Challenges
Datasets
Workspaces
Papers
Discussions
Leaderboard
Log inSign up
Challenges
Datasets
Workspaces
Papers
Discussions
Leaderboard
Blog
Job Board
Q3AS

© 2026 Aqora Quantum S.A.S.

TermsPrivacyLegal Notice

Entropy

Living Systems are Dynamically Stable by Computing Themselves at the Quantum Level

Abir U. Igamberdiev

Published Jun 30, 2003• 6 citations
Publisher

Abstract

The smallest details of living systems are molecular devices that operate between the classical and quantum levels, i.e. between the potential dimension (microscale) and the actual three-dimensional space (macroscale). They realize non-demolition quantum measurements in which time appears as a mesoscale dimension separating contradictory statements in the course of actualization. These smaller devices form larger devices (macromolecular complexes), up to living body. The quantum device possesses its own potential internal quantum state (IQS), which is maintained for prolonged time via error-correction being a reflection over this state. Decoherence-free IQS can exhibit itself by a creative generation of iteration limits in the real world. To avoid a collapse of the quantum information in the process of correcting errors, it is possible to make a partial measurement that extracts only the error-information and leaves the encoded state untouched. In natural quantum computers, which are living systems, the error-correction is internal. It is a result of reflection, given as a sort of a subjective process allotting optimal limits of iteration. The IQS resembles the properties of a quasi-particle, which interacts with the surround, applying decoherence commands to it. In this framework, enzymes are molecular automata of the extremal quantum computer, the set of which maintains stable highly ordered coherent state, and genome represents a concatenation of error-correcting codes into a single reflective set. Biological systems, being autopoietic in physical space, control quantum measurements in the physical universe. The biological evolution is really a functional evolution of measurement constraints in which limits of iteration are established possessing criteria of perfection and having selective values.

DOI
10.3390/e5020076

Related papers

The computation power of living systems is maintained by decoherence-free internal quantum states

Abir U. Igamberdiev

The internal quantum state (IQS) is a kind of a pilot-wave (in the Bohmian sense) attached to a macroscopic system and representing its potential field continuously reduced during its exhibition to the external world. This state is maintained as decoherence-free by applying error-correction commands to it and by screening from thermal interactions. Its effective temperature is kept down below the millikelvin range thus being screened even from the background microwave radiation. The quantum Zeno effect enables coherent superpositions and entanglement to persist for macroscopic time intervals. The IQS thus avoids the Boltzmann statistics and approaches a state when the Bose-Einstein statistics is applicable. The IQS of a living system can be viewed as a subtle individual subatomic structure reduced to a complex pattern of vibrating strings and exhibiting itself via a visible classical body-like system. Light quanta inside IQS are trapped like matter is trapped by a black hole in space. The IQS can be considered as a unified field meeting place of gravitational, electromagnetic, weak and strong nuclear forces. The phenomenon of emission of weak coherent light is an indirect evidence of coherent long-living internal quantum states in living systems. This emission is a kind of a similar phenomenon as the Hawking's radiation from black holes and it may serve for unification of the processes taking place in different subsystems of a biological system (synchronization of individual coherent states within the whole system). The external exhibition of the IQS can be expressed as a mapping from complex to real numbers where the certain rules are generated, e.g. the power law and other recursive formulae. In the simplest case when two superposed states are reduced, it has a limit of price of action equal to the Planck's constant. The reduction is non-computable and resembles the act of volition. The result is Godel number appearing above superposed states and memorizing the act of reduction. It is used by living system as an information unit in emerging computation process.

