This article proposes an approach to understanding life that overcomes reductionist and dualist approaches. Kant’s analysis of the conditions of knowing an organism shows that attempts to explain its teleology and autopoiesis from the interactions of its components is problematic. Based on an analysis by Van de Vijver and colleagues, a co-constitutive relationship between the cognitive activities of the observer and the living features of the organism is described. Using the example of a developmental series, it is shown that within (...) this active relational process, both autopoiesis and teleology of the organism manifest themselves on the mental level of the observer. The Kantian mode of objectification, which refers to the sensually perceptible appearance of an organism, can be supplemented by an active mode of relational objectification that encompasses the life of the organism. The analysis introduces a phenomenological first-person perspective on the study of life "from within", which enables an empirical investigation of the vital properties of an organism. (shrink)

These preprints were automatically compiled into a PDF from the collection of papers deposited in PhilSci-Archive in conjunction with the PSA 2018.

The foundations of biology have been a topic of debate for the past few decades. The traditional perspective of the Modern Synthesis, which portrays organisms as passive entities with limited role in evolutionary theory, is giving way to a new paradigm where organisms are recognized as active agents, actively shaping their own phenotypic traits for adaptive purposes. Within this context, this article raises the question of whether contemporary biological theory is undergoing a cognitive revolution. This inquiry can be approached in (...) two ways: from a theoretical standpoint, exploring the centrality of the cognitive sciences in current theoretical biology; and from a historical perspective, examining the resemblance between the current state of theoretical biology and the Cognitive Revolution of the mid-20th century. Both inquiries yield affirmative answers, though important nuances will be emphasized. The cognitive sciences' explanatory framework is employed to elucidate the agentic characteristics of organisms, establishing a clear parallelism between the Cognitive Revolution and the present state of theoretical biology. (shrink)

Existentialism is compatible with a broadly biological vision of who we are. This thesis is grounded in an analysis of “concrete” or “individual” possibility, which differs from standard conceptions of possibility in that it allows for possibilities to come into being or disappear through time. Concrete possibilities are introduced both in individual life and by major transitions in evolution. In particular, the advent of ultrasociality and of language has enabled human goals to be formulated in partial independence from the vestigial (...) “goal” of biological replication. The existentialist stance is validated by the necessity of choice grounded in emotion, in a way that does not require a commitment to a Kantian Will. (shrink)

Methodological reductionists practice ‘wannabe reductionism’. They claim that one should pursue reductionism, but never propose how. I integrate two strains in prior work to do so. Three kinds of activities are pursued as “reductionist”. “Successional reduction” and inter-level mechanistic explanation are legitimate and powerful strategies. Eliminativism is generally ill-conceived. Specific problem-solving heuristics for constructing inter-level mechanistic explanations show why and when they can provide powerful and fruitful tools and insights, but sometimes lead to erroneous results. I show how traditional metaphysical (...) approaches fail to engage how science is done. The methods used do so, and support a pragmatic and non-eliminativist realism. (shrink)

The social, behavioral, and a good chunk of the biological sciences concern the nature of individual agency, where our paradigm for an individual is a human being. Theories of economic behavior, of mental function and dysfunction, and of ontogenetic development, for example, are theories of how such individuals act, and of what internal and external factors are determinative of that action. Such theories construe individuals in distinctive ways.

Recently the terms “codes” and “information” as used in the context of molecular biology have been the subject of much discussion. Here I propose that a variety of structural realism can assist us in rethinking the concepts of DNA codes and information apart from semantic criteria. Using the genetic code as a theoretical backdrop, a necessary distinction is made between codes qua symbolic representations and information qua structure that accords with data. Structural attractors are also shown to be entailed by (...) the mapping relation that any DNA code is a part of (as the domain). In this framework, these attractors are higher-order informational structures that obviate any “DNA-centric” reductionism. In addition to the implications that are discussed, this approach validates the array of coding systems now recognized in molecular biology. (shrink)

