Philosophy of Biology: Naturalistic or Transcendental?

The aim of this article is to clarify the meaning of a naturalistic position within philosophy of biology, against the background of an alternative view, founded on the basic insights of transcendental philosophy. It is argued that the apparently minimal and neutral constraints naturalism imposes on philosophy of science turn out to involve a quite heavily constraining metaphysics, due to the naturalism's fundamental neglect of its own perspective. Because of its intrinsic sensitivity to perspectivity and historicity, transcendental philosophy can avoid this type of hidden metaphysics.     

Theses on Darwin.

The received view that teleology has been successfully eliminated from the modern scientific worldview is challenged. It is argued that both the theory of natural selection and molecular biology presuppose the existence of natural teleology, and so cannot explain it. A number of other issues in the foundations of biology are briefly examined, while stress is laid throughout on empirical evidence of the rational agency inherent in life. It is urged that teleology be rehabilitated and that the reigning functionalist philosophy be replaced by a realistic view of biological functions as emergent properties of living matter within a broad, selforganization framework.     

An interdisciplinary approach to certain fundamental issues in the fields of physics and biology: towards a unified theory

Recent experiments appear to have revealed the possibility of the existence of quantum entanglement between spatially separated human subjects. In addition, a similar condition might exist between basins containing human neurons adhering to printed circuit boards. In both instances, preliminary data indicates what appear to be non-local correlations between brain electrical activities in the case of the human subjects and also non-local correlations between neuronal basin electrical activities, implying entanglement at the macroscopic level. If the ongoing expanded research and the analysis of same continues to support this hypothesis, it may then make it possible to simultaneously address some of the fundamental problems facing us in both physics and biology through the adoption of an interdisciplinary empirical approach based on Bell's experimental philosophy, with the goal of unifying these two fields.     

Biodiversity, biotechnologies and the philosophy of biology.

The thesis of this paper is that in front of the development of biotechnology and of the capacity of techniques of altering the living, there is still a very old philosophy of biology. A rapid historical view is given where the rise and diffusion of the reductionistic paradigm is presented and the connections between this paradigm and biotechnologies are traced. Curiously biotechnologies are still based on the philosophy of F. Bacon. Then the necessity of a new paradigm in biology based on the recent discoveries of complexity is underlined. It is reminded that the main discovery of science of the XX century is that we are living in a small planet of limited resources and frail equilibriums. This discovery asks for a different view of the scientific progress, more linked to the conservation of the Biosphere than to its alteration. Stability is the task for the future interactions of human-kind with nature. For this reason the relationships between stability and diversity are summarised. Finally, as the species is the main step of Biodiversity, a brief discussion of the problems posed by the altering of species barriers is presented.     

Biohumanities: rethinking the relationship between biosciences, philosophy and history of science, and society

We argue that philosophical and historical research can constitute a "Biohumanities" that deepens our understanding of biology itself engages in constructive "science criticism," helps formulate new "visions of biology," and facilitates "critical science communication." We illustrate these ideas with two recent "experimental philosophy" studies of the concept of the gene and of the concept of innateness conducted by ourselves and collaborators. We conclude that the complex and often troubled relations between science and society are critical to both parties, and argue that the philosophy and history of science can help to make this relationship work.     

Making developmental biology relevant to undergraduates in an era of economic rationalism in Australia

This report describes the road map we followed at our university to accommodate three main factors: financial pressure within the university system; desire to enhance the learning experience of undergraduates; and motivation to increase the prominence of the discipline of developmental biology in our university. We engineered a novel, multi-year undergraduate developmental biology program which was "student-oriented," ensuring that students were continually exposed to the underlying principles and philosophy of this discipline throughout their undergraduate career. Among its key features are introductory lectures in core courses in the first year, which emphasize the relevance of developmental biology to tissue engineering, reproductive medicine, therapeutic approaches in medicine, agriculture and aquaculture. State-of-the-art animated computer graphics and images of high visual impact are also used. In addition, students are streamed into the developmental biology track in the second year, using courses like human embryology and courses shared with cell biology, which include practicals based on modern experimental approaches. Finally, fully dedicated third-year courses in developmental biology are undertaken in conjunction with stand-alone practical courses where students experiencefirst-hand work in a research laboratory. Our philosophy is a "cradle-to-grave" approach to the education of undergraduates so as to prepare highly motivated, enthusiastic and well-educated developmental biologists for entry into graduate programs and ultimately post-doctoral research.     

