We provide an introduction to network theory, evidence to support a connection between molecular network structure and neuropsychiatric disease, and examples of how network approaches can expand our knowledge of the molecular bases of these diseases. Without systematic methods to derive their biological meanings and inter‐relatedness, the many molecular changes associated with neuropsychiatric disease, including genetic variants, gene expression changes, and protein differences, present an impenetrably complex set of findings. Network approaches can potentially help integrate and reconcile these findings, as (...) well as provide new insights into the molecular architecture of neuropsychiatric diseases. Network approaches to neuropsychiatric disease are still in their infancy, and we discuss what might be done to improve their prospects. (shrink)

This essay argues that, while much has been gained by medicine's focus on the spatial aspects of disease in light of developments in modern pathology, too little attention has been given to the temporal experience of illness at the subjective level of the patient. In particular, it is noted that there is a radical distinction between subjective and objective time. Whereas the patient experiences his immediate illness in terms of the ongoing flux of subjective time, the physician conceptualizes the illness (...) as a disease state according to the measurements of objective time. A greater understanding of this disparity in temporal experiencing provides insights into the lived experience of illness and can preclude difficulties in communication between physician and patient. (shrink)

This paper suggests that the paradigm of lived body (as it is developed in the works of Merleau-Ponty, Sartre and Zaner) provides important insights into the experience of illness. In particular it is noted that, as embodied persons, we experience illness primarily as a disruption of lived body rather than as a dysfunction of biological body. An account is given of the manner in which such fundamental features of embodiment as bodily intentionality, primary meaning, contextural organization, body image, gestural display, (...) lived spatiality and temporality, are disrupted in illness causing a concurrent disorganization of the patient's self and world. The paradigm of lived body has important applications for medical practice. It provides a fuller account of illness than does the prevailing reductionist Cartesian paradigm of body, more directly addresses the existential predicament of illness, and orients the clinical focus around the personhood of the patient. (shrink)

C.H. Waddington is today remembered chiefly as a Drosophila developmental geneticist who developed the concepts of “canalization” and “the epigenetic landscape.” In his lifetime, however, he was widely perceived primarily as a critic of Neo-Darwinian evolutionary theory. His criticisms of Neo-Darwinian evolutionary theory were focused on what he saw as unrealistic, “atomistic” models of both gene selection and trait evolution. In particular, he felt that the Neo-Darwinians badly neglected the phenomenon of extensive gene interactions and that the “randomness” of mutational (...) effects, posited in the theory, was a false postulate. This last criticism dealt with the phenomenon known today as “developmental constraints.” Although population genetics itself has evolved considerably from its form at mid-20th century, much of Waddington’s critique, it is argued here, retains cogency. Yet, he did not attempt to develop a full-fledged alternative theory himself. Perhaps most surprisingly, in retrospect, is that he did not try to marry his work on gene interactions in development with his evolutionary interests, to create a theory of “genetic networks” and their evolution. Whether evolutionary genetics today will incorporate “network thinking” as a central element or whether there will be a general retreat to the more atomistic approach offered by genomics, remains an open question. (shrink)

In this essay I discuss Edith Stein's analysis of empathy and note its application in the field of clinical medicine. In identifying empathy as the basic mode of cognition in which one grasps the experiences of others, Stein notes, 'I grasp the Other as a living body and not merely as a physical body'. The living body is given in terms of five distinctive characteristics - characteristics that disclose important facets of the illness experience. Empathy plays an important role in (...) clinical practice in aiding physicians to grasp the content of first-person reports of bodily disorder, and to comprehend the meaning of illness-as-lived. I suggest that an important task for medical education should be that of developing students' capacity for empathic understanding and I note several ways in which this task might be accomplished. (shrink)

In this paper I briefly summarize Pellegrino’s phenomenological analysis of the ethics of the physician–patient relationship. In delineating the essential elements of the healing relationship, Pellegrino demonstrates the necessity for health care professionals to understand the patient’s lived experience of illness. In considering the phenomenon of illness, I identify certain essential characteristics of illness-as-lived that provide a basis for developing a rigorous understanding of the patient’s experience. I note recent developments in the systematic delivery of health care that make it (...) difficult for health care professionals to realize Pellegrino’s ethical model of the role of healer. Such developments limit both the physician’s freedom to act on behalf of the patient without the constraint of third parties and the physician’s freedom to act in light of his or her own ethical or religious convictions. Given these difficulties, I note MacIntyre’s call for the development of moral communities, as an alternative to the prevailing culture, and share a first-hand example illustrating how intentional Christian community provides an alternative nurturing context that permits the full development of the healing relationship. (shrink)

Book reviewed in this article: The Meaning of Illness. By S. Kay Toombs.

