The educated eye: visual culture and pedagogy in the life sciences

About the Book (from upne.com) The creation and processing of visual representations in the life sciences is a critical but often overlooked aspect of scientific pedagogy. The Educated Eye follows the nineteenth-century embrace of the visible in new spectatoria, or demonstration halls, through the twentieth-century cinematic explorations of microscopic realms and simulations of surgery in virtual reality. With essays on Doc Edgerton\u27s stroboscopic techniques that froze time and Eames\u27s visualization of scale in Powers of Ten, among others, contributors ask how we are taught to see the unseen. About the Author (from upne.com) NANCY ANDERSON is an assistant professor of visual studies at the State University of New York, Buffalo. MICHAEL R. DIETRICH is a professor in the Department of Biological Sciences at Dartmouth College. About the Electronic Publication This electronic publication of The Educated Eye was made possible with the permission of the author. The University Press of New England created EPUB and PDF files from a scanned copy of the book. Rights Information Creative Commons Attribution-NonCommercial License © Trustees of Dartmouth Collegehttps://digitalcommons.dartmouth.edu/dartmouth_press/1002/thumbnail.jp

‘Extreme’ Organisms and the Problem of Generalization: Interpreting the Krogh Principle

Many biologists appeal to the so-called Krogh principle when justifying their choice of experimental organisms. The principle states that “for a large number of problems there will be some animal of choice, or a few such animals, on which it can be most conveniently studied”. Despite its popularity, the principle is often critiqued for implying unwarranted generalizations from optimal models. We argue that the Krogh principle should be interpreted in relation to the historical and scientific contexts in which it has been developed and used. We interpret the Krogh Principle as a heuristic, i.e., as a recommendation to approach biological problems through organisms where a specific trait or physiological mechanism is expected to be most distinctively displayed or most experimentally accessible. We designate these organisms “Krogh organisms.” We clarify the differences between uses of model organisms and non-standard Krogh organisms. Among these is the use of Krogh organisms as “negative models” in biomedical research, where organisms are chosen for their dissimilarity to human physiology. Importantly, the representational scope of Krogh organisms and the generalizability of their characteristics are not fixed or assumed but explored through experimental studies. Research on Krogh organisms is steeped in the comparative method characteristic of zoology and comparative physiology, in which studies of biological variation produce insights into general physiological constraints. Accordingly, we conclude that the Krogh principle exemplifies the advantages of studying biological variation as a strategy to produce generalizable insights

How to Choose Your Research Organism

Despite August Krogh’s famous admonition that a ‘convenient’ organism exists for every biological problem, we argue that appeals to ‘convenience’ are not sufficient to capture reasoning about organism choice. Instead, we offer a detailed analysis based on empirical data and philosophical arguments for a working set of twenty criteria that interact with each other in the highly contextualized judgements that biologists make about organism choice. We propose to think of these decisions as a form of ‘differential analysis’ where researchers weigh multiple criteria for organismal choice against each other, and often utilize multidimensional refinement processes to finalize their choices. The specific details of any one case make it difficult to draw generalizations or to abstract away from specific research situations. However, this analysis of criteria for organismal choice and how these are related in practice allows us to reflect more generally on what makes a particular organism useful or ‘good.

Colour superconductivity in finite systems

In this paper we study the effect of finite size on the two-flavour colour superconducting state. As well as restricting the quarks to a box, we project onto states of good baryon number and onto colour singlets, these being necessary restrictions on any observable ``quark nuggets''. We find that whereas finite size alone has a significant effect for very small boxes, with the superconducting state often being destroyed, the effect of projection is to restore it again. The infinite-volume limit is a good approximation even for quite small systems.Comment: 14 pages RevTeX4, 12 eps figure

Influence of Chronic Exposure to Treated Sewage Effluent on the Distribution of White Blood Cell Populations in Rainbow Trout (Oncorhynchus mykiss) Spleen

