference to biology and medicine. Two types of experiments are distinguished: exploratory (or "blazing") and consolidating. They Have objectives and canons that are strikingly different. A contrast is drawn between the literalism of the most pragmatic scientists and the formalism of most statisticians. The terms and notions of the one may have imperfect correspondence with those of the other, or perhaps none at all. The dangers are (...) pointed out of both the conclusion that the gap between the two is unbridgeable and the contrary view that the gap is trivial and merits no serious attention. Substantive discussions address the choice and meaning of a metric, the idea of interaction and time series analysis, the ontology of variation, and the epistemology of randomization, hypothesis-seeking, and multiple comparisons. * From the Division of Medical Genetics, Johns Hopkins University School of Medicine, Baltimore Md. 21205. The research in this paper was supported by grants number GM24736 and RR007722 of the National Institutes of Health. Text of a lecture given to the Maryland Institute for Clinical Research and the Department of Social and Preventive Medicine, University of Maryland, October 6, 1980. CiteULike Connotea Del.icio.us What's this? (shrink)

The German–American physiologist Jacques Loeb (1859–1924) and the Polish embryologist Emil Godlewski, jr. (1875–1944) contributed many valuable works to the body of developmental biology. Jacques Loeb was world famous at the beginning of the twentieth century for his development and demonstration of artificial parthenogenesis in 1899 and his experiments on regeneration. He served as a role model for the younger Polish experimenter Emil Godlewski, who began his career as a researcher like Loeb at the Zoological Station in Naples. (...) Following Godlewski’s first visit to Naples in 1901 a close relationship between the two scientists developed. Until Loeb’s death in 1924 the two exchanged ideas via correspondence that was only interrupted during the First World War. The aim of the paper is to examine the transatlantic transfer of knowledge in the field of biological experimentation that was fostered by these two protagonists. Using a modification of Bruno Latour’s model of the ‘Circulatory System of Science’ as a heuristic tool, different mechanisms of scientific exchange are displayed. With the help of Loeb’s and Godlewski’s correspondence the role of scientific communities, methods, allies, the public and institutions in the process of knowledge transfer are analysed. Preconditions for success and failure in transferring science are examined. (shrink)

: Most work done in philosophy of experiment has focused on experiments taken from the domain of physics. The present essay tests whether Allan Franklin's (1984, 1986, 1989, 1990) philosophy of experiment developed in the context of high energy physics can be extended to include examples from evolutionary biology, such as H. B. D. Kettlewell's (1955, 1956, 1958) famous studies of industrial melanism in the peppered moth, Biston betularia. The analysis demonstrates that many of the techniques used by (...) evolutionary biologists exemplify the strategies Franklin lists, and identifies an additional strategy that can likewise be justified by appeal to Bayes's Theorem. (shrink)

Placing Goodenough and Deacon’s “From Biology to Consciousness to Morality” against the background of the ethical naturalism of seventeenth- and eighteenth-century British moral theory, Yeager highlights the contribution the authors make to the moral sense tradition as well as indicating the limitations of such accounts of moral agency, judgment, and conduct. Yeager also identifies two strands of the essay that seem to open toward a more comprehensive account than the authors actually give. The first concerns the “interplay between self-interest (...) and pro-sociality,” and the other concerns the ethical implications of coevolution. On the latter point, the work of G. H. Mead is offered as an illuminating contrast. (shrink)

‘‘Theoretical biology’’ is a surprisingly heter- ogeneous field, partly because it encompasses ‘‘doing the- ory’’ across disciplines as diverse as molecular biology, systematics, ecology, and evolutionary biology. Moreover, it is done in a stunning variety of different ways, using anything from formal analytical models to computer sim- ulations, from graphic representations to verbal arguments. In this essay I survey a number of aspects of what it means to do theoretical biology, and how they compare with the (...) allegedly much more restricted sense of theory in the physical sciences. I also tackle a recent trend toward the presentation of all-encompassing theories in the biological sciences, from general theories of ecology to a recent attempt to provide a conceptual framework for the entire set of biological disciplines. Finally, I discuss the roles played by philosophers of science in criticizing and shap- ing biological theorizing. (shrink)

Essentialism in philosophy is the position that things, especially kinds of things, have essences, or sets of properties, that all members of the kind must have, and the combination of which only members of the kind do, in fact, have. It is usually thought to derive from classical Greek philosophy and in particular from Aristotle’s notion of “what it is to be” something. In biology, it has been claimed that pre-evolutionary views of living kinds, or as they are sometimes (...) called, “natu-ral kinds”, are essentialist. This static view of living things presumes that no tran-sition is possible in time or form between kinds, and that variation is regarded as accidental or inessential noise rather than important information about taxa. In contrast it is held that Darwinian, and post-Darwinian, biology relies upon varia-tion as important and inevitable properties of taxa, and that taxa are not, therefore, kinds but historical individuals. Recent attempts have been made to undercut this account, and to reinstitute essentialism in biological kind terms. Others argue that essentialism has not ever been a historical reality in biology and its predecessors. In this chapter, I shall outline the many meanings of the notion of essentialism in psychology and social science as well as science, and discuss pro- and anti-essentialist views, and some recent historical revisionism. It turns out that nobody was essentialist to speak of in the sense that is antievolutionary in biology, and that much confusion rests on treating the one word, “essence” as meaning a single notion when in fact there are many. I shall also discuss the philosophical implica-tions of essentialism, and what that means one way or the other for evolutionary biology. Teaching about evolution relies upon narratives of change in the ways the living world is conceived by biologists. This is a core narrative issue. (shrink)

Martha Nussbaum has argued in support of the view (supposedly that of Aristotle) that we can, through thought-experiments involving personal identity, find an objective foundation for moral thought without having to appeal to any authority independent of morality. I compare the thought-experiment from Plato’s Philebus that she presents as an example to other thought-experiments involving identity in the literature and argue that this reveals a tension between the sources of authority which Nussbaum invokes for her thought-experiment. I also (...) argue that each of her sources of authority presents further difficulties for her project. Finally, I argue that it is not clear that her thought-experiment is one that actually involves identity in any crucial way. As a result, the case she offers does not offer any satisfactory support for her view on the relation between identity, morality and thought-experiments, but we do gain some insights into what that relation really is along the way. (shrink)

In this piece, I advocate and motivate a new understanding of thought experiments, which avoids problems with the rival accounts of Brown and Norton.

