2022. OUR GENES: 
A Philosophical Perspective on Human Evolutionary Genomics
[Book website @ Cambridge University Press
20% Discount with code: OUGE2022
Cambridge University Press.

2023. With Eske Willerslev. "Wilson and Sarich (1969): The birth of a molecular evolution research paradigm,"
Proceedings of the National Academy of Sciences (PNAS)
[PNAS Website Open Access]

2022. "Models and Maps,"
For _The Routledge Handbook of Philosophy of Scientific Modeling_
(Knuuttila, T., Carrillo, N., and Koskinen, R., eds.) Routledge.
[Download PDF]

2022. "Dawkins or Lewontin or Both?" Review of J. Arvid Ågren Gene’s-Eye View of Evolution, Oxford University Press,
In _Evolution_
[Download PDF]

Remapping Race in a Global Context
[Book website @ Routledge]
(Routledge, 2022; co-edited with Ludovica Lorusso)

2022. "Richard Lewontin as Master Dialectician. Rest in Power, Dick."
Science for the People 
Alternate Figure: "Lewontin's Globe"  

2022. "Lewontin (1972)" 
For: _Remapping Race in a Global Context_
(L. Lorusso and R.G. Winther, eds.), Routledge.
[Download PDF

2022. "Map Thinking across the Life Sciences," 
For: _The Routledge Handbook of Geospatial Technologies and Society_ 
(A.J. Kent and D. Specht, eds.), Routledge.
[Download PDF]

2022. "Race and Human Genomic Variation,"
For: _Speciesism: How Human Exceptionalism is Pushing Planetary Boundaries_
(B. Swartz and B.D. Mishler, eds.), Springer Nature (Open Access).
[Download PDF]

2022. With Annika Döring. “The Human Condition is an Ocean: 
Philosophy and the Mediterranean Sea,” 
For: _Words and Worlds: Use and Abuse of Analogies and Metaphors within Sciences and Humanities_ 
(S. Wuppuluri and A.C. Grayling, eds.), Synthese Library Series. 
[Download PDF]

2021. ¿El ombligo del mundo? Mapas y contramapas
_Revista de la Universidad de México_ (Guadalupe Nettel, ed.) “Imperialismo,” noviembre, pp. 60-67
[Download PDF]

2020. WHEN MAPS BECOME THE WORLD (University of Chicago Press, 2020) 
[Book website @ University of Chicago Press]
• Perhaps because of my nomadic life, my strong attraction to all scientific theories across the disciplines, and my simultaneous and mutually constitutive obsessions with philosophy and cartography, I suspect that I am the right person to write a book that, I also feel, _needed_ to be written. When I was a graduate student, a close friend offered me advice in the form of a quote from computer scientist Edsger W. Dijkstra: “Do only what only you can do.” This book is my attempt to make that contribution. Hopefully it will inspire you in ways you might not have imagined, and I look forward to hearing from you about your response to the book, but also about where I can improve its thesis and structure, and how I can work with you to build a better world.

2020. "On Conspiracy Theories and Real Science," Ludus Vitalis 28(53): 109-110.
[Download PDF]

2022. "Philosophical Cartography" 
For: Routledge Volume on _Global Epistemologies and Philosophies of Science_, edited by David Ludwig, Inkeri Koskinen, Zinhle Mncube, Luana Poliseli, Luis Reyes-Galindo
[Download PDF]
• Following discussions in my _When Maps Become the World_ (2020), I here explore how mapping and the map analogy have received sustained philosophical attention, as well as how the cartographic impulse to map our worlds spatially lies deep in our cognitive structure and cultural history. The role of map thinking is briefly reviewed in three philosophical fields: Anglo-American analytic philosophy, “continental” European philosophy, and pragmatic philosophy. By analyzing an Ancient Chinese map, and Marshall Island mapping practices, I also show map thinking in action regarding the philosophy of politics, and overcoming philosophical debates around constructivism, empiricism, and realism.

2019. Review of Future Humans by Scott Solomon, for The Quarterly Review of Biology.
[Download PDF]

2019. "A Beginner's Guide to the New Population Genomics of Homo sapiens: Origins, Race, and Medicine." The Harvard Review of Philosophy [Download PDF]
• It is important to understand the science underlying philosophical debates. In particular, careful reflection is needed on the scientific study of the origins of Homo sapiens, the division of current human populations into ethnicities, populations, or races, and the potential impact of genomics on personalized medicine. Genomic approaches to the origins and divisions of our species are among the most multi-dimensional areas of contemporary science, combining mathematical modeling, computer science, medicine, bioethics, and philosophy of biology. The best evidence suggests that we are a young species, with a cradle in Africa. While prejudice, misunderstanding, and violence grow in many corners of the world, our best genomic science suggests a deep biological connection among all peoples.

