查看更多>>摘要：How can a living system escape the solipsistic self-making process? This problem has been ignored in mainstream biology. This study seeks a reasonable mechanism by which a living system produces symbols that signify external states. To this end, the inverse causality model proposed in previous studies was theoretically improved by refining the core concepts. Inverse causality is an epistemic principle operating in a subject system to produce symbols internally, signifying the past states of the external reality hidden to the subject. Inverse causality yields an important theorem for a system to produce symbols for external states. It asserts that if a system changes from state x to y(1) in some instances, and from x to y(2) in others (y(1) &NOTEQUexpressionL; y(2)), then x bar right arrow y(1) produces a symbol that signifies one external state, and x bar right arrow y(2) produces a different symbol for another state. These symbols are embodied as the states of the system components. The model postulates the equivalence principle in the subject-reality relationship, asserting that inverse causality is equivalent to causality in the external view. Living systems operate with inverse causality using biological devices called measurers, which include membrane receptors, second messengers, and molecular switches in cells, and neurons in multicellular organisms. A measurer is a medium of symbols signifying external states. Biological subsystems functioning as measurers are ubiquitous and essential in contemporary living systems for adaptation to their environments in particular ways by manipulating the symbols they produce. By the inverse causality operation, living systems can reduce the uncertainty of events and manage the probability distribution of future events favorable to survival and reproduction. Due to this function, their measurer systems were sophisticated and diversified in evolution. In philosophy and science, there has been endless debate between determinism and indeterminism. However, surprisingly, contemporary living systems use the inverse causality operation (ICW) to adapt to their environments, which is logically equivalent to the causal principle of determinism.
查看更多>>摘要：Environmental variability often degrades the performance of algorithms designed to capture the global convergence of a given search space. Several approaches have been developed to challenge environmental uncertainty by incorporating biologically inspired notions, focusing on crossover, mutation, and selection. This study proposes a bio-inspired approach called NEAT-HD, which focuses on parent selection based on genetic similarity. The originality of the proposed approach rests on its use of a sigmoid function to accelerate species formation and contribute to population diversity. Experiments on two classic control tasks were performed to demonstrate the performance of the proposed method. The results show that NEAT-HD can dynamically adapt to its environment by forming hybrid individuals originating from genetically distinct parents. Additionally, an increase in diversity within the population was observed due to the formation of hybrids and novel individuals, which has never been observed before. Comparing two tasks, the characteristics of NEAT-HD were improved by appropriately setting the algorithm to include the distribution of genetic distance within the population. Our key finding is the inherent potential of newly formed individuals for robustness against dynamic environments.
Baluska, FrantisekReber, Arthur S.Miller Jr, William B.
9页
查看更多>>摘要：All life is cellular, starting some 4 billion years ago with the emergence of the first cells. In order to survive their early evolution in the face of an extremely challenging environment, the very first cells invented cellular sentience and cognition, allowing them to make relevant decisions to survive through creative ad-aptations in a continuously running evolutionary narrative. We propose that the success of cellular life has crucially depended on a biological version of Maxwell's demons which permits the extraction of relevant sensory information and energy from the cellular environment, allowing cells to sustain anti-entropic actions. These sensor-effector actions allowed for the creative construction of biological order in the form of diverse organic macromolecules, including crucial polymers such as DNA, RNA, and cytoskeleton. Ordered biopolymers store analogue (structures as templates) and digital (nucleotide sequences of DNA and RNA) information that functioned as a form memory to support the development of organisms and their evolution. Crucially, all cells are formed by the division of previous cells, and their plasma membranes are physically and informationally continuous across evolution since the beginning of cellular life. It is argued that life is supported through life-specific principles which support cellular sentience, distinguishing life from non-life. Biological order, together with cellular cognition and sentience, allow the creative evolution of all living organisms as the authentic authors of evolutionary novelty.
Adamatzky, AndrewChiolerio, AlessandroDehshibi, Mohammad MahdiManfredi, Diego...
9页
查看更多>>摘要：A reactive bacterial glove is a cotton glove colonised by Acetobacter aceti, an example of biofabrication of a living electronic sensing device. The bacterial colony, supported by a cellulose-based hydrogel, forms a several millimetres-thick living coating on the surface of the glove. This paper proposes a novel method for analysing the complex electrical activity of trains of spikes generated by a living colony. The proposed method, which primarily focuses on dynamic entropy analysis, shows that the bacterial glove responds to mechanical triaxial stimuli by producing travelling patterns of electrical activity. Kolmogorov complexity further supports our investigation into the evolution of dynamic patterns of such waves in the hydrogel and shows how stimuli initiate electrical activity waves across the glove. These waves are diffractive and ultimately are suppressed by depression. Our experiments demonstrate that living substrates could be used to enable reactive sensing wearable by means of living colonies of bacteria, once the paradigm of excitation wave propagation and reflection is implemented.
