Reconceiving autoimmunity: An overview.

Three interconnected positions are advocated: (1) although serving as a useful model, the immune self does not exist as such; (2) instead of a self/nonself demarcation, the immune system 'sees' itself, i.e., it does not ignore the 'self' or attack the 'other;' but exhibits a spectrum of responses, which when viewed from outside the system appear as discrimination of 'self' and 'nonself' based on certain criteria of reactivity. When immune reactions are conceived in terms of normal physiology and open exchange with the environment, where borders dividing host and foreign are elusive and changing, host defense is only part of the immune system's functions, which actually comprise two basic tasks: protection, i.e., to preserve host integrity, and maintenance of organismic identity. And thus (3) if the spectrum of immunity is enlarged, differentiating low reactive 'autoimmune' reactions from activated immune responses against the 'other' is only a matter of degree. Simply, all immunity is 'autoimmunity,' and the pathologic state of immunity directed at normal constituents of the organism is a particular case of dis-regulation, which appropriately is designated, autoimmune. Other uses of 'autoimmunity' and its congeners function as the semantic remnants of Burnet's original self/nonself theory and should be replaced. A new nomenclature is proposed, concinnity, which more accurately designates the physiology of the animal's ordinary housekeeping economy mediated by the immune system than 'autoimmunity' when used to describe such normal functions.

Individual and meta-immune networks.

Networks can be found everywhere-in technology, in nature and in our bodies. In this paper we present how antigen networks can be used as a model to study network interaction and architecture. Utilizing antigen microarray data of the reactivity of hundreds of antibodies of sera of ten mothers and their newborns, we reconstruct networks, either isotype specific (IgM or IgG) or person specific-mothers or newborns-and investigate the network properties. Such an approach makes it possible to decipher fundamental information regarding the personal immune network state and its unique characteristics. In the current paper we demonstrate how we are successful in studying the interaction between two dependent networks, the maternal IgG repertoire and the one of the offspring, using the concept of meta-network provides essential information regarding the biological phenomenon of cross placental transfer. Such an approach is useful in the study of coupled networks in variety of scientific fields.

Immunology's theories of cognition.

Contemporary immunology has established its fundamental theory as a biological expression of personal identity, wherein the "immune self" is defended by the immune system. Protection of this agent putatively requires a cognitive capacity by which the self and the foreign are perceived and thereby discriminated; from such information, discernment of the environment is achieved and activation of pathways leading to an immune response may be initiated. This so-called cognitive paradigm embeds such functions as "perception," "recognition," "learning," and "memory" to characterize immune processes, but the conceptual character of such functions has meanings that vary with the particular theory adopted. When different formulations of cognition are considered, immunology's conceptual infrastructure shifts: Extensions of conventional psychological understanding of representational cognition based on a subject-object dichotomy support notions of immune agency; alternatively, formulations of perception that dispense with representations and attendant notions of agency reconfigure the predicate epistemology dominating current immune theory. Reviewing immunological literature of the past five decades, these two understandings of perception--representational and non-representational (considered here from ecological, enactivist, and autopoietic perspectives)--offer competing views of immune cognitive functions. These, in turn, provide competing philosophical understandings of immunology's conceptual foundations, which reflect parallel controversies dominating current debates in philosophy of mind and attendant discussions about personal identity.

A symbiotic view of life: we have never been individuals.

The notion of the "biological individual" is crucial to studies of genetics, immunology, evolution, development, anatomy, and physiology. Each of these biological subdisciplines has a specific conception of individuality, which has historically provided conceptual contexts for integrating newly acquired data. During the past decade, nucleic acid analysis, especially genomic sequencing and high-throughput RNA techniques, has challenged each of these disciplinary definitions by finding significant interactions of animals and plants with symbiotic microorganisms that disrupt the boundaries that heretofore had characterized the biological individual. Animals cannot be considered individuals by anatomical or physiological criteria because a diversity of symbionts are both present and functional in completing metabolic pathways and serving other physiological functions. Similarly, these new studies have shown that animal development is incomplete without symbionts. Symbionts also constitute a second mode of genetic inheritance, providing selectable genetic variation for natural selection. The immune system also develops, in part, in dialogue with symbionts and thereby functions as a mechanism for integrating microbes into the animal-cell community. Recognizing the "holobiont"--the multicellular eukaryote plus its colonies of persistent symbionts--as a critically important unit of anatomy, development, physiology, immunology, and evolution opens up new investigative avenues and conceptually challenges the ways in which the biological subdisciplines have heretofore characterized living entities.

Analyses of antigen dependency networks unveil immune system reorganization between birth and adulthood.