An expanded role for microbial physiology in metabolic engineering and functional genomics: moving towards systems biology

Microbial physiology has traditionally played a very important role in both fundamental research and in industrial applications of microorganisms. The classical approach in microbial physiology has been to analyze the role of individual components (genes or proteins) in the overall cell function. With the progress in molecular biology it has become possible to optimize industrial fermentations through introduction of directed genetic modification - an approach referred to as metabolic engineering. Furthermore, as a consequence of large sequencing programs the complete genomic sequence has become available for an increasing number of microorganisms. This has resulted in substantial research efforts in assigning function to all identified open reading frames - referred to as functional genomics. In both metabolic engineering and functional genomics there is a trend towards application of a macroscopic view on cell function, and this leads to an expanded role of the classical approach applied in microbial physiology. With the increased understanding of the molecular mechanisms it is envisaged that in the future it will be possible to describe the interaction between all the components in the system (the cell), also at the quantitative level, and this is the goal of systems biology. Clearly this will have a significant impact on microbial physiology as well as on metabolic engineering.     

Interdisciplinary integration in biology? An overview

Philosophical theories about reduction and integration in science are at variance with what is happenign in science. A realistic approach to science show that possibilities for reduction and integration are limited. The classical ideal of a unified science has since long been rejected in philosophy. But the current emphasis on interdisciplinary integration in philosophy and in science shows that it survives in a different guise. It is necessary to redress the balance, specifically in biology. Methodological analysis shows that many of the grand interdisciplinary theories involving biology actually represent pseudo-integration covered up by inappropriate, overgeneral concepts. Integrationism is not bad, but it must be kept within reasonable bounds. If the present analysis is appropriate, there will have to be fundamental changes in research strategy both in science and in the philosophy of science.     

The roles of integration in molecular systems biology

A common way to think about scientific practice involves classifying it as hypothesis- or data-driven. We argue that although such distinctions might illuminate scientific practice very generally, they are not sufficient to understand the day-to-day dynamics of scientific activity and the development of programmes of research. One aspect of everyday scientific practice that is beginning to gain more attention is integration. This paper outlines what is meant by this term and how it has been discussed from scientific and philosophical points of view. We focus on methodological, data and explanatory integration, and show how they are connected. Then, using some examples from molecular systems biology, we will show how integration works in a range of inquiries to generate surprising insights and even new fields of research. From these examples we try to gain a broader perspective on integration in relation to the contexts of inquiry in which it is implemented. In today's environment of data-intensive large-scale science, integration has become both a practical and normative requirement with corresponding implications for meta-methodological accounts of scientific practice. We conclude with a discussion of why an understanding of integration and its dynamics is useful for philosophy of science and scientific practice in general.     

Again,What the Philosophy of Biology is not

There are many things that philosophy of biology might be. But, given the existence of a professional philosophy of biology that is arguably a progressive research program and, as such, unrivaled, it makes sense to define philosophy of biology more narrowly than the totality of intersecting concerns biologists and philosophers (let alone other scholars) might have. The reasons for the success of the “new” philosophy of biology remain poorly understood. I reflect on what Dutch and Flemish, and, more generally, European philosophers of biology could do to improve the situation of their discipline locally, regionally, and internationally, paying particular attention to the lessons to be learned from the “Science Wars.” This paper grew out of my contribution to the symposium Philosophy of Biology in the Netherlands and Flanders organized by Thomas Reydon and Sabina Leonelli in Amsterdam in February 2004. It is a rather personal reaction to many of the opinions voiced in the quite heated atmosphere of the Symposium. My main concern is to convey an idea of what, according to me, is required to turn “our” philosophy of biology into a more successful enterprise than it currently is. This is motivated by a disconcerting discovery I made at the Symposium: Contrary to my expectations, a sensitivity for the sorts of things that make possible philosophy of biology of the best kind available today seems to be largely lacking in our part of the world. I wish to stress from the outset that although I will be quite polemical at times, this is always intended in the spirit of constructive dialogue.     

What history tells us

The history of science was long considered to be something peripheral to science itself. By supplying interesting stories and gossip, it seemed, at best, to provide material for enlivening lectures. In general, it was deemed a suitable activity for retired scientists. This view has been revised considerably in the past years and indeed, today seems hopelessly out of date. History and philosophy of science are increasingly held to be an essential component of the education of scientists. By becoming acquainted with these areas, practicing scientists — and in particular biologists — can better appreciate the significance of the models and theories that underpin their research, especially with the accelerating succession of one idea by the next. The present series, of which the article that follows is the first, aims to give historical glimpses that bear on contemporary biology. The hope is that these glimpses will be both a source of inspiration and of help in resisting useless fashions.     

Mass spectrometric approaches for characterizing bacterial proteomes

The emergence of advanced liquid chromatography mass spectrometry technologies for characterizing very complex mixtures of proteins has greatly propelled the field of proteomics, the goal of which is the simultaneous examination of all the proteins expressed by an organism. This research area represents a paradigm shift in molecular biology by attempting to provide a top-down qualitative and quantitative view of all the proteins (including their modifications and interactions) that are essential for an organism's life cycle, rather than targeting a particular protein family. This level of global protein information about an organism such as a bacterium can be combined with genomic and metabolomic data to enable a systems biology approach for understanding how these organisms live and function.     

