Molecules and Meaning:
How Do Molecules Become Biochemical Signals?
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The objective of this paper is to reflect on how molecules can acquire macroscopic meaning (i.e., carry a message to macroscopic levels) in a context of biological evolution. First, the structure of molecules is explained in terms of form (molecular geometry), function (measurable or computable molecular properties), and fluctuation. Fluctuations in form and function create distinct molecular states, and the ensemble of all molecular states defines a molecular space (also known as a property space).
The second part examines molecules in a chemical context. The interplay between a chemical compound and its environment creates a complex system in its own right, as exemplified by solutions. A solute influences the solvent by affecting its organization and some colligative properties, while the solvent often has a marked influence on the solute by constraining its property space and so selecting some of its molecular states. Solutions may display emergent properties not existing in the separate components, e.g. chemical reactivity, implying that information has been created upon formation of the complex system.
The third part of the paper discusses the interaction of
chemical compounds with biological media. In contrast to abiotic environments
such as solvents whose degree of organization is comparatively low, biological
media are characterized by a high degree of organization. Examples at the
macromolecular level include functional proteins (receptors, enzymes,
transporters, ...) or nucleic acids. When a molecule is recognized by such a
macromolecule and interacts (binds) productively with it, a complex system is
produced whose emergent property is the functional response, and which strongly
constrains both of its components. The chemical is frozen into a single or a
very limited number of molecular states (induced fit), whereas the macromolecule
is activated by a conformational change (e.g. an allosteric effect). Here
again, emergent information appears in the complex. However, there is an
essential difference with abiotic systems since the emergent information can
now be translated into a functional biochemical reaction that in turn will be
amplified into a macroscopic biological response. In other words, information
emerging in the molecule-macromolecule complex is a signal that becomes meaning
as it is recognized in the higher hierarchy of nested biological contexts.