Bennett and Hacker criticize a number of neuroscientists and philosophers for attributing capacities which belong to the human being as a whole, like perceiving or deciding, to a “part” of the human being, viz. the brain. They call this type of mistake the “mereological fallacy”. Interestingly, the authors say that these capacities cannot be ascribed to the mind either. They reject not only materialistic monism but also Cartesian dualism, arguing that many predicates describing human life do not refer to physical (...) or mental properties, nor to the sum of such properties. I agree with this important principle and with the critique of the mereological fallacy which it underpins, but I have two objections to the authors’ view. Firstly, I think that the brain is not literally a part of the human being, as suggested. Secondly, Bennett and Hacker do not offer an account of body and mind which explains in a systematic way how the domain of phenomena which transcends the mental and the physical relates to the mental and the physical. I first argue that Helmuth Plessner’s philosophical anthropology provides the kind of account we need. Then, drawing on Plessner, I present an alternative view of the mereological relationships between brain and human being. My criticism does not undercut Bennett and Hacker’s diagnosis of the mereological fallacy but rather gives it a more solid philosophical–anthropological foundation. (shrink)

Recalling the title of Yoxen’s classical paper on the influence of Schrödinger’s book, I analyze the role that the work of H. Pattee might have played, if any, in the development of Biosemiotics. I take his 1969 paper “How does a molecule become a message?” (Developmental Biology Supplement) as a first target due to several circumstances that make it especially salient. On the one hand, even if Pattee has obviously developed further his ideas on later papers, the significance of this (...) one springs out right from the title, the journal and date of publication and, of course, its content. On the other, this paper in particular has been somehow rediscovered recently and not only within the frame of biosemiotics (eg, in history and philosophy of biology by E.F. Keller). Following the parallelism with Yoxen’s perspective, I contend that Pattee’s work was relatively influential with respect to a good amount of attempts to rethink living systems within theoretical biology around the 70s. This influence diminished together with the decay or even collapse of those attempts under the impact of molecular biology as it was being developed those years. Eventually, Pattee’s work has been taken up again. Notwithstanding, it is quite clear that Pattee himself was not intending to contribute specifically to Biosemiotics and that he was probably unaware of any such discipline, at least until recently. Then, we should as well ask (as Yoxen wonders with respect to Schrödinger) to which extent Pattee’s influence has been a direct one or rather an indication of the relevance of his ideas and the resonance of his hypotheses with those of biosemiotics. For this task I will sketch a few points of convergence and divergence and examine the work of some authors who either address directly this issue or have contributed significantly to build up the history of Biosemiotics. (shrink)

There has been a long-standing opposition to genetically modified organisms worldwide. Some studies have tried to identify the deep-lying philosophical, conceptual as well as psychological motivations for this opposition. Philosophical essentialism, psychological essentialism, and vitalism have been proposed as possible candidates. I approach the plausibility of the claim that these notions are related to GMO opposition from a historical perspective. Vitalism and philosophical essentialism have been associated with anti-GMO stance on account of their purported hostility to species and organismic mutability. (...) I show that vitalism has often been associated to various mutabilist theories, whereas the case for philosophical essentialism as motivating GMO opposition depends on the now discredited Essentialism Story that had constructed essentialism as a predominant view in pre-Darwinian science. Further, as philosophical essentialism taken seriously is incompatible with the reality of genetic engineering, it is unlikely to be a reason for opposition. Psychological essentialism, involving an instinctive repulsion from the practice of manipulating what is thought to be the essence of living beings, is a more likely reason for resistance to transgenesis. Yet even here, historical considerations are crucial. Not only lay people tend to essentialize genes, but scientists themselves can be shown to have been complicit in essentialist tendencies. From the advent of modern genetics, the imagery of the all-powerful genes, often depicted by scientists themselves metaphorically as material counterparts of the now obsolete vitalistic agent, has permeated the language of leading scientific figures, whose influence in shaping public opinion should not be downplayed. Enthusiasm for genetic engineering and the abhorrence from it might both derive from the same unrealistic image of the essential gene, the revision of which thus holding out the hope for transcending the present impasse of the GMO controversy. (shrink)

