Defining Glomerular Disease in Mechanistic Terms: Implementing an Integrative Biology Approach in Nephrology

Advances in biomedical research allow for the capture of an unprecedented level of genetic, molecular, and clinical information from large patient cohorts, where the quest for precision medicine can be pursued. An overarching goal of precision medicine is to integrate the large–scale genetic and molecular data with deep phenotypic information to identify a new mechanistic disease classification. This classification can ideally be used to meet the clinical goal of the right medication for the right patient at the right time. Glomerular disease presents a formidable challenge for precision medicine. Patients present with similar signs and symptoms, which cross the current disease categories. The diseases are grouped by shared histopathologic features, but individual patients have dramatic variability in presentation, progression, and response to therapy, reflecting the underlying biologic heterogeneity within each glomerular disease category. Despite the clinical challenge, glomerular disease has several unique advantages to building multilayered datasets connecting genetic, molecular, and structural information needed to address the goals of precision medicine in this population. Kidney biopsy tissue, obtained during routine clinical care, provides a direct window into the molecular mechanisms active in the affected organ. In addition, urine is a biofluid ideally suited for repeated measurement from the diseased organ as a liquid biopsy with potential to reflect the dynamic state of renal tissue. In our review, current approaches for large–scale data generation and integration along the genotype-phenotype continuum in glomerular disease will be summarized. Several successful examples of this integrative biology approach within glomerular disease will be highlighted along with an outlook on how achieving a mechanistic disease classification could help to shape glomerular disease research and care in the future

Is defining life pointless? Operational definitions at the frontiers of Biology

Despite numerous and increasing attempts to define what life is, there is no consensus on necessary and sufficient conditions for life. Accordingly, some scholars have questioned the value of definitions of life and encouraged scientists and philosophers alike to discard the project. As an alternative to this pessimistic conclusion, we argue that critically rethinking the nature and uses of definitions can provide new insights into the epistemic roles of definitions of life for different research practices. This paper examines the possible contributions of definitions of life in scientific domains where such definitions are used most (e.g., Synthetic Biology, Origins of Life, Alife, and Astrobiology). Rather than as classificatory tools for demarcation of natural kinds, we highlight the pragmatic utility of what we call operational definitions that serve as theoretical and epistemic tools in scientific practice. In particular, we examine contexts where definitions integrate criteria for life into theoretical models that involve or enable observable operations. We show how these definitions of life play important roles in influencing research agendas and evaluating results, and we argue that to discard the project of defining life is neither sufficiently motivated, nor possible without dismissing important theoretical and practical research

Q & A with Dean Victoria McGillin

After 11 months on the job, Victoria McGillin, dean of faculty, discusses how success of a Linfield education can be measured

Brain Death as the End of a Human Organism as a Self-moving Whole

The biophilosophic justification for the idea that “brain death” is death needs to support two claims: that what dies in human death is a human organism, not merely a psychological entity distinct from it; that total brain failure signifies the end of the human organism as a whole. Defenders of brain death typically assume without argument that the first claim is true and argue for the second by defending the “integrative unity” rationale. Yet the integrative unity rationale has fallen on hard times. In this article, I give reasons for why we should think of ourselves as organisms, and why the “fundamental work” rationale put forward by the 2008 President’s Council is better than the integrative unity rationale, despite persistent objections to it

Scaling and Accommodation of Jaw Adductor Muscles in Canidae

© 2016 The Authors The Anatomical Record: Advances in Integrative Anatomy and Evolutionary Biology Published by Wiley Periodicals, Inc.The masticatory apparatus amongst closely related carnivoran species raises intriguing questions about the interplay between allometry, function, and phylogeny in defining interspecific variations of cranial morphology. Here we describe the gross structure of the jaw adductor muscles of several species of canid, and then examine how the muscles are scaled across the range of body sizes, phylogenies, and trophic groups. We also consider how the muscles are accommodated on the skull, and how this is influenced by differences of endocranial size. Data were collected for a suite of morphological metrics, including body mass, endocranial volume, and muscle masses and we used geometric morphometric shape analysis to reveal associated form changes. We find that all jaw adductor muscles scale isometrically against body mass, regardless of phylogeny or trophic group, but that endocranial volume scales with negative allometry against body mass. These findings suggest that head shape is partly influenced by the need to house isometrically scaling muscles on a neurocranium scaling with negative allometry. Principal component analysis suggests that skull shape changes, such as the relatively wide zygomatic arches and large sagittal crests seen in species with higher body masses, allow the skull to accommodate a relative enlargement of the jaw adductors compared with the endocranium. Anat Rec, 299:951–966, 2016. © 2016 The Authors The Anatomical Record: Advances in Integrative Anatomy and Evolutionary Biology Published by Wiley Periodicals, Inc

Natural Kinds in Evolution and Systematics: Metaphysical and Epistemological Considerations

Despite the traditional focus on metaphysical issues in discussions of natural kinds in biology, epistemological considerations are at least as important. By revisiting the debate as to whether taxa are kinds or individuals, I argue that both accounts are metaphysically compatible but one or the other approach can be pragmatically preferable depending on the epistemic context. Recent objections against construing species as homeostatic property cluster kinds are also addressed. The second part of the paper broadens the perspective by considering homologues as another example of natural kinds, comparing them with analogues as functionally defined kinds. Given that there are various types of natural kinds, I discuss the different theoretical purposes served by diverse kind concepts, suggesting that there is no clear-cut distinction between natural kinds and other kinds, such as functional kinds. Rather than attempting to offer a unique metaphysical account of ‘natural’ kind, a more fruitful approach consists in the epistemological study of how different natural kind concepts are employed in scientific reasoning

Article Addendum: Ecocultural basis of cognition: Farmers and fishermen are more holistic than herders

It has been hypothesized that interdependent (versus independent) social orientations breed more holistic (versus analytic) cognitions. If so, farming and small-scale fishing, which require more cooperation (and represent a more interdependent mode of being) than does herding, may encourage a more holistic mode of cognition. To test this hypothesis we compared responses to tasks measuring categorization, reasoning, and attention by members of herding, fishing, and farming communities in the eastern Black Sea Region of Turkey. The samples did not differ from each other in important demographic variables such as nationality, ethnicity, language, and religion, as well as age and education. As hypothesized, in all three tasks, results indicated a greater degree of holistic mode of cognition exhibited by the members of fishing and farming communities than members of herding communities. The findings support the notion that level of special interdependence fostered by ecocultural settings is likely to shape the ways in which individuals perceive and attend to their surrounding world