Features Covers the philosophical and historical development of the concept of "species" Documents that variation was recognized by pre-Darwinian scholars Includes a section on the debates since the time of the New Synthesis Better suited to non-philosophers Summary Over time the complex idea of "species" has evolved, yet its meaning is far from resolved. This comprehensive work is a fresh look at an idea central to the field of biology by tracing its history from antiquity to today. Species is a (...) benchmark exploration and clarification of a concept fundamental to the past, present, and future of the natural sciences. In this edition, a section is added on the debate over species since the time of the New Synthesis, and brings the book up to date. A section on recent philosophical debates over species has also been added. This edition is better suited non-specialists in philosophy, so that it will be of greater use for scientists wishing to understand how the notion came to be that living organisms form species. (shrink)

Defining Species: A Sourcebook from Antiquity to Today provides excerpts and commentary on the definition of «species from source material ranging from the ...

The Nature of Classification discusses an old and generally ignored issue in the philosophy of science: natural classification. It argues for classification to be a sometimes theory-free activity in science, and discusses the existence of scientific domains, theory-dependence of observation, the inferential relations of classification and theory, and the nature of the classificatory activity in general. It focuses on biological classification, but extends the discussion to physics, psychiatry, meteorology and other special sciences.

We provide a suitable theoretical foundation for the notion of the quantum coherent state which describes the electrostatic field due to a static external macroscopic charge distribution introduced by the author in 1998 and use it to rederive the formulae obtained in 1998 for the inner product of a pair of such states. (We also correct an incorrect factor of 4π\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$4\pi$$\end{document} in some of those formulae.) Contrary to what one might expect, (...) this inner product is usually non-zero whenever the total charges of the two charge distributions are equal, even if the charge distributions themselves are different. We actually display two different frameworks that lead to the same inner-product formulae, in the second of which Gauss’s law only holds in expectation value. We propose an experiment capable of ruling out the latter framework. We then address the problem of finding a product picture for QED—i.e. a reformulation in which it has a total Hamiltonian, arising as a sum of a free electromagnetic Hamiltonian, a free charged-matter Hamiltonian and an interaction term, acting on a Hilbert space which is a subspace (the physical subspace) of the full tensor product of a charged-matter Hilbert space and an electromagnetic-field Hilbert space. (The traditional Coulomb gauge formulation of QED isn’t a product picture in this sense because, in it, the longitudinal part of the electric field is a function of the charged matter operators.) Motivated by the first framework for our coherent-state construction, we find such a product picture and exhibit its equivalence with Coulomb gauge QED both for a charged Dirac field and also for a system of non-relativistic charged balls. For each of these systems, in all states in the physical subspace (including the vacuum in the case of the Dirac field) the charged matter is entangled with longitudinal photons and Gauss’s law holds as an operator equation; albeit the electric field operator (and therefore also the full Hamiltonian) while self-adjoint on the physical subspace, fails to be self-adjoint on the full tensor-product Hilbert space. The inner products of our electrostatic coherent states and the product picture for QED are relevant as analogues to quantities that play a rôle in the author’s matter-gravity entanglement hypothesis. Also, the product picture provides a temporal gauge quantization of QED which appears to be free from the difficulties which plagued previous approaches to temporal-gauge quantization. (shrink)

In this paper I reflect upon my personal experience of chronic progressive multiple sclerosis in order to provide a phenomenological account of the human experience of disability. In particular, I argue that the phenomenological notion of lived body provides important insights into the profound disruptions of space and time that are an integral element of changed physical capacities such as loss of mobility. In addition, phenomenology discloses the emotional dimension of physical disorder. The lived body disruption engendered by loss of (...) mobility includes a change in the character of surrounding space, an alteration in one's taken-for-granted awareness of objects, the disruption of corporeal identity, a disturbance in one's relations with others, and a change in the character of temporal experience. The loss of upright posture is of particular significance since it not only concretely diminishes autonomy but affects the way one is treated by others. Such a change in posture is, therefore, particularly disruptive in the social world of everyday life. An understanding of the lived body disruption engendered by disability has important applications for the clinical context in devising effective therapies, as well as for the social arena in determining how best to resolve the various challenges posed by chronic disabling disorders. (shrink)