•Jan 1, 2005•1 citation

Internal Quantum Measurements and the Growth of Information

Abir U. Igamberdiev

Introduction In the processes of adaptation, development and evolution, living systems interpret themselves in the environment resulting in changes of both. This leads to the growth of information via rescaling of internal time (heterochrony) followed by spatial reconstructions of morphology (heterotopy). The growth of information is based on perpetual changes in its interpretation in the changing world. Biological evolution involves the anticipatory epigenetic changes in interpretation of the genetic information which cannot be generally forecasted but can provide canalization of structural changes defined by the existing organization leading to predictable patterns of form generation. Social evolution is accompanied by unprecedented growth of the informational field that leads to progressive development of human society. In modern theoretical biology, the internal measurement concept was suggested as a background for explanation of the phenomenon of life (Matsuno, 1995). The quantum measurement represents the action of a measuring device on the measured system. The quantum measurement is an irreversible phenomenon exhibiting itself as a reduction of the potential field. It has also a relation to the irreversibility of time (Igamberdiev, 1993). The collapse of wave function is not equivalent to time until it does not generate a measurable duration, but when its pattern is repeated consistently, the clock can be set, and the system becomes organized in time. When the measuring device is a part of measured system, the measurement proceeds internally in relation to the whole system and the latter becomes more complex as a result of measurement itself. The aim of this study is to discuss the role of internal measurement in the growth of information in evolving systems. This can refer to biological evolution, social evolution, and as well to the cosmic evolution, which is represented in the phenomenon of expansion of the Universe. Internal Measurement and the Generation of New Information The internal measurement leads to an iterative recursive process which appears as the development and evolution of the combined system containing the measuring device and the measured object. The quantum measuring device can be organized in such way that it “encodes” the system in the course of interaction with the measured object, and makes it possible for the measurement to proceed in a regular way. In this case, such system can memorize the evolutionary complication of organization in a digital information-bearing subsystem and evolve further; in other words it contains an internal description memorizing the result of measurement. The logical precondition of the growth of information in this evolving process is the incompleteness of biosystem’s internal description, while the physical precondition is the uncertainty of quantum measurement. The evolutionary increase of complexity becomes possible when genotype appears as a system distinct from phenotype and is embedded into it, which separates energy-degenerate rate-independent genetic symbols from the rate-dependent dynamics of construction that they control (Pattee, 2001). Evolutionary growth of information becomes its own cause, a universal property of our world. The growth of information accompanies the appearance of measurable time that occurs in the systems performing quantum measurements in a regular way, with low dissipation of energy (Igamberdiev, 1993, 2004). These systems are modelled as hypercycles and can be defined as structures in which the subset of a substrate set of the catalytic system happens to be the matrix for generating and reproducing the set of catalysts itself (Igamberdiev, 1999). This definition keeps the main features of the original notion of hypercycle given by Eigen and Schuster (1979). The hypercyclic system is closed in the way that all of the catalysts needed for an organism to stay alive (representing an efficient causation according to Aristotle and forming organism’s spatiotemporal structure) must be produced by the organism itself, only relying on matter and energy from the outside (Letelier et al., 2011). When hypercycles appear in evolution, time becomes an independent measurable variable due to the internal reproducible changes. Hypercycle organizes irreversibility of quantum measurement into a measurable duration. Eigen’s hypercycle is a formalized representation of the autopoietic system of Maturana and Varela or Rosen’s (M,R) system (Leteiler et al., 2011). The system becomes an internal autonomous clock that distinguishes the past (memory), the present (life), and the future (anticipation based on the reproducible model), so the modeling, logic and digital information growth become possible within the system (Rosen, 1985). The hypercycle having own embedded description, becomes a structure that realizes computation in accordance with its internal logic defined by the embedded description. The latter has the property of incompleteness which is reflected in the fact that quantum correlations of the states of the system are associated with undecidable logic theories, i.e., they can potentially generate the statements not defined within the system. The undecidability can be interpreted in the sense similar to the Gödel’s incompleteness theorem, meaning that there exist propositions, expressible in the formal logic, which cannot be proven or disproven (Briegel et al., 2009). These propositions become the grounds of expansion of the system and its informational growth. From the quantum mechanical point of view, the emergence of a new statement results in acquiring a new error-correction meaning to support the internal quantum state (IQS) (Igamberdiev, 2004, 2007). The IQS keeps the system organizationally invariant. It is supported by the set of error-correcting commands that aim to keep IQS free from external demolitions. The error-correction information becomes an important part of the whole informational field. A new statement makes the system more complex (it leads to an increase of its informational content), with its all spatiotemporal organizational invariance be rescaled. In the course of evolution, an available element of a formal system (similarly to a word when used as a metaphor) can acquire another (in addition to already existing) value that contributes to formation of a new level of organization in the system. The logical basis of this action is the incompleteness of the existing formal system that allows assigning arbitrary values to the statements non-provable within that system, while the physical basis is the quantum uncertainty arising in quantum measurement. A new statement can arise from existing elements by acquiring the double function, however, for fixation of this new statement via expansion of existing formal system, some informational redundancy of the system is needed, which can be achieved by multiplication of some of its elements. Genome is a system which possesses an internal complementarity between the linear texts and their superposition. Relevantly to this, complementarity means that text and hypertext cannot be viewed at the same moment: they should be separated by a time interval. It is an example of uncertainty between the system and its embedding. Overlapping genes, alternatively