Atoms, molecules, cells, organisms, societies and cultures certainly ARE all built up from elementary particles. Brains are organs that evolved as the control centers of certain species of organisms, including our own species. They are vast complexes of neurons that generate electromagnetic fields. The are no "unknown nonspatial substances" in my analysis and substances do not supervene on anything. Functional or phenomenal properties, for example, are said to supervene on organisms or brains. But I don't think anyone holds that a substance could be a supervenient property. 
I introduced a substance theory as an ontological solution to the hard problem of consciousness. Elementary particles (leptons, quarks and bosons) are basic substances and the composite objects (atoms, molecules, cells...) they comprise have both intrinsic and extrinsic properties. The extrinsic properties of the neurons in the brain generate specific patterns of firings of these cells that are structurally isomorphic with recognizable sensory inputs from the environment (or memory) that are sufficiently reliable representations of the world in which we "brainy" animals live. Consciousness is identical to these patterns of representational electro-chemical magnetic field activity. It appears to the brainy animal, who can also use language to reflect upon its own conscious experience, memories and imaginings, that these experiences (i.e., "qualia") are not physical things, composed of elementary particles. The solution to the hard problem of mind is that the intrinsic nature of the representational electromagnetic activity is "like something"... in just the sense that it is like something to be a bat. Bat's are brainy animals too, so the electromagnetic fields on which the representational acoustical information is propagated in their bat brains is "like something to be". Something very, well, ... "batty". Just like the complex array of brain processes generated when you or I might enjoy a beer, marvel at a rainbow or recount a dream are typically human experiences. All substances, elementary and composite, have intrinsic natures. In the cases of composite objects that are brainy animals, it's like something to be certain parts and processes of their brains. The scientific or third-person descriptions of these neurological properties are of the extrinsic properties of brains. The first-person or phenomenal properties are explained as the intrinsic properties of theses same composite objects.


-dcd