Symmetry and Causation: A General Theory of Biological Individuality

I propose and defend a method of identifying individuals that is applicable across the biological sciences and yet sensitive to the details of particular theories. Specifically, I propose that an individual with respect to a given biological theory is an entity that instantiates the structure of a special class of transformations called the ‘dynamical symmetries’ of the theory. Here, a dynamical symmetry is understood roughly as a transformation of the state of a system that commutes with the increment of another system variable. This notion of individual is dependent upon the causal regularities in a particular domain of biology. However, the approach is completely general in that the same characterization of ‘individual’ in terms of symmetries applies across all biological domains. The metaphysical and methodological appeal of this approach to identifying individuals derives from the fact that the entities identified in this way share robust causal features and yet are causally independent of one another. To demonstrate the generality as well as the plausibility of the approach, I consider examples from evolutionary theory and ecology

How Symmetry Undid the Particle: A Demonstration of the Incompatibility of Particle Interpretations and Permutation Invariance

The idea that the world is made of particles — little discrete, interacting objects that compose the material bodies of everyday experience — is a durable one. Following the advent of quantum theory, the idea was revised but not abandoned. It remains manifest in the explanatory language of physics, chemistry, and molecular biology. Aside from its durability, there is good reason for the scientific realist to embrace the particle interpretation: such a view can account for the prominent epistemic fact that only limited knowledge of a portion of the material universe is needed in order to make reliable predictions about that portion. Thus, particle interpretations can support an abductive argument from the epistemic facts in favor of a realist reading of physical theory. However, any particle interpretation with this property is untenable. The empirical adequacy of modern particle theories requires adoption of a postulate known as permutation invariance (PI) — the claim that interchanging the role of two particles of the same kind in a dynamical state description results in a description of the identical state. It is the central claim of this essay that PI is incompatible with any particle interpretation strong enough to account for the epistemic facts. This incompatibility extends across all physical theories. To frame and motivate the inconsistency argument, I begin by fixing the relevant notion of particle. To single out those accounts of greatest appeal to the realist, I develop the logically weakest particle ontology that entails the epistemic fact that the world is piecewise predictable, an ontology I call ‘minimal atomism’ (MA). The entire series of scientific conceptions of the particle, from Newton’s mechanically interacting corpuscles to the ‘centers of force’ in classical field theories, all comport with MA. As long as PI is left out, even quantum mechanics can be viewed this way. To assess the impact of PI on this picture, I present a framework for rigorously connecting interpretations to physical theories. In particular, I represent MA as a set of formal conditions on the models of physical theories, the mathematical structures taken to represent states of the world. I also formulate PI — originally introduced as a postulate of non-relativistic quantum mechanics — in theory independent terms. With all of these pieces in hand, I am then able to present a proof of the inconsistency of PI and MA. In the second part of the essay, I survey responses to the inconsistency result open to the scientific realist. The two most plausible approaches involve abandoning particles in one way or another. The first alternative interpretation considered takes the property bearing objects of the world to be regions of space rather than particles. In this view, the properties once attributed to particles in quantum states are attributed instead to one or more regions of space. PI no longer obtains in this case, at least not as a statement about the permutation symmetry of property bearers. Rather, the new interpretation naturally imposes an analogous constraint on quantum states. The second major approach to evading the inconsistency result is to dispense with objects altogether. This is the recommendation of so-called ‘Ontic Structural Realism’ (OSR). The central OSR thesis is that structure rather than entities are the basic ontological components of the world. OSR is intended to embrace the ‘miracle’ argument in favor of scientific realism (it would be a miracle if a scientific theory were predictively successful unless it were also approximately true with regard to its description of reality) while avoiding the pessimistic meta-induction (most predictively successful theories along with their associated ontologies have been overturned, so we should expect the same of our current theories). I demonstrate that one principal motivation for OSR based on the under-determination of interpretations in QM is actually dissolved by the incompatibility result. At the same time, I suggest reasons to think that OSR fares no better with respect to the pessimistic meta-induction than traditional realism does. Thus, while PI and MA may be incompatible, object ontologies remain the best option for the realist

Symmetry and Causation: A General Theory of Biological Individuality

I propose and defend a method of identifying individuals that is applicable across the biological sciences and yet sensitive to the details of particular theories. Specifically, I propose that an individual with respect to a given biological theory is an entity that instantiates the structure of a special class of transformations called the ‘dynamical symmetries’ of the theory. Here, a dynamical symmetry is understood roughly as a transformation of the state of a system that commutes with the increment of another system variable. This notion of individual is dependent upon the causal regularities in a particular domain of biology. However, the approach is completely general in that the same characterization of ‘individual’ in terms of symmetries applies across all biological domains. The metaphysical and methodological appeal of this approach to identifying individuals derives from the fact that the entities identified in this way share robust causal features and yet are causally independent of one another. To demonstrate the generality as well as the plausibility of the approach, I consider examples from evolutionary theory and ecology

How Symmetry Undid the Particle: A Demonstration of the Incompatibility of Particle Interpretations and Permutation Invariance