This essay argues that philosophical phenomenology can provide important insights into the patient-physician relationship. In particular, it is noted that the physician and patient encounter the experience of illness from within the context of different "worlds", each "world" providing a horizon of meaning. Such phenomenological notions as focusing, habits of mind, finite provinces of meaning, and relevance are shown to be central to the way these "worlds" are constituted. An eidetic interpretation of illness is proposed. Such an interpretation discloses certain (...) essential characteristics that pertain to the experience of illness, per se , regardless of its manifestation in terms of a particular disease state. It is suggested that, if a shared world of meaning is to be constituted between physician and patient, the eidetic characteristics of illness must be recognized by the physician. Keywords: phenomenology, patient-physician relationship, illness-as-lived, habits of mind, relevance, eidetic CiteULike Connotea Del.icio.us What's this? (shrink)

Yet, the central conviction that informs this volume is that phenomenology provides extraordinary insights into many of the issues that are directly addressed ...

This study examined the ethical issues experienced by nurses working in a small group of elderly persons’ care settings in the UK, using a survey questionnaire previously used in other countries for examining the cultural aspects of ethical issues. However ‘culture’ relates not only to ethnicity but also the organizational culture in which care is delivered. Nurses working in elderly persons’ care settings described a range of issues faced when caring for elderly terminally ill people, which illustrated the different needs (...) of patients, relatives, professionals and society. These issues related to the unique needs of elderly people (such as dementia sufferers) and could have an impact on patients’ quality of death. (shrink)

The power of sexual selection to influence the evolution of morphological traits was first proposed more than 130 years ago by Darwin. Though long a controversial idea, it has been documented in recent decades for a host of animal species. Yet few of the established sexually selected features have been explored at the level of their genetic or molecular foundations. In a recent report, Zauner et al.1 describe some of the molecular features associated with one of the best characterized of (...) sexually selected traits, the male‐specific tail “sword” seen in certain species of the fish genus Xiphophorus. Zauner et al. find that the msxC gene, a gene previously implicated in fin development from work in zebrafish, is dramatically and specifically upregulated in the development of the ventral caudal fin rays, which give rise to the sword, in males. The results provide the first molecular insight into the development of this sexually selected trait while prompting new questions about the structure of the entire genetic network that underlies this trait. To fully understand the molecular‐genetic and evolutionary history of this network, however, it will be essential to determine whether sword‐development is a basal or derived trait in Xiphophorus. BioEssays 26:116–119, 2004. © 2004 Wiley Periodicals, Inc. (shrink)

In 1988, David Hull presented an evolutionary account of science. This was a direct analogy to evolutionary accounts of biological adaptation, and part of a generalized view of Darwinian selection accounts that he based upon the Universal Darwinism of Richard Dawkins. Criticisms of this view were made by, among others, Kim Sterelny, which led to it gaining only limited acceptance. Some of these criticisms are, I will argue, no longer valid in the light of developments in the formal modeling of (...) evolution, in particular that of Sergey Gavrilets’ work on adaptive landscapes. If we can usefully recast the Hullian view of science as being driven by selection in terms of Gavrilets’ and Kaufmann’s view of there being “giant components” of high-fitness networks through any realistic adaptive landscape, we may now find it useful to ask what the adaptive pressures on science are, and to extend the metaphor into a full analogy. This is in effect to reconcile the Fisherianism of the Dawkins–Hull approach to selection and replicators, with a Wrightean drift account of social constructionist views of science, preserving, it is to be hoped, the valuable aspects of both. (shrink)

Donald MacKay's description of the embodiment of an efficacious conscious mind is reviewed as a version of non-reductive physicalism. Particular focus is given to MacKay's analysis of the emergence of consciousness in the capacity for self-evaluation which results from informational feedback regarding the results of action. Unique to MacKay's posthumously published Gifford Lectures is his analysis of agents in dialog as a particular form of an environmental feedback loop. His analysis of dialog is reviewed and expanded to encompass concepts of (...) a First and Second Order Theory of Mind. Finally, MacKay's view of the status of the soul is considered, and the particular role of dialogue as critical to the instantiation of soul is suggested. (shrink)

"--Joel Cracraft, American Museum of Natural History "This is not the potted history that one usually finds in texts and review articles.

