A historical and critical analysis of the concept of the gene that attempts to provide new perspectives and metaphors for the transformation of biology and its philosophy.

Abstract: Many believe that, in addition to cognitive capacities, autonomous robots need something similar to affect. As in humans, affect, including specific emotions, would filter robot experience based on a set of goals, values, and interests. This narrows behavioral options and avoids combinatorial explosion or regress problems that challenge purely cognitive assessments in a continuously changing experiential field. Adding human-like affect to robots is not straightforward, however. Affect in organisms is an aspect of evolved biological systems, from the taxes of (...) single-cell organisms to the instincts, drives, feelings, moods, and emotions that focus human behavior through the mediation of hormones, pheromones, neurotransmitters, the autonomic nervous system, and key brain structures. We argue that human intelligence is intimately linked to biological affective systems and to the unique repertoire of potential behaviors, sometimes conflicting, they facilitate. Artificial affect is affect in name only and without genes and biological bodies, autonomous robots will lack the goals, interests, and value systems associated with human intelligence. We will take advantage of their general intelligence and expertise, but robots will not enter our intellectual world or apply for legal status in the community. -/- . (shrink)

The concept of the gene has been the central organizing theme of 20th century biology. Biology has become increasingly influential both for philosophers seeking a naturalized basis for epistemology, ethics, and the understanding of the mind, as well as for the human sciences generally. The central task of this work is to get the story right about genes and in so doing provide a critical and enabling resourse for use in the further pursuit of human self-understanding. ;The work begins (...) with a wide-ranging historical reconstruction and conceptual analysis of the meaning of "the gene" that results in defining and distinguishing two different "genes". Each of these can be seen as an heir to one of the two major historical trends in explaining the source of biological order---preformationism and epigenesis. The preformationist gene predicts phenotypes but only on an instrumental basis where immediate medical and/or economic benefits can be had. The gene of epigenesis , by contrast, is a developmental resource that provides templates for RNA and protein synthesis but has in itself no determinate relationship to organismal phenotypes. The seemingly prevalent idea that genes constitute information for traits is based, I argue, upon an unwarranted conflation of these two senses which is in effect held together by rhetorical glue. Beyond this historical, conceptual, and rhetorical inquiry the bulk of the dissertation then concerns itself with an empirically up-to-date analysis of the cell and molecular basis of biological order and of the pathological loss of same. In each of these chapters I structure my analysis with the idea in mind that the "conflated" view can be held empirically accountable. Major touchpoints in this work include the ideas of I. Kant, J. Blumenbach, K. E. von Baer, J. Muller, R. Virchow, W. Johannsen, R. Falk, J. Sapp, E. Schrodinger, M. Delbruick, G. Gamow, R. Doyle, L. Kay, S. Kauffman, E. Jablonka, J. Rothman, K. Yamamoto, P. Rous, H. Temin, J. M. Bishop, H. Harris, E. Stanbridge, D. L. Smithers, B. Vogelstein, E. Farber and H. Rubin. (shrink)

Radically new or unexpected findings in a science demand an openness to new concepts and styles of explanation. The time is more than ripe for asking ourselves what we have learned from the research program of comparative genomics. Where not long ago the human genome was expected to reveal a close association of complexity with the quantitative expansion of the roster of unique genes, more recent findings, especially in relation to comparisons between human and chimp, have raised the bracing possibility (...) that when it comes to complexity, it may be that `less is more'. But `less is more' is not the only observation or inference that follows from the data. The idea of `progressive detachment' will be introduced and set forth as the most perspicuous conceptual resource for unifying and interpreting the overall findings from comparative genomics to date. (shrink)

If the question ``What is a gene?'' proves to be worth asking it must be able to elicit an answer which both recognizes and address the reasons why the concept of the gene ever seemed to be something worth getting excited about in the first place as well analyzing and evaluating the latest develops in the molecular biology of DNA. Each of the preceding papers fails to do one of these and sufferrs the consequences. Where Rolston responds to (...) the apparent failure of molecular biology to make good on the desideratum of the classical gene by veering off into fanciful talk about ``cybernetic genes,'' Griffiths and Stotz lose themselves in the molecular fine print and forget to ask themselves why ``genes'' should be of any special interst anyway. (shrink)