In the history of genetics, the information-theoretical description of the gene, beginning in the early 1960s, had a significant effect on the concept of the gene. Information is a highly complex metaphor which is applicable in view of the description of substances, processes, and spatio-temporal organisation. Thus, information can be understood as a functional particle of many different language games (some of them belonging to subdisciplines of genetics, as the biochemical language game, some of them belonging to linguistics and informatics). (...) It is this wide covering of different language games that justifies the common description of genes x, y, z as containing information for the phenotypic traits X, Y, Z (or the genome as storage for the information of a whole organism). However, if information is taken as the explanans and phenotypic traits or organisms as the explananda, then a description of the explanandum is of prior importance before the explanans can be characterised. This way of thinking could be useful for future discussions on the strikingly dominant information -metaphor, and the different gene concepts as well. The article illustrates this in two steps. First, a condensed overview on the history of genetics is given, which can be divided into three parts: (1) genetics without genes, (2) genetics with genes, but without information, (3) genetics with genes and information. It is assumed that this provides not only some historical knowledge about the origin of genetics and the introduction of technical terms, but offers at least preliminary insight into the methodological structure of genetic descriptions. In a second step, we redraw Spemann’s disturbation experiments to discuss our thesis that genetic information is not a natural entity, but part of a causality-language game which is secondarily added to the descriptions of interventionalistic practices, viz. experimental approaches. (shrink)

I use a recent ‘experimental philosophy’ study of the concept of the gene conducted by myself and collaborators to discuss the broader epistemological framework within which that research was conducted, and to reflect on the relationship between science, history and philosophy of science, and society.Keywords: Experimental philosophy; Biohumanities; Representing Genes Project; Gene concept; Science criticism; Conceptual ecology.

A central idea of developmental systems theory is ‘parity’ or ‘symmetry’ between genes and non-genetic factors of development. The precise content of this idea remains controversial, with different authors stressing different aspects and little explicit comparisons among the various interpretations. Here I characterise and assess several influential versions of parity.

The somatic mutation theory has been the prevailing paradigm in cancer research for the last 50 years. Its premises are: (1) cancer is derived from a single somatic cell that has accumulated multiple DNA mutations, (2) the default state of cell proliferation in metazoa is quiescence, and (3) cancer is a disease of cell proliferation caused by mutations in genes that control proliferation and the cell cycle. From this compelling simplicity, an increasingly complicated picture has emerged as more than 100 (...) oncogenes and 30 tumor suppressor genes have been identified. To accommodate this complexity, additional ad hoc explanations have been postulated. After a critical review of the data gathered from this perspective, an alternative research program has been proposed. It is based on the tissue organization field theory, the premises of which are that carcinogenesis represents a problem of tissue organization, comparable to organogenesis, and that proliferation is the default state of all cells. The merits of these competing theories are evaluated herein. BioEssays 26:1097–1107, 2004. © 2004 Wiley Periodicals, Inc. (shrink)

David Waldron Smithers was, among other things, a physician and a pioneer of cancer radiotherapy and a well-respected figure in British medicine and public health. From the 1940s until his retirement from medical practice in 1973, he was the director of the Radiotherapy Department at the Royal Marsden Hospital and London University Chair of Radiotherapy at the Institute of Cancer Research. Using massive amounts of clinical observations, which he interpreted from an organicist viewpoint, and his impressive synthetic thinking, he proposed (...) a coherent alternative perspective to the somatic mutation theory (SMT) which was then, and still is, the dominant theory of cancer. The purpose of this essay is to acquaint the modern audience with his seminal paper, published in 1962, because it deserves to be recognized as a true classic. In it, he examined the lack of fit between clinical observations and the SMT and proposed the rejection of this reductionist perspective. In addition, he built an organicist alternative in which carcinogenesis is seen as a problem of biological organization. His conceptual contribution to the cancer problem has inspired us and other authors over the last two decades. His essay “Cancer: An Attack on Cytologism,” originally published in The Lancet in 1962, is available as supplementary material in the online version of this article. (shrink)