2019. "As Though They Are Real: The five horsemen of the ecological apocalypse (and the return of hope)." MEDIUM.COM (online)
• The five horsemen of the environmental apocalypse are galloping towards you. Will it be business as usual, or will you try something different? Think quick, there’s not much time. Seventeenth-century Pascal’s wager might help you answer.

2019. "Take Your Time: Your greatest accomplishment may still be unfolding." MEDIUM.COM (online)

2019. "¿De dónde venimos? Orígenes humanos y genómica," ORÍGENES Revista de la Universidad de México  (Guadalupe Nettel, ed.), pp. 8-15 [Online ArticleDownload Entire PDF]
• ¿El _Homo sapiens_ del año 2020 es más parecido a los habitantes del planeta Unidad o de Galápagos a gran escala? ¿Y qué nos dice esto sobre nuestra historia evolutiva y hacia dónde podríamos dirigirnos? La genética y la genómica modernas nos enseñan que nuestra especie es mucho más cercana a la de Unidad. La variación genética humana muestra que nuestra especie es relativamente joven, se ha expandido con rapidez y presenta una variación genética bastante continua a lo largo de toda nuestra geografía. Sin embargo, abundan las controversias.

2019. "Mapping the Deep Blue Oceans," The Philosophy of GIS (Timothy Tambassi, ed.), 
Springer Verlag [Download PDF.]
• The ocean terrain spanning the globe is vast and complex – far from an immense flat plain of mud. To map this terrain accurately and wisely, we must understand how cartographic abstraction and generalization work both in analog cartography and digital GIS. This chapter explores abstraction practices such as selection and exaggeration with respect to mapping the oceans, showing significant continuity in such practices across cartography and contemporary GIS. The role of measurement and abstraction—as well as of political and economic power, and sexual and personal bias—in these sciences is illustrated by the biographies of Marie Tharp and Bruce Heezen, whose mapping of the Mid-Atlantic Ridge precipitated a paradigm shift in geology.

2020. "Cutting the Cord: A Corrective for World Navels in Cartography and Science," The Cartographic Journal (British Cartographic Society) [Download PDF.]
• A map is not its territory. Taking a map too seriously may lead to _pernicious reification_: map and world are conflated. As one family of cases of such reification, I focus on maps exuding the omphalos syndrome, whereby a centred location on the map is taken to be the world navel of, for instance, an empire. I build on themes from my book _When Maps Become the World_, in which I analogize scientific theories to maps, and develop the tools of _assumption archaeology_ and _integration platforms_. Here I argue that excavating assumptions helps fill cartographic silences, showing the limitations of perspectives often at war. Furthermore, integrating perspectives permits resisting imperial central or master images. A worthwhile future project would be a repository of world-navel maps, critically annotated with cultural context and imperial information. Mutual understanding may result from such an integration platform, perhaps implemented online or in a museum.

2018. Phylogenetic Inference, Selection Theory, and History of Science: Selected Papers of A. W. F. Edwards with Commentaries. Cambridge University Press.
• A. W. F. Edwards is one of the most influential mathematical geneticists in the history of the discipline. One of the last students of R. A. Fisher, Edwards pioneered the statistical analysis of phylogeny in collaboration with L. L. Cavalli-Sforza, and helped establish Fisher's concept of likelihood as a standard of statistical and scientific inference. In this book, edited by philosopher of science Rasmus Grønfeldt Winther, Edwards's key papers are assembled alongside commentaries by leading scientists, discussing Edwards's influence on their own research and on thinking in their field overall. In an extensive interview with Winther, Edwards offers his thoughts on his contributions, their legacy, and the context in which they emerged. This book is a resource both for anyone interested in the history and philosophy of genetics, statistics, and science, and for scientists seeking to develop new algorithmic and statistical methods for understanding the genetic relationships between and among species both extant and extinct.

2015. (2020 revision) The Structure of Scientific Theories. 
The Stanford Encyclopedia of Philosophy
  • ​This entry in the SEP scrutinizes the structure of scientific theories from the perspective of three major positions: the Syntactic, Semantic, and Pragmatic Views. These views have decidedly different implications about how best to characterize the composition and function of theories, how to link up theory with the world, and how one should go about describing or reconstructing a theory. In fact, they do not even agree on which aspects of scientific practice must be accounted for when providing an analysis of scientific theories. However, it is suggested that further work in this area may show that these three viewpoints are best understood, not as competitors, but as complimentary tools within the philosopher’s toolbox. 

2018. "Race and Biology," The Routledge Companion to the Philosophy of Race (Linda Alcoff, Luvell Anderson, and Paul Taylor, eds.), Routledge, New York, pp. 305-320. [Download PDF from academia.com.]
  • The ontology of race is replete with moral, political, and scientific implications. This book chapter surveys proposals about the reality of race, distinguishing among three levels of analysis: biogenomic, biological, and social. The relatively homogeneous structure of human genetic variation casts doubt upon the practice of postulating distinct biogenomic races that might be mapped onto socially recognized race categories.

