The human genome project: a reply to Rosenberg

In this paper we discuss the scientific value of the human genome project. To what extent is the data obtained by sequencing the entire human genome useful in the gene dicovery process? Responding to Alex Rosenberg' skepticism about the value of such data, we maintain that brute sequence data is much more useful than he suggests.     

How to be an anti-reductionist about developmental biology: Response to Laubichler and Wagner

Alexander Rosenberg recently claimed (1997) that developmental biology is currently being reduced to molecular biology. cite several concrete biological examples that are intended to impugn Rosenberg's claim. I first argue that although Laubichler and Wagner's examples would refute a very strong reductionism, a more moderate reductionism would escape their attacks. Next, taking my cue from the antireductionist's perennial stress on the importance of spatial organization, I describe one form an empirical finding that refutes this moderate reductionism would take. Finally, I point out an actual example, anterior-posterior axis determination in the chick, that challenges the reductionist's belief that all developmental regularities can be explained by molecular biology. In short, I argue that Rosenberg's position can be saved from Laubichler and Wagner's criticisms and putative counter-examples, but it would not survive a different kind of counter-example.     

Overcoming the Newtonian paradigm: The unfinished project of theoretical biology from a Schellingian perspective

Defending Robert Rosen's claim that in every confrontation between physics and biology it is physics that has always had to give ground, it is shown that many of the most important advances in mathematics and physics over the last two centuries have followed from Schelling's demand for a new physics that could make the emergence of life intelligible. Consequently, while reductionism prevails in biology, many biophysicists are resolutely anti-reductionist. This history is used to identify and defend a fragmented but progressive tradition of anti-reductionist biomathematics. It is shown that the mathematico–physico–chemical morphology research program, the biosemiotics movement, and the relational biology of Rosen, although they have developed independently of each other, are built on and advance this anti-reductionist tradition of thought. It is suggested that understanding this history and its relationship to the broader history of post-Newtonian science could provide guidance for and justify both the integration of these strands and radically new work in post-reductionist biomathematics.     

Nutritional biology: a neglected basic discipline of nutritional science

On the basis of a scientific-philosophical analysis, this paper tries to show that the approaches in current nutritional science—including its subdisciplines which focus on molecular aspects—are predominantly application-oriented. This becomes particularly evident through a number of conceptual problems characterized by the triad of ‘dearth of theoretical foundation,’ ‘particularist research questions,’ and ‘reductionist understanding of nutrition.’ The thesis presented here is that an interpretive framework based on nutritional biology is able to shed constructive light on the fundamental problems of nutritional science. In this context, the establishment of ‘nutritional biology’ as a basic discipline in research and education would be a first step toward recognizing the phenomenon of ‘nutrition’ as an oecic process as a special case of an organism–environment interaction. Modern nutritional science should be substantively grounded on ecological—and therefore systems biology as well as organismic—principles. The aim of nutritional biology, then, should be to develop near-universal ‘law statements’ in nutritional science—a task which presents a major challenge for the current science system.     

Studying populations without molecular biology: Aster Models and a new argument against reductionism

During the past few decades, philosophers of biology have debated the issue of reductionism versus anti-reductionism, with both sides often claiming a 'pluralist' position. However, both sides also tend to focus on a single research paradigm, which analyzes living things in terms of certain macromolecular components. I offer a case study where biologists pursue other analytic pathways, in a tradition of quantitative genetics that originates with the initially purely mathematical theories of R. A. Fisher, J. B. S. Haldane, and Sewall Wright in the 1930s. Aster Models (developed by Ruth Shaw and Charles Geyer) offers a class of statistical models designed for studying the fitness of plant and animal populations, by integrating the measurements of separate, sequential, non-normally distributed fitness components in novel ways. Their work generates important theoretical and practical results that do not require elaboration by molecular biology, and thus serves as a counterexample to the claims of philosophers whose 'pluralism' still harbors reductionist assumptions.     

Values at stake: autonomy, responsibility, and trustworthiness in relation to genetic testing and personalized nutrition advice

Personalized nutrition has the potential to enhance individual health control. It could be seen as a means to strengthen people’s autonomy as they learn more about their personal health risks, and receive dietary advice accordingly. We examine in what sense personalized nutrition strengthens or weakens individual autonomy. The impact of personalized nutrition on autonomy is analyzed in relation to responsibility and trustworthiness. On a societal level, individualization of health promotion may be accompanied by the attribution of extended individual responsibility for one’s health. This constitutes a dilemma of individualization, caused by a conflict between the right to individual freedom and societal interests. The extent to which personalized nutrition strengthens autonomy is consequently influenced by how responsibility for health is allocated to individuals. Ethically adequate allocation of responsibility should focus on prospective responsibility and be differentiated with regard to individual differences concerning the capacity of adults to take responsibility. The impact of personalized nutrition on autonomy also depends on its methodological design. Owing to the complexity of information received, personalized nutrition through genetic testing (PNTGT) is open to misinterpretation and may not facilitate informed choices and autonomy. As new technologies, personalized nutrition and PNTGT are subject to issues of trust. To strengthen autonomy, trust should be approached in terms of trustworthiness. Trustworthiness implies that an organization that develops or introduces personalized nutrition can show that it is competent to deal with both the technical and moral dimensions at stake and that its decisions are motivated by the interests and expectations of the truster.     

The autonomy of biological individuals and artificial models

This paper aims to offer an overview of the meaning of autonomy for biological individuals and artificial models rooted in a specific perspective that pays attention to the historical and structural aspects of its origins and evolution. Taking autopoiesis and the recursivity characteristic of its circular logic as a starting point, we depart from some of its consequences to claim that the theory of autonomy should also take into account historical and structural features. Autonomy should not be considered only in internal or constitutive terms, the largely neglected interactive aspects stemming from it should be equally addressed. Artificial models contribute to get a better understanding of the role of autonomy for life and the varieties of its organization and phenomenological diversity.     