In her recent book Lindley Darden has endeavored to reclaim for philosophy an active role in the elaboration of good science. She has done this, not by holding up some set of rational standards derived from outside of scientific practice, but rather by delving into the history of science and coming out with a set of scientific strategies. Unconcerned about whether any particular strategy wasin fact employed in a given historical case her project depends upon two claims, first that these (...) strategiescould have been successfully deployed in the particular cases from which they were construed, and second and more importantly, that these strategies can be generalized beyond any particular context and be put to future use. It will be argued that Darden''s conception of the possible context independence of scientific strategies is based upon an overly cognitivist misconstrual. An alternative account of the relationship of context dependent and context independent aspects of scientific theory formation will be offered as well as its implications for philosophy. (shrink)

Recognition of the plasticity of development — from gene expression to neuroplasticity — is increasingly undermining the traditional distinction between structure and function, or anatomy and behavior. At the same time, dynamic systems theory — a set of tools and concepts drawn from the physical sciences — has emerged as a way of describing what Maurice Merleau-Ponty calls the “dynamic anatomy” of the living organism. This article surveys and synthesizes dynamic systems models of development from biology, neuroscience, and psychology (...) in order to propose an integrated account of growth, learning, and behavior. Key to this account is the concept of self-differentiation or symmetry-breaking. I argue that development can be understood as a cascade of symmetry-breaking events brought about by the ongoing interactions of multiple, nested, nonlinear dynamic systems whose self-organizing behaviors gradually alter their own anatomical conditions. I begin by introducing the concept of symmetry-breaking as a way of understanding anatomical development. I then extend this approach to motor development by arguing that the organism’s behavior grows along with its body, like a new organ. Finally, I argue that the organism’s behavior and its world grow together dialectically, each driving the other to become more complex and asymmetrical through its own increasing asymmetry. Thus development turns out to be a form of cognition or sense-making, and cognition a form of development. (shrink)

Vaccinia virus, the world's oldest vaccine, was used originally for the eradication of smallpox. It is now being genetically engineered to create new live vaccines for use against other infectious agents of medical and veterinary importance. Genes coding for antigens of several pathogens have been linked to vaccinia virus transcriptional regulatory signals and inserted into the vaccinia virus genome. The resultant recombinant viruses are infectious, express the foreign gene, stimulate specific immune responses in vaccinated animals and can protect against (...) disease caused by the corresponding pathogen. (shrink)

The essays in this book discuss human behavior and the institutions of capitalism. The essays are non-technical and are written so as to be accessible to students of all disciplines and to all other persons interested in capitalism and in economic behavior. They often present unconventional views of the topics they discuss. Those containing unconventional views discuss self-interested behavior, selfish gene theory, the meaning and social function of private ownership, the externality problem, the nature of the firm and the (...) rise of capitalism. The essays are not meant to be a textbook, but they offer a useful supplementary reading source for courses in business, economics and law that deal with human behavior in the marketplace and with capitalism, ownership, markets and firms. (shrink)

Representing species-specific proteins and protein complexes in ontologies that are both human and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. Although existing protin-centric informatics resources provide the biomedical research community with well-curated compendia of protein sequence and structure, these resources lack formal ontological representations of the relationships among the proteins themselves. The Protein Ontology (PRO) Consortium is filling this informatics resource gap by developing ontological representations and relationships among proteins and their variants and modified forms. Because (...) proteins are often functional only as members of stable protein complexes, the PRO Consortium, in collaboration with existing protein and pathway databases, has launched a new initiative to implement logical and consistent representation of protein complexes. We describe here how the PRO Consortium is meeting the challenge of representing species-specific protein complexes, how protein complex representation in PRO supports annotation of protein complexes and comparative biology, and how PRO is being integrated into existing community bioinformatics resources. The PRO resource is accessible at http://pir.georgetown.edu/pro/. (shrink)

Book review of Lenny Moss, What Genes Can’t Do. Cambridge, MA: MIT Press , 256 pp. -/- Many philosophers of science will have encountered the core distinction between two different gene concepts found in What Genes Can’t Do. Moss argues that contemporary uses of the term ‘gene’ that denote an information bearing entity result from the conflation of two concepts (‘Gene-P’ and ‘Gene-D’).

