Structural and organisational conditions for being a machine

Abstract

Although the analogy between macroscopic machines and biological molecular devices plays an important role in the conceptual framework of both neo-mechanistic accounts and nanotechnology, it has recently been claimed that certain complex molecular devices (consisting of biological or synthetic macromolecular aggregates) cannot be considered machines since they are subject to physicochemical forces that are different from those of macroscopic machines. However, the structural and physicochemical conditions that allow both macroscopic machines and microscopic devices to work and perform new functions, through a combination of elemental functional parts, have not yet been examined. In order to fill this void, this paper has a threefold aim: first, to clarify the structural and organisational conditions of macroscopic machines and microscopic devices; second, to determine whether the machine-like analogy fits nanoscale devices; and third, to assess whether the machine-like analogy is appropriate for describing the behaviour of some biological macromolecules. Finally, the paper gives an account of 'machine' which, while acknowledging the physicochemical and organisational differences between man-made machines and biological microscopic devices, nevertheless identifies a common conceptual core that allows us to consider the latter 'machines'.

Understanding the SARS-CoV-2-Human Liver Interactome Using a Comprehensive Analysis of the Individual Virus-Host Interactions.

“…We can see these molecular complexes in the peripheral areas of the network. They operate as metabolic nano-machines that carry out specific molecular processes [59,60]. For example, the subgraph at the bottom left is rich in proteins of the Splicing Factor 3B complex that, together with other 17S U2 small nuclear ribonucleoprotein particle (snRNP) components, may play a role in Spliceosome during the selective processing of microRNAs (miRNAs) [61].…”

Understanding the SARS-CoV-2–Human Liver Interactome Using a Comprehensive Analysis of the Individual Virus–Host Interactions

“…We can see these molecular complexes in the peripheral areas of the network. They operate as metabolic nano-machines that carry out specific molecular processes [54,55]. For example, the subgraph at the bottom left is rich in proteins of the Splicing Factor 3B complex that, together with other 17S U2 small nuclear ribonucleoprotein particle (snRNP) components, may play a role in the spliceosome during the selective processing of microRNAs (miRNAs) [56].…”

Mechanism, autonomy and biological explanation

“…A similar consideration applies at smaller scales. The activity of complex molecular machinery such as ATPases and how they perform their function in the cell, can be explained if they are described in mechanistic terms as ordered structures of interacting constraints (Militello and Moreno 2018). Mechanistic details are useful for understanding allosteric enzymes in which it is informative to distinguish as different constraints the allosteric and catalytic sites, as well as additional phosphorylation sites.…”