Mechanists Must be Holists Too! Perspectives from Circadian Biology

Mechanistic decomposition and reduction in complex, context-sensitive systems

Standard arguments in philosophy of science infer from the complexity of biological and neural systems to the presence of emergence and failure of mechanistic/reductionist explanation for those systems. I argue against this kind of argument, specifically focusing on the notion of context-sensitivity. Context-sensitivity is standardly taken to be incompatible with reductionistic explanation, because it shows that larger-scale factors influence the functioning of lower-level parts. I argue that this argument can be overcome if there are mechanisms underlying those context-specific reorganizations. I argue that such mechanisms are frequently discovered in neuroscience.

Understanding the genetics of neuropsychiatric disorders: the potential role of genomic regulatory blocks

Recent genome-wide association studies have identified numerous loci associated with neuropsychiatric disorders. The majority of these are in non-coding regions, and are commonly assigned to the nearest gene along the genome. However, this approach neglects the three-dimensional organisation of the genome, and the fact that the genome contains arrays of extremely conserved non-coding elements termed genomic regulatory blocks (GRBs), which can be utilized to detect genes under long-range developmental regulation. Here we review a GRB-based approach to assign loci in non-coding regions to potential target genes, and apply it to reanalyse the results of one of the largest schizophrenia GWAS (SWG PGC, 2014). We further apply this approach to GWAS data from two related neuropsychiatric disorders-autism spectrum disorder and bipolar disorder-to show that it is applicable to developmental disorders in general. We find that disease-associated SNPs are overrepresented in GRBs and that the GRB model is a powerful tool for linking these SNPs to their correct target genes under long-range regulation. Our analysis identifies novel genes not previously implicated in schizophrenia and corroborates a number of predicted targets from the original study. The results are available as an online resource in which the genomic context and the strength of enhancer-promoter associations can be browsed for each schizophrenia-associated SNP.

Earthquake prediction, biological clocks, and the cold war psy-ops: Using animals as seismic sensors in the 1970s California

A familiar story of seismology is that of a small field originally focused on local studies of earthquakes through diverse disciplinary perspectives being transformed, in the second half of the twentieth century, into a highly specialized field focused on global studies of the earth's deep interior via sophisticated instruments and transnational networks of seismological stations. Against this backdrop, this essay offers a complementing account, highlighting the significance of local circumstances and disciplinary agendas that were contingent not only on transformations in the geophysical sciences but also on the concurrently changing biological sciences during the Cold War. Using examples of the studies of unusual animal behavior prior to earthquakes conducted under the auspices of the US Geological Survey on the West Coast of the United States in the 1970s, this essay examines a variety of motivations behind the attempts to bridge geophysics and biology. These examples illustrate the ways in which earthquake prediction became entangled with concerns over the use of seismological data, pioneering research on biological rhythms, and the troubled field of Cold War-driven military brain studies.