splicing sequences, RNA and DNA editing, introns, and recombination according to molecular addresses are the features of this hypertext generating a potentially infinite number of language games. Genome as a complete language exists as a complementary set of its alternative combinations resulting in logical paradoxes which determine its temporal dynamics (Isalan, 2009). This superposition is a basis for ontogenesis, adaptation and evolution. Thus, the total “true” genome is a superposition of contradictory arrangements, which generate one single arrangement at a concrete moment of time. The pool of mobile genetic elements expands the combinatorial capacity of the genome by many times. An ambiguity in meaning is analogous to the quantum uncertainty principle in which it is impossible to define strictly the position and impulse of a particle simultaneously, or to fix certain energy in a very short period of time necessary for its registration. The question of a minimal size of the autocatalytic self-reproducing system and its composition has been discussed in several works (Sharov, 2009; Steel et al., 2013). Self-reproduction itself is a creative process of placing text in text with following self-growing of this joint structure. Any evolutionary change also begins from the placing of “text into text”. This is possible because genome is structurally adapted for realization of such a non-trivial function. Moreover, even a point mutation or deletion may be considered as generative if it is placed in the repeated (e.g., diploid) structure. The doubling is a premise of metasystem transition, which includes duplication of the original system and the establishment of control over multiple copies (Turchin, 1977). The evolutionary significance of gene duplication was considered by Ohno (1970) as a premise of neofunctionalization. The advantage of sexual reproduction is in the casual combinatorial generating of new statements from two separate texts that can acquire meanings, thus it resists evolutionary degradation. It becomes a prerequisite for growing of information and complexity (Igamberdiev, 2014). The combinatorial interaction of heterochronic texts generates a new system in which the internal time is rescaled in a new way that generally cannot be forecasted. The heterochronic duplication (via hybridization of temporally different organisms) generates more possibilities for the metasystem transition. Thus, the incompleteness of embedded set of symbols is the formal cause of evolution. The physical representation of this incompleteness is a quantum uncertainty in the course of measurement (Matsuno, 1992). It spans from the level of elementary particles to biological evolution and to the phenomenon of free will and consciousness. Growth of Information in the Expanding Universe The growth of information that we discuss here mainly in relation to biological evolution is relevant also to the physical space-time scales. The self-growing principle of quantum measurement has a property of intrinsic expansion of the informational field. The relationship between observable nature and a hidden “potential” nature is modeled, according to Kineman (2010), as an imaginary space-time domain geometrically represented as radial “Minkowski-space”. Despite of the fact that local space and time are normally represented as real numbers, the general relationship in this geometry is hyperbolic in accordance with the special theory of relativity. When mapped as a radial geometry, the space-time is seen to be intrinsically dynamic (expanding) and self-similar across all scales. The geometry has the properties of early and present acceleration. This representation eliminates the “light cone” and thus all regions in this model are the domains of existence and are observable over time. Nevertheless a domain of general, non-local reality is represented in the imaginary axes that exist simultaneously with measurable, local domains. The Universe in the concept of Kineman (2010) consists of the units called “holons”, which vaguely correspond to Leibniz’s monads. They possess simultaneous properties of location and non-location, as a point of non-differentiated whole appearing in a subject-object relation. The Everett’s interpretation of quantum mechanics works in these isolated domains but not between the domains, the same idea has been suggested by Matsuno (2012) for the individual biological systems taken as separate domains. The reality of superposition of the wave function is limited by the single monad and does not expand outside it, and in this sense monads do not have windows as originally proposed by Leibniz. Conclusion The growth of information is the basic property of evolving systems and it follows from the interaction between non-local and local domains in the course of internal quantum measurements. The internal measurement leads to an iterative recursive process which appears as evolution of the combined system containing the measuring device and the measured object. The system through measurement acquires the property of expansion, which is seen in biological evolution, social development, and at cosmic scales as expansion of the Universe. References Briegel, H.J.; Browne, D.E.; Dur, W.; Raussendorf, R.; Van den Nest, M. Measurement-based quantum computation. Nature Physics 2009, 5, 19-26. Eigen, M.; Schuster, P. The Hypercycle: A Principle of Natural Self-Organization. Springer, Berlin, 1979. Igamberdiev, A.U. Quantum mechanical properties of biosystems: A framework for complexity, structural stability and transformations. Biosystems 1993, 31, 65‐ Igamberdiev, A.U. Foundations of metabolic organization: coherence as a basis of computational properties in metabolic networks. Biosystems 1999, 50, 1-16. Igamberdiev, A.U. Quantum computation, non-demolition measurements, and reflective control in living systems. Biosystems 2004, 77, 47–56. Igamberdiev, A.U. Physical limits of computation and emergence of life. Biosystems 2007, 90, 340–349. Igamberdiev, A.U. Time rescaling and pattern formation in biological evolution. Biosystems 2014, 123, 19-26. Isalan, M. Gene networks and liar paradoxes. Bioessays 2009, 31, 1110-1115. Letelier, J.C.; Cárdenas, M.L.; Cornish-Bowden, A. From L'Homme Machine to metabolic closure: steps towards understanding life. Journal of Theoretical Biology 2011, 286, 100-113. Matsuno, K. The uncertainty principle as an evolutionary engine. Biosystems 1991, 27, 63-76. Matsuno, K. Quantum and biological computation. Biosystems 1995, 35, 209-212. Matsuno, K. Chemical evolution as a concrete scheme for naturalizing the relative-state of quantum mechanics. Biosystems 2012, 109, 159-168. Kineman, J.J. Relational self-similar space-time cosmology revisited. Proceedings of the 54th Meeting of the International Society for System Sciences. Waterloo, Canada, 2010. Ohno, S. Evolution by Gene Duplication. Springer, New York, 1970. Pattee, H.H. The physics of symbols: bridging the epistemic cut. Biosystems 2001, 60, 5-21. Sharov, A.A., 2009. Coenzyme autocatalytic network on the surface of oil microspheres as a model for the origin of life. International Journal of Molecular Sciences 2009, 10, 1838-1852. Steel, M.; Hordijk, W.; Smith, J. Minimal autocatalytic networks. Journal of Theoretical Biology 2013, 332, 96-107. Turchin, V. Phenomenon of Science. Columbia University Press, New York, 1977.