The Protein Ontology (PRO) is designed as a formal and principled Open Biomedical Ontologies (OBO) Foundry ontology for proteins. The components of PRO extend from a classification of proteins on the basis of evolutionary relationships at the homeomorphic level to the representation of the multiple protein forms of a gene, including those resulting from alternative splicing, cleavage and/or posttranslational modifications. Focusing specifically on the TGF-beta signaling proteins, we describe the building, curation, usage and dissemination of PRO. PRO provides a (...) framework for the formal representation of protein classes and protein forms in the OBO Foundry. It is designed to enable data retrieval and integration and machine reasoning at the molecular level of proteins, thereby facilitating cross-species comparisons, pathway analysis, disease modeling and the generation of new hypotheses. (shrink)

The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms and interrelations. Protein entities represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence and modification metaclasses, and there is a separate metaclass for protein complexes. All metaclasses also have organism-specific derivatives. PRO complements established sequence databases such as UniProtKB, and interoperates with other biomedical and biological ontologies such as the Gene Ontology (GO). PRO (...) relates to UniProtKB in that PRO’s organism-specific classes of proteins encoded by a specific gene correspond to entities documented in UniProtKB entries. PRO relates to the GO in that PRO’s representations of organism-specific protein complexes are subclasses of the organism-agnostic protein complex terms in the GO Cellular Component Ontology. The past few years have seen growth and changes to the PRO, as well as new points of access to the data and new applications of PRO in immunology and proteomics. Here we describe some of these developments. (shrink)

This article examines how minimal genome research mobilizes philosophical concepts such as minimality and essentiality. Following a historical approach the article aims to uncover what function this terminology plays and which problems are raised by them. Specifically, four historical moments are examined, linked to the work of Harold J. Morowitz, Mitsuhiro Itaya, Eugene Koonin and Arcady Mushegian, and J. Craig Venter. What this survey shows is a historical shift away from historical questions about life or descriptive questions about specific (...) organisms towards questions that explore biological possibilities: what are possible forms of minimal genomes, regardless of whether they exist in nature? Moreover, it highlights a fundamental ambiguity at work in minimal genome research between a universality claim and a standardization claim: does a minimal genome refer to the minimal gene set for any organism whatsoever? Or does it refer rather to a gene set that will provide stable, robust and predictable behaviour, suited for biotechnological applications? Two diagnoses are proposed for this ambiguity: a philosophical diagnosis of how minimal genome research either misunderstands the ontology of biological entities or philosophically misarticulates scientific practice. Secondly, a historical diagnosis that suggests that this ambiguity is part of a broader shift towards technoscience. (shrink)

In March 1996, the General Accounting Office (GAO) issued the reportScientific Research: Continued Vigilance Critical to Protecting Human Subjects.It stated that “an inherent conflict of interest exists when physician-researchers include their patients in research protocols. If the physicians do not clearly distinguish between research and treatment in their attempt to inform subjects, the possible benefits of a study can be overemphasized and the risks minimized.” The report also acknowledged that “the line between research and treatment is not always cleartoclinicians. Controversy (...) exists regarding whether certain medical procedures should be categorized as research.”This problem currently plagues gene transfer research. A few months prior to the GAO report, an ad hoc committee appointed by National Institutes of Health (NIH) Director Harold Varmus expressed similar concerns in its assessment of NIH investment in research on gene therapy. (shrink)

In March 1996, the General Accounting Office issued the report Scientific Research: Continued Vigilance Critical to Protecting Human Subjects. It stated that “an inherent conflict of interest exists when physician-researchers include their patients in research protocols. If the physicians do not clearly distinguish between research and treatment in their attempt to inform subjects, the possible benefits of a study can be overemphasized and the risks minimized.” The report also acknowledged that “the line between research and treatment is not always clear (...) to clinicians. Controversy exists regarding whether certain medical procedures should be categorized as research.”This problem currently plagues gene transfer research. A few months prior to the GAO report, an ad hoc committee appointed by National Institutes of Health Director Harold Varmus expressed similar concerns in its assessment of NIH investment in research on gene therapy. (shrink)

