Research

Plethodon cinereus red-back phase.

Nagel, Bartlett, Quinn, & Goldsby, in progress

With Ben Bartlett (Dept. of Physics, Stanford), Michael Goldsby (Philosophy, WSU), & Todd Nagel (Philosophy, Western): Brandon's arguments that genetic drift constitutes the inertial state for evolutionary biology are faulty. Applying Brandon's criteria, drift constitutes an evolutionary force. 

Plethodon cinereus lead-back phase.

Mole Kingsnake, Lampropeltis calligaster. Multiple new species have been proposed within this genus, but the putative contact zones were not sampled.

Revise & resubmit

A critical analysis of the use of mtDNA barcoding and the Multi-Species Coalescent for species delimitation. New data and methods enable splitting lineages on the basis of more or less ephemeral population structure.

Philosophy of Biology at the Mountains, University of Utah, 14-18 May 2018

Research supported by a SEED grant from the Office of Research and Educational Development, University of Idaho

Black Rat Snake, Pantherophis obsoletus, in shed. The number of species in this complex is contested.

Degnan & Rosenberg 2009. Species tree may not match all gene trees.

Revise & resubmit

I explicate the claim that one family of computational models in contemporary studies of biodiversity (concatenation) constitutes a special case of a more general set of models (coalescence). I clarify Edwards et al.'s (2016) claims that phylogenetics is a "special case" of population genetics. By comparison with earlier debates and mathematical reductions, I show that (pace Edwards) the concatenation vs. coalescence disputes reflect competing paradigms. The debate turns on competing interpretations of "first principles".

International Congress of History of Science and Technology, Federal University of Rio de Janeiro, 23-29 July 2017

International Society for the History, Philosophy, and Social Studies of Biology, Federal University of Sao Paulo, 16-21 July 2017 (NSF supported)

Species in the Age of Discordance, University of Utah, 23-25 March 2017 (NSF supported)

Forthcoming in Philosophy, Theory, and Practice in Biology 

I trace the connection between parsimony vs. likelihood, taxonomic congruence vs. simultaneous analysis, and concatenation vs. coalescence debates, via the principle of total evidence.

Models and Simulations 8, University of South Carolina, 15-17 March 2018

Northwestern Philosophy Conference, Washington State University, 5-7 October 2017

Interpretation of Edwards et al.'s claims about the relationships between theories/models.

The Multi-Species Coalescent. Widely used to  infer relationships between species, and increasingly (but problematically) for species delimitation.

Bateson's publication and defense of Mendel's experiments. 

Forthcoming in Unnatural Kinds: Perspectives on Classification in Synthetic Sciences (Julia Bursten, ed.). London: Routledge History and Philosophy of Technoscience Book Series. 

I analyze analogies of the units of genetics to the units of chemistry, focusing on William Bateson. Bateson did not intend an empirical claim about the nature of characters, genes, or species, but rather a theoretical claim that he hoped would advance the science of genetics. I also demonstrate that Bateson thought that species were not regarded as fixed entities until the eighteenth century, and that the fixation of species was an important scientific advance. Bateson expected his readers to understand his analogies in light of this historical background.

History of Science Society Annual Meeting, 1-4 November 2018

Canadian Society for History and Philosophy of Science, 26-28 May 2018

Bateson's work on variation and the relationship between genetics and development.

Ambystoma maculatum. 

2018 Pp. 187-198 in Living with Animals: Bonds Across Species (Natalie Porter & Ilana Gershon, eds.). Ithaca, NY: Cornell University Press

A sociological essay on scientists who study biodiversity, written as a [fictional] letter to an aspiring biologist. The volume explores human/animal interactions from multi-disciplinary perspectives.

http://www.cornellpress.cornell.edu/book/?GCOI=80140101657200

Batrachospes major from the most disturbed habitat I can imagine. 

Branch length calculation using maximum parsimony. "Cladists" in the sense used by many biologists  favor this methodology.

2017 Biology and Philosophy 32(4): 581-598.

This paper clarifies substantial confusion in use of the term "cladist" by biologists and philosophers. Resolving this confusion reveals what is at stake in ongoing debates between proponents of distinct mathematical models for studying biodiversity.

Joint Meetings of the American Society of Ichthyologists and Herpetologists, Rochester NY 11-15 July 2018

Common mechanism version of maximum likelihood model. Biologists who favor this methodology fit many philosophers' use of "cladist", but not (now) many biologists'. 

Candolle's Theorie Elementaire was Whewell's main source for classificatory history and theory.

2017 Studies in History and Philosophy of Biological and Biomedical Sciences 64: 65-74.

I analyze Whewell's attempts to impose order on classificatory mineralogy, in Whewell's day (1794-1866) a confused science of uncertain prospects. By comparison with biological classification, Whewell proposed methodological reforms that he claimed would lead to a natural classification of minerals, which in turn would support advances in causal understanding of the properties of minerals. Whewell's comparison to successful biological classification is particularly striking given that classificatory biologists did not share an understanding of the causal structure underlying the natural classification of life (the common descent with modification of all organisms).