ISIS Summit: The Information Society at the Crossroads•Jun 23, 2015•0 citations

Practical Advances in Quantum Error Correction & Communication

Daniel Benjamin Criger

Quantum computing exists at the intersection of mathematics, physics, chemistry, and engineering; the main goal of quantum computing is the creation of devices and algorithms which use the properties of quantum mechanics to store, manipulate and measure information. There exist many families of algorithms, which, using non-classical logical operations, can outperform traditional, classical algorithms in terms of memory and processing requirements. In addition, quantum computing devices are fundamentally smaller than classical processors and memory elements; since the physical models governing their performance are applicable on all scales, as opposed to classical logic elements, whose underlying principles rely on the macroscopic nature of the device in question. \n \nQuantum algorithms, for the most part, are predicated on a theory of resources. It is often assumed that quantum computers can be placed in a precise fiducial state prior to computation, and that logical operations are perfect, inducing no error on the system which they affect. These assumptions greatly simplify algorithmic design, but are fundamentally unrealistic. In order to justify their use, it is necessary to develop a framework for using a large number of imperfect devices to simulate the action of a perfect device, with some acceptable probability of failure. This is the study of fault-tolerant quantum computing. In order to pursue this study effectively, it is necessary to understand the fundamental nature of generic quantum states and operations, as well as the means by which one can correct quantum errors. Additionally, it is important to attempt to minimize the use of computational resources in achieving error reduction and fault-tolerant computing. \n \nThis thesis is concerned with three projects related to the use of error-prone quantum systems to transmit and manipulate information. The first of these is concerned with the use of imperfectly-prepared states in error-correction routines. Using optimal quantum error correction, we are able to deduce a method of partially protecting encoded quantum information against preparation errors prior to encoding, using no additional qubits. The second of these projects details the search for entangled states which can be used to transmit classical information over quantum channels at a rate superior to classical states. The third of these projects concerns the transcoding of data from one quantum code into another using few ancillary resources. The descriptions of these projects are preceded by a brief introduction to representations of quantum states and channels, for completeness. \n \nThree techniques of general interest are presented in appendices. The first is an introduction to, and a minor advance in the development of optimal error correction codes. The second is a more efficient means of calculating the action of a quantum channel on a given state, given that the channel acts non-trivially only on a subsystem, rather than the entire system. Finally, we include documentation on a software package developed to aid the search for quantum transcoding operations.

•Oct 25, 2013•1 citation

Quantum codes and macroscopic superpositions

Julio R. Gea-Banacloche

It is shown that encoding the state of a quantum computer (or other quantum information-processing device) for error correction has the effect of making its operating states macroscopically indistinguishable; all the more, the more ``stable'' the code is, that is, the more errors it can correct in each pass. It is also shown that for nondegenerate codes the expectation values of macroscopic observables in such encoded states are identical to those that would be obtained for a totally mixed state of maximum entropy, where again the degree of indistinguishability increases with the number of errors corrected by the code. The results can be used to estimate the decoherence rates for systems of qubits under certain forms of interaction with the environment: it is found that when the qubits are encoded all coherent superpositions decay, to lowest order, at the same rate, which scales more slowly with the number of physical qubits than the decoherence rate for macroscopic coherent superpositions (``Schr\"odinger cats'') of the bare qubits.

Physical Review A•Jan 4, 2000•4 citations

Foreword

Tony Leggett

When the revolutionary conceptual structure for the description of the physical world which we know as quantum mechanics was first formulated nearly 90 years ago, and its predictions tested in the laboratory, most of the experiments in question were on systems which were both very well characterized and reasonably well isolated from their environments, such as single electrons and atoms, small molecules and near-perfect crystalline solids. While from the very start most physicists have taken it for granted that the formalism of quantum mechanics, when combined with appropriate system-specific information, can “in principle” account for all phenomena occurring in the physical world, including those usually regarded as the subject-matter of biology, until quite recently the overwhelmingly majority opinion has been that in a biological context the role of quantum theory is confined to elucidating the equilibrium structures of the relevant molecules and their reaction processes, and that subtle phenomena such as superposition and entanglement, of which we can now routinely exhibit spectacular effects at the level of a few well-isolated photons or atoms, play at most a very indirect role in any phenomena of biological interest. A major reason conventionally given for this view has been that biological systems, at least working ones, are by their very nature “warm and wet” – a phrase which in the physicist's lexicon translates to “prone to massive decoherence”; it looks as though any interesting superposition, say of different energy eigenstates of one's system, would be rapidly decohered by the ever-present, and usually microscopically very complex, environment.

Cambridge University Press eBooks•Aug 6, 2014•0 citations

Internal quantum constraints of natural computation in autopoietic systems

Abir U. Igamberdiev

Time relates to actualization, which is physically interpreted as a quantum measurement. The measurement has a dual structure consisting of the reality being measured (externality) and the reality by which the measurement takes place (an agent or ontolon). These two constituents refer to the two types of time: physical time measured by clocks, and internal time, defined by Bergson as la durée (duration). The latter holds the coherent internal quantum state of entangled potentialities, while the former represents the collapse of this state, thereby flowing through quantum transactions. This view unifies the Everett (Many-worlds) and the Copenhagen (Wave function collapse) interpretations of the quantum measurement. Time as a duration can be estimated via the energy-time uncertainty relation, which links the precision of the measurement result to the value of energy dissipation during it and to its span. The precision of the measurement result enables the process of quantum computation, which emerges in the systems characterized by internal closure, i.e., autopoietic (living) systems operating at the state of sustainable non-equilibrium. Energy dissipation in the process of measurement occurs as the emission of quanta that trigger the collapse of the coherent entangled state. These quanta are recognized in the system, enabling the performance of higher-level control over elementary computational actions through their integration within the complex system. It is concluded that the energy-time uncertainty relation represents the fundamental internal quantum constraint of natural computation, the process that spans from enzymatic catalysis to complex regulatory and adaptive activities, and finally to reflexive consciousness.