Much effort has been devoted to assess the importance of nodes in complex biological networks (such as gene transcriptional regulatory networks, protein interaction networks, and neural networks). Examples of commonly used measures of node importance include node degree, node centrality, and node vulnerability score (the effect of the node deletion on the network efficiency). Here, we present a new approach to compute and investigate the mutual dependencies between network nodes from the matrices of node-node correlations. To this end, we first define the dependency of node i on node j (or the influence of node j on node i), D(i, j) as the average over all nodes k of the difference between the i - k correlation and the partial correlations between these nodes with respect to node j. Note that the dependencies, D(i, j) define a directed weighted matrix, since, in general, D(i, j) differs from D( j, i). For this reason, many of the commonly used measures of node importance, such as node centrality, cannot be used. Hence, to assess the node importance of the dependency networks, we define the system level influence (SLI) of antigen j, SLI( j) as the sum of the influence of j on all other antigens i. Next, we define the system level influence or the influence score of antigen j, SLI( j) as the sum of D(i, j) over all nodes i. We introduce the new approach and demonstrate that it can unveil important biological information in the context of the immune system. More specifically, we investigated antigen dependency networks computed from antigen microarray data of autoantibody reactivity of IgM and IgG isotypes present in the sera of ten mothers and their newborns. We found that the analysis was able to unveil that there is only a subset of antigens that have high influence scores (SLI) common both to the mothers and newborns. Networks comparison in terms of modularity (using the Newman's algorithm) and of topology (measured by the divergence rate) revealed that, at birth, the IgG networks exhibit a more profound global reorganization while the IgM networks exhibit a more profound local reorganization. During immune system development, the modularity of the IgG network increases and becomes comparable to that of the IgM networks at adulthood. We also found the existence of several conserved IgG and IgM network motifs between the maternal and newborns networks, which might retain network information as our immune system develops. If correct, these findings provide a convincing demonstration of the effectiveness of the new approach to unveil most significant biological information. Whereas we have introduced the new approach within the context of the immune system, it is expected to be effective in the studies of other complex biological social, financial, and manmade networks.

Network theory analysis of antibody-antigen reactivity data: the immune trees at birth and adulthood.

MOTIVATION: New antigen microarray technology enables parallel recording of antibody reactivities with hundreds of antigens. Such data affords system level analysis of the immune system's organization using methods and approaches from network theory. Here we measured the reactivity of 290 antigens (for both the IgG and IgM isotypes) of 10 healthy mothers and their term newborns. We constructed antigen correlation networks (or immune networks) whose nodes are the antigens and the edges are the antigen-antigen reactivity correlations, and we also computed their corresponding minimum spanning trees (MST)--maximal information reduced sub-graphs. We quantify the network organization (topology) in terms of the network theory divergence rate measure and rank the antigen importance in the full antigen correlation networks by the eigen-value centrality measure. This analysis makes possible the characterization and comparison of the IgG and IgM immune networks at birth (newborns) and adulthood (mothers) in terms of topology and node importance. RESULTS: Comparison of the immune network topology at birth and adulthood revealed partial conservation of the IgG immune network topology, and significant reorganization of the IgM immune networks. Inspection of the antigen importance revealed some dominant (in terms of high centrality) antigens in the IgG and IgM networks at birth, which retain their importance at adulthood.

Reframing developmental biology and building evolutionary theory's new synthesis.

Gilbert and Epel present a new approach to developmental biology: embryogenesis must be understood within the full context of the organism's environment. Instead of an insular embryo following a genetic blueprint, this revised program maintains that embryogenesis is subject to inputs from the environment that generate novel genetic variation with dynamic consequences for development. Beyond allelic variation of structural genes and of regulatory loci, plasticity-derived epigenetic variation completes the triad of the major types of variation required for evolution. Developmental biology and ecology, disciplines that have previously been regarded as distinct, are presented here as fully integrated under the rubric of "eco-devo," and from this perspective, which highlights how the environment not only selects variation, it helps construct it, another synthesis with evolutionary biology must also be made, "eco-evo-devo." This second integration has enormous implications for expanding evolution theory, inasmuch as the Modern Synthesis (Provine 1971), which combined classical genetics and Darwinism in the mid-20th century, did not account for the role of development in evolution. The eco-evo-devo synthesis thus portends a major theoretical inflection in evolutionary biology. Following a description of these scientific developments, comment is offered as to how this new integrated approach might be understood within the larger shifts in contemporary biology.

Freud's dreams of reason: the Kantian structure of psychoanalysis.