2015. "Introduction: Genomics and Philosophy of Race," Studies in the History and Philosophy of Science, Part C 52: 1-4. Co-edited with Roberta Millstein and Rasmus Nielsen. Contributors include: Jonathan M. Kaplan, Massimo Pigliucci, Noah Rosenberg, Quayshawn Spencer, the three co-editors, and others. 
[Editorial Introduction: Download PDF from philpapers.com.]
  • Productive interdisciplinary conversation requires openness, patience, and charity; physical proximity is also an important consideration. During the 2013-2014 academic year, a group of biologists, philosophers, and social scientists met for two workshops (Stanford, UC Davis) and a public conference (UC Santa Cruz) to discuss a variety of concerns surrounding genomics and race. As a group we shared a commitment to thinking critically about how theoretical population genetics and genomics conceptualize and model certain constructs, such as “populations,” which, in turn, are deemed by some to be “races.” Of course there was not complete agreement, but we benefited tremendously from becoming more philosophically informed scientists and more scientifically informed philosophers.

2015. "Evo-Devo as a Trading Zone" in Conceptual Change in Biology: Scientific and Philosophical Perspectives on Evolution and Development. (A. Love, ed.), Springer Verlag, Boston Studies in the Philosophy of Science, pp. 459-482. [Download PDF.]
  • Evolutionary developmental biology (Evo-devo) can be usefully understood as a trading zone (Galison 1997). That is, Evo-devo is constituted by a variety of disciplines, styles, and paradigms negotiating heavily with one another. I am concerned with the differences, interactions, and relative openness and flexibility of these cultures. When are the cultures acting—individually or collectively—in ways that further research empirically, theoretically, and ethically? When do they become imperialistic, in the sense of excluding and subordinating other cultures? The goal of this chapter is to identify six cultures of Evo-devo (three styles and three paradigms) and provide an assumption archaeology of their internal structure, and mutual relations, through the concept of a trading zone. My main excavation site is Bonner (1982), a founding text of Evo-devo and product of the 1981 Dahlem conference on evolution and development. 

2015. With Ryan Giordano, Michael D. Edge, and Rasmus Nielsen. The Mind, the Lab, and the Field: Three Kinds of Populations in Scientific Practice. Studies in the History and Philosophy of Science, Part C 52: 12-21 [Download PDF.]
  • Three different kinds of populations in studies of ecology and evolution are distinguished: theoretical, laboratory, and natural (as exemplified by the work of R. A. Fisher, Thomas Park, and David Lack, respectively). We adduce three examples in order to examine the interplay between these different kinds of populations: first, the notion of “effective” population size; second, the work of Thomas Park on Tribolium populations; and third, model-based clustering algorithms such as STRUCTURE. We conclude by discussing ways to move safely between the three population types while avoiding the mistake of confusing models with reality.

2014. World Navels. Cartouche. Canadian Cartographic Association 89: 15-21. [Download PDF from academia.com.]
  • This piece examines how hegemonic power is graphically represented through maps that place the seat of a nation or empire at the center – a complex set of representational practices that has been baptized the “omphalos syndrome.” Such mapping practices demonstrate that “the habit of equating one’s age with the apogee of civilization, one’s town with the hub of the universe, one’s horizons with the limits of human awareness, is paradoxically widespread” (Levin 1963, 268). In fact, although the omphalos syndrome is most obviously exhibited by powerful empires, it could be argued that this form of thinking is an inescapable feature of c​ulture in general.

2014. Determinism and Total Explanation in the Biological and Behavioral Sciences. Encyclopedia of Life Sciences. [Download PDF from academia.com]
  • Which methods are available for studying such complex and multi-factorial phenomena as sexuality, intelligence, and autism, and is there any way of aggregating multiple perspectives so as to arrive at a “total explanation”? This article inspects thinking about causation in the temporal evolution of biological and behavioral systems, with special attention paid to statistical methods and the role of determinism. In the end, it is suggested that apparently incommensurable projects and methodologies might in fact produce a “floodlight” vision of reality constituted by various particular “spotlights.” ​

2014. With Carlos Montemayor. Review of Stanislas Dehaene and Elizabeth Brannon Space, Time and Number in the Brain. Searching for the Foundations of Mathematical Thought. (Academic Press; Elsevier), The Mathematical Intelligencer. [Download PDF from philpapers.com.] 
  • This co-written piece reviews Dehaene and Brannon’s book about the neurological and psychological foundations of mathematical cognition. This anthology searches for the foundations of mathematical thought through an impressive collection of twenty-one articles divided into five sections: (1) Mental Magnitudes and Their Transformations, (2) Neural Codes for Space, Time and Number, (3) Shared Mechanisms for Space, Time and Number?, (4) Origins of Proto-Mathematical Intuitions, (5) Representational Change and Education. While this book represents an important contribution by leading scholars, there remain a number of unsolved problems pertaining to the interpretation of empirical data, the cognitive-epistemic foundations of mathematics, and linguistic representation. 