Simulating autonomous anticipation: the importance of Dubois' conjecture

Anticipation allows a system to adapt to conditions that have not yet come to be, either externally to the system or internally. Autonomous systems actively control their own conditions so as to increase their functionality (they self-regulate). Living systems self-regulate in order to increase their own viability. These increasingly stronger conditions, anticipation, autonomy and viability, can give an insight into progressively stronger classes of models of autonomy. I will argue that stronger forms are the relevant ones for Artificial Life. This has consequences for the design of and accurate simulation of living systems.     

The Taung endocast: a reply to Holloway

Indices of rostrality (ir, ir') are developed to assess the extent to which the medial end of the lunate sulcus (L) is rostrally positioned in photographs and figures of lateral views of primate brains and endocasts, and indices are determined for chimpanzees, SK 1585 and the Taung endocast. Ir quantifies the extent of rostrality as it has traditionally been viewed (in A-P projections) while ir' takes dorsal curvature into account. The ir of the feature that I have identified as the lunate sulcus of Taung is within one standard deviation of the mean ir for Pan and its ir' is within 1.5 standard deviations from the mean ir' for Pan. Both findings are compatible with my earlier statement that the medial end of the lunate sulcus of the Taung endocast is in a pongid-like position. Use of stereoplotting to transfer the position of L from chimpanzee endocasts and brains to australopithecine endocasts is critically assessed: Holloway stereoplotted five chimpanzee brains and then transferred their mean coordinates that describe the lunate sulcus to the Taung endocast. If stereoplotting successfully transfers the extent to which L is rostrally located, one would expect the mean L of Pan and its transferred counterpart in Taung to have identical index values of rostrality. However, the ir of the lunate sulcus that Holloway located on Taung is over two standard deviations lower than the mean ir for the five chimpanzees he stereoplotted to determine its angular coordinates, and Holloway's ir' for Taung is one standard deviation lower than the five chimpanzees' mean ir'. These discrepancies are shown to be due to shape differences, and it is concluded that stereoplotting should not be used to transfer sulci between differently shaped endocasts without correcting for these differences. I also reply to Holloway's criticisms of my use of L/H indices, palpation, techniques for sampling endocasts, and illustration of the Taung endocast. It is shown that there is room on the Taung specimen for the lateral end of L, and the pongid-like sulcal pattern of Taung is reaffirmed. Thus, we do not yet know when human-like sulcal patterns first appeared in the hominid fossil record.     

The friendship model: a reply to Illingworth

Patricia M.L. Illingworth, in an article in the January 1988 issue of Bioethics, maintained that a friendship model of the physician patient relationship violates the autonomy of patients who do not want to be friends with their physicians and diminishes the autonomy of patients who seek such friendship based on "psychological oppression" stemming from internalization of feelings of inferiority. James contends in this reply that much of Illingworth's critique of the model was beside the point. He argues that trust between doctor and patient is a moral good in the therapeutic relationship and that this trust has enough similarities to trust between friends to make a model which develops these similarities well worth exploring.     

Distinguishing between convergence and parallelism is central to comparative biology: a reply to Williams and Ebach

The definitions of character similarity, homology, homoplasy, heterology, parallelism and convergence are clarified in the framework of current phylogenetic methodology. They are all associated with definite patterns of character change and can consequently be tested by phylogeny building. Their crucial significance in comparative biology is illustrated using demonstrative examples. © The Willi Hennig Society 2006.     

鞘糖脂的新陈代谢与生理学功能（英文）

鞘糖脂由一个神经酰胺的脂骨架与一个或多个糖基连接形成,存在于细胞膜中,承担多种生理学功能。我们将对鞘糖脂的生物化学及生理学方面研究做一概述,随后简要介绍近年来鞘糖脂的临床研究进展。在讨论鞘糖脂生物化学方面的研究中,我们把重点放在介绍鞘脂类及鞘糖脂的结构和生合成途径。脂类生物合成和降解是通过一系列酶的参与紧密调控的,如果一种酶参与代谢失败会导致酶底物的大量堆积,会引起溶酶体贮积症,这种疾病是由具有分解代谢活性的水解酶缺失所造成的。随后,我们介绍鞘糖脂在细胞及动物体内的生理学方面的功能,以及鞘糖脂在临床方面的一些病症中所起的作用,即使许多细节还有待于进一步研究。     

The theory of organism and the culturalist foundation of biology

Summary After the disappearance of organism was diagnosed, the discussion about the role of a theory of organism in biology is characterised by a significant contradiction. On the one hand, the importance of a theory of organism is stated. Particularly developmental biology demands organism-centred approaches as a basis for conceptual integration. On the other hand, several modern biological disciplines such as genetics and molecular biology simply don’t need a theory of organism for their work. Consequently, the determination of the status of the organism and its relevance for biology at all is an unsolved problem. In order to clarify the methodological status of the organism in biology we start with the reconstruction of three important propositions. A life oriented approach and a hierarchy concept - which both are from a neo-Darwinian origin - are confronted with a structuralist approach of organism, that can be characterised as a non-Darwinist approach. Our own attempt for the solution of the organism problem applies the tools of culturalist methodology. In accordance to this pragmatic approach, the term organism is introduced as a concept of notion. A constructional morphological case study exemplifies the applicability of this concept. From the culturalist point of view a methodological foundation of biology can be achieved, that provides a consistent basis for a comprehensive integration of biological knowledge.