The physics of symbols: bridging the epistemic cut

Evolution requires the genotype–phenotype distinction, a primeval epistemic cut that separates energy-degenerate, rate-independent genetic symbols from the rate-dependent dynamics of construction that they control. This symbol–matter or subject–object distinction occurs at all higher levels where symbols are related to a referent by an arbitrary code. The converse of control is measurement in which a rate-dependent dynamical state is coded into quiescent symbols. Non-integrable constraints are one necessary condition for bridging the epistemic cut by measurement, control, and coding. Additional properties of heteropolymer constraints are necessary for biological evolution.     

Quantum monadology: a consistent world model for consciousness and physics

The NL world model presented in the previous paper is embodied by use of relativistic quantum mechanics, which reveals the significance of the reduction of quantum states and the relativity principle, and locates consciousness and the concept of flowing time consistently in physics. This model provides a consistent framework to solve apparent incompatibilities between consciousness (as our interior experience) and matter (as described by quantum mechanics and relativity theory). Does matter have an inside? What is the flowing time now? Does physics allow the indeterminism by volition? The problem of quantum measurement is also resolved in this model.     

电针模拟中医按摩手法产生方法的研究

在提取传统中医按摩手法特征的基础上,提出了一种模拟中医按摩手法的电针产生方法该方法应用符号化测量理论,采用不同域间的问题映射,结合按摩手法的力学和动力学特征,科学地将传统中医按摩手法映射到电气参数域,并以按法为例,设计了模拟按法的电针仪及同心圆电极,解决了传统中医按摩与现代工程技术仪器仪表学科之间结合的问题。     

Protein domain annotation with predicted domain-domain interaction networks

This paper presents a framework for annotating protein domains with predicted domain-domain interaction networks. Specially, domain annotation is formalized as a multi-class classification problem in this work. The numerical experiments on InterPro domains show promising results, which proves the efficiency of our proposed methods.     

Quantum computation, non-demolition measurements, and reflective control in living systems

Internal computation underlies robust non-equilibrium living process. The smallest details of living systems are molecular devices that realize non-demolition quantum measurements. 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 a prolonged time via reflective error-correction. Decoherence-free IQS can exhibit itself by a creative generation of iteration limits in the real world. It 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 highly ordered robust coherent state, and genome represents a concatenation of error-correcting codes into a single reflective set. The biological evolution can be viewed as a functional evolution of measurement constraints in which limits of iteration are established, possessing criteria of perfection and having selective values.     

Bridging the gap between physics and biology.

The work is devoted to the historical development of physics and biology. Various aspects of their interactions are shown: antagonism, mutual penetration and a lot of bridges, built or being built between them. The gradual "evolution of the world picture" from going away of the "pre-scientific" animated Universe and the appearance of mechanicism and vitalism to the development of systems and field approaches is traced. The last part of the paper is concerned with some present-day works at the joint between physics and biology.     

A Formalized Design Process for Bacterial Consortia That Perform Logic Computing

The concept of microbial consortia is of great attractiveness in synthetic biology. Despite of all its benefits, however, there are still problems remaining for large-scaled multicellular gene circuits, for example, how to reliably design and distribute the circuits in microbial consortia with limited number of well-behaved genetic modules and wiring quorum-sensing molecules. To manage such problem, here we propose a formalized design process: (i) determine the basic logic units (AND, OR and NOT gates) based on mathematical and biological considerations; (ii) establish rules to search and distribute simplest logic design; (iii) assemble assigned basic logic units in each logic operating cell; and (iv) fine-tune the circuiting interface between logic operators. We in silico analyzed gene circuits with inputs ranging from two to four, comparing our method with the pre-existing ones. Results showed that this formalized design process is more feasible concerning numbers of cells required. Furthermore, as a proof of principle, an Escherichia coli consortium that performs XOR function, a typical complex computing operation, was designed. The construction and characterization of logic operators is independent of “wiring” and provides predictive information for fine-tuning. This formalized design process provides guidance for the design of microbial consortia that perform distributed biological computation.     

Ritual,emotion, and sacred symbols

This paper considers religion in relation to four recurrent traits: belief systems incorporating supernatural agents and counterintuitive concepts, communal ritual, separation of the sacred and the profane, and adolescence as a preferred developmental period for religious transmission. These co-occurring traits are viewed as an adaptive complex that offers clues to the evolution of religion from its nonhuman ritual roots. We consider the critical element differentiating religious from non-human ritual to be the conditioned association of emotion and abstract symbols. We propose neurophysiological mechanisms underlying such associations and argue that the brain plasticity of human adolescence constitutes an “experience expectant” developmental period for ritual conditioning of sacred symbols. We suggest that such symbols evolved to solve an ecological problem by extending communication and coordination of social relations across time and space. Candace Alcorta is currently a doctoral student in the Department of Anthropology at the University of Connecticut. Her research interests include the behavioral ecology and evolution of religion, and the interrelationship between cultural and neurophysiological systems. She is currently conducting research on adolescent religious participation, stress, and health. Richard Sosis is an associate professor in the Department of Anthropology at the University of Connecticut and a senior lecturer in the Department of Sociology and Anthropology at The Hebrew University of Jerusalem. His current research interests include the evolution of cooperation, utopian societies, and the behavioral ecology of religion. He has conducted fieldwork on Ifaluk Atoll in the Federated States of Micronesia and is currently pursuing various projects in Israel aimed at understanding the benefits and costs associated with religious behavior.     