Biosystems•Jan 17, 2026•6 citations
The smallest details of living systems are molecular devices that operate between the classical and quantum levels, i.e. between the potential dimension (microscale) and the actual three-dimensional space (macroscale). They realize non-demolition quantum measurements in which time appears as a mesoscale dimension separating contradictory statements in the course of actualization. These smaller devices form larger devices (macromolecular complexes), up to living body. The quantum device possesses its own potential internal quantum state (IQS), which is maintained for prolonged time via error-correction being a reflection over this state. Decoherence-free IQS can exhibit itself by a creative generation of iteration limits in the real world. To avoid a collapse of the quantum information in the process of correcting errors, it is possible to make a partial measurement that extracts only the error-information and leaves the encoded state untouched. In natural quantum computers, which are living systems, the error-correction is internal. It is a result of reflection, given as a sort of a subjective process allotting optimal limits of iteration. The IQS resembles the properties of a quasi-particle, which interacts with the surround, applying decoherence commands to it. In this framework, enzymes are molecular automata of the extremal quantum computer, the set of which maintains stable highly ordered coherent state, and genome represents a concatenation of error-correcting codes into a single reflective set. Biological systems, being autopoietic in physical space, control quantum measurements in the physical universe. The biological evolution is really a functional evolution of measurement constraints in which limits of iteration are established possessing criteria of perfection and having selective values.
The internal quantum state (IQS) is a kind of a pilot-wave (in the Bohmian sense) attached to a macroscopic system and representing its potential field continuously reduced during its exhibition to the external world. This state is maintained as decoherence-free by applying error-correction commands to it and by screening from thermal interactions. Its effective temperature is kept down below the millikelvin range thus being screened even from the background microwave radiation. The quantum Zeno effect enables coherent superpositions and entanglement to persist for macroscopic time intervals. The IQS thus avoids the Boltzmann statistics and approaches a state when the Bose-Einstein statistics is applicable. The IQS of a living system can be viewed as a subtle individual subatomic structure reduced to a complex pattern of vibrating strings and exhibiting itself via a visible classical body-like system. Light quanta inside IQS are trapped like matter is trapped by a black hole in space. The IQS can be considered as a unified field meeting place of gravitational, electromagnetic, weak and strong nuclear forces. The phenomenon of emission of weak coherent light is an indirect evidence of coherent long-living internal quantum states in living systems. This emission is a kind of a similar phenomenon as the Hawking's radiation from black holes and it may serve for unification of the processes taking place in different subsystems of a biological system (synchronization of individual coherent states within the whole system). The external exhibition of the IQS can be expressed as a mapping from complex to real numbers where the certain rules are generated, e.g. the power law and other recursive formulae. In the simplest case when two superposed states are reduced, it has a limit of price of action equal to the Planck's constant. The reduction is non-computable and resembles the act of volition. The result is Godel number appearing above superposed states and memorizing the act of reduction. It is used by living system as an information unit in emerging computation process.
Introduction In the processes of adaptation, development and evolution, living systems interpret themselves in the environment resulting in changes of both. This leads to the growth of information via rescaling of internal time (heterochrony) followed by spatial reconstructions of morphology (heterotopy). The growth of information is based on perpetual changes in its interpretation in the changing world. Biological evolution involves the anticipatory epigenetic changes in interpretation of the genetic information which cannot be generally forecasted but can provide canalization of structural changes defined by the existing organization leading to predictable patterns of form generation. Social evolution is accompanied by unprecedented growth of the informational field that leads to progressive development of human society. In modern theoretical biology, the internal measurement concept was suggested as a background for explanation of the phenomenon of life (Matsuno, 1995). The quantum measurement represents the action of a measuring device on the measured system. The quantum measurement is an irreversible phenomenon exhibiting itself as a reduction of the potential field. It has also a relation to the irreversibility of time (Igamberdiev, 1993). The collapse of wave function is not equivalent to time until it does not generate a measurable duration, but when its pattern is repeated consistently, the clock can be set, and the system becomes organized in time. When the measuring device is a part of measured system, the measurement proceeds internally in relation to the whole system and the latter becomes more complex as a result of measurement itself. The aim of this study is to discuss the role of internal measurement in the growth of information in evolving systems. This can refer to biological evolution, social evolution, and as well to the cosmic evolution, which is represented in the phenomenon of expansion of the Universe. Internal Measurement and the Generation of New Information The internal measurement leads to an iterative recursive process which appears as the development and evolution of the combined system containing the measuring device and the measured object. The quantum measuring device can be organized in such way that it “encodes” the system in the course of interaction with the measured object, and makes it possible for the measurement to proceed in a regular way. In this case, such system can memorize the evolutionary complication of organization in a digital information-bearing subsystem and evolve further; in other words it contains an internal