But what are functions? Here, 15 leading scholars of philosophy of psychology and philosophy of biology present new essays on functions.

The idea of integrating evolutionary biology and psychology has great promise, but one that will be compromised if psychological functions are conceived too abstractly and neuroscience is not allowed to play a contructive role. We argue that the proper integration of neuroscience, psyychology, and evolutionary biology requires a telelogical as opposed to a merely componential analysis of function. A teleological analysis is required in neuroscience itself; we point to traditional and curent research methods in neuroscience, which make critical (...) use of distinctly teleological functional considerations in brain cartography. Only by invoking teleological criteria can researchers distinguish the fruitful ways of identifying brain components from the myriad of possible ways. One likely reason for reluctance to turn to neuroscience is fear of reduction, but we argue that, in the context of a teleological perspective on function, this concern is misplaced. Adducing such theoretical considerations as top-down and bottom-up constraints on neuroscientific and psychological models, as well as existing cases of productive, multidisciplinary cooperation, we argue that integration of neuroscience into psychology and evolutionary biology is likely to be mutually beneficial. We also show how it can be accommodated methodologically within the framework of an interfield theory. (shrink)

The Perky experiments are taken to demonstrate the phenomenal similarity between perception and visualization. Robert Hopkins argues that this interpretation should be resisted because it ignores an important feature of the experiments, namely, that they involve picture perception, rather than ordinary seeing. My aim is to point out that the force of this argument depends on one’s views on picture perception. On what I take to be the most mainstream account of picture perception, Hopkins’s argument does not work. (...) But even if we accept Hopkins’s own account, we have good reasons to believe that his conclusion does not follow. (shrink)

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 pay-off 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. (shrink)

After the discovery of the structure of DNA in 1953, scientists working in molecular biology embraced reductionism—the theory that all complex systems can be understood in terms of their components. Reductionism, however, has been widely resisted by both nonmolecular biologists and scientists working outside the field of biology. Many of these antireductionists, nevertheless, embrace the notion of physicalism—the idea that all biological processes are physical in nature. How, Alexander Rosenberg asks, can these self-proclaimed physicalists also be antireductionists? With (...) clarity and wit, Darwinian Reductionism navigates this difficult and seemingly intractable dualism with convincing analysis and timely evidence. In the spirit of the few distinguished biologists who accept reductionism—E. O. Wilson, Francis Crick, Jacques Monod, James Watson, and Richard Dawkins—Rosenberg provides a philosophically sophisticated defense of reductionism and applies it to molecular developmental biology and the theory of natural selection, ultimately proving that the physicalist must also be a reductionist. (shrink)

A collection of essays investigating key historical and scientific questions relating to the concept of natural purpose in Kant's philosophy of biology.

There appears much new in philosophy of biology, the exploding field in philosophy of science over the past few decades.

Exploring central philosophical issues concerning scientific research in modern experimental biology, this book clarifies the strategies, concepts, reasoning, approaches, tools, models and experimental systems deployed by researchers. It also integrates recent developments in historical scholarship, in particular, the New Experimentalism, making this work of interest to philosophers and historians of science as well as to biological researchers.

Starting with a discussion of what I call Koyré’s paradox of conceptual novelty, I introduce the ideas of Damerow et al. on the establishment of classical mechanics in Galileo’s work. I then argue that although the view of Damerow et al. on the nature of Galileo’s conceptual innovation is convincing, it misses an essential element: Galileo’s use of the experiments described in the first day of the Two New Sciences. I describe these experiments and analyze their function. Central (...) to my analysis is the idea that Galileo’s pendulum experiments serve to secure the reference of his theoretical models in actually occurring cases of free fall. In this way Galileo’s experiments constitute an essential part of the meaning of the new concepts of classical mechanics. (shrink)

An influential position in the philosophy of biology claims that there are no biological laws, since any apparently biological generalization is either too accidental, fact-like or contingent to be named a law, or is simply reducible to physical laws that regulate electrical and chemical interactions taking place between merely physical systems. In the following I will stress a neglected aspect of the debate that emerges directly from the growing importance of mathematical models of biological phenomena. My main aim is (...) to defend, as well as reinforce, the view that there are indeed laws also in biology, and that their difference in stability, contingency or resilience with respect to physical laws is one of degrees, and not of kind . (shrink)

Sorensen presents a general theory of thought experiments: what they are, how they work, what are their virtues and vices. On Sorensen's view, philosophy differs from science in degree, but not in kind. For this reason, he claims, it is possible to understand philosophical thought experiments by concentrating on their resemblance to scientific relatives. Lessons learned about scientific experimentation carry over to thought experiment, and vice versa. Sorensen also assesses the hazards and pseudo-hazards of thought experiments. Although (...) he grants that there are interesting ways in which the method leads us astray, he attacks most scepticism about thought experiments as arbitrary. They should be used, he says, as they generally are used--as part of a diversified portfolio of techniques. All of these devices are individually susceptible to abuse, fallacy, and error. Collectively, however, they provide a network of cross-checks that make for impressive reliability. (shrink)

John Dupré explores recent revolutionary developments in biology and considers their relevance for our understanding of human nature and human society. Epigenetics and related areas of molecular biology have eroded the exceptional status of the gene and presented the genome as fully interactive with the rest of the cell. Developmental systems theory provides a space for a vision of evolution that takes full account of the fundamental importance of developmental processes. Dupré shows the importance of microbiology for a (...) proper understanding of the living world, and reveals how it subverts such basic biological assumptions as the organisation of biological kinds on a branching tree of life, and the simple traditional conception of the biological organism. -/- These topics are considered in the context of a view of science as realistically grounded in the natural order, but at the same time as pluralistic and inextricably integrated within a social and normative context. The volume includes a section that recapitulates and expands some of the author's general views on science; a section addressing a range of topics in biology, including the significance of genomics, the nature of the organism and the current status of evolutionary theory; and a section exploring some implications of contemporary biology for humans, for example on the reality or unreality of human races, and the plasticity of human nature. (shrink)

Thought experiments play an important cognitive role in many fields of inquiry, especially in physics and philosophy. Do they also matter in revealed theology? In addressing this question, I will argue first why it is important to do so, then elaborate on the characteristic features of such thought experiments in revealed theology, and finally discuss two instances of thought experimenting in Augustine.