Impairment of immune function in aquatic animals has been proposed as a possible consequence of low-level contamination of surface waters with anthropogenic substances such as through the discharge of wastewater into rivers, lakes, and oceans. The study at hand investigated the effects of chronic (32 weeks) exposure to sewage treatment plant (STP) effluent on the prevalence and distribution of different leucocyte populations in spleen samples of rainbow trout (Oncorhynchus mykiss). To simulate an infection, fish were injected intraperitoneally (ip) with inactivated Aeromonas salmonicida salmonicida, 6 weeks prior to the termination of the experiment. Immunohistological analysis revealed a marked decrease in thrombocyte numbers, an increase of monocytes, altered distribution of B-cells, and higher surface immunoglobulin expression, as well as activation of MHC class II expression in the spleen after exposure to 15% (v/v) effluent. The most prominent finding of the present study, however, was the occurrence of intraplasmatic deposits or inclusions with strong autofluorescence in spleen sections from effluent-exposed trout. In addition to effluent effects, injection of trout with A. salmonicida stimulated infiltration of monocytes, increased staining intensity on thrombocytes, and enhanced MHC class I expression in larger leucocytes surrounding melanomacrophage centres. In general, the current study demonstrates a marked, potentially adverse effect of STP effluent on spleen leucocytes and on the integrity of spleen tissue. The observed response suggests a constant unspecific stimulation of different leucocyte populations and is reminiscent of chronic inflammatio

Machine Learning Nucleation Collective Variables with Graph Neural Networks

The efficient calculation of nucleation collective variables (CVs) is one of the main limitations to the application of enhanced sampling methods to the investigation of nucleation processes in realistic environments. Here we discuss the development of a graph-based model for the approximation of nucleation CVs that enables orders-of-magnitude gains in computational efficiency in the on-the-fly evaluation of nucleation CVs. By performing simulations on a nucleating colloidal system mimicking a multistep nucleation process from solution, we assess the model's efficiency in both postprocessing and on-the-fly biasing of nucleation trajectories with pulling, umbrella sampling, and metadynamics simulations. Moreover, we probe and discuss the transferability of graph-based models of nucleation CVs across systems using the model of a CV based on sixth-order Steinhardt parameters trained on a colloidal system to drive the nucleation of crystalline copper from its melt. Our approach is general and potentially transferable to more complex systems as well as to different CVs

Extrinsic intestinal denervation modulates tumor development in the small intestine of ApcMin/+ mice

Background Innervation interacts with enteric immune responses. Chronic intestinal inflammation is associated with increased risk of colorectal cancer. We aimed to study potential extrinsic neuronal modulation of intestinal tumor development in a mouse model. Methods Experiments were performed with male ApcMin/+ or wild type mice (4 weeks old, body weight approximately 20 g). Subgroups with subdiaphragmatic vagotomy (apcV/wtV), sympathetic denervation of the small intestine (apcS/wtS) or sham operated controls (apcC/wtC) were investigated (n = 6-14 per group). Three months after surgical manipulation, 10 cm of terminal ileum were excised, fixed for 48 h in 4% paraformaldehyde and all tumors were counted and their area determined in mm2 (mean ± standard error of the mean (SEM)). Whole mounts of the muscularis of terminal ileum and duodenum (internal positive control) were also stained for tyrosine hydroxylase to confirm successful sympathetic denervation. Results Tumor count in ApcMin/+ mice was 62 ± 8 (apcC), 46 ± 11 (apcV) and 54 ± 8 (apcS) which was increased compared to wildtype controls with 4 ± 0.5 (wtC), 5 ± 0.5 (wtV) and 5 ± 0.6 (wtS; all p < 0.05). For ApcMin/+ groups, vagotomized animals showed a trend towards decreased tumor counts compared to sham operated ApcMin/+ controls while sympathetic denervation was similar to sham ApcMin/+. Area covered by tumors in ApcMin/+ mice was 55 ± 10 (apcC), 31 ± 8 (apcV) and 42 ± 8 (apcS) mm2, which was generally increased compared to wildtype controls with 7 ± 0.6 (wtC), 7 ± 0.4 (wtV) and 7 ± 0.6 (wtS) mm2 (all p < 0.05). In ApcMin/+ groups, tumor area was decreased in vagotomized animals compared to sham operated controls (p < 0.05) while sympathetically denervated mice showed a minor trend to decreased tumor area compared to controls. Conclusions Extrinsic innervation of the small bowel is likely to modulate tumor development in ApcMin/+ mice. Interrupted vagal innervation, but not sympathetic denervation, seems to inhibit tumor growth