American Institute of Physics Biennial Early-Career Conference, Annapolis, 6-10 April 2016

Whewell studied with Moh to produce a mineralogical classification.

Girard's draft of mammal classification. SI Archives

2017 Journal of the History of Biology 50(3): 609-643

What did pre-Darwinian biologists think they were doing when they made claims about species and relationships between species? And how did they get anything right? Girard argued for three distinct forms of natural relationship, which compelled him to represent biodiversity via diagrams intended to be read in three dimensions.

Biological Sciences Seminar Series, University of Idaho, 12 January 2018

Ecology & Evolutionary Biology Seminar, University of California at Santa Barbara, TBD

Burke Museum of Natural History, TBD

Vertebrate Zoology Seminar, National Museum of Natural History, 24 August 2016

International Society for the History, Philosophy, and Social Studies of Biology, Université du Québec à Montréal, 5-10 July 2015

Girard intended this chart to be viewed as a cone.

2016 de Ethica 3(2): 5-21

Market forces have driven commercialized biomedical research to a structure that cannot take responsible account of scientific and social values.

Canadian Society for History and Philosophy of Science, Brock University, 24-26 May 2014

Long Island Philosophical Society, Molloy College, 26 April 2014

APA Pacific, San Diego, 15-18 April 2014

2016 Studies in History and Philosophy of Biological and Biomedical Sciences 59: 11-19

Whewell developed a theory of historical inference: how to make and defend scientific claims about what happened in the past. Following Darwin's publication, biological inference changed in some of the ways that Whewell analyzed. Karl Gegenbaur reasoned about the construction of organisms in much the same way that Whewell reasoned about the historical development of Gothic architecture.

The Making of the Humanities V, Johns Hopkins University, 5-7 October 2016

History of Science Society, Chicago, 6-9 November 2014

2016 Synthese 193(9): 3025-39.

Biologists who study biodiversity have devised a formal structure of inference that answers the bad lot objection to abductive inference. Modern computational approaches to biodiversity provide methodological solutions to this philosophical challenge.

Olinguito. Photo credit Mark Gurney.

Helgen, K.M., C.M. Pinto, R. Kays, L.E. Helgen, M.T.N. Tsuchiya, A. Quinn, D.E. Wilson, & J.E. Maldonado. 2013. Zookeys 324: 1-83.

We used morphological, genetic, and bioegeographic analyses to review the genus Bassaricyon. We discovered the first new species of Carnivore in the Western hemisphere in 35 years. The Olinguito was named one of the Top 10 New Species of the year by the International Institute for Species Exploration, and our paper is currently the all-time most downloaded paper in the journal.

Press conference at the Smithsonian Castle, attended by CNN, NBC, ABC, BBC, NYT, etc.

Cathedral of Learning, University of Pittsburgh.

Work-in-progress talks with graduate students at Pitt.

2015 Dissertation, History & Philosophy of Science, University of Pittsburgh. James Lennox (HPS), Director. Sandra Mitchell (HPS), Kenneth Schaffner (HPS, Psychology, & Psychiatry), and Jeffrey Schwartz (Anthropology & HPS).

I critique the view that scientists use causal theories to hypothesize what past chains of events must have been, and then form hypotheses that identify segments of a network of events and causal transactions between events. Twentieth century philosophers of science tacitly adopted this assumption in otherwise distinct models of explanation. As Whewell pointed out in his critique of J.S. Mill, the problem with this assumption is that the delineation of events via properties is itself the hard part of science. Whewell’s account of historical science and of consilience provide a better foothold for understanding the study of biodiversity after Darwin’s revolution as a form of abductive inference. I conclude by showing how two challenges that are frequently pressed against abductive inference are met in the context of phylogenetic inference.

21st Annual Kent State May 4th Philosophy Graduate Student Conference, 15 March 2014

North Carolina Philosophical Society Meeting, Durham, 22-23 February 2014

Western Michigan University Graduate Philosophy Conference, Kalamazoo, 6-8 December 2013

Bassaricyon study (see above) served as an example in my diss.

Quinn, A. & D.E. Wilson 2005 Journal of Mammalogy 86(3): 639-40.

Quinn, A., & D.E. Wilson 2005 Journal of Mammalogy 86(3): 639

Aye-aye, Daubentonia madagascariensis. Photo credit Duke University Lemur Center.

Quinn, A., & D.E. Wilson 2004. Mammalian Species 740: 1-6

Quinn, A., & D.E. Wilson 2002. Mammalian Species 694: 1-5

Indri, Indri indri. Photo credit Russ Mittermeier.