Statistical Physics of Adaptation

Perunov, Nikolay; Marsland, Robert; England, Jeremy L.

doi:10.1103/physrevx.6.021036

Cited by 82 publications

(109 citation statements)

References 24 publications

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“…As anticipated in previous theoretical works (7,17), our central finding was that kinetically stable behaviors of such a system are indeed biased toward appearing to be finely tuned to the external drive: In other words, the long-time behavior of the system is enriched in outcomes that would be observed only with small likelihood in a random and uniform sampling of the whole space of possibilities.…”

Section: Discussionsupporting

confidence: 56%

Spontaneous fine-tuning to environment in many-species chemical reaction networks

Horowitz

England

2017

Proc. Natl. Acad. Sci. U.S.A.

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A chemical mixture that continually absorbs work from its environment may exhibit steady-state chemical concentrations that deviate from their equilibrium values. Such behavior is particularly interesting in a scenario where the environmental work sources are relatively difficult to access, so that only the proper orchestration of many distinct catalytic actors can power the dissipative flux required to maintain a stable, far-from-equilibrium steady state. In this article, we study the dynamics of an in silico chemical network with random connectivity in an environment that makes strong thermodynamic forcing available only to rare combinations of chemical concentrations. We find that the long-time dynamics of such systems are biased toward states that exhibit a fine-tuned extremization of environmental forcing.A n arrangement of matter may be said to be finely tuned to its environment if it is configured to interact with that environment in a way that is highly atypical for random rearrangements of its components. Whereas some of the most striking examples of such matching between system and environment are found in the architecture of living things (1, 2), the category is in principle far broader, and one might therefore hope to provide an account of emergent fine-tuning in general physical terms.Recent progress in theoretical nonequilibrium statistical mechanics (3-7) has helped to clarify a general relationship between the likelihood of a system adopting a particular microscopic configuration and the amount of energy absorbed and dissipated during the system's dynamical history. Essentially, the irreversibility of being driven into a kinetically stable state must be compensated by the release of heat in the surroundings, which frequently occurs when the system absorbs and dissipates energy from an environmental source of work. The implications of this thermodynamic frame are particularly clear in systems where the specific configuration adopted has a large influence on the accessibility of energy from external drives, such that strongly driven states are rare. In such a scenario, having a highly dissipative history becomes tantamount to having a configurational history that includes the rare, finely tuned states that make dissipation possible. This observation suggests that there may be a broad class of nonequilibrium systems for which state-dependent drive strength is the relevant thermodynamic parameter for describing the bias in their exploration of configuration space.Motivated by these considerations, we carried out simulations of a complexly driven, randomly wired, many-species chemical reaction network, with the aim of identifying a thermodynamic principle governing self-organization far from equilibrium. We found that such networks have a pronounced bias toward settling into rare states in chemical space with extremal forcing, suggesting that emergent fine-tuning is a general tendency of their dynamical behavior. Two-Species ModelIn this study, we are ultimately interested in the thermodynamic propert...

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Section: Discussionsupporting

confidence: 56%

Spontaneous fine-tuning to environment in many-species chemical reaction networks

Horowitz

England

2017

Proc. Natl. Acad. Sci. U.S.A.

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“…adjust to their environment has been challenged in a very recent proposal known as "dissipative adaptation" (59,60) that asserts that molecules adapt to maximize the dissipation of energy and that makes no mention of kinetic asymmetry. Despite much attention given to the dissipative adaptation model, particularly in the lay literature, the basic claim of the dissipative adaptation model is wrong (55).…”

Section: Prospective and Conclusionmentioning

confidence: 99%

Stochastically pumped adaptation and directional motion of molecular machines

Astumian

2018

Proc. Natl. Acad. Sci. U.S.A.

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Recent developments in synthetic molecular motors and pumps have sprung from a remarkable confluence of experiment and theory. Synthetic accomplishments have facilitated the ability to design and create molecules, many of them featuring mechanically bonded components, to carry out specific functions in their environment-walking along a polymeric track, unidirectional circling of one ring about another, synthesizing stereoisomers according to an external protocol, or pumping rings onto a long rod-like molecule to form and maintain high-energy, complex, nonequilibrium structures from simpler antecedents. Progress in the theory of nanoscale stochastic thermodynamics, specifically the generalization and extension of the principle of microscopic reversibility to the single-molecule regime, has enhanced the understanding of the design requirements for achieving strong unidirectional motion and high efficiency of these synthetic molecular machines for harnessing energy from external fluctuations to carry out mechanical and/or chemical functions in their environment. A key insight is that the interaction between the fluctuations and the transition state energies plays a central role in determining the steady-state concentrations. Kinetic asymmetry, a requirement for stochastic adaptation, occurs when there is an imbalance in the effect of the fluctuations on the forward and reverse rate constants. Because of strong viscosity, the motions of the machine can be viewed as mechanical equilibrium processes where mechanical resonances are simply impossible but where the probability distributions for the state occupancies and trajectories are very different from those that would be expected at thermodynamic equilibrium. molecular machine | stochastic pumping | kinetic asymmetry The molecular machines necessary for life must carry out their function in the fluctuating environment of a biological cell. Nowhere is the dynamic aspect of biology at the molecular level more evident than in the bilayer membrane surrounding most cells and organelles, a small portion of which is shown schematically in Fig. 1. Three transmembrane proteins are included in the depiction: (i) an ion channel that provides a conduit for conduction of ions across the membrane; (ii) a molecule that facilitates the transport of some substance, S, across the membrane; and (iii), an NaATPase that uses energy from ATP hydrolysis to maintain ion gradients across the membrane. The transporter acts as a catalyst to reduce the barrier for transport of S. In and of itself, the transporter cannot drive the substance S from low to high chemical potential. The transporter, however, is near a possible source of energy, the ion channel. The ion channel provides a path for conduction of ions from high to low electrochemical potential, thus dissipating energy. Every time the ion channel opens or closes, the local electric field across the membrane changes, and because the flow of ions down the electrochemical gradient when the channel is open dissipates energy, the resulting ...