Philosophy of biology, perhaps more than any other philosophy of science, is a discipline in flux. What counts as consensus and key arguments in certain areas changes rapidly.The publication of Contemporary Debates in Philosophy of Biology (2010 Wiley-Blackwell) is reviewed and is used as a catalyst to a discussion of the recent expansion of subjects and perspectives in the philosophy of biology as well as their diverse epistemological and methodological commitments.

Systems biology is a vigorous and expanding discipline, in many ways a successor to genomics and perhaps unprecendented in its combination of biology with a ...

Natural selection [Darwin 1859] is perhaps the most important component of evolutionary theory, since it is the only known process that can bring about the adaptation of living organisms to their environments [Gould 2002]. And yet, its study is conceptually and methodologically complex, and much attention needs to be paid to a variety of phenomena that can limit the efficacy of selection [Antonovics 1976; Pigliucci and Kaplan 2000]. In this essay, I will use examples of recent work carried out in (...) my laboratory to illustrate basic research on natural selection as conducted using a variety of approaches, including field work, laboratory experiments, and molecular genetics. I also discuss the application of this array of tools to questions pertinent to conservation biology, and in particular to the all-important problem of what makes invasive species so good at creating the sort of problems they are infamous for [Lee 2002]. (shrink)

The `developmental systems'' perspective in biology is intended to replace the idea of a genetic program. This new perspective is strongly convergent with recent work in psychology on situated/embodied cognition and on the role of external `scaffolding'' in cognitive development. Cognitive processes, including those which can be explained in evolutionary terms, are not `inherited'' or produced in accordance with an inherited program. Instead, they are constructed in each generation through the interaction of a range of developmental resources. The attractors (...) which emerge during development and explain robust and/or widespread outcomes are themselves constructed during the process. At no stage is there an explanatory stopping point where some resources control or program the rest of the developmental cascade. `Human nature'' is a description of how things generally turn out, not an explanation of why they turn out that way. Finally, we suggest that what is distinctive about human development is its degree of reliance on external scaffolding. (shrink)

Some foundational debates in philosophy of biology Content Type Journal Article DOI 10.1007/s11016-010-9517-x Authors Stavros Ioannidis, Department of Philosophy, University of Bristol, 9 Woodland Rd, Bristol, BS8 1TB UK Journal Metascience Online ISSN 1467-9981 Print ISSN 0815-0796.

The Oxford Handbook of Philosophy of Biology is an exciting collection of new essays written especially to give the reader an introduction to one of the most vibrant areas of scholarship today, and at the same time to move the subject forward dramatically. Written in a clear and rigorous style it will give the more experienced scholar much to think about and will also be of great value to the new student of the subject. The handbook covers the history (...) of the topic, then moves into important analyses of contemporary evolutionary thinking, and continues with discussions of genetics and the moral and epistemological foundations of our understanding of heredity. The book goes on to cover ecology, behavior and morality, and does not neglect religion or feminist issues. Finally, it takes up matters to do with language and metaphor. The authors range from the senior and experienced to new and exciting young scholars. The Oxford Handbook of Philosophy of Biology is a collection that will be of interest to philosophers of science, to philosophers generally, as well as biologists of all kinds. There is no better way to learn about this dynamic field than through the essays in this volume. (shrink)

Brown (The laboratory of the mind. Thought experiments in the natural science, 1991a , 1991b ; Contemporary debates in philosophy of science, 2004 ; Thought experiments, 2008 ) argues that thought experiments (TE) in science cannot be arguments and cannot even be represented by arguments. He rest his case on examples of TEs which proceed through a contradiction to reach a positive resolution (Brown calls such TEs “platonic”). This, supposedly, makes it impossible to represent them as arguments (...) for logical reasons: there is no logic that can adequately model such phenomena. (Brown further argues that this being the case, “platonic” TEs provide us with irreducible insight into the abstract realm of laws of nature). I argue against this approach by describing how “platonic” TEs can be modeled within the logical framework of adaptive proofs for prioritized consequence operations. To show how this mundane apparatus works, I use it to reconstruct one of the key examples used by Brown, Galileo’s TE involving falling bodies. (shrink)

The idea of integrating evolutionary biology and psychology has great promise, but one that will be compromised if psychological functions are conceived too abstractly and neuroscience is not allowed to play a contructive role. We argue that the proper integration of neuroscience, psychology, and evolutionary biology requires a telelogical as opposed to a merely componential analysis of function. A teleological analysis is required in neuroscience itself; we point to traditional and curent research methods in neuroscience, which make critical (...) use of distinctly teleological functional considerations in brain cartography. Only by invoking teleological criteria can researchers distinguish the fruitful ways of identifying brain components from the myriad of possible ways. One likely reason for reluctance to turn to neuroscience is fear of reduction, but we argue that, in the context of a teleological perspective on function, this concern is misplaced. Adducing such theoretical considerations as top-down and bottom-up constraints on neuroscientific and psychological models, as well as existing cases of productive, multidisciplinary cooperation, we argue that integration of neuroscience into psychology and evolutionary biology is likely to be mutually beneficial. We also show how it can be accommodated methodologically within the framework of an interfield theory. (shrink)

In her landmark book, Language, Thought, and Other Biological Categories (Millikan1984),1 Ruth Garrett Millikan utilizes the idea of a biological function to solve philosophical problems associated with the phenomena of language, thought, and meaning. Language and thought are activities of biological organisms, according to Millikan, and we should treat them as such when trying to answer related philosophical questions. Of special interest is Millikan’s treatment of intentionality. Here Millikan employs the notion of a biological function to explain what it is (...) for one thing in nature, a bee dance (43), for example, to be about another, in this case, the location of a nectar source. My concern in this paper is to understand whether Millikan’s account of intentionality adequately explains how humans achieve reference, in language or thought, to individuals and groups in their environment. In bringing her theory of intentional content to bear on human activities, Millikan focuses largely on natural language. Thus, in what follows, I begin by laying out the biology-based principles that underlie Millikan’s theory of content, then proceed with an explanation of how the theory is to apply to natural language. As it appears, Millikan’s account of how content is determined for natural language terms and sentences rests on the determinacy of intentional content at the psychological level. This leads me to take a careful look at what Millikan says about the content of mental representations, in hopes of finding a sufficient basis there for the application of Millikan’s theory of content to natural language. Ultimately, I conclude that Millikan’s theory faces a problem of vacuity. If we approach the theory as a theory of intentional content, intended to explain the nature of reference, the theory is lacking in an extremely important respect: Millikan explains how it could be one of the biological functions of a mental or natural language term to refer, without telling us precisely what in the natural order constitutes the reference relation.. (shrink)