《分子生物学》研究性教学初探

当前高等学校教学改革的一个重要特点在于倡导进行研究性教学,研究性教学成为现代教学理念的构成要素,它是对传统的传递式——被动接受式的教育理念的革新。这种教学模式有利于培养学生研究能力,提升教学的有效性。从理论教学、问题情境教学、实验教学、科研成果的引入等4个方面阐述在《分子生物学》教学中如何运用研究性教学模式,贯穿研究性教学理念,有效培养学生的研究能力。     

Mass spectrometric approaches for characterizing bacterial proteomes

The emergence of advanced liquid chromatography mass spectrometry technologies for characterizing very complex mixtures of proteins has greatly propelled the field of proteomics, the goal of which is the simultaneous examination of all the proteins expressed by an organism. This research area represents a paradigm shift in molecular biology by attempting to provide a top-down qualitative and quantitative view of all the proteins (including their modifications and interactions) that are essential for an organism’s life cycle, rather than targeting a particular protein family. This level of global protein information about an organism such as a bacterium can be combined with genomic and metabolomic data to enable a systems biology approach for understanding how these organisms live and function.     

The philosophy of modelling or does the philosophy of biology have any use?

Biologists in search of answers to real-world issues such as the ecological consequences of global warming, the design of species'' conservation plans, understanding landscape dynamics and understanding gene expression make decisions constantly that are based on a ‘philosophical’ stance as to how to create and test explanations of an observed phenomenon. For better or for worse, some kind of philosophy is an integral part of the doing of biology. Given this, it is more important than ever to undertake a practical assessment of what philosophy does mean and should mean to biologists. Here, I address three questions: should biologists pay any attention to ‘philosophy’; should biologists pay any attention to ‘philosophy of biology’; and should biologists pay any attention to the philosophy of biology literature on modelling? I describe why the last question is easily answered affirmatively, with the proviso that the practical benefits to be gained by biologists from this literature will be directly proportional to the extent to which biologists understand ‘philosophy’ to be a part of biology, not apart from biology.     

Understanding of basic mechanisms of β-cell function and survival

Type 1 and type 2 diabetes are both diseases of insulin insufficiency, although they develop by distinct pathways. The recent surge in the incidence of type 2 diabetes and the chronic ailments confronted by patients with either form of the disease highlight the need for better understanding of β-cell biology. In this review, we present recent work focused on this goal. Our hope is that basic research being conducted in this and other laboratories will ultimately contribute to the development of methods for enhancing β-cell function and survival in the context of both major forms of diabetes. Our strategy for understanding the β-cell involves a multidisciplinary approach in which tools from the traditional fields of biochemistry, enzymology, and physiology are teamed with newer technologies from the fields of molecular biology, gene discovery, cell and developmental biology, and biophysical chemistry. We have focused on two important aspects of β-cell biology in our studies: β-cell function, specifically the metabolic regulatory mechanisms involved in glucose-stimulated insulin secretion, and β-cell resistance to immune attack, with emphasis on resistance to inflammatory cytokines and reactive oxygen species.     

Epigenetic determinism in science and society

The epigenetic “revolution” in science cuts across many disciplines, and it is now one of the fastest-growing research areas in biology. Increasingly, claims are made that epigenetics research represents a move away from the genetic determinism that has been prominent both in biological research and in understandings of the impact of biology on society. We discuss to what extent an epigenetic framework actually supports these claims. We show that, in contrast to the received view, epigenetics research is often couched in language as deterministic as genetics research in both science and the popular press. We engage the rapidly emerging conversation about the impact of epigenetics on public discourse and scientific practice, and we contend that the notion of epigenetic determinism – or the belief that epigenetic mechanisms determine the expression of human traits and behaviors – matters for understandings of the influence of biology and society on population health.     

The Philosophy of Donald T. Campbell: A Short Review and Critical Appraisal

Aside from his remarkable studies in psychology and the social sciences, Donald Thomas Campbell (1916–1996) made significant contributions to philosophy, particularly philosophy of science,epistemology, and ethics. His name and his work are inseparably linked with the evolutionary approach to explaining human knowledge (evolutionary epistemology). He was an indefatigable supporter of the naturalistic turn in philosophy and has strongly influenced the discussion of moral issues (evolutionary ethics). The aim of this paper is to briefly characterize Campbells work and to discuss its philosophical implications. In particular, I show its relevance to some current debates in the intersection of biology and philosophy. In fact, philosophy of biology would look poorer without Campbells influence. The present paper is not a hagiography but an attempt to evaluate and critically discuss the meaning of Campbells work for philosophy of biology and to encourage scholars working in this field to read and re-read this work which is both challenging and inspiring.     

What philosophy of biology should be

This paper reviews Rosenberg’s and McShea’s textbook in philosophy of biology, entitled Philosophy of Biology. A Contemporary Introduction. I insist on the excellent quality of this textbook, then I turn to more critical comments, which deal mainly with what philosophy of biology is, and what it should be.