For the last 50 years the dominant stance in experimental biology has been reductionism in general, and genetic reductionism in particular. Philosophers were the first to realize that the belief that the Mendelian genes were reduced to DNA molecules was questionable. Soon, experimental data confirmed these misgivings. The optimism of molecular biologists, fueled by early success in tackling relatively simple problems has now been tempered by the difficulties encountered when applying the same simple ideas to complex problems. We analyze three (...) examples taken from experimental data that illustrate the shortcomings of this sort of reductionism. In the first, alterations in the expression of a large number of genes coexist with normal phenotypes at supra-cellular levels of organization; in the second, the supposed intrinsic specificity of hormonal signals is negated; in the third, the notion that cancer is a cellular problem caused by mutated genes is challenged by data gathered both from the reductionist viewpoint and the alternative view proposing that carcinogenesis is development gone awry. As an alternative to reductionism, we propose that the organicist view is a good starting point from which to explore these phenomena. However, new theoretical concepts are needed to grapple with the apparent circular causality of complex biological phenomena. (shrink)

Several influential psychologists have attempted to estimate to what extent human happiness levels are directly controlled by genes by comparing the happiness levels of identical twins raised apart. If we discover that the happiness levels of identical twins raised apart tend to be closer than the happiness levels of fraternal twins raised apart, this is taken as evidence that average happiness levels are largely controlled by genes. However, if it turns out that identical twins' happiness levels tend to be substantially (...) different, as different as fraternal twins raised apart, it has been argued that this implies that the environment largely determines happiness levels. I contend that this interpretation of the data rests on a set of questionable, closely related assumptions: a) that pairs of identical twins raised apart are raised in substantially different environments; b) that genetically identical twins aren't identical in other pertinent ways; and c) that average levels of affect that are correlated with certain sets of genes in the environments the twin studies were conducted in will be correlated with those genes in other relevant environments because those genes govern average affect levels. In this paper, I will show that these assumptions are false and explain how to properly go about investigating the contingent causal links between genes and happiness. In the end, I argue that there is no good evidence that our genes delimit our hedonic potential and that the fact that this misinterpretation of the data has been widely disseminated is potentially harmful to human well-being. (shrink)

There is ongoing controversy as to whether the genome is a representing system. Although it is widely recognised that DNA carries information, both correlating with and coding for various outcomes, neither of these implies that the genome has semantic properties like correctness or satisfaction conditions, In the Scope of Logic, Methodology, and the Philosophy of Sciences, Vol. II. Kluwer, Dordrecht, pp. 387–400). Here a modified version of teleosemantics is applied to the genome to show that it does indeed have semantic (...) properties – there is representation in the genome. The account differs in three respects from previous attempts to apply teleosemantics to genes. It emphasises the role of the consumer of representations. It rejects the standard assumption that genetic representation can be used to explain the course of an organism’s development. And it identifies the explanatory role played by representational properties of the genome. A striking consequence of this account is that other inheritance systems could also be representational. Thus, a version of the parity thesis is accepted. However, the criteria for being an inheritance system are demanding, so semantic properties are not ubiquitous. (shrink)

The concept of innateness is used to make inferences between various better-understood properties, like developmental canalization, evolutionary adaptation, heritability, species-typicality, and so on (‘innateness-related properties’). This article uses a recently-developed account of the representational content carried by inheritance systems like the genome to explain why innateness-related properties cluster together, especially in non-human organisms. Although inferences between innateness-related properties are deductively invalid, and lead to false conclusions in many actual cases, where some aspect of a phenotypic trait develops in reliance on (...) a genetic representation it will tend, better than chance, to have many of the innateness-related properties. The account also shows why inferences between innateness-related properties sometimes fail and argues that such inferences are especially misleading when applied to human psychology and behaviour because human psychological development is especially reliant on non-genetic inherited representations. (shrink)

I show that gene regulation networks are qualitatively consistent and therefore sufficiently similar to linearly seperable connectionist networks to warrant that the connectionist framework be applied to gene regulation. On this view, natural selection designs gene regulation networks to overcome the difficulty of development. I offer some general lessons about their evolvability that can be learned by examining the generic features of connectionist networks.

