Projects in Preparation or Under Review

(papers under review / revision are available upon request)


"Reorienting Scientific Explanation - The Case from Robustness in Biological Systems" In revision.

One striking feature of many biological systems is their high degree of robustness, or the ability of a system to maintain its function or behavior against perturbations and under a wide range of circumstances. Despite the ubiquity and importance of robustness, philosophers tend to think of it in a simple way. I trace recent developments in two fields of biology where the study of robustness has become increasingly important: ecology and evo-devo. I argue for a shift towards incorporating more top-down, system-level approaches into accounts of explanation to better reflect scientific practice seen in those two fields. I develop a general taxonomy of robustness to help clarify links between the study of robustness in different fields. I define three general kinds of robustness: redundancy, resistance and resilience. Each of these categories are further subdivided in turn.      

"Two Pitfalls for Causal Reasoning in Biology" In revision.

In this paper I examine aspects of causal reasoning in biology. In my analysis, I provide a novel distinction between two types of difficulties encountered while reasoning about biological systems. First, there is a difficulty with imagining and predicting the behaviour of biological phenomena—especially across scales or domains--that stems from the stochastic and contingent nature of many biological processes. I refer to this as the translation problem. For example, reasoning about the emerging behavior of higher-level biological phenomena from lower-level phenomena can be difficult because the intracellular stochastically-driven biological processes that make up the building blocks of life behave in a way that is alien to our everyday reasoning about the behavior of objects at our scale. Second, there is a difficulty with identifying all the numerous salient causal factors and interactions behind the production of biological phenomena. I call this the interpretation problem. It stems from the difficulty in decomposing the unique causal complexity that is found in robust, hierarchical and recursively organized biological systems. In the face of these problems I argue that approaches to explanation are best seen as heuristics, which focuses our attention on both how our conceptual tools resolve problems, and when and where they can break down.


"Integration and Discordance in Multilineage Systems" In prep. 

In this paper I discuss the complications involved in making sense of lineage integration and discordance in host-microbiota symbioses, now commonly referred to as a single unit: the holobiont. Reciprocal selection pressures emerging from gene-gene interactions between species are commonly recognized as the framework by which to understand co-evolution. I look to the field of community genetics as a better way to understand host-microbe gene interactions. One promising concept for understanding the interaction of gene lineages between species is Θ. Initially introduced for studying epistasis within genomes, Θ has recently been applied to gene interactions across genomes in the context of community genetics—a type of intergenomic epistasis. It is a measure of the degree of co-inheritance of gene combinations, and it represents the simultaneous co-variance in identity-by-descent of host and symbiont genes when two infected hosts are compared. Theoretically, Θ is increased by vertical transmission and reduced by horizontal transmission and an increased Θ facilitates selection to act on gene combinations across genomes. A high average overall Θ between the host genome and microbial genes might indicate the action of selection at the level of the holobiont and the integration of formerly separate lineages into a single lineage. I explore the consequences of this framework for combining ecological and evolutionary perspectives—one of the recognized aims of community genetics--in the context of the holobiont. 

"A Framework for Individualization and Individuality in Biology" In prep. 

The study of individuality is primarily concerned with how to carve up a particular domain into basic units and with how to tell those units apart. There are a host of particular interests or practices, scientific or otherwise, which inform that general endeavor but the central aim remains the same. In the last few decades, biologists and philosophers of biology have worked towards finding biological criteria for the individuation of biological entities, as opposed to earlier approaches based on the “phenomenal individuation” of organisms that uses categories derived from more familiar things, such as vertebrate animals and large plants. This has resulted in some of the most active debates within philosophy of biology. In this paper I develop a framework for different grades of individuality that is tied to both scientific practices of individuation (i.e. description vs. explanation) and different features of living systems . I suggest four kinds of individuals: marks (the product of descriptive bookkeeping), components (the product of network analysis), distinguishables (entities, such as an ecosystem, that are distinguishable only when indexed to a feature of explanatory interest), biological individuals (entities, like evolutionary individuals, that are required to exist if an accepted theoretical framework is true).      


​"Can Host-microbiome Systems be Healthy? Shaping Ecosystems vs Curing Disease" In prep. 
     An upcoming talk for The Future of Microbiome Research workshop I am co-organizing with Maureen O'Malley and Paul
     Griffiths.

Host-associated microbiomes play a variety of important roles in host health and disease. Attempts to understand and make predictions about complex host-microbiome interactions have led many researchers to talk about microbiomes—especially human-associated ones—in terms of being either healthy or dysbiotic. In this presentation I will look at some alternatives for making sense of “healthy microbiome” talk. I will argue that existing “naturalistic”, or non-evaluative, accounts of human health are not appropriate for microbiomes, and that notions of ecosystem health face similar shortcomings. These problems suggest that “microbiome health” might only be definable in evaluative terms and may never extend beyond a metaphor to organismal health. I will end by looking at some possibilities for understanding overall host health given the importance and ubiquity of microbiomes.


