Mathematics, structuralism and biology

A new approach is gaining ground in biology, one that has much in common with the structuralist tradition in other fields. It is very much in the spirit of an earlier view of biology and indeed of science in general. It is also, though this is not generally recognized, in the spirit of twentieth century physics. As in modern physics, however, it is not a question of ignoring all the progress that has been made within the former paradigm. On the contrary, the aim is to use it as a basis for setting out in a somewhat different direction. Complex phenomena do not generally lend themselves to reductionist analyses which seek explanation only in terms of detailed mechanisms, but a proper scientific discussion of structure must make full use of what we have already learned - by whatever means - about the processes that underly the phenomena we are trying to understand.     

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.     

Biological physics in México

Biological and physical sciences possess a long-standing tradition of cooperativity as separate but related subfields of science. For some time, this cooperativity has been limited by their obvious differences in methods and views. Biological physics has recently experienced a kind of revival (or better a rebirth) due to the growth of molecular research on animate matter. New avenues for research have been opened for both theoretical and experimental physicists. Nevertheless, in order to better travel for such paths, the contemporary biological physicist should be armed with a set of specialized tools and methods but also with a new attitude toward multidisciplinarity. In this review article, we intend to somehow summarize what has been done in the past (in particular, as an example we will take a closer look at the Mexican case), to show some examples of fruitful investigations in the biological physics area and also to set a proposal of new curricula for physics students and professionals interested in applying their science to get a better understanding of the physical basis of biological function.     

Structured exploratory data analysis (SEDA) of finger ridge-count inheritance: I. Major gene index, midparental correlation, and offspring-between-parents function in 125 south Indian families

Fourteen dermatoglyphic traits measured on 125 Velanadu Brahmin families were analyzed for mode of inheritance using three Structured Exploratory Data Analysis (SEDA) statistics: the major gene index, the offspring between parents function, and the traditional midparental correlation coefficient. Since the traits are integer valued with restricted ranges of variation, we simulated various transmission models with discrete expression to better understand the nature of the SEDA statistics for such variables. In addition, permutation procedures were employed to aid the interpretation of the SEDA results. These analyses suggest that corresponding homologous fingers on the left and right hands exhibit similar transmission characteristics. The relationship of the parent and child total ridge-counts of the two hands separately, as well as their combined total, virtually simulate complete Galtonian blending inheritance. Results for the individual digital ridge-counts as well as the pattern-intensity-index variable also suggest a multifactorial mode of transmission or possibly one involving several genes.     

The splendid isolation of biological nomenclature

Recent arguments against phylogenetic nomenclature (PN) rest on the assumption that, generally, consensus about the meaning of taxon names arises spontaneously. A brief historical review shows that this is not the case. Comparisons with other fields as diverse as physics, geology and geopolitics show that precision in the meaning of terms is essential to produce consensus, which is precisely the opposite as the avowed aims of rank-based nomenclature (RN). The difficulty in reaching consensus increases with the weight of tradition and decreases with the number of objective tests to falsify competing theories. In both respects, biological nomenclature is handicapped because the weight of tradition is extreme and rules of nomenclature cannot be discovered in nature. These facts may explain the difficulty in reaching consensus on the most appropriate system of nomenclature for the 21st century. Therefore, comparisons between RN and PN should focus on minimal taxonomic stability, rather than realized or maximal stability. A four-taxon example shows that in this respect, PN vastly outperforms RN. Opponents of PN often predict that implementation of PN will cause considerable confusion. A comparison with computer science shows that confusion is often associated with progress, and may be unavoidable for nomenclature to prosper in the new millennium.     

The presence and influence of religion in American bioethics

From the inception of the relatively short history of American bioethics in the mid-to-late 1960s, the place of religion in this field has been complex and controversial. It has also been a subject of more than casual interest and concern to bioethicists, and to an array of medical and non-medical groups in U.S. society for whom the activities and issues in which bioethics is engaged have ongoing import. The questions and the tensions linked to the status and influence of religion in the sphere of bioethics have ramifications that extend beyond bioethics and biomedicine into matters involving the relationship of religion to the institutional structure of American society--most particularly its political, legal foundations, and realm of public affairs--and to its cultural attributes and tradition. It is within this larger perspective that we will consider the association between American bioethics and religion. Our analysis includes two case studies: (1) how, in the early years of bioethics, a pioneering organization in the field dealt with the "redefinition of death" in its discussions and in a major medical journal publication; and (2) the way in which the most recently appointed federal bioethics commission, the National Bioethics Advisory Commission, involved religion in its work on cloning and stem cell research.     

