Patterns, Information, and Causation

This paper articulates an account of causation as a collection of information-theoretic relationships between patterns instantiated in the causal nexus. I draw on Dennett’s account of real patterns to characterize potential causal relata as patterns with specific identification criteria and noise tolerance levels, and actual causal relata as those patterns instantiated at some spatiotemporal location in the rich causal nexus as originally developed by Salmon. I develop a representation framework using phase space to precisely characterize causal relata, including their degree of counterfactual robustness, causal profiles, causal connectivity, and privileged grain size. By doing so, I show how the philosophical notion of causation can be rendered in a format that is amenable for direct application of mathematical techniques from information theory such that the resulting informational measures are causal informational measures. This account provides a metaphysics of causation that supports interventionist semantics and causal modeling and discovery techniques

Bi-directional and shared epigenomic signatures following proton and 56Fe irradiation.

The brain's response to radiation exposure is an important concern for patients undergoing cancer therapy and astronauts on long missions in deep space. We assessed whether this response is specific and prolonged and is linked to epigenetic mechanisms. We focused on the response of the hippocampus at early (2-weeks) and late (20-week) time points following whole body proton irradiation. We examined two forms of DNA methylation, cytosine methylation (5mC) and hydroxymethylation (5hmC). Impairments in object recognition, spatial memory retention, and network stability following proton irradiation were observed at the two-week time point and correlated with altered gene expression and 5hmC profiles that mapped to specific gene ontology pathways. Significant overlap was observed between DNA methylation changes at the 2 and 20-week time points demonstrating specificity and retention of changes in response to radiation. Moreover, a novel class of DNA methylation change was observed following an environmental challenge (i.e. space irradiation), characterized by both increased and decreased 5hmC levels along the entire gene body. These changes were mapped to genes encoding neuronal functions including postsynaptic gene ontology categories. Thus, the brain's response to proton irradiation is both specific and prolonged and involves novel remodeling of non-random regions of the epigenome

How Philosophy of Mind Needs Philosophy of Chemistry

By the 1960s many (perhaps most) philosophers had adopted ‘physicalism’ ─ the view that physical causes fully account for mental activities. However, controversy persists about what count as ‘physical causes’. ‘Reductive’ physicalists recognize only microphysical (elementary-particle-level) causality. Many (perhaps most) physicalists are ‘non-reductive’ ─ they hold that entities considered by other (‘special’) sciences have causal powers. Philosophy of chemistry can help resolve main issues in philosophy of mind in three ways: developing an extended mereology applicable to chemical combination, testing whether ‘singularities’ prevent reduction of chemistry to microphysics, and demonstrating ‘downward causation’ in complex networks of chemical reactions

How Philosophy of Mind Needs Philosophy of Chemistry

By the 1960s many (perhaps most) philosophers had adopted ‘physicalism’ ─ the view that physical causes fully account for mental activities. However, controversy persists about what count as ‘physical causes’. ‘Reductive’ physicalists recognize only microphysical (elementary-particle-level) causality. Many (perhaps most) physicalists are ‘non-reductive’ ─ they hold that entities considered by other (‘special’) sciences have causal powers. Philosophy of chemistry can help resolve main issues in philosophy of mind in three ways: developing an extended mereology applicable to chemical combination, testing whether ‘singularities’ prevent reduction of chemistry to microphysics, and demonstrating ‘downward causation’ in complex networks of chemical reactions

Being Emergence vs. Pattern Emergence: Complexity, Control, and Goal-Directedness in Biological Systems

Emergence is much discussed by both philosophers and scientists. But, as noted by Mitchell (2012), there is a significant gulf; philosophers and scientists talk past each other. We contend that this is because philosophers and scientists typically mean different things by emergence, leading us to distinguish being emergence and pattern emergence. While related to distinctions offered by others between, for example, strong/weak emergence or epistemic/ontological emergence (Clayton, 2004, pp. 9–11), we argue that the being vs. pattern distinction better captures what the two groups are addressing. In identifying pattern emergence as the central concern of scientists, however, we do not mean that pattern emergence is of no interest to philosophers. Rather, we argue that philosophers should attend to, and even contribute to, discussions of pattern emergence. But it is important that this discussion be distinguished, not conflated, with discussions of being emergence. In the following section we explicate the notion of being emergence and show how it has been the focus of many philosophical discussions, historical and contemporary. In section 3 we turn to pattern emergence, briefly presenting a few of the ways it figures in the discussions of scientists (and philosophers of science who contribute to these discussions in science). Finally, in sections 4 and 5, we consider the relevance of pattern emergence to several central topics in philosophy of biology: the emergence of complexity, of control, and of goal-directedness in biological systems