"The Ecology of Holobionts" w/ Christopher Lean. In revision. 
     To be a part of special issue on the Philosophy of Holobionts in Philosophy, Theory and Practice in Biology.
Owing to the rapid uptick in microbiome research, experimental data and correlational studies have started to outpace the theories and conceptual frameworks by which we understand the biology of holobiont systems. The evidence accumulated so far shows--fairly decisively--that holobionts are full of complex interactions that range across developmental, ecological, and evolutionary scales. Understanding holobiont dynamics will surely require the tools of theoretical ecology in addition to those of evolutionary theory. The biggest debate is over which forces shape holobionts and host-microbiome systems at the level of the whole. Views here can be roughly split into two conflicting camps. There is the ecological account that sees holobionts as a particular kind of ecosystem: multispecies microbial assemblages or networks of causal relations indexed to a host organism--and nothing over and above that. On the ecological view, resident microbiomes are complex and dynamic ecosystems that are constantly in flux and shaped by interactions from the bottom up. This view is in opposition to the evolutionary account that sees holobionts as organisms, evolutionary individuals, or units of selection--wholes that can be acted upon by natural selection with corresponding selected-effect functions. Our view is that holobionts are best understood as a particular kind of ecological system. We develop how holobionts are best explained as ecological communities emphasizing the similarity of holobiont to other network arrangements of mutualistic and competitive populations. We outline an approach to individuality consistent with this view of holobionts that we also think serves as a helpful framework for the further investigation of holobiont biology.


​"Physiological Individuality and Syntrophic Individuality" w/ Leonardo Bich. In prep.

Philosophical research on biological individuality has primarily focused on evolutionary individuality, an important topic that has helped clarify talk about units of selection and what is required for evolution by natural selection. Less attention has been paid to other kinds of individuality. Non-evolutionary accounts of biological individuality are often underdeveloped and/or imprecise, especially in cases (i.e. host-microbe symbioses, microbe-microbe symbioses (biofilms), colonies) that transcend the “traditional organism”. Where generalization is attempted criteria involved in physiology, metabolism, organisms, anatomy, and ecology all tend to get bundled up together with very few distinctions to be made about why they go together. Or individuality becomes just descriptive of scientific practice; for each field there is a different kind of individual indexed to the objects of study in that field: anatomical individual, immunological individual, physiological individual, ecological individual, etc. This paper develops two complementary accounts of biological individuality that are based on non-evolutionary theoretical approaches developed to explain biological systems. Physiological individuals are described in terms of the theory of biological autonomy and causal closure of constraints in self-maintaining systems. Syntrophic individuals are described in terms of metabolic complementarity in recurring self-organized systems.   

A few dusty side-projects


"Complexity, Organization and Life in the Philosophy of Sir Kenelm Digby" In revision
One of the central themes of the history of early-modern philosophy and science is the rise of mechanical philosophy
and the fall of Aristotelian views of the natural world. In this paper I look at the philosophy of Sir Kenelm
Digby, a now mostly obscure figure who wrote early on in the transition to mechanical philosophy. Digby was a
thorough-going mechanist in respect to matter and the physical world. He attempted to wed the emerging mechanical
and corpuscular philosophies to the Aristotelian notion of composite substances in his most famous
philosophical work, the 1644 Two Treatises. It is Digby’s views on living creatures and machines that concern
me here, specifically the role of organization in delimiting the types of things in the world. Though he has not
been very well appreciated, I hope to show that his views on life were quite insightful and bear some striking
similarities to modern-day theories of the organism.


"The Emptiness of the Species Problem - A Buddhist Approach to the Metaphysics of Species" In revision.

The dominant view in biology and philosophy of biology is that species do not have essences. This is notable because at one time biological species were used as paradigmatic examples of essence-bearers. The search for essences has been historically productive for the sciences of physics and chemistry. As a discipline Biology matured much later than physics and chemistry, and an approach to science modeled on what worked for physics has been ill-suited for biology. The search for essences in biology has been by-and-large given up. So while the consensus view is that species have no essences, there is much less agreement about the current ontological status of species. A view of the world which holds that entities have essences--like the ones found in much of Western philosophy--contrasts sharply with views that are found in the equally-rich traditions of Buddhist philosophy. There we find it denied that the furniture of the world includes anything that might be thought of as an essence. Indeed, a distinguishing feature of reality is the lack of anything like an essence. I suggest that Buddhist metaphysics gives us some very useful tools for understanding species, the doctrines of interdependence, impermanence, and emptiness. I show how a Buddhist understanding of species might proceed. I don’t give a “Buddhist account” of species, but rather try to show how adopting these concepts sheds light on the species debate, as well as offering a good way forward. 

Contrasting phylogeographic patterns in two Pacific brittle stars, Ophiocoma Erinaceous and Ophiocoma pica
      w/ Matt Iacchei and Robert Toonen. In revision.