There has been a strong recent interest in applying quantum theory (QT) outside physics, including in cognitive science. We analyze the applicability of QT to two basic properties in opinion polling. The first property (response replicability) is that, for a large class of questions, a response to a given question is expected to be repeated if the question is posed again, irrespective of whether another question is asked and answered in between. The second property (question order effect) is that the response probabilities frequently depend on the order in which the questions are asked. Whenever these two properties occur together, it poses a problem for QT. The conventional QT with Hermitian operators can handle response replicability, but only in the way incompatible with the question order effect. In the generalization of QT known as theory of positive-operator-valued measures (POVMs), in order to account for response replicability, the POVMs involved must be conventional operators. Although these problems are not unique to QT and also challenge conventional cognitive theories, they stand out as important unresolved problems for the application of QT to cognition. Either some new principles are needed to determine the bounds of applicability of QT to cognition, or quantum formalisms more general than POVMs are needed.

We present the novel approach to mathematical modeling of information processes in biosystems. It explores the mathematical formalism and methodology of quantum theory, especially quantum measurement theory. This approach is known as quantum-like and it should be distinguished from study of genuine quantum physical processes in biosystems (quantum biophysics, quantum cognition). It is based on quantum information representation of biosystem's state and modeling its dynamics in the framework of theory of open quantum systems. This paper starts with the non-physicist friendly presentation of quantum measurement theory, from the original von Neumann formulation to modern theory of quantum instruments. Then, latter is applied to model combinations of cognitive effects and gene regulation of glucose/lactose metabolism in Escherichia coli bacterium. The most general construction of quantum instruments is based on the scheme of indirect measurement, in that measurement apparatus plays the role of the environment for a biosystem. The biological essence of this scheme is illustrated by quantum formalization of Helmholtz sensation-perception theory. Then we move to open systems dynamics and consider quantum master equation, with concentrating on quantum Markov processes. In this framework, we model functioning of biological functions such as psychological functions and epigenetic mutation.