Research

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

 

When is a cladist a cladist?

In progress

 

I trace the connection between parsimony vs. likelihood, supermatrix vs. supertree, and concatenation vs. coalescence debates, via the principle of total evidence.

 

Concatalypse Now: Competing methods and paradigms in phylogenetics

In progress

 

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)

 

Edwards et al. 2016. Coalescence uses the discordance between gene trees to infer a species tree.

 

On Brandon's zero-force law

Bartlett & Quinn, in progress

 

With Ben Bartlett, physics student at Caltech: Brandon's arguments that genetic drift constitutes the inertial state for evolutionary biology are faulty. Applying Brandon's criteria, drift constitutes an evolutionary force. 

 

Whewell on classification and consilience

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

 

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

 

 

When is a cladist not a cladist?

2017 Biology and Philosophy 32(4): 581-598. 10.1007/s10539-017-9577-z

 

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.

 

 

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

 

Sceloporus occidentalis push pigment through skin layers to display blue chins and bellies when warm and for sexual displays.

 

How to classify animals

Forthcoming in How to Do Things With Animals: Imagined Field Guides for Social Tasks (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.

 

 

 

Field expedition with ichthyologist Luke Tornabene (UW, BM) in search of lizards.

 

 

 

Run the experiment, publish the study, close the sale: commercialized biomedical research

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

 

 

 

Girard's draft of mammal classification. SI Archives

Charles Girard: relationships and representation in 19th century systematics

2016 Journal of the History of Biology 10.1007/s10739-016-9447-6

 

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 three dimensional structures.

 

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, University of Quebec a Montreal, 5-10 July 2015

 

Girard intended this chart to be viewed as a cone

 

William Whewell's philosophy of architecture and the historicization of biology

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

 

Phylogenetic inference to the best explanation and the bad lot argument

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.

 

Taxonomic revision of the Olingos (Bassaricyon) with description of a new species, the Olinguito

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.

 

Biological systematics and evolutionary theory

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.

 

Tasmanian Tiger - the tragic tale of how the world lost its most mysterious predator [book review]

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

 

The last Tasmanian Tiger: the history and extinction of the Thylacine [book review]

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

 

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

 

Daubentonia madagascariensis

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

 

Indri indri

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

 

Indri, Indri indri. Photo credit Russ Mittermeier.

 

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