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arXiv:1312.4440

Comment on Masanari Asano et al. A model of epigenetic evolution based on theory of open quantum systems. Syst Synth Biol, 2013

Vasily V. Ogryzko

Published Dec 16, 2013• 0 citations
arXivHTMLPDF

Abstract

The comment mostly concerns mis-representation of my position on Quantum Biology, by stating that I am 'reducing cell's behavior to quantum particles inside the cell'. I contrast my position with that of McFadden-Al-Khalili, as well as with the position of Asano et al. I also advertise an idea, described in our latest paper (Bordonaro, Ogryzko. Quantum Biology at the Cellular level - elements of the research program, BioSystems, 2013), for the need of synthetic biology in testing some predictions that follow from our approach.

DOI
10.48550/arxiv.1312.4440

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The comment mostly concerns mis-representation of my position on Quantum Biology, by stating that I am 'reducing cell's behavior to quantum particles inside the cell'. I contrast my position with that of McFadden-Al-Khalili, as well as with the position of Asano et al. I also advertise an idea, described in our latest paper (Bordonaro, Ogryzko. Quantum Biology at the Cellular level - elements of the research program, BioSystems, 2013), for the need of synthetic biology in testing some predictions that follow from our approach.
We apply theory of open quantum systems to modeling of epigenetic evolution. This is an attempt to unify Darwinian and Lamarckian viewpoints on evolution on the basis of a quantum-like model. The state of uncertainty of cell's epigenome is resolved to a stable and inherited epigenetic configuration. This process of evolution and stabilization is described by the quantum master equation (the Gorini-Kossakowski-Sudarshan-Lindblad equation). The initial state of epigenome starting interaction with a new environment is represented as a pure quantum state. It evolves to a steady state solution of the quantum master equation given by a diagonal density matrix. The latter represents the state resulting from a series of epimutations induced by the environment. We use the information interpretation of the wave function which was elaborated by C. Fuchs and A. Zeilinger.
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.