Molecules into Cells: Specifying Spatial Architecture

Abstract

SUMMARY A living cell is not an aggregate of molecules but an organized pattern, structured in space and in time. This article addresses some conceptual issues in the genesis of spatial architecture, including how molecules find their proper location in cell space, the origins of supramolecular order, the role of the genes, cell morphology, the continuity of cells, and the inheritance of order. The discussion is framed around a hierarchy of physiological processes that bridge the gap between nanometer-sized molecules and cells three to six orders of magnitude larger. Stepping stones include molecular self-organization, directional physiology, spatial markers, gradients, fields, and physical forces. The knowledge at hand leads to an unconventional interpretation of biological order. I have come to think of cells as self-organized systems composed of genetically specified elements plus heritable structures. The smallest self that can be fairly said to organize itself is the whole cell. If structure, form, and function are ever to be computed from data at a lower level, the starting point will be not the genome, but a spatially organized system of molecules. This conclusion invites us to reconsider our understanding of what genes do, what organisms are, and how living systems could have arisen on the early Earth.

From Systems to Organisations

“…Organisation appears everywhere. It may be a collective aspect, as in simple oscillatory chemical reactions, consensus bio-chemical setups of cells [33], and "self-organising" phenomena; or a structural, individual-centred aspect present in macro-molecules, cell compartments, and cellular functional modules [14,34,35].…”

“…Both terms refer to the same idea-the relative position, connection, or interaction channel of things and thing components with respect to one another, that become hierarchically arranged as a consequence of encapsulation into wholes or units [30]. Organisation is a central characteristic of biological entities and biological phenomena [1,11,14,27,28,31,32]. Organisation appears everywhere.…”

“…This perspective hypothesises that things in a phenomenon are organisations, rather than particles, substances, individuals etc, that interact predominantly exchanging signals and a specific kind of in-formation (see Sections 3.2 and 5) that pictures in(side)formation. In this way, living things and phenomena may be seen as a fifth state of matter (organised-matter), that maintains, reproduces, multiplies, and enchains organisations [3], as proposed by F. Harold [11,14] and R. Rosen [8] (see also [3])…”

“…These entangled factors encapsulate into units, adapt themselves and integrate several dynamic scales [6,8,[13][14][15][16][17], leading to the picture described by Harold [11,14].…”

Methods for Whole Cell Detection of Microorganisms

“…Although the capacity to detect cell-specific nucleic acids without the need for culture may be considered an advantage of such acellular techniques, it is not without cost. The individual cell is the "...fundamental unit of biological organization..." (16,17). Additional layers of information are therefore intrinsically linked to the "granular" or corpuscular nature of microbes.…”