Who was... John Henri Fabre?

The books of Jean Henri Fabre, replete with lively accounts of his observations on nature, inspired generations of children from all over the world. The detail in his study of insects and the entertaining presentation allowed readers to absorb his fascination. Yet, he was a physics teacher by profession and virtually self taught on matters of entomology.     

传承与开拓：当代匠师方惠的传统造园叠山技艺及理论探究

对传统叠山匠师技艺进行考察研究，既是当代的传统风格造园实践的迫切需要，也是学术界对工匠文化研究及非物质文化遗产传承的必然要求。选择以当代匠师方惠的造园叠山技艺为研究对象，在调查访谈的基础上，从他的事业历程、创作理论和营造原则3个方面，认识其叠山技艺及其理论的核心要点，并探讨他对传统技艺的传承与开拓。     

Biochemistry on a Leash: The Roles of Tether Length and Geometry in Signal Integration Proteins

We use statistical mechanics and simple ideas from polymer physics to develop a quantitative model of proteins whose activity is controlled by flexibly tethered ligands and receptors. We predict how the properties of tethers influence the function of these proteins and demonstrate how their tether length dependence can be exploited to construct proteins whose integration of multiple signals can be tuned. One case study to which we apply these ideas is that of the Wiskott-Aldrich Syndrome Proteins as activators of actin polymerization. More generally, tethered ligands competing with those free in solution are common phenomena in biology, making this an important specific example of a widespread biological idea.     

Massively Parallel Single-Molecule Manipulation Using Centrifugal Force

Precise manipulation of single molecules has already led to remarkable insights in physics, chemistry, biology, and medicine. However, widespread adoption of single-molecule techniques has been impeded by equipment cost and the laborious nature of making measurements one molecule at a time. We have solved these issues by developing an approach that enables massively parallel single-molecule force measurements using centrifugal force. This approach is realized in an instrument that we call the centrifuge force microscope in which objects in an orbiting sample are subjected to a calibration-free, macroscopically uniform force-field while their micro-to-nanoscopic motions are observed. We demonstrate high-throughput single-molecule force spectroscopy with this technique by performing thousands of rupture experiments in parallel, characterizing force-dependent unbinding kinetics of an antibody-antigen pair in minutes rather than days. Additionally, we verify the force accuracy of the instrument by measuring the well-established DNA overstretching transition at 66 ± 3 pN. With significant benefits in efficiency, cost, simplicity, and versatility, single-molecule centrifugation has the potential to expand single-molecule experimentation to a wider range of researchers and experimental systems.     

A Matter of Taste? Quality of Life in Day-to-Day Living with ALS and a Feeding Tube

Although people often refer to quality of life and there is a respectable research tradition to establish it, the meaning of the term is unclear. In this article we qualitatively study an intervention of which the quantitative effects are documented as indecisive. We do this in order to learn more about what the meaning of the term quality of life means when it is studied in daily life. With the help of these findings we reflect on the intricacies of objectifying and measuring quality of life using quantitative research designs. Our case is the feeding tube for patients suffering from ALS, a severe motor neuron disease that rapidly and progressively incapacitates patients. We studied how these patients, who lived in the Netherlands, anticipated and lived with a feeding tube in the course of their physical deterioration. Our analysis shows that the quality of life related to the feeding tube has to be understood as a process rather than as an outcome. The feeding tube becomes a different thing as patients move through the various phases of their illness, due to changes in their condition, living circumstances, and concerns and values. There are very different appreciations of the way the feeding tube changes the body’s appearance and feel. Some patients refuse it because they feel it disfigures their body, whereas others are indifferent to its appearance. Our conclusion is that these differences are difficult to grasp with a quantitative study designs because ‘matters of taste’ and values are not distributed in a population in the same ways as physiological responses to medication. Effect studies assume physiological responses to be more or less the same for everyone, with only gradual differences. Our analysis of quality in daily life, however, shows that what a treatment comes to be and how it is valued shows shows generalities for subgroups rather than populations.     

