Studies in History and Philosophy of Science, 2024
n this paper, John E. Huss discusses the book "What is Regeneration?" by Jane Maienschein and Kat... more n this paper, John E. Huss discusses the book "What is Regeneration?" by Jane Maienschein and Kate MacCord, which explores the concept of regeneration across various biological scales and contexts. The central question is whether there is a unified logic to regeneration, from limb regeneration in axolotls to ecological recovery after a fire. Huss examines historical perspectives, such as Frederick Clements' superorganism concept, and contemporary ideas like scale-free biology and process philosophy. He proposes that regeneration might be unified by viewing life as a single individual or through systems science frameworks. The paper highlights the potential benefits of a unified theory of regeneration for understanding life and facilitating cross-disciplinary scientific collaboration.
Etyka o współczesności Współczesność w etyce, 2016
Peter Singer's views on moral intuitions shed light on his practical ethics, but also point to a ... more Peter Singer's views on moral intuitions shed light on his practical ethics, but also point to a blind spot. Through evolutionary analysis bolstered by experimental moral psychology Singer debunks moral intuitions, yet moral intuitions are often the basis for criticizing his utilitarian bioethics. On global issues, Singer calls for a twopronged strategy: overriding intuition via reason, and establishing a global institutional ethic. Yet Singer fails to see what Peter Kropotkin saw clearly: moral
In the age of genomics, public understanding of complex scientific knowledge is critical. To comb... more In the age of genomics, public understanding of complex scientific knowledge is critical. To combat reductionistic views, it is necessary to generate and organize educational material and data that keep pace with advances in genomics. The view that CCR5 is solely the receptor for HIV gave rise to demand to remove the gene in patients to create host HIV resistance, underestimating the broader roles and complex genetic inheritance of CCR5. A program aimed at providing research projects to undergraduates, known as CODE, has been expanded to build educational material for genes such as CCR5 in a rapid approach, exposing students and trainees to large bioinformatics databases and previous experiments for broader data to challenge commitment to biological reductionism. Our students organize expression databases, query environmental responses, assess genetic factors, generate protein models/dynamics, and profile evolutionary insights into a protein such as CCR5. The knowledgebase generated in the initiative opens the door for public educational information and tools (molecular videos, 3D printed models, and handouts), classroom materials, and strategy for future genetic ideas that can be distributed in formal, semiformal, and informal educational environments. This work highlights that many factors are missing from the reductionist view of CCR5, including the role of missense variants or expression of CCR5 with neurological phenotypes and the role of CCR5 and the delta32 variant in complex critical care patients with sepsis. When connected to genomic stories in the news, these tools offer critically needed Ethical, Legal, and Social Implication (ELSI) education to combat biological reductionism.
A narrative of recurrent causation, the Nemesis hypothesis, holds that the Sun has a companion st... more A narrative of recurrent causation, the Nemesis hypothesis, holds that the Sun has a companion star, Nemesis, whose orbit perturbs comets from the Oort cloud into earth-crossing orbits leading to mass extinction by impact with a nearly clocklike periodicity. Here I discuss the pursuit of the Nemesis hypothesis as the pursuit of narrative closure. Using a framework drawing on formalist analysis of narratives that distinguishes between the ordering of events in the narrative discourse (the syuzhet) and in their chronological sequence (the fabula), I describe the processes of reading and rereading the fossil and geologic records. The resulting analysis dissolves false dichotomies between nomothetic and idiographic, and catastrophic and uniformitarian approaches in the historical sciences. It also accommodates diverse philosophical views about the nature of epistemic access to the past. 3.1 1 The impact hypothesis for the extinction of the dinosaurs and other taxonomic groups at the end of the Cretaceous period was put forward by Berkeley's Alvarez group (Alvarez et al. 1979; 1980). Resistance to the idea that impact is the general cause of mass extinctions was raised by, for example, Johns Hopkins palaeontologist Steven Stanley (1987). 2 On reading (and rereading) the fossil record, see Sepkoski (2012).
ious to know more about bird cognitive neurobiology, and how that field might advance. Having sai... more ious to know more about bird cognitive neurobiology, and how that field might advance. Having said that, my overall assessment remains very positive. I found I learned a great deal from reading this volume: about cognition in general and birds in particular. The individual chapters are all strong and the book is so well assembled that it was an enjoyable study.
ious to know more about bird cognitive neurobiology, and how that field might advance. Having sai... more ious to know more about bird cognitive neurobiology, and how that field might advance. Having said that, my overall assessment remains very positive. I found I learned a great deal from reading this volume: about cognition in general and birds in particular. The individual chapters are all strong and the book is so well assembled that it was an enjoyable study.
