In the hierarchy of cognitive processes, with the highest levels being represented by human individual and social cognition, the processes at the molecular level represent the bottom of the hierarchy. Molecular recognition has become an important subject of research in molecular biology, biological and organic chemistry and in pharmacology. It has important practical implications for medicine, in particular in design of new drugs. Surprisingly, molecular recognition has been only vaguely defined and its relevance to the understanding of higher cognition has been fully neglected so far.

Do chemical reactions between simple atoms and molecules, such as hydrogen and oxygen, consists in molecular recognition? No, they do not. The process is a molecular interaction, not molecular recognition. Why does the binding of a low-molecular ligand to a receptor represent molecular recognition? Because the process is elective: it is a product of design, worked out either by trial and selection in evolution, or by rational design in a contemporary laboratory research. It begins with uncertainty, quantified by information entropy and results in a gain of information. The process is driven by a decrease in interaction free energy, and both its constituents, an enthalpy and an entropy term, play a role in the interaction. A simple model of molecular recognition with only two interacting sites has been worked out allowing quantitative description of the process.

The molecular recognition is only the first step of a molecular process in which a ligand and a receptor interact in vivo to enable transfer of information to other molecules and a relevant molecular response. The entire process is called molecular cognition. In it, a semantic interpretation is being given to the information received.

This analysis provides a revealing importance for the interpretation of cognition at higher levels, including human cognition. In generalizing the free energy description, it can be implied that the human cognition does also involve two distinct, but unseparable terms. Isomorphy between the object and the subject, no matter how coarse and partial, reflects the information term. Affinity between the two, an attraction of the subject to the object, an interest in it, reflects a generalized enthalpy, or energy, term and represents a motivational, emotional component present in the interaction process.

Cognition, even though distinct from its emotional accompaniment, is inseparable from emotion. No cognition without emotion. A molecular analysis provides a strong argument against all variants of radical constructivism in epistemology. A receptor, a molecular "subject", does certainly not "construct" its ligand, its "object"; the structure of the receptor does copy the structure of the ligand, not invent it.