Archive for the ‘Biology’ Category

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Charles Darwin’s Reaction to William Sharp MacLeay

September 11, 2014

Aaron Novick

Abstract: Charles Darwin, in his notebooks of the late 1830s, engaged in a sustained attempt to sort out the merits and demerits of the quinarian system (developed by William Sharp MacLeay and William Swainson in the 1820s and 1830s). By 1844, he could quickly dismiss the quinarian system as incompatible with his transmutationist theory. As yet there is no fully satisfying account (a) of this shift in opinion and (b) of the nature of Darwin’s engagement with the quinarian system. I aim to provide such an account.

 

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DAY-O-WIPs 4.0

July 14, 2014

“The Nature of Models and Modeling: Two Perspectives” Yoichi Ishida

“The Curious History of the Footless Tortoise” Aaron Novick

Evan Pence

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Four Issues in the History of the Quinarian System

January 24, 2014

Aaron Novick

Abstract: The secondary literature on the Quinarian system in biology, developed in the early 1800s by William Sharp MacLeay, is sparse. As a result, it is beset by insufficiencies. In part, it is simply missing information. All descriptions of the system (that I have read, which is most of them) have left out important aspects that are clear even on a first reading of MacLeay’s main work. In other parts, it is flatly contradictory: no one can agree on MacLeay’s philosophical influences, and the two sentences that exist discussing how the system developed over time are polar opposites. In one part, at least, the story of the Quinarian system’s death, there is a received view. But we cannot breathe easily, because I suspect it is wrong or least only partial. My presentation is aimed at helping me move from this mess to a clear history comp topic. As such, I will isolate four promising issues—what was the Quinarian system?; how was it born?; how did it live?; how did it die?—and then solicit advice on how to proceed.

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Realism, Instrumentalism, and Uses of Models in Science

January 13, 2014

Yoichi Ishida

Abstract: This paper argues in support of Howard Stein’s idea that in successful scientific research, a scientist uses a model according to the methodological principles of realism and instrumentalism despite the tension that they create among the scientist’s uses of the model over time. After giving precise formulations of the realist and instrumentalist methodological principles, I argue for my thesis through a detailed analysis of successful scientific research done by Seymour Benzer in the 1950s and 60s. I then argue that epistemic realism or epistemic instrumentalism—forms of realism and instrumentalism familiar in the philosophical literature—by itself prohibits a scientist from adopting both the realist and instrumentalist methodological principles. Stein’s conjecture thus poses new challenges to realists and instrumentalists, and I briefly suggest possible avenues of response that realists and instrumentalists may take.
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The Use of Usus and the Function of Functio: Teleology and its Limits in Descartes’ Physiology

January 11, 2013
Peter M. Distelzweig
Descartes frequently, explicitly, and controversially rejected appeals to final causes (glossed as divine ends) in natural philosophy. Nonetheless, Descartes employs the apparently teleological language of functio and usus in his physiology. Recently, scholars have given increased attention to the nature, extent, and consistency of this apparent teleology. However, little consensus has emerged. In this paper I examine this interpretive difficulty employing a new, two-pronged strategy. I seek to overcome the potential ambiguities in Descartes language by (1) turning our attention especially to the explanatory structures Descartes uses and by (2) focusing on the medical context of his physiology and the language of usus and functio. I employ work on the concept of ‘function’ in contemporary philosophy of biology in order to clarify my interpretive claims.
I argue that Descartes intends and primarily does employ usus and functio to provide ‘function-analytical’ explanations of the complex behavior of organisms and their organ systems. This was a familiar project, exemplified in (e.g.) the work of Jean Fernel (an influential medical writer of the 16th century). In it, usus are treated like Cummins-functions. Descartes’ goal in his physiology is to provide mechanical explanations to replace the metaphysically more extravagant versions in the medical tradition. I argue further that Descartes, nonetheless, does occasionally employ explanations like the final causal explanations characteristic of the work of anatomists Hieronymus Fabricius ab Aquapendente and his more famous student, William Harvey. In these, usus are treated like Wright-functions. I analyze two examples in Descartes: his explanation of the bicuspid character of the mitral valve of the heart and his explanation of the pscho-corporeal physiology of sensation. Finally, I argue that this kind of explanation is problematic for Descartes’ system: his only explicit strategy for grounding such explanations (appealing to divine non-deceptiveness) has significant difficulties—especially in the case of the mitral valve.
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Cartographers, Cardboard, and Wellington Boots

October 12, 2012
Yoichi Ishida

I’m going to give a true work-in-progress talk: I will briefly describe my dissertation project and then present some of my ideas from the first two chapters. I plan to discuss what sort of objects we should think models are and what it is to study their uses in everyday scientific research. I also present my tentative formulation of the distinction between representational and non-representational uses of models. Representational uses include those uses that philosophers commonly recognize as uses of models in science, such as descriptive or explanatory uses. But non-representational uses tend to be neglected or characterized (mistakenly, in my view) as representational uses, because we lack appropriate conceptual resources. So I will develop the necessary conceptual resources to recognize non-representational uses and illustrate them with a variety of examples, including some drawn from the research I did at the Caltech Archives. If time remains in the discussion period, we can explore some of the implications of these ideas for other philosophical topics—e.g., our understanding of realism and instrumentalism, the idea of a good model, as well as approaches to the evaluation of models—which I plan to discuss in the second half of my dissertation.

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Random Sampling, Offspring Distribution, and Genetic Drift

March 30, 2012

Yoichi Ishida

In population genetics, genetic drift as a phenomenon refers to non-directional or random changes in the frequency of types, such as alleles or genotypes, in a population. In its pure form, drift occurs in a population of finite size in the absence of any other evolutionary factors, such as selection, mutation, and migration. Both in biology and philosophy of biology, the common way of thinking about drift is in terms of random sampling. For example, each generation of a population of diploid organisms (like us) is thought to be a relatively small sample drawn randomly from an infinitely large pool of gametes produced by the previous generation of organisms. Because each generation may be an unrepresentative sample from the large pool of gametes, the allele frequency in a population may change randomly from generation to generation. In the paper I’m co-authoring with Alirio Rosales (UBC), we challenge this sampling-based thinking and suggest a viable alternative. This WIP talk will present our basic idea, and I will try to make it accessible to those without any detailed knowledge of population genetics or philosophy of biology.