A narrative of recurrent causation, the Nemesis hypothesis, holds that the Sun has a companion st... more A narrative of recurrent causation, the Nemesis hypothesis, holds that the Sun has a companion star, Nemesis, whose orbit perturbs comets from the Oort cloud into earth-crossing orbits leading to mass extinction by impact with a nearly clocklike periodicity. Here I discuss the pursuit of the Nemesis hypothesis as the pursuit of narrative closure. Using a framework drawing on formalist analysis of narratives that distinguishes between the ordering of events in the narrative discourse (the syuzhet) and in their chronological sequence (the fabula), I describe the processes of reading and rereading the fossil and geologic records. The resulting analysis dissolves false dichotomies between nomothetic and idiographic, and catastrophic and uniformitarian approaches in the historical sciences. It also accommodates diverse philosophical views about the nature of epistemic access to the past.
Is philosophy of medicine a subfield of philosophy of science? Of philosophy of biology? Should i... more Is philosophy of medicine a subfield of philosophy of science? Of philosophy of biology? Should it overlap with bioethics? Or is it its own field like philosophy of technology or philosophy of law? Should we worry about the reliability of medical knowledge? With such questions in mind, I briefly review three books in the philosophy of medicine: an introductory survey by R. Paul Thompson and Ross E.G. Upshur, a philosophical critique of medicine by Jacob Stegenga, and a breast cancer survivor's bid for philosophical consolation by Mary Ann Cutter. To philosophers of science, Thompson and Upshur's and Stegenga's contributions will be recognizable as an application of the tools of philosophy of science to medicine. Cutter's book comes from a different tradition, traceable to the philosophy of medicine of Tristram Engelhardt. Thus, while the nature and reliability of medical knowledge takes up most of this review, the issue of demarcation-what philosophy of medicine is and how it relates to philosophy of science, bioethics, and perhaps social and political philosophy-is raised just by virtue of the variety in the books reviewed. In my view, philosophy of medicine should be aware of its relationship to these other fields of philosophy and draw upon them. Thompson and Upshur's Philosophy of Medicine: An Introduction goes well beyond offering a survey of issues in the field. Distinguishing between bench medicine (experimental research and model-building closely allied to biology, chemistry, and physics) and clinical medicine (13), their core thesis-introduced early with contrasting capsule summaries of James Lind's 1753 discovery of the cure for scurvy (6) and Victor Bolie's 1960 glucose-insulin model (7)-is that the mathematical and mechanistic
In this paper, I discuss several temporal aspects of paleontology from a philosophical perspectiv... more In this paper, I discuss several temporal aspects of paleontology from a philosophical perspective. I begin by presenting the general problem of "taming" deep time to make it comprehensible at a human scale, starting with the traditional geologic time scale: an event-based, relative time scale consisting of a hierarchy of chronological units. Not only does the relative timescale provide a basis for reconstructing many of the general features of the history of life, but it is also consonant with the cognitive processes humans use to think about time. Absolute dating of rocks, fossils, and evolutionary events (such as branching events on the tree of life) can be accomplished through the use of radiometric dating, chronological signals extractable from fossil growth patterns, and the "molecular clock." Sometimes these different methods of absolute dating, which start from largely independent assumptions and evidentiary bases, converge in their temporal estimates, resulting in a consilience of inductions. At other times they fail to agree, either because fossils and molecules are giving temporal information about different aspects of nature and should not be expected to agree, or because of flawed assumptions that give rise to an inaccurate estimate. I argue that in general, despite the fact that it can be difficult to integrate disparate kinds of evidence, the principle of total evidence should be applied to the dating of evolutionary events. As a historical science, paleontology studies past events we cannot observe directly. This raises questions of epistemic access, meaning that due to the fragmentary nature of the fossil record we may find ourselves without access to the relevant traces to adjudicate between rival hypotheses about the past. The problems and prospects of epistemic access are explored through a case study of the reconstruction of the colors of dinosaurs. The paper closes with a reflection on the Darwin-Lyell metaphor of the fossil record as a highly fragmentary history book, and a call for a reconsideration of the book metaphor in favor of a systems view of the geologic and fossil records.
Sciences 2016). These elements should be taken into account when designing research that involves... more Sciences 2016). These elements should be taken into account when designing research that involves vulnerable populations. CONCLUDING THOUGHTS: GET REAL When it comes to FMT, the concern about uncertainties, vulnerabilities, and protections may actually be beside the point. Today, do-it-yourself FMT is a fact of life. Instructions abound on the Internet so that anyone with a willing fecal material donor can accept the risks and give it a try for any purpose. In this environment, it is important to be realistic about the effects of overly cautious constraints that would limit research participation. Although it is important to study FMT's therapeutic potential, to the extent that desperate patients are eager to try it, creating barriers to their research participation will only drive them to the do-it-yourself option. Because we need to learn about which uses of FMT are safe and effective, we should try to make the research environment as accepting and supportive as possible. Because all of society will be paying the price, instead of building walls, we should be extending helping hands.