Kenneth F. Schaffner compares the practice of biological and medical research and shows how traditional topics in philosophy of science--such as the nature of theories and of explanation--can illuminate the life sciences. While Schaffner pays some attention to the conceptual questions of evolutionary biology, his chief focus is on the examples that immunology, human genetics, neuroscience, and internal medicine provide for examinations of the way scientists develop, examine, test, and apply theories. Although traditional philosophy of science has regarded scientific (...) discovery--the questions of creativity in science--as a subject for psychological rather than philosophical study, Schaffner argues that recent work in cognitive science and artificial intelligence enables researchers to rationally analyze the nature of discovery. As a philosopher of science who holds an M.D., he has examined biomedical work from the inside and uses detailed examples from the entire range of the life sciences to support the semantic approach to scientific theories, addressing whether there are "laws" in the life sciences as there are in the physical sciences. Schaffner's novel use of philosophical tools to deal with scientific research in all of its complexity provides a distinctive angle on basic questions of scientific evaluation and explanation. (shrink)

Aristotle's biological works - constituting over 25% of his surviving corpus and for centuries largely unstudied by philosophically oriented scholars - have been the subject of an increasing amount of attention of late. This collection brings together some of the best work that has been done in this area, with the aim of exhibiting the contribution that close study of these treatises can make to the understanding of Aristotle's philosophy. The book is divided into four parts, each with an introduction (...) which places its essays in relation to each other and to the wider issues of the book as a whole. The first part is an overview of the relationship of Aristotle's biology to his philosophy; the other three each concentrate on a set of issues central to Aristotelian study - definition and demonstration; teleology and necessity in nature; and metaph themes such as the unity of matter and form and the nature of substance. (shrink)

Do the sciences aim to uncover the structure of nature, or are they ultimately a practical means of controlling our environment? In Instrumental Biology, or the Disunity of Science, Alexander Rosenberg argues that while physics and chemistry can develop laws that reveal the structure of natural phenomena, biology is fated to be a practical, instrumental discipline. Because of the complexity produced by natural selection, and because of the limits on human cognition, scientists are prevented from uncovering the basic (...) structure of biological phenomena. Consequently, biology and all of the disciplines that rest upon it--psychology and the other human sciences--must aim at most to provide practical tools for coping with the natural world rather than a complete theoretical understanding of it. (shrink)

What are the agents of life? Central to our conception of the biological world is the idea that it contains various kinds of individuals, including genes, organisms, and species. How we conceive of these agents of life is central to our understanding of the relationship between life and mind, the place of hierarchical thinking in the biological sciences, and pluralistic views of biological agency. Genes and the Agents of Life rethinks the place of the individual in the biological sciences, drawing (...) parallels with the cognitive and social sciences. Genes, organisms, and species are all agents of life, but how are each of these conceptualized within genetics, developmental biology, evolutionary biology, and systematics? The book includes highly accessible discussions of genetic encoding, species and natural kinds, and pluralism above the levels of selection, drawing on work from across the biological sciences. A companion to Boundaries of the Mind, (Cambridge, 2004) where the focus is on the cognitive sciences, this volume will appeal to professionals and students in philosophy, biology, and the history of science. Robert A. Wilson is Professor of Philosophy at the University of Alberta. He is the author of Cartesian Psychology and Physical Minds (Cambridge, 1995). (shrink)

The philosophy of biology is one of the most exciting new areas in the field of philosophy and one that is attracting much attention from working scientists. This Companion, edited by two of the founders of the field, includes newly commissioned essays by senior scholars and up-and-coming younger scholars who collectively examine the main areas of the subject - the nature of evolutionary theory, classification, teleology and function, ecology, and the problematic relationship between biology and religion, among other (...) topics. Up-to-date and comprehensive in its coverage, this unique volume will be of interest not only to professional philosophers but also to students in the humanities and researchers in the life sciences and related areas of inquiry. (shrink)

Comprised of essays by top scholars in the field, this volume offers concise overviews of philosophical issues raised by biology. Brings together a team of eminent scholars to explore the philosophical issues raised by biology Addresses traditional and emerging topics, spanning molecular biology and genetics, evolution, developmental biology, immunology, ecology, mind and behaviour, neuroscience, and experimentation Begins with a thorough introduction to the field Goes beyond previous treatments that focused only on evolution to give equal attention (...) to other areas, such as molecular and developmental biology Represents both an authoritative guide to philosophy of biology, and an accessible reference work for anyone seeking to learn about this rapidly-changing field. (shrink)

The formal systems of logic have ordinarily been regarded as independent of biology, but recent developments in evolutionary theory suggest that biology and logic may be intimately interrelated. In this book, Cooper outlines a theory of rationality in which logical law emerges as an intrinsic aspect of evolutionary biology. This biological perspective on logic, though at present unorthodox, could change traditional ideas about the reasoning process. Cooper examines the connections between logic and evolutionary biology and illustrates (...) how logical rules are derived directly from evolutionary principles, and therefore have no independent status of their own. Laws of decision theory, utility theory, induction, and deduction are reinterpreted as natural consequences of evolutionary processes. Cooper's connection of logical law to evolutionary theory results in a unified foundation for an evolutionary science of reason. (shrink)

The genetic code appeared on Earth with the first cells. The codes of cultural evolution arrived almost four billion years later. These are the only codes that are recognized by modern biology. In this book, however, Marcello Barbieri explains that there are many more organic codes in nature, and their appearance not only took place throughout the history of life but marked the major steps of that history. A code establishes a correspondence between two independent 'worlds', and the codemaker (...) is a third party between those 'worlds'. Therefore the cell can be thought of as a trinity of genotype, phenotype and ribotype. The ancestral ribotypes were the agents which gave rise to the first cells. The book goes on to explain how organic codes and organic memories can be used to shed new light on the problems encountered in cell signalling, epigenesis, embryonic development, and the evolution of language. (shrink)