Keith Thomas: Gerald Edward Aylmer, 1926-2000 Adrian Hollis: William Spencer Barrett, 1914-2001 Bruce Williams: Charles Frederick Carter, 1919-2002 Malcolm Mackintosh: John Erickson, 1929-2002 J. H .R. Davis: Raymond William Firth, 1901-2002 F. M. L. Thompson: Hrothgar John Habakkuk, 1915-2002 A. W. Price: Richard Mervyn Hare, 1919-2002 Hugh Lloyd-Jones: Geoffrey Stephen Kirk, 1921-2003 Michael Lapidge and Peter Matthews: Vivien Anne Law, 1954-2002 Ann Moss: John Lough, 1913-2000 Terence Cave: Ian Dalrymple McFarlane, 1915-2002 Ludwig Paul: David Neil MacKenzie, 1926-2001 Peter Birks: (...) John Kieran Barry Moylan Nicholas, 1919-2002 Jonathan Shepard: Dimitri Dimitrievich Obolensky, 1918-2001 David Cannadine: John Harold Plumb, 1911-2001 Daniel Waley: Nicolai Rubinstein, 1911-2002 Ian Wood: John Michael Wallace-Hadrill, 1916-1985 R. G. M. Nisbet: William Smith Watt, 1913-2002 G. W. Bernard: Richard Bruce Wernham, 1906-1999. (shrink)

This 1996 book defends the prospects for a science of society. It argues that behind the diverse methods of the natural sciences lies a common core of scientific rationality that the social sciences can and sometimes do achieve. It also argues that good social science must be in part about large-scale social structures and processes and thus that methodological individualism is misguided. These theses are supported by a detailed discussion of actual social research, including theories of agrarian revolution, organizational ecology, (...) social theories of depression, and supply-demand explanations in economics. Professor Kincaid provides a general picture of explanation and confirmation in the social sciences and discusses the nature of scientific rationality, functional explanation, optimality arguments, meaning and interpretation, the place of microfoundations in social explanation, the status of neo-classical economics, the role of idealizations and non-experimental evidence, and other specific controversies. (shrink)

This paper has three aims: to define autonomism clearly and charitably, to offer a positive argument in its favour, and to defend a larger view about what is at stake in the debate between autonomism and its critics. Autonomism is here understood as the claim that a valuer does not make an error in failing to bring her moral and aesthetic judgements together, unless she herself values doing so. The paper goes on to argue that reason does not require the (...) valuer to make coherent her aesthetic and moral evaluations. Finally, the paper shows that the denial of autonomism has realist commitments that autonomism does not have, and concludes that issues of value realism and irrealism are relevant to the debates about autonomism in ways that have not hitherto been recognized. (shrink)

Ancient Chinese and Greek thinkers alike were preoccupied with the moral value of music; they distinguished between good and bad music by looking at the music’s effect on moral character. The idea can be understood in terms of two closely related questions. Does music have the power to affect the ethical character of either listener or performer? If it does, is it better as music for doing so? I argue that an affirmative answers to both questions are more plausible than (...) it might seem at first. (shrink)

The aim of the paper is to discuss some recent variants of familiar puzzles concerning the relations of parts to wholes put forward by Trenton Merricks and Eric Olson. The argument is put forward that so long as the familiar distinction between 'loose and popular' and 'strict and philosophical' senses of identity claims is accepted the paradoxical conclusions at which Merricks and Olson arrive can be resisted. It is not denied that accepting the distinction between 'loose and popular' and 'strict (...) and philosophical' senses of identity claims is itself a departure from common-sense, but it is argued that it is the smallest such departure available to us. (shrink)