Resumo: A partir de uma análise sobre a utilização das biotecnologias médicas, este artigo pretende compreender como a disseminação de uma lógica e um discurso "informacional", na área de saúde, mascaram as intervenções médicas efetuadas no corpo humano. Argumenta-se que frequentemente as práticas biotecnológicas são tratadas como meras relações linguísticas, como se não fossem operações de carne e sangue realizadas nos corpos. Para abordar a forma como essa lógica se processa, será feita, neste texto, uma breve discussão sobre como as (...) disputas em torno do que são, e como operam os genes, acabam por reforçar um paradigma informacional, ainda que tal resolução não seja amparada pelas evidências empíricas, mas em metáforas bem-sucedidas.: Starting with an analysis of the use of medical biotechnology, this article aims to understand how medical interventions in the human body are masked by a certain logic and by an "informational" discourse on health care. We argue that biotechnological practices are often treated as linguistic relations, as if they were not flesh and blood operations on bodies. To address how this logic is processed, we discuss how disputes over the nature and functioning of genes end up strengthening an informational paradigm that is not based on empirical evidence, but rather on successful metaphors. (shrink)

The question of specific properties of life compared to nonliving things accompanied biology throughout its history. At times this question generated major controversies with largely diverging opinions. Basically, mechanistic thinkers, who tried to understand organismic functions in terms of nonliving machines, were opposed by those who tried to describe specific properties or even special forces being active within living entities. As this question included the human body, these controversies always have been of special relevance to our self-image and also touched (...) practical issues of medicine. During the second half of the twentieth century, it seemed to be resolved that organisms are explainable basically as physicochemical machines. Especially from the perspective of molecular biology, it seemed to be clear that organisms need to be explained solely by the chemical functions of their component parts, although some resistance to this view never ceased. This research program has been working quite successfully, so that science today knows a lot about the physiological and chemical processes within organisms. However, again new doubts arise questioning whether the mere continuation of this analytical approach will finally generate a fundamental understanding of living entities. At the beginning of the twenty-first century the quest for a new synthesis actually comes from analytical empiricists themselves. The hypothesis of the present paper is that empirical research has been developed far enough today, that it reveals by itself the materials and the prerequisites to understand more of the specific properties of life. Without recourse to mysterious forces, it is possible to generate answers to this age-old question, just using recent, empirically generated knowledge. This view does not contradict the results of reductionistic research, but rather grants them meaning within the context of organismic systems and also may increase their practical usefulness. Although several of these properties have been discussed before, different authors usually concentrated on a single one or some of them. The paper describes ten specific properties of living entities as they can be deduced from contemporary science. The aim is to demonstrate that the results of empirical research show both the necessity as well as the possibility of the development of a new conception of life to build a coherent understanding of organismic functions. (shrink)

According to a recent suggestion, the names of gene taxa should be conceived of as referring to individuals with concrete genes as their parts, just as the names of biological species are often understood as denoting individuals with organisms as their parts. Although prima facie this suggestion might advance the debate on gene concepts in a similar way as the species-are-individuals thesis advanced the debate on species concepts, I argue that the principal arguments in support of the gene-individuality thesis are (...) much less compelling than the parallel arguments in the species case. In addition, I argue that the notion of biological function invoked in the gene-individuality thesis (selected effect) is not the one that biologists actually use when individuating genes. Contra the gene-individuality thesis, I argue that gene names refer to kinds, defined primarily (though not exclusively) by causal-role functions. (shrink)