Is life different from the non-living? If so, how? And how, in that case, does biology as the study of living things differ from other sciences? These questions are traced through an exploration of episodes in the history of biology and philosophy. The book begins with Aristotle, then moves on to Descartes comparing his position with that of Harvey. In the eighteenth century the authors consider Buffon and Kant. In the nineteenth century the authors examine the Cuvier-Geoffroy debate, (...) pre-Darwinian geology and natural theology, Darwin and the transition from Darwin to the revival of Mendelism. Two chapters deal with the evolutionary synthesis and such questions as the species problem, the reducibility or otherwise of biology to physics and chemistry, and the problem of biological explanation in terms of function and teleology. The final chapters reflect on the implications of the philosophy of biology for philosophy of science in general. (shrink)

Research in ecology and evolutionary biology (evo-eco) often tries to emulate the “hard” sciences such as physics and chemistry, but to many of its practitioners feels more like the “soft” sciences of psychology and sociology. I argue that this schizophrenic attitude is the result of lack of appreciation of the full consequences of the peculiarity of the evo-eco sciences as lying in between a-historical disciplines such as physics and completely historical ones as like paleontology. Furthermore, evo-eco researchers have gotten (...) stuck on mathematically appealing but philosophi- cally simplistic concepts such as null hypotheses and p-values defined according to the frequentist approach in statistics, with the consequence of having been unable to fully embrace the complexity and subtlety of the problems with which ecologists and evolutionary biologists deal with. I review and discuss some literature in ecology, philosophy of science and psychology to show that a more critical methodological attitude can be liberating for the evo-eco scientist and can lead to a more fecund and enjoyable practice of ecology and evolutionary biology. With this aim, I briefly cover concepts such as the method of multiple hypotheses, Bayesian analysis, and strong inference. (shrink)

. Introductory Remarks THEODOSIUS DOBZHANSKY The problems of reduction in biology are currently of considerable theoretical interest and practical ...

Joshua Glasgow argues against the existence of races. His experimental philosophy asks subjects questions involving racial categorization to discover the ordinary concept of race at work in their judgments. The results show conflicting information about the concept of race, and Glasgow concludes that the ordinary concept of race is inconsistent. I conclude, rather, that Glasgow’s results fit perfectly fine with a social-kind view of races as real social entities. He also presents thought experiments to show that social-kind views give (...) the wrong results, but intuitions might differ on which results are the wrong ones, and social-kind views can resist the implications he derives from these cases. Widespread false beliefs about a concept or category need not undermine anything’s existence, and a sufficiently context-sensitive approach to races will allow for competing criteria for race-membership in different contexts without contradictory criteria in any one context. Glasgow’s arguments are therefore unsuccessful. (shrink)

Philip Kitcher is one of the leading figures in the philosophy of science today. Here he collects, for the first time, many of his published articles on the philosophy of biology, spanning from the mid-1980's to the present. The book's title refers to Gregor Mendel, an Augustinian monk who was one of the first scientists to develop a theory of heredity. Mendel's work has been deeply influential to our understanding of our selves and our world, just as the study (...) of genetics today will have a profound and long-term impact on future scientific research. Kitcher's articles cover a broad range of topics with similar philosophical and social significance: sociobiology, evolutionary psychology, species, race, altruism, genetic determinism, and the rebirth of creationism in Intelligent Design. Kitcher's work on the intersection of biology and the philosophy of science is both unprecedented and wide-ranging, and will appeal not only to philosophers of science, but to scholars and students across disciplines. (shrink)

A is for Alice and astronomers arguing about acceleration -- B is for Bernard's body-exchange machine -- C is for the Catholic cannibal -- D is for Maxwell's demon -- E is for evolution (and an embarrassing problem with it) -- F is for the forms lost forever to the prisoners of the cave -- G is for Galileo's gravitational balls -- H is for Hume's shades -- I is for the identity of indiscernibles -- J is for Henri Poincaré (...) and alternative geometries -- K is for the Kritik and Kant's kind of thought experiments -- L is for Lucretius' spear -- M is for Mach's motionless chain -- N is for Newton's bucket -- O is for Olbers' paradox -- P is for Parfit's person -- Q is for the questions raised by thought experiments quotidiennes -- R is for the rule-ruled room -- S is for Salvatius' ship, sailing along its own space-time line -- T is for the time-travelling twins -- U is for the universe, and Einstein's attempts to understand it -- V is for the vexed case of the violinist -- W is for Wittgenstein's beetle -- X is for xenophanes and thinking by examples -- Y is for counterfactuals and a backwards approach to history -- Z is for Zeno and the mysteries of infinity. (shrink)

Marco Buzzoni has presented a Kantian account of thought experiments in science as a serious rival to the current empiricist and Platonic accounts. This paper takes the first steps of a comprehensive assessment of this account in order to further the more general discussion of the feasibility of a Kantian theory of scientific thought experiments. Such a discussion is overdue. To this effect the broader question is addressed as to what motivates a Kantian approach. Buzzoni's account and the (...) assessment developed in this paper are warranted by the fact that the history of philosophical inquiry into thought experiments is deeply interwoven with Kant's philosophy. This history will be depicted here for the first time in more comprehensive terms to contextualize Buzzoni's account in historical and systematic perspective. (shrink)

Systems Biology and the Modern Synthesis are recent versions of two classical biological paradigms that are known as structuralism and functionalism, or internalism and externalism. According to functionalism (or externalism), living matter is a fundamentally passive entity that owes its organization to external forces (functions that shape organs) or to an external organizing agent (natural selection). Structuralism (or internalism), is the view that living matter is an intrinsically active entity that is capable of organizing itself from within, with purely (...) internal processes that are based on mathematical principles and physical laws. At the molecular level, the basic mechanism of the Modern Synthesis is molecular copying, the process that leads in the short run to heredity and in the long run to natural selection. The basic mechanism of Systems Biology, instead, is self-assembly, the process by which many supramolecular structures are formed by the spontaneous aggregation of their components. In addition to molecular copying and self-assembly, however, molecular biology has uncovered also a third great mechanism at the heart of life. The existence of the genetic code and of many other organic codes in Nature tells us that molecular coding is a biological reality and we need therefore a framework that accounts for it. This framework is Code biology, the study of the codes of life, a new field of research that brings to light an entirely new dimension of the living world and gives us a completely new understanding of the origin and the evolution of life. (shrink)