Gender specificity and interdisciplinarity. Methodological-theoretical observations

In public, sex specifity of humans is under a lively discussion, dominated by Social Sciences. It could be observed that between the theoretically involved disciplines natural sciences, social sciences and liberal arts exist very little flow of information and discussion. It was pointed out that sex specifity matters several disciplines because of the complexity of the phenomenon, but the research still lacks epistemological prerequisites to apply to this goal. The contribution makes methodological and theoretical remarks in order to promote an interdisciplinary approach. Obstacles from tradition and organisation of research are mentioned as well as dominating epistemological and theoretical advances.     

Ethical issues in ethnomusicological filmmaking

This paper investigates ethical issues which the author had to face in making a series of four ethnomusicological films in central Switzerland. Specifically related as well to an experience in filming music, the subjects considered raise questions of general concern in ethnographic filmmaking. Three main matters are discussed: revealing editing devices, which is rarely done in the film itself; the risk of the musicians becoming the laughing stock of the village if they appear to have weaknesses in their performance; and the return of research to those being studied, for their own benefit.     

The Moral Economy of Water: Equity and Antiquity in the Andean Commons

This article focuses on irrigation and water use in a community in the Peruvian Andes, one of numerous villages in the region where these activities are carried out in an unusual way. The practices and principles that make up this tradition, defining the rights and duties of community members in making use of the resource most vital for life, are identified and evaluated based on comparative ethnographic research. It is argued that they provide a highly effective way of managing a scarce and fluctuating resource that is held in common, an older Andean tradition that may have been adopted by the Incas and endorsed as an official policy—all of which might help to account for its wide distribution in the region today. In this particular case, the principles help to create an extraordinary kind of community, a transparent and equitable one in which a basic material symmetry or proportionality is expressed at many levels. This symmetry is closely related to other basic commonalities among community members, but of particular interest are its effects on social solidarity and cooperation and its association with a strong sense of ethnic identity. The implications of this tradition for solving contemporary problems in water management are also briefly discussed, [sociocultural anthropology, irrigation, Andes, common-property]     

离子束生物效应及应用中值得研究的几个问题

重离子束生物效应及重离子束在生命科学中的应用研究,在国内外物理学与生命科学领域中得到了广泛的开展,但对出现的一些现象还没有深刻地揭露其本质,作出机理性解释。为了深入研究,本文提出一些值得研究的问题供参考,如:重离子径迹结构及能量沉积分布模型,DNA辐射敏感位点,质量沉积-分子改造,直接作用与间接作用,放射性核束的应用等。     

Hidden Implications of Clumps and Masses

In a recent study on the spawn of the common frog (Rana temporaria) surveyed over several breeding sites, a significant linear relationship (p < 0.001) was found to exist between the number of spawn 'clumps' making up a bouyant spawn 'mass' and the area of the mass visible from above the water surface (Griffiths and Raper, 1994). An open question exists, as to why such a strong linear relationship is to be found. Using elementary physics, I suggest some factors which may underly the observed linearity and how it may reveal characteristics other than size of a breeding population. A follow-up experiment is outlined to test for these in the field and some ecological implications are discussed.     

神山森林文化传统的生态伦理学意义

在云南山地民族的传统文化里 ,对绿的图腾和对树的崇拜无处不在 ,神山森林传统已经成为一种生态文化传统 ,几乎所有的民族都会在自己居住的村寨附近选一片葱绿茂密的山林作为自己的风水林或水源林 ,有的甚至作为神山森林顶礼膜拜 ,严禁任何人砍伐和破坏。村寨和神山上的参天古树也往往成为神树和村寨的标记加以崇拜和保护。我们把山地民族这种文化传统称为神山森林文化传统。这是一种朴素的生态伦理观 ,体现一种敬畏生命的生态伦理学 ,有着深刻的自然保护意义。1　神山森林文化的生态学内涵及生态学意义文化 ,是人类对环境的一种社会生态适…     

Molecule by molecule, the physics and chemistry of life: SMB 2007

Interdisciplinary work in the life sciences at the boundaries of biology, chemistry and physics is making enormous strides. This progress was showcased at the recent Single Molecule Biophysics conference.     

The composition and antianemia efficacy of the iron-containing waters of the Skhodnitsa spring

Slight-mineralized chalybeate waters of the Skhodnitsa deposit containing organic matters are distinguished by high-molecular organic iron complexes present in waters. It is shown that such natural complex iron compounds are characterized by high biological accessibility making these mineral waters very useful for posthemorrhagic anemia due to their therapeutic action.