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“…Furthermore, also experiments investigating stochastic resonance (SR) within and between brain areas imply that "SR-mediated neural synchronization is a general mechanism of brain functioning" (Ward et al, 2006) and that "noise could play a fundamental role in biological information processing" (Keppler, 2013 (Keppler, 2016;Tononi, 2008 This dynamic, yet harmonic, field structuretherefore suggests a "bootstrap" approach to understanding how consciousness might universally weave through quantum processes of complex systems both micro and macro cosmically (Wolchover, 2017). Within living systems, the ubiquitous access to these background signals means that self-organizing information can plausibly be represented across entropic discontinuities via stochastic resonance (SR) processing to drive biological development of agency in close correlation to the thermodynamic work energy driving reproduction (Perunov, Marsland, & England, 2016).…”

Section: J Adlermentioning

confidence: 99%

“…Therefore, creativity in the face of stochastic possibilities provides adaptively rewarding feed forward phenomena in the development of conscious systems, including intrapsychic phenomena (McCrae, 1996;Kaufman et al, 2015). These considerations suggest that "emergent 'adaptive' resonance in the system" is correlated (both in terms of energy and information) to the system's openness to interpreting frequencies of driving field harmonics despite noise, interference, or perturbation during absorption (Perunov, Marsland, & England, 2016). As a conscious perceiver remains more open more willfully, as in socio-behavioral studies of human generosity, the richness of stimuli via qualia producing architectures optimizes the organism's responsiveness (i.e., tunes and dilates) (Grant & Dutton, 2012).…”

Section: Conscious Systems Theory (Cst)mentioning

confidence: 99%

The Open Mind: A Phenomenology

Adler¹

2017

OJPP

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What does it mean to keep an "open mind"? In casual conversation it's a popular phrase with enough common sense to negate much need for debate about what the speaker means. Someone with an open mind might be considered considerate, equanimous, empathetic, a good listener, curious, or flexible in opinion. In Western culture an open-minded person might be receptive to new ideas, possibilities, and interpretations, suggesting that they successfully maintain an engaged yet dynamic mental relationship to various subjects or challenges. Yet in science's nascent study of consciousness, the notion of a mind "opening" is complicated by the field's inability to clearly articulate what a mind is, let alone how, or into what, it might open. It is the purpose of this research to present the biological significance of "open-mindedness" in order to discuss possible phenomenological implications pertaining to neural correlates of consciousness (NCC). In his seminal book The Open Work, Umberto Eco describes "openness" as a phenomenon of conscious organization that "locates the infinite at the very core of the finite," and "invites us to conceive, feel, and thus see the world as possibility." Utilizing the methods of MDA analysis, my critical phenomenological inquiry extends Eco's lens of cultural semiotics into quantum biology to provide key insights for understanding the aesthetic role of field dynamics in qualia physics-as interpretive events (i.e., watching a film, tasting a dessert, or drawing). In particular, pairing Eco's semiotic analyses of openness with Hameroff and Penrose's OR Theory concerning cognitive qualia-producing architectures such as microtubules, raises how sensations (i.e., interpretive events) between organisms and the ZPF are-as Antero Alli conceives-absorbed, integrated, and transmitted through quantum SED information states proposed by Joachim Keppler. Therefore, we can say that living systems are those systems that have adapted their material capabilities (including fundamental principles of self-organization and complexity in common cognitive architectures like awareness and attention) to perceive and interpret coherently. That is to say-biology has evolved to make meaning through its very aliveness. Our conscious ability to open our minds in order to interpret and communicate J. Adler our sensations, thoughts, and complete experiences, therefore reveals a radically multidimensional bio-geometry and biolinguistics based on a phenomenological field dynamics Eco's work constructs. Via an aesthetic information theory, Eco describes as, "a practical level of poetics that acts as programmatic projects for creation." The writings of Rumi, Husserl, Dewey, Emerson, Merleau-Ponty, Hegel, and others confer depth to the emergent mechanics of perception found throughout biotic systems. Eco's ideas thereby provoke discourse on the role of openness within recent theoretical works by Jeremy England, Anirban Bandyopadhyay, Robert Lanza, Deepak Chopra, Ervin Laszlo, Giulio Tononi, Stuart Kauffman, Walter J. Fr...

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Statistical Physics of Adaptation

Cited by 82 publications

References 24 publications

Spontaneous fine-tuning to environment in many-species chemical reaction networks

Spontaneous fine-tuning to environment in many-species chemical reaction networks

Stochastically pumped adaptation and directional motion of molecular machines

The Open Mind: A Phenomenology

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