description memorizing the result of measurement. The logical precondition of the growth of information in this evolving process is the incompleteness of biosystem’s internal description, while the physical precondition is the uncertainty of quantum measurement. The evolutionary increase of complexity becomes possible when genotype appears as a system distinct from phenotype and is embedded into it, which separates energy-degenerate rate-independent genetic symbols from the rate-dependent dynamics of construction that they control (Pattee, 2001). Evolutionary growth of information becomes its own cause, a universal property of our world. The growth of information accompanies the appearance of measurable time that occurs in the systems performing quantum measurements in a regular way, with low dissipation of energy (Igamberdiev, 1993, 2004). These systems are modelled as hypercycles and can be defined as structures in which the subset of a substrate set of the catalytic system happens to be the matrix for generating and reproducing the set of catalysts itself (Igamberdiev, 1999). This definition keeps the main features of the original notion of hypercycle given by Eigen and Schuster (1979). The hypercyclic system is closed in the way that all of the catalysts needed for an organism to stay alive (representing an efficient causation according to Aristotle and forming organism’s spatiotemporal structure) must be produced by the organism itself, only relying on matter and energy from the outside (Letelier et al., 2011). When hypercycles appear in evolution, time becomes an independent measurable variable due to the internal reproducible changes. Hypercycle organizes irreversibility of quantum measurement into a measurable duration. Eigen’s hypercycle is a formalized representation of the autopoietic system of Maturana and Varela or Rosen’s (M,R) system (Leteiler et al., 2011). The system becomes an internal autonomous clock that distinguishes the past (memory), the present (life), and the future (anticipation based on the reproducible model), so the modeling, logic and digital information growth become possible within the system (Rosen, 1985). The hypercycle having own embedded description, becomes a structure that realizes computation in accordance with its internal logic defined by the embedded description. The latter has the property of incompleteness which is reflected in the fact that quantum correlations of the states of the system are associated with undecidable logic theories, i.e., they can potentially generate the statements not defined within the system. The undecidability can be interpreted in the sense similar to the Gödel’s incompleteness theorem, meaning that there exist propositions, expressible in the formal logic, which cannot be proven or disproven (Briegel et al., 2009). These propositions become the grounds of expansion of the system and its informational growth. From the quantum mechanical point of view, the emergence of a new statement results in acquiring a new error-correction meaning to support the internal quantum state (IQS) (Igamberdiev, 2004, 2007). The IQS keeps the system organizationally invariant. It is supported by the set of error-correcting commands that aim to keep IQS free from external demolitions. The error-correction information becomes an important part of the whole informational field. A new statement makes the system more complex (it leads to an increase of its informational content), with its all spatiotemporal organizational invariance be rescaled. In the course of evolution, an available element of a formal system (similarly to a word when used as a metaphor) can acquire another (in addition to already existing) value that contributes to formation of a new level of organization in the system. The logical basis of this action is the incompleteness of the existing formal system that allows assigning arbitrary values to the statements non-provable within that system, while the physical basis is the quantum uncertainty arising in quantum measurement. A new statement can arise from existing elements by acquiring the double function, however, for fixation of this new statement via expansion of existing formal system, some informational redundancy of the system is needed, which can be achieved by multiplication of some of its elements. Genome is a system which possesses an internal complementarity between the linear texts and their superposition. Relevantly to this, complementarity means that text and hypertext cannot be viewed at the same moment: they should be separated by a time interval. It is an example of uncertainty between the system and its embedding. Overlapping genes, alternatively splicing sequences, RNA and DNA editing, introns, and recombination according to molecular addresses are the features of this hypertext generating a potentially infinite number of language games. Genome as a complete language exists as a complementary set of its alternative combinations resulting in logical paradoxes which determine its temporal dynamics (Isalan, 2009). This superposition is a basis for ontogenesis, adaptation and evolution. Thus, the total “true” genome is a superposition of contradictory arrangements, which generate one single arrangement at a concrete moment of time. The pool of mobile genetic elements expands the combinatorial capacity of the genome by many times. An ambiguity in meaning is analogous to the quantum uncertainty principle in which it is impossible to define strictly the position and impulse of a particle simultaneously, or to fix certain energy in a very short period of time necessary for its registration. The question of a minimal size of the autocatalytic self-reproducing system and its composition has been discussed in several works (Sharov, 2009; Steel et al., 2013). Self-reproduction itself is a creative process of placing text in text with following self-growing of this joint structure. Any evolutionary change also begins from the placing of “text into text”. This is possible because genome is structurally adapted for realization of such a non-trivial function. Moreover, even a point mutation or deletion may be considered as generative if it is placed in the repeated (e.g., diploid) structure. The doubling is a premise of metasystem transition, which includes duplication of the original system and the establishment of control over multiple copies (Turchin, 1977). The evolutionary significance of gene duplication was considered by Ohno (1970) as a premise of neofunctionalization. The advantage of sexual