Intelligent design theorist William Dembski hasproposed an ``explanatory filter'' fordistinguishing between events due to chance,lawful regularity or design. We show that ifDembski's filter were adopted as a scientificheuristic, some classical developments inscience would not be rational, and thatDembski's assertion that the filter reliablyidentifies rarefied design requires ignoringthe state of background knowledge. Ifbackground information changes even slightly,the filter's conclusion will vary wildly.Dembski fails to overcome Hume's objections toarguments from design.

The phenomenon of ‘canalization’ ‐ the genetic capacity to buffer developmental pathways against mutational or environmental perturbations ‐ was first characterized in the late 1930s and early 1940s. Despite enormous subsequent progress in understanding the nature of the genetic material and the molecular basis of gene expression, there have been few attempts to interpret the classical work on canalization in molecular genetic terms. Some recent findings, however, bear on one form of canalization, ‘genetic canalization’, the stabilization of development against mutational (...) effects. These data indicate that co‐expressed paralogous genes can function as mutual ‘back‐up’ elements in developmental processes. Paralogues, however, are far from the only basis of canalization: other genetic sources can be readily envisaged and some of these are described here. The evolutionary questions about genetic canalization and the mechanistic questions about developmental instability that still need to be addressed are also briefly discussed. (shrink)

The biological species (biospecies) concept applies only to sexually reproducing species, which means that until sexual reproduction evolved, there were no biospecies. On the universal tree of life, biospecies concepts therefore apply only to a relatively small number of clades, notably plants andanimals. I argue that it is useful to treat the various ways of being a species (species modes) as traits of clades. By extension from biospecies to the other concepts intended to capture the natural realities of what keeps (...) taxa distinct, we can treat other modes as traits also, and so come to understand that theplurality of species concepts reflects the biological realities of monophyletic groups.We should expect that specialists in different organisms will tend to favour those concepts that best represent the intrinsic mechanisms that keep taxa distinct in their clades. I will address the question whether modes ofreproduction such as asexual and sexual reproduction are natural classes, given that they are paraphyletic in most clades. (shrink)

A hypothesis on the evolutionary origin of the genetic pathway of sex determination in the nematode Caenorhabditis elegans is presented here. It is suggested that the pathway arose in steps, driven by frequency‐dependent selection for the minority sex at each step, and involving the sequential acquisition of dominant negative, neomorphic genetic switches, each one reversing the action of the previous one. A central implication is that the genetic pathway evolved in reverse order from the final step in the hierarchy up (...) to the first. The possible applicability of the model to the other well‐characterized sex determination pathway, that of Drosophila melanogaster, and to sex determination in mammals, is discussed, along with some potential implications for pathway evolution in general. Finally, the specific molecular and population genetic questions that the model raises are described and some tests are proposed. (shrink)

Species concepts for bacteria and other microbes are contentious, because they are often asexual. There is a Problem of Homogeneity: every mutation in an asexual lineage forms a new strain, of which all descendents are clones until a new mutation occurs. We should expect that asexual organisms would form a smear or continuum. What causes the internal homogeneity of asexual lineages, if they are in fact homogeneous? Is there a natural “species concept” for “microbes”? Two main concepts devised for metazoans (...) and metaphytes have been applied to bacteria. One is the Recombination Concept, a revised form of the Biological Species Concept in which the homogenizing mechanism is the sharing of genome fragments, somewhat akin to sexual recombination. The other is the Ecological Species Concept, in which the ecological niche is that which maintains lineages as cohesive. In this paper I will discuss these two concepts, and offer an underlying model that conjoins them, and consider the implications for species concepts in general. In short, my argument is that asexual species are instances of the most primitive and underived notion of species, which I will call “quasispecies”, following Eigen, and that sexual species are merely one derived kind of species. Moreover, I will argue that there is a continuum of recombination from simple viral models in which each strain is a clone, through to obligate recombination of 50% of the parents’ genome, and that consequently there is no sharp division between “microbial” and more familiar species. (shrink)