2015. "Mapping Kinds in GIS and Cartography," in Natural Kinds and Classification in Scientific Practice (Catherine Kendig ed.), Routledge, New York, pp. 197-216. [Download PDF from academia.com.]
  • This book chapter delves into the use of natural kinds in the data modeling and map generalization practices of GIS and cartography. Collecting and collating geographical data, building geographical databases, and engaging in spatial analysis, visualization, and map-making all require organizing, typologizing, and classifying geographic space, objects, relations, and processes. These practices of making and using kinds are contextual, fallible, plural, and purposive. The mapping of kinds is just one aspect of a possible philosophy of GIS and cartography (PGISC), which may provide a novel method for addressing concerns of realism, representation, explanation, reduction, and theory structure in philosophy of science more generally.

2014. James and Dewey on Abstraction. The Pluralist 9 (2): 1-28. [Download PDF.]
  • This article examines both the danger and usefulness of abstraction in science and philosophy through an examination of the writings of William James and John Dewey. According to these two pragmatists, whenever one forgets (1) the particular function, (2) historical conditions of emergence, and/or (3) appropriate analytical level of an abstraction, the products and processes of abstraction become inappropriately universalized, narrowed, and/or ontologized. This article elucidates the abstraction-reification account diagnosed by James and Dewey and locates it in contemporary scientific work, dubbing the problem at hand “pernicious reification.”

2014. The Genetic Reification of "Race"? A Story of Two Mathematical Methods. Critical Philosophy of Race 2 (2): 204-223. [Download PDF from philpapers.com.]
  • Two families of mathematical methods lie at the heart of investigating the hierarchical structure of genetic variation in Homo sapiens: diversity partitioning, which assesses genetic variation within and among predetermined groups, and clustering analysis, which simultaneously produces clusters and assigns individuals to these “unsupervised” cluster classifications. While mathematically consistent, these two methodologies seem to ground diametrically opposed claims about the reality of human races. Moreover, modeling results are subject to being perniciously reified – conflated and confused with the world – because they are sensitive to preexisting theoretical commitments to certain linguistic, anthropological, and geographic human groups. This fact belies standard realist and antirealist interpretations of “race,” and supports a pluralist conventionalist interpretation.

2014. With Jonathan Michael Kaplan. Realism, Antirealism, and Conventionalism about Race. Philosophy of Science 81 (5):1039-1052. [Download PDF.]
  • Three concepts of “race” are distinguished: bio-genomic cluster/race, biological race, and social race. It maps out realism, antirealism, and conventionalism about each of these concepts, across three important historical episodes. Upon inspection, each episode also reveals a variety of commitments to the metaphysics of race. The article concludes by interrogating the relevance of these scientific discussions for political positions and a post-racial future.

2013. With Fabrizzio Guerrero McManus. Review of Michael Ruse The Philosophy of Human Evolution. (Cambridge University Press), Evolution. [Download PDF from philpapers.com.]
  • This co-authored book review covers several topics relevant to human evolution: evolutionary theory, the concept of progress, knowledge, morality, sex and race, and evolutionary medicine. Although Ruse’s book is clearly and effectively written and foregrounds a diversity of important questions regarding human evolution, it would benefit our understanding of both human evolution and the role of the historian and philosopher of science to consider further theoretical frames from evolutionary biology that go beyond his Dawkins-style view of evolution. Such frames include multilevel and hierarchical selection theories, epigenetics, feminist science, and developmental systems and niche construction theory. One role of the philosopher and historian of science is to identify, negotiate, and potentially integrate multiple theoretical perspectives.

2013. Review of Stephen Stich Collected Papers. Vol 2. Knowledge, Rationality, and Morality (Oxford University Press), Notre Dame Philosophical Reviews. [Read review on NDPR's website.]
  • This is a review of a volume of papers by Stephen Stitch, a philosopher who has consistently argued that our conceptions of knowledge and morality must be responsive to cognitive science and cultural context. Stitch puts real concrete individuals back into analytic philosophy, as a welcome corrective to overly idealized notions of reasoning and reasoning agents. After exploring Stitch’s themes of (1) cognitive diversity, (2) biases and heuristics, (3) psychological foundations of morality, and (4) philosophical methodology, the review concludes by recommending this volume to a broad audience of analytic philosophers, psychologists, and cognitive scientists.