reproduction is in the casual combinatorial generating of new statements from two separate texts that can acquire meanings, thus it resists evolutionary degradation. It becomes a prerequisite for growing of information and complexity (Igamberdiev, 2014). The combinatorial interaction of heterochronic texts generates a new system in which the internal time is rescaled in a new way that generally cannot be forecasted. The heterochronic duplication (via hybridization of temporally different organisms) generates more possibilities for the metasystem transition. Thus, the incompleteness of embedded set of symbols is the formal cause of evolution. The physical representation of this incompleteness is a quantum uncertainty in the course of measurement (Matsuno, 1992). It spans from the level of elementary particles to biological evolution and to the phenomenon of free will and consciousness. Growth of Information in the Expanding Universe The growth of information that we discuss here mainly in relation to biological evolution is relevant also to the physical space-time scales. The self-growing principle of quantum measurement has a property of intrinsic expansion of the informational field. The relationship between observable nature and a hidden “potential” nature is modeled, according to Kineman (2010), as an imaginary space-time domain geometrically represented as radial “Minkowski-space”. Despite of the fact that local space and time are normally represented as real numbers, the general relationship in this geometry is hyperbolic in accordance with the special theory of relativity. When mapped as a radial geometry, the space-time is seen to be intrinsically dynamic (expanding) and self-similar across all scales. The geometry has the properties of early and present acceleration. This representation eliminates the “light cone” and thus all regions in this model are the domains of existence and are observable over time. Nevertheless a domain of general, non-local reality is represented in the imaginary axes that exist simultaneously with measurable, local domains. The Universe in the concept of Kineman (2010) consists of the units called “holons”, which vaguely correspond to Leibniz’s monads. They possess simultaneous properties of location and non-location, as a point of non-differentiated whole appearing in a subject-object relation. The Everett’s interpretation of quantum mechanics works in these isolated domains but not between the domains, the same idea has been suggested by Matsuno (2012) for the individual biological systems taken as separate domains. The reality of superposition of the wave function is limited by the single monad and does not expand outside it, and in this sense monads do not have windows as originally proposed by Leibniz. Conclusion The growth of information is the basic property of evolving systems and it follows from the interaction between non-local and local domains in the course of internal quantum measurements. The internal measurement leads to an iterative recursive process which appears as evolution of the combined system containing the measuring device and the measured object. The system through measurement acquires the property of expansion, which is seen in biological evolution, social development, and at cosmic scales as expansion of the Universe. References Briegel, H.J.; Browne, D.E.; Dur, W.; Raussendorf, R.; Van den Nest, M. Measurement-based quantum computation. Nature Physics 2009, 5, 19-26. Eigen, M.; Schuster, P. The Hypercycle: A Principle of Natural Self-Organization. Springer, Berlin, 1979. Igamberdiev, A.U. Quantum mechanical properties of biosystems: A framework for complexity, structural stability and transformations. Biosystems 1993, 31, 65‐ Igamberdiev, A.U. Foundations of metabolic organization: coherence as a basis of computational properties in metabolic networks. Biosystems 1999, 50, 1-16. Igamberdiev, A.U. Quantum computation, non-demolition measurements, and reflective control in living systems. Biosystems 2004, 77, 47–56. Igamberdiev, A.U. Physical limits of computation and emergence of life. Biosystems 2007, 90, 340–349. Igamberdiev, A.U. Time rescaling and pattern formation in biological evolution. Biosystems 2014, 123, 19-26. Isalan, M. Gene networks and liar paradoxes. Bioessays 2009, 31, 1110-1115. Letelier, J.C.; Cárdenas, M.L.; Cornish-Bowden, A. From L'Homme Machine to metabolic closure: steps towards understanding life. Journal of Theoretical Biology 2011, 286, 100-113. Matsuno, K. The uncertainty principle as an evolutionary engine. Biosystems 1991, 27, 63-76. Matsuno, K. Quantum and biological computation. Biosystems 1995, 35, 209-212. Matsuno, K. Chemical evolution as a concrete scheme for naturalizing the relative-state of quantum mechanics. Biosystems 2012, 109, 159-168. Kineman, J.J. Relational self-similar space-time cosmology revisited. Proceedings of the 54th Meeting of the International Society for System Sciences. Waterloo, Canada, 2010. Ohno, S. Evolution by Gene Duplication. Springer, New York, 1970. Pattee, H.H. The physics of symbols: bridging the epistemic cut. Biosystems 2001, 60, 5-21. Sharov, A.A., 2009. Coenzyme autocatalytic network on the surface of oil microspheres as a model for the origin of life. International Journal of Molecular Sciences 2009, 10, 1838-1852. Steel, M.; Hordijk, W.; Smith, J. Minimal autocatalytic networks. Journal of Theoretical Biology 2013, 332, 96-107. Turchin, V. Phenomenon of Science. Columbia University Press, New York, 1977.
Quantum computing exists at the intersection of mathematics, physics, chemistry, and engineering; the main goal of quantum computing is the creation of devices and algorithms which use the properties of quantum mechanics to store, manipulate and measure information. There exist many families of algorithms, which, using non-classical logical operations, can outperform traditional, classical algorithms in terms of memory and processing requirements. In addition, quantum computing devices are fundamentally smaller than classical processors and memory elements; since the physical models governing their performance are applicable on all scales, as opposed to classical logic elements, whose underlying principles rely on the macroscopic nature of the device in question. \n \nQuantum algorithms, for the most part, are predicated on a theory of resources. It is often assumed that quantum computers can be placed in a precise fiducial state prior to computation, and that logical operations are perfect, inducing no error on the system