ENCODE and the parts of the human genome

This paper examines a specific kind of part-whole relations that exist in the molecular genetic domain. The central question is under which conditions a particular molecule, such as a DNA sequence, is a biological part of the human genome. I address this question by analyzing how biologists in fact partition the human genome into parts. This paper thus presents a case study in the metaphysics of biological practice. I develop a metaphysical account of genomic parthood by analyzing the investigative and reasoning practices in the ENCODE (ENCyclopedia Of DNA Elements) project. My account reveals two conditions that determine whether a molecule is a part of the human genome (i.e., a genomic part). First, genomic parts must possess a causal role function in the genome as a whole, that is, their functions must contribute to the genome directing the overall functioning of the cell. Second, genomic parts must have a specific chemical structure and be actual segments of the DNA sequence of the genome.

Saving the mutual manipulability account of constitutive relevance

Constitutive mechanistic explanations are said to refer to mechanisms that constitute the phenomenon-to-be-explained. The most prominent approach of how to understand this relation is Carl Craver's mutual manipulability approach (MM) to constitutive relevance. Recently, MM has come under attack (Baumgartner and Casini 2017; Baumgartner and Gebharter 2015; Harinen 2014; Kästner 2017; Leuridan 2012; Romero 2015). It is argued that MM is inconsistent because, roughly, it is spelled out in terms of interventionism (which is an approach to causation), whereas constitutive relevance is said to be a non-causal relation. In this paper, I will discuss a strategy of how to resolve this inconsistency-so-called fat-handedness approaches (Baumgartner and Casini 2017; Baumgartner and Gebharter 2015; Romero 2015). I will argue that these approaches are problematic. I will present a novel suggestion for how to consistently define constitutive relevance in terms of interventionism. My approach is based on a causal interpretation of manipulability in terms of causal relations between the mechanism's components and what I will call temporal EIO-parts of the phenomenon. Still, this interpretation accounts for the fundamental difference between constitutive relevance and causal relevance.

Deeper insights into semantic relations: an fMRI study of part-whole and functional associations

Cognitive neuroscience research on semantics recognizes a distinction between categorical and associated relations. However, associations can be divided further, such as into part-whole and functional relations. We investigated the neural basis of both relations using a picture-word interference task in an fMRI study. While the left supramarginal gyrus and the right inferior temporal sulcus were activated by part-whole over functional relations, the same applies to the right parahippocampal complex contrasting the functional over part-whole relations. The small effect sizes of our analyses have to be interpreted with caution. While the parahippocampal complex might reflect global scene processing across objects, the inferior temporal sulcus might be involved in the perceptual encoding of object related knowledge and the supramarginal gyrus might represent a convergence zone which implements within object related perceptual features. The current study gives a first indication that the neural bases for part-whole and functional relations seem to be distinguishable.