2013. With Jonathan Michael Kaplan. Ontologies and Politics of Biogenomic 'Race.' Theoria. A Journal of Social and Political Theory (South Africa). 60 (3): 54-80 [Download PDF.]
  • Genomic data and models will not unequivocally settle questions about the reality of race. First, different sub-disciplines of biology interested in population structure employ distinct concepts, aims, and measures and models, thereby producing cross-cutting categorizations of population subdivisions rather than a single, universal biogenomic concept of ‘race.’ Second, within each sub-discipline, genomic results are consistent with, and map multiply to, racial realism and anti-realism. We thus defend a constructivist conventionalism about biogenomic racial ontology. Political agendas, social programmes, and moral questions premised on the existence of naturalistic race should accept that no scientifically grounded racial ontology is forthcoming, and adjust presumptions, practices and projects accordingly.

2013. With Michael J. Wade and Christopher C. Dimond. Pluralism in Evolutionary Controversies: Styles and Averaging Strategies in Hierarchical Selection Theories. Biology and 
Philosophy 28: 957-979. [Download PDF.]  
  • Two controversies regarding the appropriate characterization of hierarchical and adaptive evolution in natural populations are here examined. First, there is the controversy over the relative roles of random genetic drift, natural selection, population structure, and interdemic selection in adaptive evolution begun by Sewall Wright and Ronald Aylmer Fisher. Second, there is the Units of Selection debate, spanning both the biological and the philosophical literature and including the impassioned group-selection debate. We postulate that the reason for the lack of interaction between these debates can be found in the differing focus of each controversy, which is itself determined by distinct general styles of scientific research guiding each discourse: a focus on adaptive process in the Wright-Fisher debate, instructed by the mathematical modeling style; and a focus on adaptive product in the Units of Selection controversy, guided by the function style.

2013. With Jonathan M. Kaplan. Prisoners of Abstraction? The Theory and Measure of Genetic Variation, and the Very Concept of "Race." Biological Theory 7 (4): 401-412. [Download PDF from philpapers.com.]
  • Biological theory does not force the concept of ‘‘race’’ upon us. Indeed, there is no single agreed-upon criterion for defining and distinguishing populations given a particular set of genetic variation data. By analyzing three formal senses of ‘‘genetic variation’’ - diversity, differentiation, and heterozygosity - we argue that the use of biological theory for making claims about race inevitably amounts to pernicious reification.

2012. Interweaving Categories: Styles, Paradigms, and Models. Studies in History and Philosophy of Science, Part A 43: 628-639. [Download PDF from philpapers.com.]
  • The major analytical categories of scientific cultures – styles (à la Hacking and Crombie), paradigms (à la Kuhn), and models (à la van Fraassen and Cartwright) – have typically been used both exclusively and universally. For instance, when styles of scientific research are employed in attempts to understand and narrate science, styles alone are usually employed. Taking the science of systematics as a case study, I ask what we might learn about both theory and practice if we applied styles, paradigms, and models simultaneously. 

2012. Mathematical Modeling in Biology: Philosophy and Pragmatics. Frontiers in Plant Evolution and Development[Download open access publication here.]
  • Philosophy can shed light on mathematical modeling and on the juxtaposition of modeling and empirical data. Scientific debate sometimes arises from different philosophies of modeling. This paper researches three philosophical traditions of the structure of scientific theory – Syntactic, Semantic, and Pragmatic – to show that each illuminates mathematical modeling. The pragmatic view identifies four critical functions of mathematical modeling: (1) unification of both models and data, (2) model fitting to data, (3) mechanism identification accounting for observation, and (4) prediction of future observations. Such facets are here explored using a recent exchange between two groups of mathematical modelers in plant biology. 

2011. Part-Whole Science. Synthese 178: 397-427. [Download PDF.] 
  • ​Part-whole science is premised on identifying, investigating, and using parts and wholes. In the biological sciences this includes mechanistic, structuralist, and historical explanations, each of which implies different norms, explananda, and aims. My diagnosis of part-whole explanation can be applied to various evolved, complex, and integrated systems (e.g. in cognitive science) and cross-cuts standard philosophical analyses of explanation such as causal and unificationist views.

2011. Darwin's Pluralism, Then and Now. Review of David N. Reznick's The Origin Then and Now. An Interpretative Guide to the Origin of Species (Princeton UP, 2010). 
Metascience 21: 157-161. [Download PDF from philpapers.com.]
  • The greatest value-add of David Reznick’s The Origin Then and Now – as against typical interpretations of Darwin’s text – is that it clarifies that Darwin’s position consisted of theories of mechanism and speciation and not only of mechanism and history. Sadly, however, Reznick continues the all-too-strong tradition of presenting Darwin’s theory of evolution from a monistic point of view. First, he reduces the complexity of Darwin’s historical theories of speciation and of the common descent of all life; and second, he erroneously construes natural selection on Darwin’s view as the sole agent of evolutionary change. Whereas Darwin was a pluralist about historical theses and about mechanisms of variation and adaptation, Reznick reads Darwin through limited and limiting monistic glasses.