Communication is an important feature of the living world that mainstream biology fails to adequately deal with. Applying two main disciplines can be contemplated to fill in this gap: semiotics and information theory. Semiotics is a philosophical discipline mainly concerned with meaning; applying it to life already originated in biosemiotics. Information theory is a mathematical discipline coming from engineering which has literal communication as purpose. Biosemiotics and information theory are thus concerned with distinct and complementary possible meanings of the (...) word ‘communication’. Since literal communication needs to be secured so as to enable semantics being communicated, information theory is a necessary prerequisite to biosemiotics. Moreover, heredity is a purely literal communication process of capital importance fully relevant to literal communication, hence to information theory. A short introduction to discrete information theory is proposed, which is centred on the concept of redundancy and its use in order to make sequences resilient to errors. Information theory has been an extremely active and fruitful domain of researches and the motor of the tremendous progress of communication engineering in the last decades. Its possible connections with semantics and linguistics are briefly considered. Its applications to biology are suggested especially as regards error-correcting codes which are mandatory for securing the conservation of genomes. Biology needs information theory so biologists and communication engineers should closely collaborate. (shrink)

Bionic technologies connecting biological nervous systems to computer or robotic devices for therapeutic purposes have been recently claimed to provide novel experimental tools for the investigation of biological mechanisms. This claim is examined here by means of a methodological analysis of bionics-supported experimental inquiries on adaptive sensory-motor behaviours. Two broad classes of bionic systems (regarded here as hybrid simulations of the target biological system) are identified, which differ from each other according to whether a component of the biological target system (...) is replaced by an artificial component, or else a component of an artificial system is replaced by a biological component. The role of these hybrid systems in the modelling of adaptive sensory-motor biological behaviours is discussed with reference to bionics-supported experiments on the mechanisms of body stabilization in lampreys. Methodological problems emerging from these case studies often arise in computer-based and biorobotic simulations of biological behaviours too. Accordingly, the present analysis contributes to identifying a more general regulative methodological framework for the machine-based modelling of biological systems. (shrink)

Livings things are so very strange -- The quest for a theory of life -- Understanding 'understanding' -- Stability and instability -- The knotty origin of life problem -- Biology's crisis of identity -- Biology is chemistry -- What is life?

Thought experiments being central to contemporary philosophy and science, the following questions were asked in recent literature. What is their definition? Are they heuristic devices, arguments, paradoxes? Are they comparable to real experiments? Do intuition and conceivability intervene? Equally imaginative thought experiments are found in ancient, medieval, and Renaissance texts. Paying attention to prime historical examples of thought experiments, we show that historical perspectives help answer these general questions.

"By combining recent advances in the physical sciences with some of the novel ideas, techniques, and data of modern biology, this book attempts to achieve a new and different kind of evolutionary synthesis. I found it to be challenging, fascinating, infuriating, and provocative, but certainly not dull."--James H, Brown, University of New Mexico "This book is unquestionably mandatory reading not only for every living biologist but for generations of biologists to come."--Jack P. Hailman, Animal Behaviour , review of the (...) first edition "An important contribution to modern evolutionary thinking. It fortifies the place of Evolutionary Theory among the other well-established natural laws."--R.Gessink, TAXON. (shrink)

This set of original essays by some of the best names in philosophy of science explores a range of diverse issues in the intersection of biology and epistemology. It asks whether the study of life requires a special biological approach to knowledge and concludes that it does not. The studies, taken together, help to develop and deepen our understanding of how biology works and what counts as warranted knowledge and as legitimate approaches to the study of life. The (...) first section deals with the nature of evidence and evolutionary theory as it came to dominate nineteenth-century philosophy of science; the second and third parts deal with the impact of laboratory and experimental research. This is an impressive team of authors, bringing together some of the most distinguished philosophers of science today. The volume will interest professionals and graduate students in biology and the history and philosophy of science. (shrink)

Are living organisms--as Descartes argued--just machines? Or is the nature of life such that it can never be fully explained by mechanistic models? In this thought-provoking and controversial book, eminent geophysicist Walter M. Elsasser argues that the behavior of living organisms cannot be reduced to physico-chemical causality. Suggesting that molecular biology today is at the same point as Newtonian physics on the eve of the quantum revolution, Elsasser lays the foundation for a theoretical biology that points the way (...) toward a natural philosophy of organic life. Explicitly repudiating "vitalism" (the notion that the laws of nature need to be modified when applied to living organisms), Elsasser argues instead that the structural complexity of even a single living cell is "transcomputational"--that is, beyond the power of any imaginable system to compute. Beginning from this insight, Elsasser leads the reader through a step-by-step process that ultimately arrives at the conclusion that living and non-living matter are separated by "a no-man's land of irrationality." Trained in Germany as a physicist, Elsasser first pondered the implications of quantum mechanics for biology as early as 1951. The more closely he studied the inherent complexity of life, the more skeptical he became of the reductionist view of organisms as tiny machines. "An organism," he concluded, "is a source of causal chains which cannot be traced beyond a terminal point because they are lost in the unfathomable complexity of the organism." Like the physicist who works within the bounds of an unfathomable universe, Elsasser argues, the biologist must seek answers within a system that is no less unfathomable. (shrink)

Drawing on work of the past decade, this volume brings together articles from the philosophy, history, and sociology of science, and many other branches of the biological sciences. The volume delves into the latest theoretical controversies as well as burning questions of contemporary social importance. The issues considered include the nature of evolutionary theory, biology and ethics, the challenge from religion, and the social implications of biology today (in particular the Human Genome Project).

In addition to being one of the world's most influential philosophers, Aristotle can also be credited with the creation of both the science of biology and the philosophy of biology. He was the first thinker to treat the investigations of the living world as a distinct inquiry with its own special concepts and principles. This book focuses on a seminal event in the history of biology - Aristotle's delineation of a special branch of theoretical knowledge devoted to (...) the systematic investigation of animals. Aristotle approached the creation of zoology with the tools of subtle and systematic philosophies of nature and of science that were then carefully tailored to the investigation of animals. The papers collected in this volume, written by a pre-eminent figure in the field of Aristotle's philosophy and biology, examine Aristotle's approach to biological inquiry and explanation, his concepts of matter, form and kind, and his teleology. (shrink)