A number of philosophers have argued that a naturalized epistemology cannot be normative, and thus that the norms that govern science cannot themselves be established empirically. Three arguments for this conclusion are here developed and then responded to on behalf of naturalized epistemology. The response is developed in three stages. First, if we view human knowers as part of the natural world, then the attempt to establish epistemic norms that are immune to scientific evaluation faces difficulties that are at least (...) as severe as the purported difficulties for naturalized epistemology. Second, some examples of the ways in which norms are proposed and evaluated in the course of scientific research are considered and it is concluded that science has no need for trans?scientific norms. Finally, the three arguments introduced at the outset have no force when they are viewed in the light of the preceding discussion. (shrink)

How is the debate between presentism and eternalism to be characterized? It is usual to suggest that this debate about time is analogous to the debate between the actualist and the possibilist about modality. I think that this suggestion is right. In what follows I pursue the analogy more strictly than is usual and offer a characterization of what is at the core of the dispute between presentists and eternalists that may be immune to worries often raised about the substantiality (...) of the debate. I suggest that the debate be characterized in Lewisean terms and define positions I call *Lewisean* eternalism and anti-*Lewisean*' presentism (analogous to Lewisean possibilism and anti-Lewisean actualism). I explain some advantages of the proposal and discuss some objections. I conclude that pursuing the analogy strictly offers the prospect of giving clear sense to a controversy which otherwise seems to many deeply obscure. (shrink)

This paper explores the explanatory adequacy of lower-level theories when their higher-level counterparts are irreducible. If some state or entity described by a high-level theory supervenes upon and is realized in events, entities, etc. described by the relevant lower-level theory, does the latter fully explain the higher-level event even if the higher-level theory is irreducible? While the autonomy of the special sciences and the success of various eliminativist programs depends in large part on how we answer this question, neither the (...) affirmative or negative answer has been defended in detail. I argue, contra Putnam and others, that certain facts about causation and explanation show that such lower-level theories do explain. I also argue, however, that there may be important questions about counterfactuals and laws that such explanations cannot answer, thereby showing their partial inadequacy. I defend the latter claim against criticisms based on eliminativism about higher-level explanations and sketch a number of empirical conditions that lower-level explanations would have to meet to fully explain higher-level events. (shrink)

I briefly argue that some issues in the individualism-holism debate have been fairly clearly settled and other issues still plagued by unclarity. The main argument of the paper is that there are a set of clear empirical issues around the holism-individualism debate that are central problems in current social science research. Those include questions about when we can be holist and how individualist we can be in social explanation.

Aesthetic internalism claims a link between judgement and motivation: aesthetic judgements bring with them motivations to act in characteristic ways. Critics object that there is a difference between merely liking something and judging it to be aesthetically good, and that it is our likings, not our aesthetic judgements, that motivate us. This paper develops a version of aesthetic internalism that can respond to this criticism. Wholehearted aesthetic judgements are characterized by stability, attention, and motivation. Making such judgements is an important (...) part of a good life, and so at least some aesthetic judgements are motivating. So we have reason to think that this version of aesthetic internalism is true. This paper defends wholehearted aesthetic internalism against objections, and assesses an argument from aesthetic internalism to aesthetic non-cognitivism. While wholehearted aesthetic internalism can only offer qualified support to non-cognitivism, it nonetheless offers a number of fruitful avenues for further work. (shrink)

The topic of this essay is how non-realistic novels challenge our philosophical understanding of the moral significance of literature. I consider just one case: Joseph Heller’s Catch-22. I argue that standard philosophical views, based as they are on realistic models of literature, fail to capture the moral significance of this work. I show that Catch-22 succeeds morally because of the ways it resists using standard realistic techniques, and suggest that philosophical discussion of ethics and literature must be pluralistic if it (...) is to include all morally salient literature, and not just novels in the “Great Tradition” and their ilk. (shrink)

Considered ahead of its time since the first publication in 1981, Medical Choices, Medical Chances provides a telescope for viewing how developments in the fields of medical research, medical technology, and health care organization are likely to influence the doctor-patient relationship in the 21st Century. The book explores this intricate web of relationships among doctors, patients, and families and offers a new framework for mastering the emotional and intellectual challenges of uncertainty, while at the same time providing tools for all (...) concerned to regain control from managed care. It is a must-read for all those interested in medicine and where it is headed in the new millennium. (shrink)

Originally published in 1950 by Yale University Press.