2011. "Una revisión crítica de los estilos de investigación científica: Teoría, práctica y estilos," in Historia, prácticas y estilos en la filosofía de la ciencia. Hacia una epistemología plural. (S. Martínez, X. Huang, and G. Guillaumin, eds.), Universidad Autónoma Metropolitana, Mexico City, pp. 259-287 (in Spanish). [Download PDF from philpapers.com.]

2011. Consciousness Modeled: Reification and Promising Pluralism. Pensamiento (Madrid, Spain) 67 (254): 617-630. [Download PDF from philpapers.com.]
  • Explorers of the territory of consciousness seem to be studying consciousness out of existence, from inside the field of “consciousness studies.” Through their love of the phenomenon/process, they have developed powerful single models – whether socio-cultural or neurobiological – through which to understand consciousness. Our imploration is to stop the dichotomous thinking and pernicious reification of single models, and instead search for divisions of labor, complementarities, and legitimate redescriptions among the various extant models. This paper present compact descriptions of three models of consciousness – computationalnetworked, and embodied – before sketching a methodology of promising pluralism that employs multiple models in order to explain, understand, and intervene in complex phenomena.

2011. "¿La cosificación genética de la 'raza'? Un análisis crítico", in Genes (&) mestizos. Genómica y raza en la biomedicina mexicana. (C. López Beltrán, ed.), UNAM, Mexico City, pp. 237-258
 (in Spanish). 
[Download PDF from philpapers.com.]

2009. Schaffner's Model of Theory Reduction: Critique and Reconstruction. Philosophy of Science 76: 119-142.  [Download PDF.]
  • Although Kenneth Schaffner’s model of theory reduction has played an important role in philosophy of science and philosophy of biology, it suffers from an internal tension that has not yet been noticed by standard external criticisms concerning reduction functions and laws in biology. Despite the internal tension here analyzed, however, Schaffner’s model usefully highlights the importance of regulative ideals associated with the search for derivational, and embedding, deductive relations among mathematical structures in theoretical biology. A reconstructed Schaffnerian model could therefore shed light on mathematical theory development in the biological sciences and on the epistemology of mathematical practices more generally. 

2009. Prediction in Selectionist Evolutionary Theory. Philosophy of Science 76: 889-901. [Download PDF]
  • ​Selectionist evolutionary theory has often been faulted for not making predictions that are surprising, risky, and correct. I argue that it in fact exhibits the theoretical virtue of predictive capacity in addition to two other virtues: explanatory unification and model fitting. Two case studies show the predictive capacity of selectionist evolutionary theory: parallel evolutionary change in E. coli and the origin of eukaryotic cells through endosymbiosis.

2009. Character Analysis in Cladistics: Abstraction, Reification, and the Search for Objectivity. Acta Biotheoretica 57: 129-162.  [Download PDF]
  • This paper probes the dangers of character reification for cladistic inference. How can we separate robustly real biological characters from uncritically reified characters when the identification and analysis of characters always involves theory-laden abstraction? It is important to minimize character reification, because poor character analysis leads to dismal cladograms, even when proper phylogenetic analysis is employed. Given the deep and systemic problems associated with character reification, it is ironic that philosophers have focused almost entirely on phylogenetic analysis and neglected character analysis. One way to avoid reification is through the employment of objectivity criteria that give us good methods for identifying robust primary homology statements. I identify six such criteria and consider each with examples. 

2009. Introduction: From a Philosophical Point of View. Acta Biotheoretica 57: 5-10.  [Download PDF]
  • This essay introduces a set of pieces exploring philosophical questions of comparative biology, elaborating on the questions arising therein. We find ourselves today at a dizzying time in biological research. Astounding data-driven progress is being made in a variety of broad biological fields including: (1) genomics, proteomics, and systems biology, (2) biodiversity and ecology, and (3) evolutionary developmental biology (‘‘evo-devo’’). Each of these growth fields relies heavily—if sometimes only implicitly—on comparative biology. Comparative biology is essential to biological research and hence worth exploring philosophically. Yet its methods and knowledge are also influenced by biological research; philosophical analysis can and should therefore also provide insight into the complex theoretical and practice relations across various porous disciplinary boundaries in the biological sciences. ​

2009. Missing in Action: On Science and Constructivism in the Realism Debates. A Dialogue. Review of Kyle Stanford's Exceeding Our Grasp. Science, History, and the Problem of Unconceived Alternatives (Oxford UP, 2006), Metascience 18: 370-379. [Download PDF
  • This piece is a contribution to a Review Symposium of Kyle Stanford’s Exceeding Our Grasp in Metascience. It takes the form of a dialogue among several stakeholders in debates about realism – a realist, an instrumentalist, a scientist, and a constructivist - showing how these different kinds of thinker would evaluate the central claims of Stanford’s book. It is concluded that a plurality of voices is necessary and that realism and instrumentalism have not paid sufficient heed to philosophical constructivism. 