This collection of revised and new essays argues that biology is an autonomous science rather than a branch of the physical sciences. Ernst Mayr, widely considered the most eminent evolutionary biologist of the 20th century, offers insights on the history of evolutionary thought, critiques the conditions of philosophy to the science of biology, and comments on several of the major developments in evolutionary theory. Notably, Mayr explains that Darwin's theory of evolution is actually five separate theories, each with (...) its own history, trajectory and impact. Ernst Mayr, commonly referred to as the "Darwin of the 20th century" and listed as one of the top 100 scientists of all-time, is Professor Emeritus at Harvard University. What Makes Biology Unique is the 25th book he has written during his long and prolific career. His recent books include This is Biology: The Science of the Living World (Belknap Press, 1997) and What Evolution Is (Basic Books, 2002). (shrink)

This book examines from a multidisciplinary viewpoint the question of what we mean - what we should mean - by setting sustainability as a goal for environmental management. The author, trained as a philosopher of science and language, explores ways to break down the disciplinary barriers to communication and deliberation about environment policy, and to integrate science and evaluations into a more comprehensive environmental policy. Choosing sustainability as the keystone concept of environmental policy, the author explores what we can learn (...) about sustainable living from the philosophy of pragmatism, from ecology, from economics, from planning, from conservation biology and from related disciplines. The idea of adaptive, or experimental, management provides the context, while insights from various disciplines are integrated into a comprehensive philosophy of environmental management. The book will appeal to students and professionals in the fields of environmental policy and ethics, conservation biology, and philosophy of science. (shrink)

Synthetic biology is an increasingly high-profile area of research that can be understood as encompassing three broad approaches towards the synthesis of living systems: DNA-based device construction, genome-driven cell engineering and protocell creation. Each approach is characterized by different aims, methods and constructs, in addition to a range of positions on intellectual property and regulatory regimes. We identify subtle but important differences between the schools in relation to their treatments of genetic determinism, cellular context and complexity. These distinctions tie (...) into two broader issues that define synthetic biology: the relationships between biology and engineering, and between synthesis and analysis. These themes also illuminate synthetic biology's connections to genetic and other forms of biological engineering, as well as to systems biology. We suggest that all these knowledge-making distinctions in synthetic biology raise fundamental questions about the nature of biological investigation and its relationship to the construction of biological components and systems. (shrink)

Understanding how scientific activities use naming stories to achieve disciplinary status is important not only for insight into the past, but for evaluating current claims that new disciplines are emerging. In order to gain a historical understanding of how new disciplines develop in relation to these baptismal narratives, we compare two recently formed disciplines, systems biology and genomics, with two earlier related life sciences, genetics and molecular biology. These four disciplines span the twentieth century, a period in which (...) the processes of disciplinary demarcation fundamentally changed from those characteristic of the nineteenth century. We outline how the establishment of each discipline relies upon an interplay of factors that include paradigmatic achievements, technological innovation, and social formations. Our focus, however, is the baptism stories that give the new discipline a founding narrative and articulate core problems, general approaches and constitutive methods. The highly plastic process of achieving disciplinary identity is further marked by the openness of disciplinary definition, tension between technological possibilities and the ways in which scientific issues are conceived and approached, synthesis of reductive and integrative strategies, and complex social interactions. The importance – albeit highly variable – of naming stories in these four cases indicates the scope for future studies that focus on failed disciplines or competing names. Further attention to disciplinary histories could, we suggest, give us richer insight into scientific development. (shrink)

Ludwik Fleck, Edmund Husserl : on the historicity of scientific knowledge -- Gaston Bachelard : the concept of "phenomenotechnique" -- Georges Canguilhem : epistemological history -- Pisum : Carl Correns's experiments on Xenia, 1896-99 -- Eudorina : Max Hartmann's experiments on biological regulation in protozoa, 1914-21 -- Ephestia : Alfred Kähn's experimental design for a developmental physiological -- Genetics, 1924-45 -- Tobacco mosaic virus : virus research at the Kaiser Wilhelm Institutes for Biochemistry and Biology, 1937-45 -- (...) The concept of the gene : molecular biological perspectives -- The liquid scintillation counter : traces of radioactivity -- The concept of information : the writings of François Jacob -- Intersections -- Preparations -- The economy of the scribble. (shrink)

Reductionism--understanding complex processes by breaking them into simpler elements--dominates scientific thinking around the world and has certainly proved a powerful tool, leading to major discoveries in every field of science. But reductionism can be taken too far, especially in the life sciences, where sociobiological thinking has bordered on biological determinism. Thus popular science writers such as Richard Dawkins, author of the highly influential The Selfish Gene, can write that human beings are just "robot vehicles blindly programmed to preserve the selfish (...) molecules known as genes." Indeed, for many in science, genes have become the fundamental unit for understanding human existence: genes determine every aspect of our lives, from personal success to existential despair: genes for health and illness, genes for criminality, violence, and sexual orientation. Others would say that this is reductionism with a vengeance. In Lifelines, biologist Steven Rose offers a powerful alternative to the ultradarwinist claims of Dawkins, E.O. Wilson, Daniel Dennett and others. Rose argues against an extreme reductionist approach that would make the gene the key to understanding human nature, in favor of a more complex and richer vision of life. He urges instead that we focus on the organism and in particular on the organism's lifeline: the trajectory it takes through time and space. Our personal lifeline, Rose points out, is unique--even identical twins, with identical genes at birth, will differ over time. These differences are obviously not embedded in our genes, but come about through our developmental trajectory in which genes, as part of the biochemical orchestra of trillions of cells in each human body, have an important part--but only a part--to play. To illustrate this idea, Rose examines recent research in modern biology, and especially two disciplines--genetics (which looks at the impact of genes on form) and developmental biology (which examines the interaction between the organism and the environment)--and he explores new ideas on biological complexity proposed by scientists such as Stuart Kauffman. He shows how our lifelines are constructed through the interplay of physical forces--such as the intrinsic chemistry of lipids and proteins, and the self-organizing and stabilizing properties of complex metabolic webs--and he reaches a startling conclusion: that organisms are active players in their own fate, not simply the playthings of the gods, nature, or the inevitable workings out of gene-driven natural selection. The organism is both the weaver and the pattern it weaves. Lifelines will be a rallying point for all who seek an alternative to the currently fashionable, deeply determinist accounts which dominate popular science writing and, in fact, crowd the pages of some of the major scientific journals. Based on solid, state-of-the-art research, it not only makes important contributions to our understanding of Darwin and natural selection, but will swing the pendulum back to a richer, more complex view of human nature and of life. (shrink)