Freud (and later commentators) have failed to explain how the origins of psychoanalytical theory began with a positivist investment without recognizing a dual epistemological commitment: simply, Freud engaged positivism because he believed it generally equated with empiricism, which he valued, and he rejected "philosophy," and, more specifically, Kantianism, because of the associated transcendental qualities of its epistemology. But this simple dismissal belies a deep investment in Kant's formulation of human reason, in which rationality escapes natural cause and thereby bestows humans with cognitive and moral autonomy. Freud also segregated human rationality: he divided the mind between (1) an unconscious grounded in the biological and thus subject to its own laws, and (2) a faculty of autonomous reason, lodged in consciousness and free of natural forces to become the repository of interpretation and free will. Psychoanalysis thus rests upon a basic Kantian construction, whereby reason, through the aid of analytic techniques, provides a detached scrutiny of the natural world, i.e. the unconscious mental domain. Further, sovereign reason becomes the instrument of self-knowing in the pursuit of human perfection. Herein lies the philosophical foundation of psychoanalytic theory, a beguiling paradox in which natural cause and autonomous reason - determinism and freedom - are conjoined despite their apparent logical exclusion.

Organization of the autoantibody repertoire in healthy newborns and adults revealed by system level informatics of antigen microarray data.

The immune system is essential to body defense and maintenance. Specific antibodies to foreign invaders function in body defense, and it has been suggested that autoantibodies binding to self molecules are important in body maintenance. Recently, the autoantibody repertoires in the bloods of healthy mothers and their newborns were studied using an antigen microarray containing hundreds of self molecules. It was found that the mothers expressed diverse repertoires for both IgG and IgM autoantibodies. Each newborn shares with its mother a similar repertoire of IgG antibodies, which cross the placental but its IgM repertoire is more similar to those of other newborns. Here, we took a system-level approach and analyzed the correlations between autoantibody reactivities of the previous data and extended the study to new data from newborns at birth and a week later, and from healthy young women. For the young women, we found modular organization of both IgG and IgM isotypes into antigen cliques-subgroups of highly correlated antigen reactivities. In contrast, the newborns were found to share a universal congenital IgM profile with no modular organization. Moreover, the IgG autoantibodies of the newborns manifested buds of the mothers' antigen cliques, but they were noticeably less structured. These findings suggest that the natural autoantibody repertoire of humans shows relatively little organization at birth, but, by young adulthood, it becomes sorted out into a modular organization of subgroups (cliques) of correlated antigens. These features revealed by antigen microarrays can be used to define personal states of autoantibody organizational motifs.

Medicine and the call for a moral epistemology, part II: constructing a synthesis of values.

The demands and needs of an individual patient require diverse value judgments to interpret and apply clinical data. Indeed, objective assessment takes on particular meaning in the context of the social and existential status of the patient, and thereby a complex calculus of values determines therapeutic goals. I have previously formulated how this moral thread of care becomes woven into the epistemological project as a "moral epistemology." Having argued its ethical justification elsewhere, I offer another perspective here: clinical choices employ diverse values directed at an array of goals, some of which are derived from a universal clinical science and others from the particular physiological, psychological, and social needs of the patient. Integrating these diverse elements that determine clinical care requires a complex synthesis of facts and judgments from several domains. This constructivist process relies on clinical facts, as well as on personal judgments and subjective assessments in an ongoing negotiation between patient and doctor. A philosophy of medicine must account for the conceptual basis of this process by identifying and addressing the judgments that govern the complex synthesis of these various elements.

Values and ethics: a collection of curricular reforms for a new generation of physicians.

In recent years, medical educators have expressed concern that the reductionist-positivist mode of medical education fails to equip physicians with the skills and attitudes to meet the full range of patients' physical and emotional needs. Indeed, the authors suggest that neither patients nor physicians are satisfied. Among the factors responsible are a pervasive industrialization of clinical practice, a progressive segmentation of patient care, and a deepening shortage of both primary care and specialty physicians. But underlying these system issues is a lack of adequate schooling in the values, ethics, and culture of caring. Today's physicians must simultaneously be analytical, perceptive, and self-reflective. They must have the capacity to see their patients as individuals with differing psychological, social, and historical natures. And they must have insight into their own values and behaviors. All of this contributes to making a competent and humane physician. To aid medical students in achieving these characteristics, the authors contend that medical education must be radically restructured so that knowledge and skills are taught within the context of values and ethics. This commentary explores such reform through the lens of three articles published in the current issue of Academic Medicine, by Litzelman and Cottingham, Kanter and colleagues, and Dobie. These articles are the product of a national call that resulted in more than thirty abstracts, testimony to the fertile thinking already being applied to this problem. It is the authors' hope that this series of papers will stimulate still more thinking and lead to the curricular reform that future generations of physicians deserve.