2008. Systemic Darwinism. Proceedings of the National Academy of Sciences (USA). 105 (33): 11833-11838. [Download PDF from philpapers.com.]
  • Darwin’s theory of natural selection opened up a multidimensional and integrative conceptual space for biology. We explore three dimensions of this space: explanatory pattern, levels of selection, and degree of difference among units of the same type. Each dimension is defined by a respective pair of poles: law and narrative explanation, organismic and hierarchical selection, and variational and essentialist thinking. As a consequence of conceptual debates in the 20th century biological sciences, the poles of each pair came to be seen as mutually exclusive opposites. Following a ‘‘compositional paradigm’’ according to which complex systems and their hierarchical networks of parts are the focus of biological investigation, Systemic Darwinism promises to reintegrate each dimension of Darwin’s original logical space, provide a deeper understanding of biological reality.​

2007. "Estilos de investigación científica, modelos e insectos sociales", in Variedad Infinita. Ciencia y representación. Un enfoque histórico y filosófico (E. Suárez, ed.). 
UNAM and Editorial Limusa, pp. 55-89.  [Download PDF]

2006. Parts and Theories in Compositional Biology. 
Biology and Philosophy 21: 471-499.  [Download PDF.]
  • ​The role of parts in the style of biological theorizing that I call compositional biology is here analyzed. I investigate partitioning frames and explanatory accounts of theoretical perspectives guided by compositional biology. This examination is grounded in a comparative analysis of three disciplines and their associated compositional perspectives: comparative morphology, functional morphology, and developmental biology. I end with a discussion of the importance of recognizing formal biology and compositional biology as two genuinely different ways of doing biology whose differences arise more from their distinct methodologies than from disciplinary boundaries or domain of study.

2006. On the Dangers of Making Scientific Models Ontologically Independent: Taking Richard Levins' Warnings Seriously. Biology and Philosophy 21: 703-724. [Download PDF.]
  • Here I explore Levins and Lewontin’s separate and joint pleas to avoid conflating our scientific models with the world. I differentiate two views of theorizing and modeling, orthodox and dialectical, in order to examine Levins and Lewontin’s, among others’, advocacy of the latter view. I compare these two views with respect to four points regarding ontological assumptions: (1) the origin of ontological assumptions, (2) the relation of such assumptions to the formal models of the same theory, (3) their use in integrating and negotiating different formal models of distinct theories, and (4) their employment in explanatory activity. I investigate three case studies that show the relevance and power of the dialectical understanding, taking ‘dialectic’ in both its Hegelian–Marxist sense of opposition and tension and its Platonic sense of dialogue between advocates of distinct theories.​

2006. Fisherian and Wrightian Perspectives in Evolutionary Genetics and Model-Mediated Imposition of Theoretical Assumptions. 
Journal of Theoretical Biology 240: 218-232.  [Download PDF from philpapers.com.]
  • This paper inspects how theoretical assumptions operative in the modeling process are central in determining how nature is actually taken to be. A case study is considered: two different models by Michael Turelli and Steve Frank of the evolution of parasite-mediated cytoplasmic incompatibility, guided by Fisherian and Wrightian perspectives, respectively. Since both models are commensurable with respect to both mathematics and data, the differences between them in (1) mathematical presentation of the models, (2) explanations, and (3) objectified ontologies stem neither from differences in mathematical method nor employed data, but rather from differences in theoretical assumptions, especially regarding ontology. I conclude with a discussion of the general implications of this analysis for the controversy between Fisherian and Wrightian perspectives.

2005. An Obstacle to Unification in Biological Social Science: Formal and Compositional Styles of Science. Graduate Journal of Social Sciences 2: 40-100.  [Download PDF from philpapers.com.]
  • ​The use of the category ‘styles of scientific research’ in historical and philosophical studies of science is motivated. In particular, the possibility of the unification of biology and social science is interrogated by examining the possibility of unifying two styles of scientific research: formal and compositional. Recent attempts at unifying biology and social science have been premised almost exclusively on the formal style. However, through the use of a historical example of defenders of compositional biological social science – the Ecology Group at the University of Chicago from, roughly, the 1930s to the 1950s – the coherence and possibility of effecting this synthesis by employing the compositional style is shown.