Research on the human microbiome has generated a staggering amount of sequence data, revealing va... more Research on the human microbiome has generated a staggering amount of sequence data, revealing variation in microbial diversity at the community, species (or phylotype), and genomic levels. In order to make this complexity more manageable and easier to interpret, new units-the metagenome, core microbiome, and enterotype-have been introduced in the scientific literature. Here, I argue that analytical tools and exploratory statistical methods, coupled with a translational imperative, are the primary drivers of this new ontology. By reducing the dimensionality of variation in the human microbiome, these new units render it more tractable and easier to interpret, and hence serve an important heuristic role. Nonetheless, there are several reasons to be cautious about these new categories prematurely ''hardening'' into natural units: a lack of constraints on what can be sequenced metagenomically, freedom of choice in taxonomic level in defining a ''core microbiome,'' typological framing of some of the concepts, and possible reification of statistical constructs. Finally, lessons from the Human Genome Project have led to a translational imperative: a drive to derive results from the exploration of microbiome variation that can help to articulate the emerging paradigm of personalized genomic medicine (PGM). There is a tension between the typologizing inherent in much of this research and the personal in PGM.
The exploration of popular culture topics by academic philosophers for non-academic audiences has... more The exploration of popular culture topics by academic philosophers for non-academic audiences has given rise to a distinctive genre of philosophical writing. Edited volumes with titles such as Black Sabbath and Philosophy or Buffy the Vampire Slayer and Philosophy contain chapters by multiple philosophical authors that attempt to bring philosophy to popular audiences. Two dominant models have emerged in the genre. On the pedagogical model, authors use popular culture examples to teach the reader philosophy. The end is to promote philosophical literacy, defined as acquaintance with the key problems, ideas, and figures in the history of philosophy. In contrast, on the applied philosophy model, authors use philosophy to open up new dimensions of the popular culture topic for fans. The end is to illustrate the value of philosophy in understanding the popular culture topic, and ultimately, to demonstrate the value of philosophy in general. Taking stock of the relative strengths and weaknesses of these two models provides an opportunity to reflect more broadly on whether, why, and how philosophers should engage the public.
In the age of genomics, public understanding of complex scientific knowledge is critical. To comb... more In the age of genomics, public understanding of complex scientific knowledge is critical. To combat reductionistic views, it is necessary to generate and organize educational material and data that keep pace with advances in genomics. The view that CCR5 is solely the receptor for HIV gave rise to demand to remove the gene in patients to create host HIV resistance, underestimating the broader roles and complex genetic inheritance of CCR5. A program aimed at providing research projects to undergraduates, known as CODE, has been expanded to build educational material for genes such as CCR5 in a rapid approach, exposing students and trainees to large bioinformatics databases and previous experiments for broader data to challenge commitment to biological reductionism. Our students organize expression databases, query environmental responses, assess genetic factors, generate protein models/dynamics, and profile evolutionary insights into a protein such as CCR5. The knowledgebase generated...
As the international genomic research community moves from the tool-making efforts of the Human G... more As the international genomic research community moves from the tool-making efforts of the Human Genome Project into biomedical applications of those tools, new metaphors are being suggested as useful to understanding how our genes work-and for understanding who we are as biological organisms. In this essay we focus on the Human Microbiome Project as one such translational initiative. The HMP is a new 'metagenomic' research effort to sequence the genomes of human microbiological flora, in order to pursue the interesting hypothesis that our 'microbiome' plays a vital and interactive role with our human genome in normal human physiology. Rather than describing the human genome as the 'blueprint' for human nature, the promoters of the HMP stress the ways in which our primate lineage DNA is interdependent with the genomes of our microbiological flora. They argue that the human body should be understood as an ecosystem with multiple ecological niches and habitats in which a variety of cellular species collaborate and compete, and that human beings should be understood as 'superorganisms' that incorporate multiple symbiotic cell species into a single individual with very blurry boundaries. These metaphors carry interesting philosophical messages, but their inspiration is not entirely ideological. Instead, part of their cachet within genome science stems from the ways in which they are rooted in genomic research techniques, in what philosophers of science have called a 'tools-totheory' heuristic. Their emergence within genome science illustrates the complexity of conceptual change in translational research, by showing how it reflects both aspirational and methodological influences.
Book Reviews Planet of the Apes and Philosophy: Great Apes Think Alike
Perhaps only a handful of fictional works can compete with Pierre Boulle’s (1912-1994) novel Plan... more Perhaps only a handful of fictional works can compete with Pierre Boulle’s (1912-1994) novel Planet of the Apes (La planète des singes, 1963) in terms of cinematographic fecundity and longevity; the original narrative sparked a franchise comprising (so far) nine motion pictures: Planet of the Apes (Franklin J. Schaffner, 1968); Beneath the Planet of the Apes (Ted Post, 1970); Escape from the Planet of the Apes (Don Taylor, 1971); Conquest of the Planet of the Apes (J. Lee Thompson, 1972); Battle for the Planet of the Apes (J. Lee Thompson, 1973); Planet of the Apes (Tim Burton, 2001); Rise of the Planet of the Apes (Rupert Wyatt, 2011); Dawn of the Planet of the Apes (Matt Reeves, 2014); War for the Planet of the Apes (Matt Reeves, 2017). To the films one must add a fourteen-episode TV series also titled Planet of the Apes (1974) and a thirteen-episode animated series titled Return to the Planet of the Apes (1975). And perhaps only a handful of franchises can compete with Planet of ...
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