The moral domain of the medical record: the routine ethics evaluation.

The structure, content, and orientation of the contemporary medical record inadequately reflect the appropriate influence of patients' rights and bioethics on health care. Most tellingly, the medical chart reveals a remarkable absence of attention to medical ethics, except in the case of crisis management. But medical ethics informs both crisis decision-making and virtually all clinical interventions. Indeed, clinical care embodies a complex array of choices influenced by individual and cultural values, themselves reflecting religious beliefs, personal histories, psychologies, and social mores. But the typical medical chart, which records clinical descriptions, analyses, and rationales for treatment, rarely identifies or accounts for this value-laden dimension of care and thus both over-simplifies and distorts the depiction of a patient's illness and its treatment. To better reflect the complex moral domain of clinical care, and assist in organizing its complex structure, a systematic procedure is proposed here to evaluate the ethical status of every patient: As a routine part of the clinical evaluation, in a designated Ethical Concerns section of the medical record, an "ethics work-up' is designed to serve as a moral 'diagnostic' analogous to its scientific counterpart. Adapted to the needs of individual patients, such evaluations should identify ethical problems, coordinate related data, resources, and opinion, and define the rationale for choices made and actions pursued. In establishing improved integration of the 'epistemologies' of care and the 'ethics' of care, the goals of a more humane, patient-centered medicine may be better met.

Viewpoint: New physicians for a new century.

How to train competent and compassionate physicians has assumed a new urgency. The authors propose that these concerns be approached by radically restructuring the medical school curriculum in ways that place facts and skills within the context of ethics and values. Doing so will require that the positivist stance of medical education be coupled to strategies that deal with ambiguity and uncertainty, communication and empathy, and, most important, physician self-awareness. Achieving such balance will require fundamental change in medicine's education philosophy along five general lines: (1) assertion of medical ethics as the foundation of clinical medicine; (2) recognition of the central place of values in clinical decision making; (3) cultivation of the ethos of humane care; (4) selection of medical students with the dual capacities of strong cognitive skills and empathy; and (5) encouragement and support of faculty who can transmit the knowledge of clinical science coupled to the principles of humane care. Such changes are both timely and necessary. Although they will be difficult to accomplish, they offer an opportunity for medical educators to foster the development of physicians with the range attributes that this new century demands.

Medicine and the call for a moral epistemology.

For over a century, medicine has prided itself on its scientific orientation and technological accomplishments. But a conceptual crack lies at the foundation of contemporary medicine, one that may be characterized as a conflict between medicine's scientific epistemology and its moral philosophy. Moral refers to value, and more specifically in the clinical setting, to how facts must be ordered by the values attached to them. A "moral epistemology" seeks to bring these two domains into closer proximity. Clinical facts always reside in a complex array of systems that confer specific and often unique meanings to any finding. An integration of unsteady norms and the intuitive inference arising from the individuality of disease expression require that judgments order facts into their proper placement. And beyond this relaxed view of objectivity, clinical care must also incorporate judgments arising from the patient's (as well as the physician's) social and psychological realms that are removed from scientific concerns. Together, these various kinds of value judgments erect the scaffold of clinical care, in which a more complex moral epistemology emerges. A comprehensive biopsychosocial model of illness and its treatment articulates this integrated orientation, but until medicine embraces a philosophy that legitimates the full integration of facts and values, the appeal of such an approach will remain limited and its application ineffective.

Sick autonomy.

Complex social and economic forces have placed patient autonomy at the center of medical ethics, and thereby displaced an older ethic of physician beneficence. This development arose, and is sustained, by waning trust in the traditional doctor-patient relationship. As patients have increasingly become clients and consumers, a contract basis for medical care has put the ancient covenant of care in jeopardy. Here, a philosophical approach to harmonize the apparent conflicting claims of patient autonomy and physician beneficence is offered by demonstrating that autonomy need not be understood as protecting a threatened identity. If persons are regarded as atomistic, certain defensive notions of individualistic rights-based autonomy prevail; if a relational construction of personal identity is employed instead, then respect for autonomy becomes part of a wider morality of relationship and care. By reconfiguring trust within this latter understanding of personhood, bioethics better balances its concerns over choices and actions with those of relationship and responsibility. Neither atomistic autonomy nor the ethics of responsibility can claim hegemony, for they are mutually interdependent, and a complete account of medicine's moral axis requires that they be integrated. This reorientation is crucial for reasserting the ethos of clinical medicine, whose fundamental mandate remains the care of others.