2005. "Evolutionary Developmental Biology Meets Levels of Selection: Modular Integration or Competition, or Both?" in Modularity: Understanding the Development and Evolution of Complex Natural Systems (W. Callebaut and D. Rasskin-Gutman, eds.), MIT Press, pp. 61-97.   [Download PDF from philpapers.com.]
  • Many biological researchers now posit ‘modules,’ defined as parts – such as conserved morphological structures or developmental units – in terms of which biological wholes may be analyzed. This paper investigates two ways of approaching the question of whether modules mechanistically interact or selectively compete (or both): Whereas the integration perspective focuses on how modules interact to form an individual and on the patterns of evolutionary change of mechanisms and modules, the competition perspective emphasizes the selective dynamics that lead to changes in replicator (e.g. gene) frequencies. I suggest that these perspectives are complementary, while also emphasizing the utility for all researchers of considering both a partitioning strategy, which explains an individual as a direct and linear aggregation of its modules, and an articulation strategy, which stresses the nonlinear interaction among parts. ​

[Writing HPS Dissertation & Biology Masters, 2001-2004] 

2001. Varieties of Modules: Kinds, Levels, Origins, and Behaviors. Journal of Experimental Zoology (Molecular and Developmental Evolution) 291: 116-129.  [Download PDF from philpapers.com.]
  • This literature and concept review distinguishes three kinds of modules: structural, developmental, and physiological. Every module fulfills none, one, or multiple functional roles. Two further orthogonal distinctions are important in this context: module-kinds versus module-variants-of-a-kind and reproducer versus nonreproducer modules. I review criteria for individuation of modules and mechanisms for the phylogenetic origin of modularity. I discuss conceptual and methodological differences between developmental and evolutionary biologists, in particular the difference between integration and competition perspectives on individualization and modular behavior. The variety in views regarding modularity presents challenges that require resolution in order to attain a comprehensive, rather than a piecemeal and fragmentary, evolutionary developmental biology​

2001. August Weismann on Germ-Plasm Variation. Journal of the History of Biology 34: 517-555.  [Download PDF from philpapers.com]
  • August Weismann is famous for having argued against the inheritance of acquired characters. However, a close analysis of his work indicates that Weismann always held that changes in external conditions, acting during development, were the necessary causes of variation in the hereditary material. Ironically and in tension with much of the standard twentieth-century history of biology, Weismann was not a Weismannian. I distinguish three claims regarding the germ-plasm: (1) its continuity, (2) its morphological sequestration, and (3) its variational sequestration. I divide his career into four stages, analyzing his views at each stage on the relative importance of changes in external conditions and sexual reproduction as causes of variation in the hereditary material. Weismann believed, and Weismannism denies, that variation, heredity, and development are deeply intertwined processes.

2001. Review of Deborah Gordon's Ants at Work: The Organization of a Social Insect Colony (Free Press, 1999). Philosophy of Science 68: 268-270. [Download PDF
  • This review takes Deborah Gordon’s Ants at Work as a concrete case study in the philosophy of science rather than focusing (like others) on controversies relating to her rejection of the caste perspective on social insects. In particular, this piece examines Gordon’s balanced treatment of the relative importance of relations among units and properties of units in scientific theories and in nature, as well as her complementary use of reductionistic and holistic analyses. Any philosopher of science interested in a cogent biological research program, rich in material for philosophical analysis, should read Ants at Work.

2000. Darwin on Variation and Heredity. Journal of the History of Biology 33: 425-455. [Download PDF from philpapers.com.]
  • Darwin’s ideas on variation, heredity, and development differ significantly from twentieth century views. First, Darwin held that environmental changes, acting either on the reproductive organs or the body, were necessary to generate variation. Second, he held heredity to be a developmental, not a transmissional, process; variation was a change in the developmental process of change. An analysis of Darwin’s elaboration and modification of these two positions from his early notebooks (1836–1844) to the last edition of the Variation of Animals and Plants Under Domestication (1875) complements previous Darwin scholarship on these issues. 

Co-Authored Publications (Professional):

Vergara-Silva F, Winther RG. 2009. Editorial: Systematics, Darwinism, and the Philosophy of Science. Acta Biotheoretica 57: 1-3. [Download PDF]

Wade MJ, Winther RG, Agrawal AF, Goodnight CJ. 2001. Alternative Definitions of Epistasis: Dependence and Interaction. Trends in Ecology and Evolution 16: 498-504. [Download PDF from philpapers.com.]

van Syoc RJ, Winther R. 1999. Sponge-Inhabiting Barnacles of the Americas: A New Species of Acasta (Cirripedia, Archaeobalanidae), First Record from the Eastern Pacific, Including Discussion of the Evolution of Cirral Morphology. Crustaceana 72: 467-486. [Download PDF

2004. A Molecular and Evolutionary Study of the Obligate Endosymbiont Wolbachia in Tribolium confusum. [Masters Thesis in the biological sciences; download PDF]

2003. Formal Biology and Compositional Biology as Two Kinds of Biological Theorizing. [PhD Thesis in philosophy of science; PDF from philpapers.com.] 

In Progress:
"Free to Universalize or Bound by Culture? Multicultural and Public Philosophy: A White Paper." [Conference paper; Scientia Salon paper, with discussion.]

I am also working on various general public "mini-essays", which have received positive feedback and praise. Feel free to email me about these.  (Homes)