This essay proposes an alternative way of studying video games: as thought experiments akin to the narrative thought experiments that are frequently used in philosophy. This perspective incorporates insights from the narratological and ludological perspectives in game studies and highlights the philosophical significance of games. Video game thought experiments are similar to narrative thought experiments in many respects and can perform the same functions. They also have distinctive advantages over narrative thought experiments, as they situate (...) counterfactuals in more complex, developed contexts and present them to players who are participants in game worlds, rather than simply observers. (shrink)

Perhaps because of it implications for our understanding of human nature, recent philosophy of biology has seen what might be the most dramatic work in the philosophies of the ”special” sciences. This drama has centered on evolutionary theory, and in the second edition of this textbook, Elliott Sober introduces the reader to the most important issues of these developments. With a rare combination of technical sophistication and clarity of expression, Sober engages both the higher level of theory and the (...) direct implications for such controversial issues as creationism, teleology, nature versus nurture, and sociobiology. Above all, the reader will gain from this book a firm grasp of the structure of evolutionary theory, the evidence for it, and the scope of its explanatory significance. (shrink)

The fundamental concept of structured chemical system has been introduced and analysed in this paper. This concept, as in biology but not in physics, is very important in chemistry. In fact, the main chemical concepts (molecule and compound) have been identified as systemic concepts and their use in chemical explanation can only be justified in this approach. The fundamental concept of “environment” has been considered and then the system concept in mechanics, chemistry and biology. The differences and the (...) analogies between the use of the systemic approach in these disciplines have been analyzed and correlated to the general problem of reductionism and complexity perspectives. The inanimate–animate dichotomy can be reconsidered in this new approach. Since the chemical systemic concepts of molecule and compound can be dated to the nineteenth century, chemistry can be considered the first true systemic science and its historical evolution can be a model for other sciences (such as the humanities) where the systemic concepts are important. (shrink)

William Morton Wheeler -- The anti-colony as an organism -- Jean-Henri Fabre -- On instincts -- The termitodoxa, or biology and society -- The organization of research -- The dry-rot of our academic biology -- Emergent evolution and the development of societies -- Carl Akeley's early work and environment -- Present tendencies in biological theory -- Hopes in the biological sciences -- Some attractions of the field study of ants -- Animal societies.

In the second half of their recent, critically acclaimed book Unto Others: The Evolution and Psychology of Unselfish Behavior , Elliott Sober and David Sloan Wilson discuss psychological hedonism. This is the view that avoiding our own pain and increasing our own pleasure are the only ultimate motives people have. They argue that none of the traditional philosophical arguments against this view are good, and they go on to present theirownevolutionary biological argument against it. Interestingly, the first half of their (...) book, which is a defense of group selectionism, has received almost all of the attention of those people who have published reactions to the book. No one has published a detailed reaction to the argument of the latter half of the book. In this article, the author explains and critically discusses their evolutionary biological argument against psychological hedonism, concluding that in its current form it is not strong enough to support its conclusion. However, the author goes on to argue that despite recent criticisms of Robert Nozick’s experience-machine argument, it is still a good argument against psychological hedonism. In support of the latter point, the author responds to the objections of Sober and Wilson and to the more recent criticisms offered by Matthew Silverstein. Key Words: hedonism • psychological egoism • evolution • Robert Nozick • Elliott Sober. (shrink)

The paper aims to clarify and scrutinize Searle"s somewhat puzzling statement that collective intentionality is a biologically primitive phenomenon. It is argued that the statement is not only meant to bring out that "collective intentionality" is not further analyzable in terms of individual intentionality. It also is meant to convey that we have a biologically evolved innate capacity for collective intentionality.The paper points out that Searle"s dedication to a strong notion of collective intentionality considerably delimits the scope of his endeavor. (...) Furthermore, evolutionary theory does not vindicate that an innate capacity for collective intentionality is a necessary precondition for cooperative behavior. 1. (shrink)

This volume presents an interconnected set of sixteen essays, four of which are previously unpublished, by Allan Gotthelf--one of the leading experts in the study of Aristotle's biological writings. Gotthelf addresses three main topics across Aristotle's three main biological treatises. Starting with his own ground-breaking study of Aristotle's natural teleology and its illuminating relationship with the Generation of Animals, Gotthelf proceeds to the axiomatic structure of biological explanation (and the first principles such explanation proceeds from) in the Parts of Animals. (...) After an exploration of the implications of these two treatises for our understanding of Aristotle's metaphysics, Gotthelf examines important aspects of the method by which Aristotle organizes his data in the History of Animals to make possible such a systematic, explanatory study of animals, offering a new view of the place of classification in that enterprise. In a concluding section on 'Aristotle as Theoretical Biologist', Gotthelf explores the basis of Charles Darwin's great praise of Aristotle and, in the first printing of a lecture delivered worldwide, provides an overview of Aristotle as a philosophically-oriented scientist, and 'a proper verdict' on his greatness as scientist. (shrink)

Provides a philosophical analysis of such biological concepts as natural selection, adaptation, speciation, and evolution.

Human aesthetic experiences are pervasive; they are triggered by faces, art, natural scenery, foods, ideas, theories, and decision-making situations, among many sources, and seem to be a distinctive trait of our species. Our moral sense, understood as our capacity to judge events, actions, or people as good or bad, appropriate or inappropriate, also seems to be an exclusively human endowment (Ayala 2010). As part of the scientific efforts to characterize the biological foundations of our human uniqueness, recently there has been (...) interest in the brain’s underpinnings of aesthetic reactions to art on the one hand, and in the neural correlates of moral judgment and decision-making on the other (Greene and Paxton .. (shrink)

This stimulating and wide-ranging book mounts a profound enquiry into some of the most pressing questions of our age, by examining the relationship between biological science and Christianity. The history of biological discovery is explored from the point of view of a leading philosopher and ethicist. What effect should modern biological theory and practice have on Christian understanding of ethics? How much of that theory and practice should Christians endorse? Can Christians, for example, agree that biological changes are not governed (...) by transcendent values, or that there are no clear or essential boundaries between species? To what extent can 'Nature' set our standards? Professor Clark takes a reasoned look at biological theory since Darwin and argues that an orthodox Christian philosophy is better able to accommodate the truth of such theory than is the sort of progressive, meliorist interpretation of Christian doctrine which is usually offered as the properly 'modern' option. (shrink)