The idea that the world is made of particles — little discrete, interacting objects that compose the material bodies of everyday experience — is a durable one. Following the advent of quantum theory, the idea was revised but not abandoned. It remains manifest in the explanatory language of physics, chemistry, and molecular biology. Aside from its durability, there is good reason for the scientific realist to embrace the particle interpretation: such a view can account for the prominent epistemic fact that only limited knowledge of a portion of the material universe is needed in order to make reliable predictions about that portion. Thus, particle interpretations can support an abductive argument from the epistemic facts in favor of a realist reading of physical theory. However, any particle interpretation with this property is untenable. The empirical adequacy of modern particle theories requires adoption of a postulate known as permutation invariance (PI) — the claim that interchanging the role of two particles of the same kind in a dynamical state description results in a description of the identical state. It is the central claim of this essay that PI is incompatible with any particle interpretation strong enough to account for the epistemic facts. This incompatibility extends across all physical theories. To frame and motivate the inconsistency argument, I begin by fixing the relevant notion of particle. To single out those accounts of greatest appeal to the realist, I develop the logically weakest particle ontology that entails the epistemic fact that the world is piecewise predictable, an ontology I call ‘minimal atomism’ (MA). The entire series of scientific conceptions of the particle, from Newton’s mechanically interacting corpuscles to the ‘centers of force’ in classical field theories, all comport with MA. As long as PI is left out, even quantum mechanics can be viewed this way. To assess the impact of PI on this picture, I present a framework for rigorously connecting interpretations to physical theories. In particular, I represent MA as a set of formal conditions on the models of physical theories, the mathematical structures taken to represent states of the world. I also formulate PI — originally introduced as a postulate of non-relativistic quantum mechanics — in theory independent terms. With all of these pieces in hand, I am then able to present a proof of the inconsistency of PI and MA. In the second part of the essay, I survey responses to the inconsistency result open to the scientific realist. The two most plausible approaches involve abandoning particles in one way or another. The first alternative interpretation considered takes the property bearing objects of the world to be regions of space rather than particles. In this view, the properties once attributed to particles in quantum states are attributed instead to one or more regions of space. PI no longer obtains in this case, at least not as a statement about the permutation symmetry of property bearers. Rather, the new interpretation naturally imposes an analogous constraint on quantum states. The second major approach to evading the inconsistency result is to dispense with objects altogether. This is the recommendation of so-called ‘Ontic Structural Realism’ (OSR). The central OSR thesis is that structure rather than entities are the basic ontological components of the world. OSR is intended to embrace the ‘miracle’ argument in favor of scientific realism (it would be a miracle if a scientific theory were predictively successful unless it were also approximately true with regard to its description of reality) while avoiding the pessimistic meta-induction (most predictively successful theories along with their associated ontologies have been overturned, so we should expect the same of our current theories). I demonstrate that one principal motivation for OSR based on the under-determination of interpretations in QM is actually dissolved by the incompatibility result. At the same time, I suggest reasons to think that OSR fares no better with respect to the pessimistic meta-induction than traditional realism does. Thus, while PI and MA may be incompatible, object ontologies remain the best option for the realist

Scientific Variables

Despite their centrality to the scientific enterprise, both the nature of scientific variables and their relation to inductive inference remain obscure. I suggest that scientific variables should be viewed as equivalence classes of sets of physical states mapped to representations (often real numbers) in a structure preserving fashion, and argue that most scientific variables introduced to expand the degrees of freedom in terms of which we describe the world can be seen as products of an algorithmic inductive inference first identified by William W. Rozeboom. This inference algorithm depends upon a notion of natural kind previously left unexplicated. By appealing to dynamical kinds—equivalence classes of causal system characterized by the interventions which commute with their time evolution—to fill this gap, we attain a complete algorithm. I demonstrate the efficacy of this algorithm in a series of experiments involving the percolation of water through granular soils that result in the induction of three novel variables. Finally, I argue that variables obtained through this sort of inductive inference are guaranteed to satisfy a variety of norms that in turn suit them for use in further scientific inferences

Ad hoc identity, Goyal complementarity, and counting quantum phenomena

I introduce a thin concept of ad hoc identity -- distinct from metaphysical accounts of either relative identity or absolute identity -- and an equally thin account of concepts and their content. According to the latter minimalist view of concepts, the content of a concept has behavioral consequences (though it may not be identical to those consequences), and so content can be bounded if not determined by appeal to linguistic and psychological evidence. In the case of counting practices, this evidence suggests that the number concept depends on a notion of identity at least as strong as ad hoc identity. In the context of nonrelativistic QM in particular, all of the counting procedures appealed to in the existing literature on nonindividuality are shown to involve ad hoc identity. I then show that Goyal Complementarity (Goyal 2019) and the associated derivation of a strong symmetrization principle in QM can be understood in terms ad hoc identity. Specifically, persistence and non-persistence models of quantum processes are seen to be complementary in the sense that they involve two relations of ad hoc identity that occasionally overlap in empirically meaningful ways. Finally, I attempt to draw out consequences for theories of nonindividuality from the above conceptual analysis. The upshot is that counting and definite cardinality are incompatible with nonindividuality, and that none of the counting procedures cited for quantum phenomena offer positive support for an interpretation in terms of nonindividuals

Probing protein-DNA interactions by unzipping a single DNA double helix.

We present unzipping force analysis of protein association (UFAPA) as a novel and versatile method for detection of the position and dynamic nature of protein-DNA interactions. A single DNA double helix was unzipped in the presence of DNA-binding proteins using a feedback-enhanced optical trap. When the unzipping fork in a DNA reached a bound protein molecule we observed a dramatic increase in the tension in the DNA, followed by a sudden tension reduction. Analysis of the unzipping force throughout an unbinding "event" revealed information about the spatial location and dynamic nature of the protein-DNA complex. The capacity of UFAPA to spatially locate protein-DNA interactions is demonstrated by noncatalytic restriction mapping on a 4-kb DNA with three restriction enzymes (BsoBI, XhoI, and EcoRI). A restriction map for a given restriction enzyme was generated with an accuracy of approximately 25 bp. UFAPA also allows direct determination of the site-specific equilibrium association constant (K(A)) for a DNA-binding protein. This capability is demonstrated by measuring the cation concentration dependence of K(A) for EcoRI binding. The measured values are in good agreement with previous measurements of K(A) over an intermediate range of cation concentration. These results demonstrate the potential utility of UFAPA for future studies of site-specific protein-DNA interactions