查看更多>>摘要：The fundamental role of symmetry in the genetic code is to decrease disorder between codons and to preserve the integrity of system. The Standard Genetic Code (SGC) table is structured alphabetically in a horizontal and vertical array of U-C-A-G bases only with aesthetic symmetry. We postulate the symmetry theory of genetic code which is based on the unique physicochemical purine - pyrimidine symmetry net between codons of our Supersymmetry genetic code (SSyGC) table. The common purine - pyrimidine symmetry net as the golden rule and a core of the SSyGC table is universal, remaining unchanged during all of evolution. It is identical for more than 30 known genetic codes including those that will be discovered in the future, as well as for all RNA and DNA species. The unique SSyGC table has five physicochemical symmetries between bases, codons, and amino acids: 1) purine - pyrimidine symmetry on the principle of the Watson - Crick pairing (A & harr;U, C & harr;G), 2) direct - complement symmetry between codons, 3) mirror symmetry between bases and codons, 4) A + T rich and C + G rich symmetry between codons, and 5) symmetry between position of amino acids. Opposite to the SGC table where the third base is inactive, in the SSyGC table the role of the third base in codons is dominant in creation of symmetries. There are also present for the first time the symmetric positions of all boxes with amino acids. Opposite of the SGC table, the SSyGC code table contains three sextets for Serine, Arginine, and Leucine, each with six codons, positioned in continuity. Multi - facet symmetries of the SSyGC table as a natural law exclude the individual random creation of amino acids even in primitive life form. Accordingly, we hypothesize that the contemporary life arose due to common activity of all natural amino acids. With discovery of the unique physicochemical Supersymmetry genetic code table, the new light is shed on the symmetry of the genetic code.
查看更多>>摘要：The existence of an environmentally regulated version of meiotic crossing-over, or eco-crossover, is proposed, and the main consequences of this hypothesis are considered. Eco-crossover is a key source of partially directed genetic diversity of eukaryotes. In stressful environment, it creates ecologically justified and topologically specific genetic changes, and hence phenotypic variability, with which the selection works. If variability were random, then, in the face of rapid environmental changes, natural selection could not create life-saving adaptations in a timely manner. Owing to the eco-crossover activity, epimutations, i.e., eco-dependently marked chromosomal sites, are transforming into mutations. In its work, eco-crossover uses the eco-stress-dependent versions of circular RNAs ("ecological" circRNAs), which, against the background of eco-stresses, are synthesized as variants of alternative splicing. These ecological circRNAs, binding to homologous epimutations on the homologous parent chromosomes of the meiocyte, involve them in topologically specific recombinations. These recombinations can create random mutations in nonrandom genomic sites. These quasi-random mutations serve as a pivotal source for creating all adaptations of any level of complexity. The drivers of the adaptive evolution of eukaryotes, both in micro- and macroevolution, are two irreplaceable factors - eco-crossover and natural selection.
查看更多>>摘要：The evolutionary lineage of neuronal phenotype is notably complex even within a limited number of species. One of the approaches resides in the realm of complex network theory. The theory reduces the connectomic data into a hallmarked set of few parameters, some of which might be correlated with a suitably chosen phylogenetic marker. In this first-of-its-kind attempt, interspecific variations of two structural complexity measures (i.e., clustering coefficient and centrality) along with two independent information-theoretic measures (i.e., von Neumann entropy and multifractality) are investigated to decipher any hidden evolutionary signature considering four mammalian connectomes (i.e., felis catus, mus musculus, macaca mulatta, and homo sapiens). All network complexity measures partially corroborate with the phylogenetic order. Nevertheless, monotonicity of the measures with the chosen phylogenetic marker of genome size has been majorly violated because of the mus musculus data point. On the other hand, von Neumann entropy was found to exhibit an allometric scaling behavior with the community structure of all connectomes (p < 0.0001, and R-2 > 0.95). The respective scaling exponent was noted to be monotonic with the genome size. Singularities of the real connectomes were also investigated upon carrying out a similar analysis in three equivalent synthetic network models.
查看更多>>摘要：We present a Monte Carlo simulation model of an epidemic spread inspired on physics variables such as temperature, cross section and interaction range, which considers the Plank distribution of photons in the black body radiation to describe the mobility of individuals. The model consists of a lattice of cells that can be in four different states: susceptible, infected, recovered or death. An infected cell can transmit the disease to any other susceptible cell within some random range R. The transmission mechanism follows the physics laws for the interaction between a particle and a target. Each infected particle affects the interaction region a number n of times, according to its energy. The number of interactions is proportional to the interaction cross section cr and to the target surface density p. The discrete energy follows a Planck distribution law, which depends on the temperature T of the system. For any interaction, infection, recovery and death probabilities are applied. We investigate the results of viral transmission for different sets of parameters and compare them with available COVID-19 data. The parameters of the model can be made time dependent in order to consider, for instance, the effects of lockdown in the middle of the pandemic.
查看更多>>摘要：Does biological computation happen at some sort of "edge of chaos", a dynamical regime somewhere between order and chaos? And if so, is this a fundamental principle that underlies self-organization, evolution, and complex natural and artificial systems that are subjected to adaptation? In this article, we will review the literature on the fundamental principles of computation in natural and artificial systems at the "edge of chaos". The term was coined by Norman Packard in the late 1980s. Since then, the concept of "adaptation to the edge of chaos"was demonstrated and investigated in many fields where both simple and complex systems receive some sort of feedback. Besides reviewing both historic and recent literature, we will also review critical voices of the concept.
NSTL
Elsevier