Morphological Evolution of Physical Robots through Model-Free Phenotype Development

Artificial evolution of physical systems is a stochastic optimization method in which physical machines are iteratively adapted to a target function. The key for a meaningful design optimization is the capability to build variations of physical machines through the course of the evolutionary process. The optimization in turn no longer relies on complex physics models that are prone to the reality gap, a mismatch between simulated and real-world behavior. We report model-free development and evaluation of phenotypes in the artificial evolution of physical systems, in which a mother robot autonomously designs and assembles locomotion agents. The locomotion agents are automatically placed in the testing environment and their locomotion behavior is analyzed in the real world. This feedback is used for the design of the next iteration. Through experiments with a total of 500 autonomously built locomotion agents, this article shows diversification of morphology and behavior of physical robots for the improvement of functionality with limited resources.     

Controlled synthesis of target strings in a class of splicing systems

This article presents an approach for synthesizing target strings in a class of computational models of DNA recombination. The computational models are formalized as splicing systems in the context of formal languages. Given a splicing system (of a restricted type) and a target string to be synthesized, we construct (i) a rule-embedded splicing automaton that recognizes languages containing strings embedded with symbols representing splicing rules, and (ii) an automaton that implicitly recognizes the target string. By manipulating these two automata, we extract all rule sequences that lead to the production of the target string (if that string belongs to the splicing language). An algorithm for synthesizing a certain type of target strings based on such rule sequences is presented.     

Computer Simulation of Magnetic Resonance Angiography Imaging: Model Description and Validation

With the development of medical imaging modalities and image processing algorithms, there arises a need for methods of their comprehensive quantitative evaluation. In particular, this concerns the algorithms for vessel tracking and segmentation in magnetic resonance angiography images. The problem can be approached by using synthetic images, where true geometry of vessels is known. This paper presents a framework for computer modeling of MRA imaging and the results of its validation. A new model incorporates blood flow simulation within MR signal computation kernel. The proposed solution is unique, especially with respect to the interface between flow and image formation processes. Furthermore it utilizes the concept of particle tracing. The particles reflect the flow of fluid they are immersed in and they are assigned magnetization vectors with temporal evolution controlled by MR physics. Such an approach ensures flexibility as the designed simulator is able to reconstruct flow profiles of any type. The proposed model is validated in a series of experiments with physical and digital flow phantoms. The synthesized 3D images contain various features (including artifacts) characteristic for the time-of-flight protocol and exhibit remarkable correlation with the data acquired in a real MR scanner. The obtained results support the primary goal of the conducted research, i.e. establishing a reference technique for a quantified validation of MR angiography image processing algorithms.     

Measurement issues in morphometry

Measurement is the instrument of morphometry. Several recurring issues of measurement are reviewed: types of measurement scales and their statistical consequences; types of measurement errors and their relationship to measurement scales; the differences between image resolution, digitization resolution and measurement resolution; and image measurement methods. The importance of formalized measurement protocols is illustrated with an example from daily morphometric practice.     

On rationalism and optimality: Responses to the Miller and Nevin Commentaries

Modern materialist rationalism is the doctrine that principles governing behaviorally important aspects of the world have become implicit in the structure of purpose-specific information-processing mechanisms through evolution by natural selection. These principles are mostly, but not entirely mathematical. Because the evolutionary process tends to optimize, the computations performed by these mechanisms tend to approximate the optimal computation. This doctrine does not imply that animals always make rational and/or optimal choices.     

Evolution of robustness to damage in artificial 3-dimensional development

GReaNs is an Artificial Life platform we have built to investigate the general principles that guide evolution of multicellular development and evolution of artificial gene regulatory networks. The embryos develop in GReaNs in a continuous 3-dimensional (3D) space with simple physics. The developmental trajectories are indirectly encoded in linear genomes. The genomes are not limited in size and determine the topology of gene regulatory networks that are not limited in the number of nodes. The expression of the genes is continuous and can be modified by adding environmental noise. In this paper we evolved development of structures with a specific shape (an ellipsoid) and asymmetrical pattering (a 3D pattern inspired by the French flag problem), and investigated emergence of the robustness to damage in development and the emergence of the robustness to noise. Our results indicate that both types of robustness are related, and that including noise during evolution promotes higher robustness to damage. Interestingly, we have observed that some evolved gene regulatory networks rely on noise for proper behaviour.     

Between history and physics

Biology has traditionally occupied a middle ground between the determinism of classical physics and the uncertainties of history. These issues are analyzed with respect to statistical laws which are applied to the prebiotic domain and strategy laws which characterize evolutionary biology. The differences in approach between biology and physics are discussed in detail. The origin of life is discussed in the context of physical chemical laws. A scenario for biogenesis is presented in terms of known molecular hardware. Evolutionary biology is then examined with respect to the kinds of laws that are possible in a domain where thermal fluctuations (mutations) have macroscopic effects. Game theory is employed to demonstrate the kinds of theory appropriate to this historical domain. The transition point between physics and history is the origin and development of the code. This is discussed and it is concluded that we are not yet able to assign the code to either the deterministic domain or to the arena of history.