which they affect. These assumptions greatly simplify algorithmic design, but are fundamentally unrealistic. In order to justify their use, it is necessary to develop a framework for using a large number of imperfect devices to simulate the action of a perfect device, with some acceptable probability of failure. This is the study of fault-tolerant quantum computing. In order to pursue this study effectively, it is necessary to understand the fundamental nature of generic quantum states and operations, as well as the means by which one can correct quantum errors. Additionally, it is important to attempt to minimize the use of computational resources in achieving error reduction and fault-tolerant computing. \n \nThis thesis is concerned with three projects related to the use of error-prone quantum systems to transmit and manipulate information. The first of these is concerned with the use of imperfectly-prepared states in error-correction routines. Using optimal quantum error correction, we are able to deduce a method of partially protecting encoded quantum information against preparation errors prior to encoding, using no additional qubits. The second of these projects details the search for entangled states which can be used to transmit classical information over quantum channels at a rate superior to classical states. The third of these projects concerns the transcoding of data from one quantum code into another using few ancillary resources. The descriptions of these projects are preceded by a brief introduction to representations of quantum states and channels, for completeness. \n \nThree techniques of general interest are presented in appendices. The first is an introduction to, and a minor advance in the development of optimal error correction codes. The second is a more efficient means of calculating the action of a quantum channel on a given state, given that the channel acts non-trivially only on a subsystem, rather than the entire system. Finally, we include documentation on a software package developed to aid the search for quantum transcoding operations.
It is shown that encoding the state of a quantum computer (or other quantum information-processing device) for error correction has the effect of making its operating states macroscopically indistinguishable; all the more, the more ``stable'' the code is, that is, the more errors it can correct in each pass. It is also shown that for nondegenerate codes the expectation values of macroscopic observables in such encoded states are identical to those that would be obtained for a totally mixed state of maximum entropy, where again the degree of indistinguishability increases with the number of errors corrected by the code. The results can be used to estimate the decoherence rates for systems of qubits under certain forms of interaction with the environment: it is found that when the qubits are encoded all coherent superpositions decay, to lowest order, at the same rate, which scales more slowly with the number of physical qubits than the decoherence rate for macroscopic coherent superpositions (``Schr\"odinger cats'') of the bare qubits.
When the revolutionary conceptual structure for the description of the physical world which we know as quantum mechanics was first formulated nearly 90 years ago, and its predictions tested in the laboratory, most of the experiments in question were on systems which were both very well characterized and reasonably well isolated from their environments, such as single electrons and atoms, small molecules and near-perfect crystalline solids. While from the very start most physicists have taken it for granted that the formalism of quantum mechanics, when combined with appropriate system-specific information, can “in principle” account for all phenomena occurring in the physical world, including those usually regarded as the subject-matter of biology, until quite recently the overwhelmingly majority opinion has been that in a biological context the role of quantum theory is confined to elucidating the equilibrium structures of the relevant molecules and their reaction processes, and that subtle phenomena such as superposition and entanglement, of which we can now routinely exhibit spectacular effects at the level of a few well-isolated photons or atoms, play at most a very indirect role in any phenomena of biological interest. A major reason conventionally given for this view has been that biological systems, at least working ones, are by their very nature “warm and wet” – a phrase which in the physicist's lexicon translates to “prone to massive decoherence”; it looks as though any interesting superposition, say of different energy eigenstates of one's system, would be rapidly decohered by the ever-present, and usually microscopically very complex, environment.
Time relates to actualization, which is physically interpreted as a quantum measurement. The measurement has a dual structure consisting of the reality being measured (externality) and the reality by which the measurement takes place (an agent or ontolon). These two constituents refer to the two types of time: physical time measured by clocks, and internal time, defined by Bergson as la durée (duration). The latter holds the coherent internal quantum state of entangled potentialities, while the former represents the collapse of this state, thereby flowing through quantum transactions. This view unifies the Everett (Many-worlds) and the Copenhagen (Wave function collapse) interpretations of the quantum measurement. Time as a duration can be estimated via the energy-time uncertainty relation, which links the precision of the measurement result to the value of energy dissipation during it and to its span. The precision of the measurement result enables the process of quantum computation, which emerges in the systems characterized by internal closure, i.e., autopoietic (living) systems operating at the state of sustainable non-equilibrium. Energy dissipation in the process of measurement occurs as the emission of quanta that trigger the collapse of the coherent entangled state. These quanta are recognized in the system, enabling the performance of higher-level control over elementary computational actions through their integration within the complex system. It is concluded that the energy-time uncertainty relation represents the fundamental internal quantum constraint of natural computation, the process that spans from enzymatic catalysis to complex regulatory and adaptive activities, and finally to reflexive consciousness.