Social Epistemology arose from the recognition that nearly all that we believe or claim to know is second hand and derived from the speech or writing of others. The “we” of “our knowledge” here is, of course, “educated members of advanced industrial societies”. Our remoter, but still identifiably, human ancestors, without speech or writing, picked up such knowledge or belief as they had on their own, apart from what they may have leant from the reactions of others to the presence (...) of quarry or danger. Palaeolithic man, having mastered speech, had access to plenty of second hand knowledge. But it was only of what the people he directly met could tell him. With writing a vast new range of informants is brought into play. Clay tablets and papyrus rolls give way to codices – in other words, books – and another gigantic step forward is made with the invention of printing. We would appear to be going through a comparable information revolution at the present day. We, as defined above, either posses or have ready access to a vast assemblage of common knowledge, actual or claimed. How are we to rationally to decide how much of this we are to accept? It is obviously not all worthy, or equally worthy of acceptance. (shrink)

Griffiths and Stotz’s Genetics and Philosophy: An Introduction offers a very good overview of scientific and philosophical issues raised by present-day genetics. Examining, in particular, the questions of how a “gene” should be defined and what a gene does from a causal point of view, the authors explore the different domains of the life sciences in which genetics has come to play a decisive role, from Mendelian genetics to molecular genetics, behavioural genetics, and evolution. In this review, I highlight what (...) I consider as the two main theses of the book, namely: genes are better conceived as tools; genes become causes only in a context. I situate these two theses in the wider perspective of developmental systems theory. This leads me to emphasize that Griffiths and Stotz reflect very well an on going process in genetics, which I call the “epigenetization” of genetics, i.e., the growing interest in the complex processes by which gene activation is regulated. I then make a factual objection, which is that Griffiths and Stotz have almost entirely neglected the perspective of ecological developmental biology, and more precisely recent work on developmental symbioses, and I suggest that this omission is unfortunate in so far as an examination of developmental symbioses would have considerably strengthened Griffiths and Stotz’s own conclusions. (shrink)

A number of debates in philosophy of biology and psychology, as well as in their respective sciences, hinge on particular views about the relationship between genotypes and phenotypes. One such view is that the genotype-phenotype relationship is relatively straightforward, in the sense that a genome contains the ?genes for? the various traits that an organism exhibits. This leads to the assumption that if a particular set of traits is posited to be present in an organism, there must be a corresponding (...) number of genes in that organism's genome to account for those traits. This assumption underlies what can be called the ?counting argument,? in which empirical estimates of the number of genes in a genome are used to support or refute particular hypotheses in philosophical debates about biology and psychology. In this paper, we assess the counting argument as it is used in discussions of the alleged massive modularity of the brain, and conclude that this argument cannot be upheld in light of recent philosophical work on gene concepts and empirical work on genome complexity. In doing so, we illustrate that there are those on both sides of the debate about massive modularity who rely on an incorrect view of gene concepts and the nature of the genotype-phenotype relationship. (shrink)

Although much has been learned about hereditary mechanisms since Gregor Mendel’s famous experiments, gene concepts have always remained vague, notwithstanding their central role in biology. During over hundred years of genetic research, gene concepts have often and dynamically changed to accommodate novel experimental findings, without ever providing a generally accepted definition of the ‘gene.’ Yet, the distinction between ‘regulatory genes’ and ‘structural genes’ has remained a common theme in modern gene concepts since the definition of the operon-model. This distinction is (...) now challenged by recent findings which suggest that, at least in eukaryotes, structural genes may in many situations have a regulatory function that is independent of the function of the gene product (protein or non-coding RNA molecule). This brief paper discusses these new findings and some possible implications for the notion of the ‘regulatory gene.’. (shrink)

Comparative genomicists seem to be convinced that the unit of measurement employed in their studies is a gene that drives the function of cells and ultimately organisms. As a result, they have come to some substantive conclusions about how similar humans are to other organisms based on the percentage of genetic makeup they share. I argue that the actual unit of measurement employed in the studies corresponds to a structural rather than a functional gene concept, thus rendering many of the (...) implications drawn from comparative genomic studies largely unwarranted, if not completely mistaken. †To contact the author, please write to: Department of Philosophy, University of Utah, 215 South Central Campus Drive, Carolyn Tanner Irish Humanities Building, 4th Floor, Salt Lake City, UT 84112; e‐mail: [email protected]. (shrink)

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

For a number of years, the debate in evolutionary biology over the ’levels of selection’ has attracted intense interest from philosophers of science. The main question concerns the level of the biological hierarchy at which natural selection occurs. Does selection act on organisms, genes, groups, colonies, demes, species, or some combination of these? According to traditional Darwinian theory the answer is the organism -- it is the differential survival and reproduction of individual organisms that drives the evolutionary process. But there (...) are alternative views too, including pluralist views which say that the choice between different levels of selection is often a matter of perspective, not empirical fact. (shrink)

Although it may seem like a truism to assert that biology is the science that studies organisms, during the second half of the twentieth century the organism category disappeared from biological theory. Over the past decade, however, biology has begun to witness the return of the organism as a fundamental explanatory concept. There are three major causes: (a) the realization that the Modern Synthesis does not provide a fully satisfactory understanding of evolution; (b) the growing awareness of the limits of (...) reductionism in molecular biology; and (c) the renewed interest in the nature of life as a genuine scientific problem. This essay examines these recent developments and considers the new epistemological roles being played by the organism in each of them. It also reflects on what the present resurgence of the organism means for the philosophy of biology. (shrink)

Biological atomism postulates that all life is composed of elementary and indivisible vital units. The activity of a living organism is thus conceived as the result of the activities and interactions of its elementary constituents, each of which individually already exhibits all the attributes proper to life. This paper surveys some of the key episodes in the history of biological atomism, and situates cell theory within this tradition. The atomistic foundations of cell theory are subsequently dissected and discussed, together with (...) the theory’s conceptual development and eventual consolidation. This paper then examines the major criticisms that have been waged against cell theory, and argues that these too can be interpreted through the prism of biological atomism as attempts to relocate the true biological atom away from the cell to a level of organization above or below it. Overall, biological atomism provides a useful perspective through which to examine the history and philosophy of cell theory, and it also opens up a new way of thinking about the epistemic decomposition of living organisms that significantly departs from the physicochemical reductionism of mechanistic biology. (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)

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)

In this paper I use a case study—the discovery of the chaperon function exerted by proteins in the various steps of the hereditary process—to re-discuss the question whether the nucleic acids are the sole repositories of relevant information as assumed in the information theory of heredity. The evidence I here present of a crucial role for molecular chaperones in the folding of nascent proteins, as well as in DNA duplication, RNA folding and gene control, suggests that the family of proteins (...) acting as molecular chaperones provides information that is complementary to that stored in the nucleic acids, and equally important. A re-evaluation of the role of proteins in the hereditary process is in order away from the gene-centric approach of the information theory of heredity, to which neo-Darwinian evolutionists adhere. (shrink)

It is frequently said that biology is emerging from a long phase of reductionism. It would be certainly more correct to say that biologists are abandoning a certain form of reductionism. We describe this past form, and the experiments which challenged the previous vision. To face the difficulties which were met, biologists use a series of concepts and metaphors - pleiotropy, tinkering, epigenetics - the ambiguity of which masks the difficulties, instead of solving them. In a similar way, the word (...) “post-genomics” has different meanings, depending upon who uses it. Which of these meanings will become dominant in the future is an open question. (shrink)

Although biologists and philosophers of science generally agree that genes cannot determine the forms of biological and psychological traits, students, journalists, politicians, and other members of the general public nonetheless continue to embrace genetic determinism. This article identifies some of the concerns typically raised by individuals when they first encounter the systems perspective that biologists and philosophers of science now favor over genetic determinism, and uses arguments informed by that perspective to address those concerns. No definitive statements can yet be (...) made about why genetic determinism has proven so resilient in the face of empirical evidence pointing up its deficiencies, but conveying the essential interdependence of 'nature' and 'nurture' to the general public will likely require deployment of the arguments that systems theorists ordinarily use to reject genetic determinism. In addition, the elaboration of new metaphors that focus attention on the dynamic nature of trait construction will likely prove valuable, because re-conceptualizing notions like 'genes' and 'nature' will probably be one of the most effective ways to help students and the general public abandon the genetic determinism that biologists now recognize as indefensible. (shrink)